Daily Papers

Breast cancer is a significant health concern affecting millions of women worldwide. Accurate survival risk stratification plays a crucial role in guiding personalised treatment decisions and improving patient outcomes. Here we present BioFusionNet, a deep learning framework that fuses image-derived features with genetic and clinical data to achieve a holistic patient profile and perform survival risk stratification of ER+ breast cancer patients. We employ multiple self-supervised feature extractors, namely DINO and MoCoV3, pretrained on histopathology patches to capture detailed histopathological image features. We then utilise a variational autoencoder (VAE) to fuse these features, and harness the latent space of the VAE to feed into a self-attention network, generating patient-level features. Next, we develop a co-dual-cross-attention mechanism to combine the histopathological features with genetic data, enabling the model to capture the interplay between them. Additionally, clinical data is incorporated using a feed-forward network (FFN), further enhancing predictive performance and achieving comprehensive multimodal feature integration. Furthermore, we introduce a weighted Cox loss function, specifically designed to handle imbalanced survival data, which is a common challenge in the field. The proposed model achieves a mean concordance index (C-index) of 0.77 and a time-dependent area under the curve (AUC) of 0.84, outperforming state-of-the-art methods. It predicts risk (high versus low) with prognostic significance for overall survival (OS) in univariate analysis (HR=2.99, 95% CI: 1.88--4.78, p<0.005), and maintains independent significance in multivariate analysis incorporating standard clinicopathological variables (HR=2.91, 95% CI: 1.80--4.68, p<0.005). The proposed method not only improves model performance but also addresses a critical gap in handling imbalanced data.

Background: Cancer remains one of the leading causes of morbidity and mortality worldwide. Comprehensive datasets that combine histopathological images with genetic and survival data across various tumour sites are essential for advancing computational pathology and personalised medicine. Results: We present SurGen, a dataset comprising 1,020 H&E-stained whole slide images (WSIs) from 843 colorectal cancer cases. The dataset includes detailed annotations for key genetic mutations (KRAS, NRAS, BRAF) and mismatch repair status, as well as survival data for 426 cases. To demonstrate SurGen's practical utility, we conducted a proof-of-concept machine learning experiment predicting mismatch repair status from the WSIs, achieving a test AUROC of 0.8316. These preliminary results underscore the dataset's potential to facilitate research in biomarker discovery, prognostic modelling, and advanced machine learning applications in colorectal cancer. Conclusions: SurGen offers a valuable resource for the scientific community, enabling studies that require high-quality WSIs linked with comprehensive clinical and genetic information on colorectal cancer. Our initial findings affirm the dataset's capacity to advance diagnostic precision and foster the development of personalised treatment strategies in colorectal oncology. Data available online at https://doi.org/10.6019/S-BIAD1285.

Causal structures for observational survival data provide crucial information regarding the relationships between covariates and time-to-event. We derive motivation from the information theoretic source coding argument, and show that incorporating the knowledge of the directed acyclic graph (DAG) can be beneficial if suitable source encoders are employed. As a possible source encoder in this context, we derive a variational inference based conditional variational autoencoder for causal structured survival prediction, which we refer to as DAGSurv. We illustrate the performance of DAGSurv on low and high-dimensional synthetic datasets, and real-world datasets such as METABRIC and GBSG. We demonstrate that the proposed method outperforms other survival analysis baselines such as Cox Proportional Hazards, DeepSurv and Deephit, which are oblivious to the underlying causal relationship between data entities.

There has been increasing interest in modeling survival data using deep learning methods in medical research. In this paper, we proposed a Bayesian hierarchical deep neural networks model for modeling and prediction of survival data. Compared with previously studied methods, the new proposal can provide not only point estimate of survival probability but also quantification of the corresponding uncertainty, which can be of crucial importance in predictive modeling and subsequent decision making. The favorable statistical properties of point and uncertainty estimates were demonstrated by simulation studies and real data analysis. The Python code implementing the proposed approach was provided.

One straightforward metric to evaluate a survival prediction model is based on the Mean Absolute Error (MAE) -- the average of the absolute difference between the time predicted by the model and the true event time, over all subjects. Unfortunately, this is challenging because, in practice, the test set includes (right) censored individuals, meaning we do not know when a censored individual actually experienced the event. In this paper, we explore various metrics to estimate MAE for survival datasets that include (many) censored individuals. Moreover, we introduce a novel and effective approach for generating realistic semi-synthetic survival datasets to facilitate the evaluation of metrics. Our findings, based on the analysis of the semi-synthetic datasets, reveal that our proposed metric (MAE using pseudo-observations) is able to rank models accurately based on their performance, and often closely matches the true MAE -- in particular, is better than several alternative methods.

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

Survival risk stratification is an important step in clinical decision making for breast cancer management. We propose a novel deep learning approach for this purpose by integrating histopathological imaging, genetic and clinical data. It employs vision transformers, specifically the MaxViT model, for image feature extraction, and self-attention to capture intricate image relationships at the patient level. A dual cross-attention mechanism fuses these features with genetic data, while clinical data is incorporated at the final layer to enhance predictive accuracy. Experiments on the public TCGA-BRCA dataset show that our model, trained using the negative log likelihood loss function, can achieve superior performance with a mean C-index of 0.64, surpassing existing methods. This advancement facilitates tailored treatment strategies, potentially leading to improved patient outcomes.

Training data quality is one of the most important drivers of final model quality. In this work, we introduce a method for evaluating data integrity based on the assumption that low-quality input prompts result in high variance and low quality responses. This is achieved by measuring the rejected response quality and the reward gap between the chosen and rejected preference pair. Our method, Rejecting Instruction Preferences (RIP) can be used to filter prompts from existing training sets, or to make high quality synthetic datasets, yielding large performance gains across various benchmarks compared to unfiltered data. Using Llama 3.1-8B-Instruct, RIP improves AlpacaEval2 LC Win Rate by 9.4%, Arena-Hard by 8.7%, and WildBench by 9.9%. Using Llama 3.3-70B-Instruct, RIP improves Arena-Hard from 67.5 to 82.9, which is from 18th place to 6th overall in the leaderboard.

Social deduction games like Werewolf combine language, reasoning, and strategy, providing a testbed for studying natural language and social intelligence. However, most studies reduce the game to LLM-based self-play, yielding templated utterances and anecdotal cases that overlook the richness of social gameplay. Evaluation further relies on coarse metrics such as survival time or subjective scoring due to the lack of quality reference data. To address these gaps, we curate a high-quality, human-verified multimodal Werewolf dataset containing over 100 hours of video, 32.4M utterance tokens, and 15 rule variants. Based on this dataset, we propose a novel strategy-alignment evaluation that leverages the winning faction's strategies as ground truth in two stages: 1) Speech evaluation, formulated as multiple-choice-style tasks that assess whether the model can adopt appropriate stances across five dimensions of social ability; and 2) Decision evaluation, which assesses the model's voting choices and opponent-role inferences. This framework enables a fine-grained evaluation of models' linguistic and reasoning capabilities, while capturing their ability to generate strategically coherent gameplay. Our experiments show that state-of-the-art LLMs show diverse performance, with roughly half remain below 0.50, revealing clear gaps in deception and counterfactual reasoning. We hope our dataset further inspires research on language, reasoning, and strategy in multi-agent interaction.

Multimodal pathology-genomic analysis is critical for cancer survival prediction. However, existing approaches predominantly integrate formalin-fixed paraffin-embedded (FFPE) slides with genomic data, while neglecting the availability of other preservation slides, such as Fresh Froze (FF) slides. Moreover, as the high-resolution spatial nature of pathology data tends to dominate the cross-modality fusion process, it hinders effective multimodal fusion and leads to modality imbalance challenges between pathology and genomics. These methods also typically require complete data modalities, limiting their clinical applicability with incomplete modalities, such as missing either pathology or genomic data. In this paper, we propose a multimodal survival prediction framework that leverages hypergraph learning to effectively integrate multi-WSI information and cross-modality interactions between pathology slides and genomics data while addressing modality imbalance. In addition, we introduce a memory mechanism that stores previously learned paired pathology-genomic features and dynamically compensates for incomplete modalities. Experiments on five TCGA datasets demonstrate that our model outperforms advanced methods by over 2.3% in C-Index. Under incomplete modality scenarios, our approach surpasses pathology-only (3.3%) and gene-only models (7.9%). Code: https://github.com/MCPathology/M2Surv

The integration of multimodal data including pathology images and gene profiles is widely applied in precise survival prediction. Despite recent advances in multimodal survival models, collecting complete modalities for multimodal fusion still poses a significant challenge, hindering their application in clinical settings. Current approaches tackling incomplete modalities often fall short, as they typically compensate for only a limited part of the knowledge of missing modalities. To address this issue, we propose a Distilled Prompt Learning framework (DisPro) to utilize the strong robustness of Large Language Models (LLMs) to missing modalities, which employs two-stage prompting for compensation of comprehensive information for missing modalities. In the first stage, Unimodal Prompting (UniPro) distills the knowledge distribution of each modality, preparing for supplementing modality-specific knowledge of the missing modality in the subsequent stage. In the second stage, Multimodal Prompting (MultiPro) leverages available modalities as prompts for LLMs to infer the missing modality, which provides modality-common information. Simultaneously, the unimodal knowledge acquired in the first stage is injected into multimodal inference to compensate for the modality-specific knowledge of the missing modality. Extensive experiments covering various missing scenarios demonstrated the superiority of the proposed method. The code is available at https://github.com/Innse/DisPro.

The human visual system is well-tuned to detect faces of all shapes and sizes. While this brings obvious survival advantages, such as a better chance of spotting unknown predators in the bush, it also leads to spurious face detections. ``Face pareidolia'' describes the perception of face-like structure among otherwise random stimuli: seeing faces in coffee stains or clouds in the sky. In this paper, we study face pareidolia from a computer vision perspective. We present an image dataset of ``Faces in Things'', consisting of five thousand web images with human-annotated pareidolic faces. Using this dataset, we examine the extent to which a state-of-the-art human face detector exhibits pareidolia, and find a significant behavioral gap between humans and machines. We find that the evolutionary need for humans to detect animal faces, as well as human faces, may explain some of this gap. Finally, we propose a simple statistical model of pareidolia in images. Through studies on human subjects and our pareidolic face detectors we confirm a key prediction of our model regarding what image conditions are most likely to induce pareidolia. Dataset and Website: https://aka.ms/faces-in-things

Pancreatic NEuroendocrine Tumors (pNETs) are very rare endocrine neoplasms that account for less than 5% of all pancreatic malignancies, with an incidence of only 1-1.5 cases per 100,000. Early detection of pNETs is critical for improving patient survival, but the rarity of pNETs makes segmenting them from CT a very challenging problem. So far, there has not been a dataset specifically for pNETs available to researchers. To address this issue, we propose a pNETs dataset, a well-annotated Contrast-Enhanced Computed Tomography (CECT) dataset focused exclusively on Pancreatic Neuroendocrine Tumors, containing data from 469 patients. This is the first dataset solely dedicated to pNETs, distinguishing it from previous collections. Additionally, we provide the baseline detection networks with a new slice-wise weight loss function designed for the UNet-based model, improving the overall pNET segmentation performance. We hope that our dataset can enhance the understanding and diagnosis of pNET Tumors within the medical community, facilitate the development of more accurate diagnostic tools, and ultimately improve patient outcomes and advance the field of oncology.

Understanding how deep learning models predict oncology patient risk can provide critical insights into disease progression, support clinical decision-making, and pave the way for trustworthy and data-driven precision medicine. Building on recent advances in the spatial modeling of the tumor microenvironment using graph neural networks, we present an explainable cell graph (xCG) approach for survival prediction. We validate our model on a public cohort of imaging mass cytometry (IMC) data for 416 cases of lung adenocarcinoma. We explain survival predictions in terms of known phenotypes on the cell level by computing risk attributions over cell graphs, for which we propose an efficient grid-based layer-wise relevance propagation (LRP) method. Our ablation studies highlight the importance of incorporating the cancer stage and model ensembling to improve the quality of risk estimates. Our xCG method, together with the IMC data, is made publicly available to support further research.

Multimodal learning significantly benefits cancer survival prediction, especially the integration of pathological images and genomic data. Despite advantages of multimodal learning for cancer survival prediction, massive redundancy in multimodal data prevents it from extracting discriminative and compact information: (1) An extensive amount of intra-modal task-unrelated information blurs discriminability, especially for gigapixel whole slide images (WSIs) with many patches in pathology and thousands of pathways in genomic data, leading to an ``intra-modal redundancy" issue. (2) Duplicated information among modalities dominates the representation of multimodal data, which makes modality-specific information prone to being ignored, resulting in an ``inter-modal redundancy" issue. To address these, we propose a new framework, Prototypical Information Bottlenecking and Disentangling (PIBD), consisting of Prototypical Information Bottleneck (PIB) module for intra-modal redundancy and Prototypical Information Disentanglement (PID) module for inter-modal redundancy. Specifically, a variant of information bottleneck, PIB, is proposed to model prototypes approximating a bunch of instances for different risk levels, which can be used for selection of discriminative instances within modality. PID module decouples entangled multimodal data into compact distinct components: modality-common and modality-specific knowledge, under the guidance of the joint prototypical distribution. Extensive experiments on five cancer benchmark datasets demonstrated our superiority over other methods.

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

Artificial intelligence-assisted imaging analysis has made substantial strides in tumor diagnosis and management. Here we present PASTA, a pan-tumor CT foundation model that achieves state-of-the-art performance on 45 of 46 representative oncology tasks -- including lesion segmentation, tumor detection in plain CT, tumor staging, survival prediction, structured report generation, and cross-modality transfer learning, significantly outperforming the second-best models on 35 tasks. This remarkable advancement is driven by our development of PASTA-Gen, an innovative synthetic tumor generation framework that produces a comprehensive dataset of 30,000 CT scans with pixel-level annotated lesions and paired structured reports, encompassing malignancies across ten organs and five benign lesion types. By leveraging this rich, high-quality synthetic data, we overcome a longstanding bottleneck in the development of CT foundation models -- specifically, the scarcity of publicly available, high-quality annotated datasets due to privacy constraints and the substantial labor required for scaling precise data annotation. Encouragingly, PASTA demonstrates exceptional data efficiency with promising practical value, markedly improving performance on various tasks with only a small amount of real-world data. The open release of both the synthetic dataset and PASTA foundation model effectively addresses the challenge of data scarcity, thereby advancing oncological research and clinical translation.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

Survival analysis is the problem of estimating probability distributions for future event times, which can be seen as a problem in uncertainty quantification. Although there are fundamental theories on strictly proper scoring rules for uncertainty quantification, little is known about those for survival analysis. In this paper, we investigate extensions of four major strictly proper scoring rules for survival analysis and we prove that these extensions are proper under certain conditions, which arise from the discretization of the estimation of probability distributions. We also compare the estimation performances of these extended scoring rules by using real datasets, and the extensions of the logarithmic score and the Brier score performed the best.

Multi-omics research has enhanced our understanding of cancer heterogeneity and progression. Investigating molecular data through multi-omics approaches is crucial for unraveling the complex biological mechanisms underlying cancer, thereby enabling effective diagnosis, treatment, and prevention strategies. However, predicting patient outcomes through integration of all available multi-omics data is an under-study research direction. Here, we present SeNMo (Self-normalizing Network for Multi-omics), a deep neural network trained on multi-omics data across 33 cancer types. SeNMo is efficient in handling multi-omics data characterized by high-width (many features) and low-length (fewer samples) attributes. We trained SeNMo for the task of overall survival using pan-cancer data involving 33 cancer sites from Genomics Data Commons (GDC). The training data includes gene expression, DNA methylation, miRNA expression, DNA mutations, protein expression modalities, and clinical data. We evaluated the model's performance in predicting overall survival using concordance index (C-Index). SeNMo performed consistently well in training regime, with the validation C-Index of 0.76 on GDC's public data. In the testing regime, SeNMo performed with a C-Index of 0.758 on a held-out test set. The model showed an average accuracy of 99.8% on the task of classifying the primary cancer type on the pan-cancer test cohort. SeNMo proved to be a mini-foundation model for multi-omics oncology data because it demonstrated robust performance, and adaptability not only across molecular data types but also on the classification task of predicting the primary cancer type of patients. SeNMo can be further scaled to any cancer site and molecular data type. We believe SeNMo and similar models are poised to transform the oncology landscape, offering hope for more effective, efficient, and patient-centric cancer care.

Discontinuing ad creatives at an appropriate time is one of the most important ad operations that can have a significant impact on sales. Such operational support for ineffective ads has been less explored than that for effective ads. After pre-analyzing 1,000,000 real-world ad creatives, we found that there are two types of discontinuation: short-term (i.e., cut-out) and long-term (i.e., wear-out). In this paper, we propose a practical prediction framework for the discontinuation of ad creatives with a hazard function-based loss function inspired by survival analysis. Our framework predicts the discontinuations with a multi-modal deep neural network that takes as input the ad creative (e.g., text, categorical, image, numerical features). To improve the prediction performance for the two different types of discontinuations and for the ad creatives that contribute to sales, we introduce two new techniques: (1) a two-term estimation technique with multi-task learning and (2) a click-through rate-weighting technique for the loss function. We evaluated our framework using the large-scale ad creative dataset, including 10 billion scale impressions. In terms of the concordance index (short: 0.896, long: 0.939, and overall: 0.792), our framework achieved significantly better performance than the conventional method (0.531). Additionally, we confirmed that our framework (i) demonstrated the same degree of discontinuation effect as manual operations for short-term cases, and (ii) accurately predicted the ad discontinuation order, which is important for long-running ad creatives for long-term cases.

We present an approach to model-based RL that achieves a new state of the art performance on the challenging Craftax-classic benchmark, an open-world 2D survival game that requires agents to exhibit a wide range of general abilities -- such as strong generalization, deep exploration, and long-term reasoning. With a series of careful design choices aimed at improving sample efficiency, our MBRL algorithm achieves a reward of 67.4% after only 1M environment steps, significantly outperforming DreamerV3, which achieves 53.2%, and, for the first time, exceeds human performance of 65.0%. Our method starts by constructing a SOTA model-free baseline, using a novel policy architecture that combines CNNs and RNNs. We then add three improvements to the standard MBRL setup: (a) "Dyna with warmup", which trains the policy on real and imaginary data, (b) "nearest neighbor tokenizer" on image patches, which improves the scheme to create the transformer world model (TWM) inputs, and (c) "block teacher forcing", which allows the TWM to reason jointly about the future tokens of the next timestep.

Accurate prediction of major adverse cardiovascular events recurrence risk in acute myocardial infarction patients based on postoperative cardiac MRI and associated clinical notes is crucial for precision treatment and personalized intervention. Existing methods primarily focus on risk stratification capability while overlooking the need for intermediate robust reasoning and model interpretability in clinical practice. Moreover, end-to-end risk prediction using LLM/VLM faces significant challenges due to data limitations and modeling complexity. To bridge this gap, we propose CardioCoT, a novel two-stage hierarchical reasoning-enhanced survival analysis framework designed to enhance both model interpretability and predictive performance. In the first stage, we employ an evidence-augmented self-refinement mechanism to guide LLM/VLMs in generating robust hierarchical reasoning trajectories based on associated radiological findings. In the second stage, we integrate the reasoning trajectories with imaging data for risk model training and prediction. CardioCoT demonstrates superior performance in MACE recurrence risk prediction while providing interpretable reasoning processes, offering valuable insights for clinical decision-making.

This paper presents a differentially private approach to Kaplan-Meier estimation that achieves accurate survival probability estimates while safeguarding individual privacy. The Kaplan-Meier estimator is widely used in survival analysis to estimate survival functions over time, yet applying it to sensitive datasets, such as clinical records, risks revealing private information. To address this, we introduce a novel algorithm that applies time-indexed Laplace noise, dynamic clipping, and smoothing to produce a privacy-preserving survival curve while maintaining the cumulative structure of the Kaplan-Meier estimator. By scaling noise over time, the algorithm accounts for decreasing sensitivity as fewer individuals remain at risk, while dynamic clipping and smoothing prevent extreme values and reduce fluctuations, preserving the natural shape of the survival curve. Our results, evaluated on the NCCTG lung cancer dataset, show that the proposed method effectively lowers root mean squared error (RMSE) and enhances accuracy across privacy budgets (epsilon). At epsilon = 10, the algorithm achieves an RMSE as low as 0.04, closely approximating non-private estimates. Additionally, membership inference attacks reveal that higher epsilon values (e.g., epsilon geq 6) significantly reduce influential points, particularly at higher thresholds, lowering susceptibility to inference attacks. These findings confirm that our approach balances privacy and utility, advancing privacy-preserving survival analysis.

TorchSurv is a Python package that serves as a companion tool to perform deep survival modeling within the PyTorch environment. Unlike existing libraries that impose specific parametric forms, TorchSurv enables the use of custom PyTorch-based deep survival models. With its lightweight design, minimal input requirements, full PyTorch backend, and freedom from restrictive survival model parameterizations, TorchSurv facilitates efficient deep survival model implementation and is particularly beneficial for high-dimensional and complex input data scenarios.

Clinical trials or studies oftentimes require long-term and/or costly follow-up of participants to evaluate a novel treatment/drug/vaccine. There has been increasing interest in the past few decades in using short-term surrogate outcomes as a replacement of the primary outcome i.e., in using the surrogate outcome, which can potentially be observed sooner, to make inference about the treatment effect on the long-term primary outcome. Very few of the available statistical methods to evaluate a surrogate are applicable to settings where both the surrogate and the primary outcome are time-to-event outcomes subject to censoring. Methods that can handle this setting tend to require parametric assumptions or be limited to assessing only the restricted mean survival time. In this paper, we propose a non-parametric approach to evaluate a censored surrogate outcome, such as time to progression, when the primary outcome is also a censored time-to-event outcome, such as time to death, and the treatment effect of interest is the difference in overall survival. Specifically, we define the proportion of the treatment effect on the primary outcome that is explained (PTE) by the censored surrogate outcome in this context, and estimate this proportion by defining and deriving an optimal transformation of the surrogate information. Our approach provides the added advantage of relaxed assumptions to guarantee that the true PTE is within (0,1), along with being model-free. Finite sample performance of our estimators are illustrated via extensive simulation studies and a real data application examining progression-free survival as a surrogate for overall survival for patients with metastatic colorectal cancer.

Decisions about managing patients on the heart transplant waitlist are currently made by committees of doctors who consider multiple factors, but the process remains largely ad-hoc. With the growing volume of longitudinal patient, donor, and organ data collected by the United Network for Organ Sharing (UNOS) since 2018, there is increasing interest in analytical approaches to support clinical decision-making at the time of organ availability. In this study, we benchmark machine learning models that leverage longitudinal waitlist history data for time-dependent, time-to-event modeling of waitlist mortality. We train on 23,807 patient records with 77 variables and evaluate both survival prediction and discrimination at a 1-year horizon. Our best model achieves a C-Index of 0.94 and AUROC of 0.89, significantly outperforming previous models. Key predictors align with known risk factors while also revealing novel associations. Our findings can support urgency assessment and policy refinement in heart transplant decision making.

As retailers around the world increase efforts in developing targeted marketing campaigns for different audiences, predicting accurately which customers are most likely to churn ahead of time is crucial for marketing teams in order to increase business profits. This work presents a deep survival framework to predict which customers are at risk of stopping to purchase with retail companies in non-contractual settings. By leveraging the survival model parameters to be learnt by recurrent neural networks, we are able to obtain individual level survival models for purchasing behaviour based only on individual customer behaviour and avoid time-consuming feature engineering processes usually done when training machine learning models.

Survival analysis can sometimes involve individuals who will not experience the event of interest, forming what is known as the cured group. Identifying such individuals is not always possible beforehand, as they provide only right-censored data. Ignoring the presence of the cured group can introduce bias in the final model. This paper presents a method for estimating a semiparametric additive hazards model that accounts for the cured fraction. Unlike regression coefficients in a hazard ratio model, those in an additive hazard model measure hazard differences. The proposed method uses a primal-dual interior point algorithm to obtain constrained maximum penalized likelihood estimates of the model parameters, including the regression coefficients and the baseline hazard, subject to certain non-negativity constraints.

The face is a rich source of information that can be utilized to infer a person's biological age, sex, phenotype, genetic defects, and health status. All of these factors are relevant for predicting an individual's remaining lifespan. In this study, we collected a dataset of over 24,000 images (from Wikidata/Wikipedia) of individuals who died of natural causes, along with the number of years between when the image was taken and when the person passed away. We made this dataset publicly available. We fine-tuned multiple Convolutional Neural Network (CNN) models on this data, at best achieving a mean absolute error of 8.3 years in the validation data using VGGFace. However, the model's performance diminishes when the person was younger at the time of the image. To demonstrate the potential applications of our remaining lifespan model, we present examples of using it to estimate the average loss of life (in years) due to the COVID-19 pandemic and to predict the increase in life expectancy that might result from a health intervention such as weight loss. Additionally, we discuss the ethical considerations associated with such models.

We present a new text-to-SQL dataset for electronic health records (EHRs). The utterances were collected from 222 hospital staff members, including physicians, nurses, and insurance review and health records teams. To construct the QA dataset on structured EHR data, we conducted a poll at a university hospital and used the responses to create seed questions. We then manually linked these questions to two open-source EHR databases, MIMIC-III and eICU, and included various time expressions and held-out unanswerable questions in the dataset, which were also collected from the poll. Our dataset poses a unique set of challenges: the model needs to 1) generate SQL queries that reflect a wide range of needs in the hospital, including simple retrieval and complex operations such as calculating survival rate, 2) understand various time expressions to answer time-sensitive questions in healthcare, and 3) distinguish whether a given question is answerable or unanswerable. We believe our dataset, EHRSQL, can serve as a practical benchmark for developing and assessing QA models on structured EHR data and take a step further towards bridging the gap between text-to-SQL research and its real-life deployment in healthcare. EHRSQL is available at https://github.com/glee4810/EHRSQL.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

Cancer is a genetic disorder whose clonal evolution can be monitored by tracking noisy genome-wide copy number variants. We introduce the Copy Number Stochastic Block Model (CN-SBM), a probabilistic framework that jointly clusters samples and genomic regions based on discrete copy number states using a bipartite categorical block model. Unlike models relying on Gaussian or Poisson assumptions, CN-SBM respects the discrete nature of CNV calls and captures subpopulation-specific patterns through block-wise structure. Using a two-stage approach, CN-SBM decomposes CNV data into primary and residual components, enabling detection of both large-scale chromosomal alterations and finer aberrations. We derive a scalable variational inference algorithm for application to large cohorts and high-resolution data. Benchmarks on simulated and real datasets show improved model fit over existing methods. Applied to TCGA low-grade glioma data, CN-SBM reveals clinically relevant subtypes and structured residual variation, aiding patient stratification in survival analysis. These results establish CN-SBM as an interpretable, scalable framework for CNV analysis with direct relevance for tumor heterogeneity and prognosis.

Reliable probability estimation is of crucial importance in many real-world applications where there is inherent (aleatoric) uncertainty. Probability-estimation models are trained on observed outcomes (e.g. whether it has rained or not, or whether a patient has died or not), because the ground-truth probabilities of the events of interest are typically unknown. The problem is therefore analogous to binary classification, with the difference that the objective is to estimate probabilities rather than predicting the specific outcome. This work investigates probability estimation from high-dimensional data using deep neural networks. There exist several methods to improve the probabilities generated by these models but they mostly focus on model (epistemic) uncertainty. For problems with inherent uncertainty, it is challenging to evaluate performance without access to ground-truth probabilities. To address this, we build a synthetic dataset to study and compare different computable metrics. We evaluate existing methods on the synthetic data as well as on three real-world probability estimation tasks, all of which involve inherent uncertainty: precipitation forecasting from radar images, predicting cancer patient survival from histopathology images, and predicting car crashes from dashcam videos. We also give a theoretical analysis of a model for high-dimensional probability estimation which reproduces several of the phenomena evinced in our experiments. Finally, we propose a new method for probability estimation using neural networks, which modifies the training process to promote output probabilities that are consistent with empirical probabilities computed from the data. The method outperforms existing approaches on most metrics on the simulated as well as real-world data.

Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is primarily used for ER+ breast cancer, which is costly, tissue destructive, requires specialized platforms and takes several weeks to obtain a result. Deep learning algorithms can effectively extract morphological patterns in digital histopathology images to predict molecular phenotypes quickly and cost-effectively. We propose a new, computationally efficient approach called hist2RNA inspired by bulk RNA-sequencing techniques to predict the expression of 138 genes (incorporated from six commercially available molecular profiling tests), including luminal PAM50 subtype, from hematoxylin and eosin (H&E) stained whole slide images (WSIs). The training phase involves the aggregation of extracted features for each patient from a pretrained model to predict gene expression at the patient level using annotated H&E images from The Cancer Genome Atlas (TCGA, n=335). We demonstrate successful gene prediction on a held-out test set (n = 160, corr = 0.82 across patients, corr = 0.29 across genes) and perform exploratory analysis on an external tissue microarray (TMA) dataset (n = 498) with known IHC and survival information. Our model is able to predict gene expression and luminal PAM50 subtype (Luminal A versus Luminal B) on the TMA dataset with prognostic significance for overall survival in univariate analysis (c-index = 0.56, hazard ratio = 2.16 (95% CI 1.12-3.06), p < 5 x 10-3), and independent significance in multivariate analysis incorporating standard clinicopathological variables (c-index = 0.65, hazard ratio = 1.85 (95% CI 1.30-2.68), p < 5 x 10-3).

Accurately predicting immunotherapy response in Non-Small Cell Lung Cancer (NSCLC) remains a critical unmet need. Existing radiomics and deep learning-based predictive models rely primarily on pre-treatment imaging to predict categorical response outcomes, limiting their ability to capture the complex morphological and textural transformations induced by immunotherapy. This study introduces ImmunoDiff, an anatomy-aware diffusion model designed to synthesize post-treatment CT scans from baseline imaging while incorporating clinically relevant constraints. The proposed framework integrates anatomical priors, specifically lobar and vascular structures, to enhance fidelity in CT synthesis. Additionally, we introduce a novel cbi-Adapter, a conditioning module that ensures pairwise-consistent multimodal integration of imaging and clinical data embeddings, to refine the generative process. Additionally, a clinical variable conditioning mechanism is introduced, leveraging demographic data, blood-based biomarkers, and PD-L1 expression to refine the generative process. Evaluations on an in-house NSCLC cohort treated with immune checkpoint inhibitors demonstrate a 21.24% improvement in balanced accuracy for response prediction and a 0.03 increase in c-index for survival prediction. Code will be released soon.

The World Health Organization added Disease X to their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. During different virus outbreaks of the past, such as COVID-19, Influenza, Lyme Disease, and Zika virus, researchers from various disciplines utilized Google Trends to mine multimodal components of web behavior to study, investigate, and analyze the global awareness, preparedness, and response associated with these respective virus outbreaks. As the world prepares for Disease X, a dataset on web behavior related to Disease X would be crucial to contribute towards the timely advancement of research in this field. Furthermore, none of the prior works in this field have focused on the development of a dataset to compile relevant web behavior data, which would help to prepare for Disease X. To address these research challenges, this work presents a dataset of web behavior related to Disease X, which emerged from different geographic regions of the world, between February 2018 and August 2023. Specifically, this dataset presents the search interests related to Disease X from 94 geographic regions. The dataset was developed by collecting data using Google Trends. The relevant search interests for all these regions for each month in this time range are available in this dataset. This paper also discusses the compliance of this dataset with the FAIR principles of scientific data management. Finally, an analysis of this dataset is presented to uphold the applicability, relevance, and usefulness of this dataset for the investigation of different research questions in the interrelated fields of Big Data, Data Mining, Healthcare, Epidemiology, and Data Analysis with a specific focus on Disease X.

Breast cancer is a prevalent form of cancer among women, with over 1.5 million women being diagnosed each year. Unfortunately, the survival rates for breast cancer patients in certain third-world countries, like South Africa, are alarmingly low, with only 40% of diagnosed patients surviving beyond five years. The inadequate availability of resources, including qualified pathologists, delayed diagnoses, and ineffective therapy planning, contribute to this low survival rate. To address this pressing issue, medical specialists and researchers have turned to domain-specific AI approaches, specifically deep learning models, to develop end-to-end solutions that can be integrated into computer-aided diagnosis (CAD) systems. By improving the workflow of pathologists, these AI models have the potential to enhance the detection and diagnosis of breast cancer. This research focuses on evaluating the performance of various cutting-edge convolutional neural network (CNN) architectures in comparison to a relatively new model called the Vision Trans-former (ViT). The objective is to determine the superiority of these models in terms of their accuracy and effectiveness. The experimental results reveal that the ViT models outperform the other selected state-of-the-art CNN architectures, achieving an impressive accuracy rate of 95.15%. This study signifies a significant advancement in the field, as it explores the utilization of data augmentation and other relevant preprocessing techniques in conjunction with deep learning models for the detection and diagnosis of breast cancer using datasets of Breast Cancer Histopathological Image Classification.

In recent years, medical information technology has made it possible for electronic health record (EHR) to store fairly complete clinical data. This has brought health care into the era of "big data". However, medical data are often sparse and strongly correlated, which means that medical problems cannot be solved effectively. With the rapid development of deep learning in recent years, it has provided opportunities for the use of big data in healthcare. In this paper, we propose a temporal-saptial correlation attention network (TSCAN) to handle some clinical characteristic prediction problems, such as predicting death, predicting length of stay, detecting physiologic decline, and classifying phenotypes. Based on the design of the attention mechanism model, our approach can effectively remove irrelevant items in clinical data and irrelevant nodes in time according to different tasks, so as to obtain more accurate prediction results. Our method can also find key clinical indicators of important outcomes that can be used to improve treatment options. Our experiments use information from the Medical Information Mart for Intensive Care (MIMIC-IV) database, which is open to the public. Finally, we have achieved significant performance benefits of 2.0\% (metric) compared to other SOTA prediction methods. We achieved a staggering 90.7\% on mortality rate, 45.1\% on length of stay. The source code can be find: https://github.com/yuyuheintju/TSCAN.

Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown promise as tools to make sense of a range of multi-variate sequences from protein-structures, music, electronic health records to weather-forecasts. We can also represent human lives in a way that shares this structural similarity to language. From one perspective, lives are simply sequences of events: People are born, visit the pediatrician, start school, move to a new location, get married, and so on. Here, we exploit this similarity to adapt innovations from natural language processing to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on arguably the most comprehensive registry data in existence, available for an entire nation of more than six million individuals across decades. Our data include information about life-events related to health, education, occupation, income, address, and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to identify new potential mechanisms that impact life outcomes and associated possibilities for personalized interventions.

Data scarcity is a common obstacle in medical research due to the high costs associated with data collection and the complexity of gaining access to and utilizing data. Synthesizing health data may provide an efficient and cost-effective solution to this shortage, enabling researchers to explore distributions and populations that are not represented in existing observations or difficult to access due to privacy considerations. To that end, we have developed a multi-task self-attention model that produces realistic wearable activity data. We examine the characteristics of the generated data and quantify its similarity to genuine samples with both quantitative and qualitative approaches.

Clinical trials disruption has always represented a non negligible part of the ending of interventional studies. While the SARS-CoV-2 (COVID-19) pandemic has led to an impressive and unprecedented initiation of clinical research, it has also led to considerable disruption of clinical trials in other disease areas, with around 80% of non-COVID-19 trials stopped or interrupted during the pandemic. In many cases the disrupted trials will not have the planned statistical power necessary to yield interpretable results. This paper describes methods to compensate for the information loss arising from trial disruptions by incorporating additional information available from auxiliary data sources. The methods described include the use of auxiliary data on baseline and early outcome data available from the trial itself and frequentist and Bayesian approaches for the incorporation of information from external data sources. The methods are illustrated by application to the analysis of artificial data based on the Primary care pediatrics Learning Activity Nutrition (PLAN) study, a clinical trial assessing a diet and exercise intervention for overweight children, that was affected by the COVID-19 pandemic. We show how all of the methods proposed lead to an increase in precision relative to use of complete case data only.

We collected a large dataset consisting of nearly 900 unique participants. For every participant we recorded two 30 second uncompressed videos, synchronized PPG waveforms and a single blood pressure measurement. Gender, age and skin color were also registered for every participant. The dataset includes roughly equal numbers of males and females, as well as participants of all ages. While the skin color distribution could have been more balanced, the dataset contains individuals from every skin color. The data was collected in a diverse set of locations to ensure a wide variety of backgrounds and lighting conditions. In an effort to assist in the research and development of remote vital sign measurement we are now opening up access to this dataset.

Laboratory test results are an important and generally high dimensional component of a patient's Electronic Health Record (EHR). We train embedding representations (via Word2Vec and GloVe) for LOINC codes of laboratory tests from the EHRs of about 80,000 patients at a cancer center. To include information about lab test outcomes, we also train embeddings on the concatenation of a LOINC code with a symbol indicating normality or abnormality of the result. We observe several clinically meaningful similarities among LOINC embeddings trained over our data. For the embeddings of the concatenation of LOINCs with abnormality codes, we evaluate the performance for mortality prediction tasks and the ability to preserve ordinality properties: i.e. a lab test with normal outcome should be more similar to an abnormal one than to the a very abnormal one.

The global cost of drug discovery and development exceeds $200 billion annually. The main results of drug discovery and development are the outcomes of clinical trials, which directly influence the regulatory approval of new drug candidates and ultimately affect patient outcomes. Despite their significance, large-scale, high-quality clinical trial outcome data are not readily available to the public. Suppose a large clinical trial outcome dataset is provided; machine learning researchers can potentially develop accurate prediction models using past trials and outcome labels, which could help prioritize and optimize therapeutic programs, ultimately benefiting patients. This paper introduces Clinical Trial Outcome (CTO) dataset, the largest trial outcome dataset with around 479K clinical trials, aggregating outcomes from multiple sources of weakly supervised labels, minimizing the noise from individual sources, and eliminating the need for human annotation. These sources include large language model (LLM) decisions on trial-related documents, news headline sentiments, stock prices of trial sponsors, trial linkages across phases, and other signals such as patient dropout rates and adverse events. CTO's labels show unprecedented agreement with supervised clinical trial outcome labels from test split of the supervised TOP dataset, with a 91 F1.

Machine learning techniques are effective for building predictive models because they identify patterns in large datasets. Development of a model for complex real-life problems often stop at the point of publication, proof of concept or when made accessible through some mode of deployment. However, a model in the medical domain risks becoming obsolete as patient demographics, systems and clinical practices change. The maintenance and monitoring of predictive model performance post-publication is crucial to enable their safe and effective long-term use. We will assess the infrastructure required to monitor the outputs of a machine learning algorithm, and present two scenarios with examples of monitoring and updates of models, firstly on a breast cancer prognosis model trained on public longitudinal data, and secondly on a neurodegenerative stratification algorithm that is currently being developed and tested in clinic.

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.

Given the dominance of dense retrievers that do not generalize well beyond their training dataset distributions, domain-specific test sets are essential in evaluating retrieval. There are few test datasets for retrieval systems intended for use by healthcare providers in a point-of-care setting. To fill this gap we have collaborated with medical professionals to create CURE, an ad-hoc retrieval test dataset for passage ranking with 2000 queries spanning 10 medical domains with a monolingual (English) and two cross-lingual (French/Spanish -> English) conditions. In this paper, we describe how CURE was constructed and provide baseline results to showcase its effectiveness as an evaluation tool. CURE is published with a Creative Commons Attribution Non Commercial 4.0 license and can be accessed on Hugging Face.

Models that can predict the occurrence of events ahead of time with low false-alarm rates are critical to the acceptance of decision support systems in the medical community. This challenging task is typically treated as a simple binary classification, ignoring temporal dependencies between samples, whereas we propose to exploit this structure. We first introduce a common theoretical framework unifying dynamic survival analysis and early event prediction. Following an analysis of objectives from both fields, we propose Temporal Label Smoothing (TLS), a simpler, yet best-performing method that preserves prediction monotonicity over time. By focusing the objective on areas with a stronger predictive signal, TLS improves performance over all baselines on two large-scale benchmark tasks. Gains are particularly notable along clinically relevant measures, such as event recall at low false-alarm rates. TLS reduces the number of missed events by up to a factor of two over previously used approaches in early event prediction.

Machine learning based decision-support tools in criminal justice systems are subjects of intense discussions and academic research. There are important open questions about the utility and fairness of such tools. Academic researchers often rely on a few small datasets that are not sufficient to empirically study various real-world aspects of these questions. In this paper, we contribute WCLD, a curated large dataset of 1.5 million criminal cases from circuit courts in the U.S. state of Wisconsin. We used reliable public data from 1970 to 2020 to curate attributes like prior criminal counts and recidivism outcomes. The dataset contains large number of samples from five racial groups, in addition to information like sex and age (at judgment and first offense). Other attributes in this dataset include neighborhood characteristics obtained from census data, detailed types of offense, charge severity, case decisions, sentence lengths, year of filing etc. We also provide pseudo-identifiers for judge, county and zipcode. The dataset will not only enable researchers to more rigorously study algorithmic fairness in the context of criminal justice, but also relate algorithmic challenges with various systemic issues. We also discuss in detail the process of constructing the dataset and provide a datasheet. The WCLD dataset is available at https://clezdata.github.io/wcld/.

The COVID-19 pandemic has posed a heavy burden to the healthcare system worldwide and caused huge social disruption and economic loss. Many deep learning models have been proposed to conduct clinical predictive tasks such as mortality prediction for COVID-19 patients in intensive care units using Electronic Health Record (EHR) data. Despite their initial success in certain clinical applications, there is currently a lack of benchmarking results to achieve a fair comparison so that we can select the optimal model for clinical use. Furthermore, there is a discrepancy between the formulation of traditional prediction tasks and real-world clinical practice in intensive care. To fill these gaps, we propose two clinical prediction tasks, Outcome-specific length-of-stay prediction and Early mortality prediction for COVID-19 patients in intensive care units. The two tasks are adapted from the naive length-of-stay and mortality prediction tasks to accommodate the clinical practice for COVID-19 patients. We propose fair, detailed, open-source data-preprocessing pipelines and evaluate 17 state-of-the-art predictive models on two tasks, including 5 machine learning models, 6 basic deep learning models and 6 deep learning predictive models specifically designed for EHR data. We provide benchmarking results using data from two real-world COVID-19 EHR datasets. One dataset is publicly available without needing any inquiry and another dataset can be accessed on request. We provide fair, reproducible benchmarking results for two tasks. We deploy all experiment results and models on an online platform. We also allow clinicians and researchers to upload their data to the platform and get quick prediction results using our trained models. We hope our efforts can further facilitate deep learning and machine learning research for COVID-19 predictive modeling.

In this paper, we present a multimodal dataset obtained from a honey bee colony in Montr\'eal, Quebec, Canada, spanning the years of 2021 to 2022. This apiary comprised 10 beehives, with microphones recording more than 2000 hours of high quality raw audio, and also sensors capturing temperature, and humidity. Periodic hive inspections involved monitoring colony honey bee population changes, assessing queen-related conditions, and documenting overall hive health. Additionally, health metrics, such as Varroa mite infestation rates and winter mortality assessments were recorded, offering valuable insights into factors affecting hive health status and resilience. In this study, we first outline the data collection process, sensor data description, and dataset structure. Furthermore, we demonstrate a practical application of this dataset by extracting various features from the raw audio to predict colony population using the number of frames of bees as a proxy.

In this article, we conduct data mining to discover the countries, universities and companies, produced or collaborated the most research on Covid-19 since the pandemic started. We present some interesting findings, but despite analysing all available records on COVID-19 from the Web of Science Core Collection, we failed to reach any significant conclusions on how the world responded to the COVID-19 pandemic. Therefore, we increased our analysis to include all available data records on pandemics and epidemics from 1900 to 2020. We discover some interesting results on countries, universities and companies, that produced collaborated most the most in research on pandemic and epidemics. Then we compared the results with the analysing on COVID-19 data records. This has created some interesting findings that are explained and graphically visualised in the article.

Purpose: Magnetic resonance imaging (MRI) to visualize anatomical motion is becoming increasingly important when treating cancer patients with radiotherapy. Hybrid MRI-linear accelerator (MRI-linac) systems allow real-time motion management during irradiation. This paper presents a multi-institutional real-time MRI time series dataset from different MRI-linac vendors. The dataset is designed to support developing and evaluating real-time tumor localization (tracking) algorithms for MRI-guided radiotherapy within the TrackRAD2025 challenge (https://trackrad2025.grand-challenge.org/). Acquisition and validation methods: The dataset consists of sagittal 2D cine MRIs in 585 patients from six centers (3 Dutch, 1 German, 1 Australian, and 1 Chinese). Tumors in the thorax, abdomen, and pelvis acquired on two commercially available MRI-linacs (0.35 T and 1.5 T) were included. For 108 cases, irradiation targets or tracking surrogates were manually segmented on each temporal frame. The dataset was randomly split into a public training set of 527 cases (477 unlabeled and 50 labeled) and a private testing set of 58 cases (all labeled). Data Format and Usage Notes: The data is publicly available under the TrackRAD2025 collection: https://doi.org/10.57967/hf/4539. Both the images and segmentations for each patient are available in metadata format. Potential Applications: This novel clinical dataset will enable the development and evaluation of real-time tumor localization algorithms for MRI-guided radiotherapy. By enabling more accurate motion management and adaptive treatment strategies, this dataset has the potential to advance the field of radiotherapy significantly.

Synthetic data generation has the potential to impact applications and domains with scarce data. However, before such data is used for sensitive tasks such as mental health, we need an understanding of how different demographics are represented in it. In our paper, we analyze the potential of producing synthetic data using GPT-3 by exploring the various stressors it attributes to different race and gender combinations, to provide insight for future researchers looking into using LLMs for data generation. Using GPT-3, we develop HEADROOM, a synthetic dataset of 3,120 posts about depression-triggering stressors, by controlling for race, gender, and time frame (before and after COVID-19). Using this dataset, we conduct semantic and lexical analyses to (1) identify the predominant stressors for each demographic group; and (2) compare our synthetic data to a human-generated dataset. We present the procedures to generate queries to develop depression data using GPT-3, and conduct analyzes to uncover the types of stressors it assigns to demographic groups, which could be used to test the limitations of LLMs for synthetic data generation for depression data. Our findings show that synthetic data mimics some of the human-generated data distribution for the predominant depression stressors across diverse demographics.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

PURPOSE: Subarachnoid hemorrhage (SAH) entails high morbidity and mortality rates. Convolutional neural networks (CNN), a form of deep learning, are capable of generating highly accurate predictions from imaging data. Our objective was to predict mortality in SAH patients by processing the initial CT scan on a CNN based algorithm. METHODS: Retrospective multicentric study of a consecutive cohort of patients with SAH between 2011-2022. Demographic, clinical and radiological variables were analyzed. Pre-processed baseline CT scan images were used as the input for training a CNN using AUCMEDI Framework. Our model's architecture leverages the DenseNet-121 structure, employing transfer learning principles. The output variable was mortality in the first three months. Performance of the model was evaluated by statistical parameters conventionally used in studies involving artificial intelligence methods. RESULTS: Images from 219 patients were processed, 175 for training and validation of the CNN and 44 for its evaluation. 52%(115/219) of patients were female, and the median age was 58(SD=13.06) years. 18.5%(39/219) were idiopathic SAH. Mortality rate was 28.5%(63/219). The model showed good accuracy at predicting mortality in SAH patients exclusively using the images of the initial CT scan (Accuracy=74%, F1=75% and AUC=82%). CONCLUSION: Modern image processing techniques based on AI and CNN make possible to predict mortality in SAH patients with high accuracy using CT scan images as the only input. These models might be optimized by including more data and patients resulting in better training, development and performance on tasks which are beyond the skills of conventional clinical knowledge.

This paper presents a dataset with over 3.3M threads and 134.5M posts from the Politically Incorrect board (/pol/) of the imageboard forum 4chan, posted over a period of almost 3.5 years (June 2016-November 2019). To the best of our knowledge, this represents the largest publicly available 4chan dataset, providing the community with an archive of posts that have been permanently deleted from 4chan and are otherwise inaccessible. We augment the data with a set of additional labels, including toxicity scores and the named entities mentioned in each post. We also present a statistical analysis of the dataset, providing an overview of what researchers interested in using it can expect, as well as a simple content analysis, shedding light on the most prominent discussion topics, the most popular entities mentioned, and the toxicity level of each post. Overall, we are confident that our work will motivate and assist researchers in studying and understanding 4chan, as well as its role on the greater Web. For instance, we hope this dataset may be used for cross-platform studies of social media, as well as being useful for other types of research like natural language processing. Finally, our dataset can assist qualitative work focusing on in-depth case studies of specific narratives, events, or social theories.

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

Background: Electronic Health Records hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Existing approaches focus mostly on structured data and a subset of single-domain outcomes. We explore how temporal modelling of patients from free text and structured data, using deep generative transformers can be used to forecast a wide range of future disorders, substances, procedures or findings. Methods: We present Foresight, a novel transformer-based pipeline that uses named entity recognition and linking tools to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, substances, procedures and findings. We processed the entire free-text portion from three different hospital datasets totalling 811336 patients covering both physical and mental health. Findings: On tests in two UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 0.68, 0.76 and 0.88 was achieved for forecasting the next disorder in a patient timeline, while precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by five clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. As a generative model, it can forecast follow-on biomedical concepts for as many steps as required. Interpretation: Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials and clinical research to study the progression of disorders, simulate interventions and counterfactuals, and educational purposes.

Currently, there is limited research investigating the phenomenon of research data repositories being shut down, and the impact this has on the long-term availability of data. This paper takes an infrastructure perspective on the preservation of research data by using a registry to identify 191 research data repositories that have been closed and presenting information on the shutdown process. The results show that 6.2 % of research data repositories indexed in the registry were shut down. The risks resulting in repository shutdown are varied. The median age of a repository when shutting down is 12 years. Strategies to prevent data loss at the infrastructure level are pursued to varying extent. 44 % of the repositories in the sample migrated data to another repository, and 12 % maintain limited access to their data collection. However, both strategies are not permanent solutions. Finally, the general lack of information on repository shutdown events as well as the effect on the findability of data and the permanence of the scholarly record are discussed.

With an estimated 160,000 deaths in 2018, lung cancer is the most common cause of cancer death in the United States. Lung cancer CT screening has been shown to reduce mortality by up to 40% and is now included in US screening guidelines. Reducing the high error rates in lung cancer screening is imperative because of the high clinical and financial costs caused by diagnosis mistakes. Despite the use of standards for radiological diagnosis, persistent inter-grader variability and incomplete characterization of comprehensive imaging findings remain as limitations of current methods. These limitations suggest opportunities for more sophisticated systems to improve performance and inter-reader consistency. In this report, we reproduce a state-of-the-art deep learning algorithm for lung cancer risk prediction. Our model predicts malignancy probability and risk bucket classification from lung CT studies. This allows for risk categorization of patients being screened and suggests the most appropriate surveillance and management. Combining our solution high accuracy, consistency and fully automated nature, our approach may enable highly efficient screening procedures and accelerate the adoption of lung cancer screening.

Missing values, irregularly collected samples, and multi-resolution signals commonly occur in multivariate time series data, making predictive tasks difficult. These challenges are especially prevalent in the healthcare domain, where patients' vital signs and electronic records are collected at different frequencies and have occasionally missing information due to the imperfections in equipment or patient circumstances. Researchers have handled each of these issues differently, often handling missing data through mean value imputation and then using sequence models over the multivariate signals while ignoring the different resolution of signals. We propose a unified model named Multi-resolution Flexible Irregular Time series Network (Multi-FIT). The building block for Multi-FIT is the FIT network. The FIT network creates an informative dense representation at each time step using signal information such as last observed value, time difference since the last observed time stamp and overall mean for the signal. Vertical FIT (FIT-V) is a variant of FIT which also models the relationship between different temporal signals while creating the informative dense representations for the signal. The multi-FIT model uses multiple FIT networks for sets of signals with different resolutions, further facilitating the construction of flexible representations. Our model has three main contributions: a.) it does not impute values but rather creates informative representations to provide flexibility to the model for creating task-specific representations b.) it models the relationship between different signals in the form of support signals c.) it models different resolutions in parallel before merging them for the final prediction task. The FIT, FIT-V and Multi-FIT networks improve upon the state-of-the-art models for three predictive tasks, including the forecasting of patient survival.

Background: Social media platforms have become a viable source of medical information, with patients and healthcare professionals using them to share health-related information and track diseases. Similarly, YouTube, the largest video-sharing platform in the world contains vlogs where individuals talk about their illnesses. The aim of our study was to investigate the use of Natural Language Processing (NLP) to identify the spoken content of YouTube vlogs related to the diagnosis of Coronavirus disease of 2019 (COVID-19) for public health screening. Methods: COVID-19 videos on YouTube were searched using relevant keywords. A total of 1000 videos being spoken in English were downloaded out of which 791 were classified as vlogs, 192 were non-vlogs, and 17 were deleted by the channel. The videos were converted into a textual format using Microsoft Streams. The textual data was preprocessed using basic and advanced preprocessing methods. A lexicon of 200 words was created which contained words related to COVID-19. The data was analyzed using topic modeling, word clouds, and lexicon matching. Results: The word cloud results revealed discussions about COVID-19 symptoms like "fever", along with generic terms such as "mask" and "isolation". Lexical analysis demonstrated that in 96.46% of videos, patients discussed generic terms, and in 95.45% of videos, people talked about COVID-19 symptoms. LDA Topic Modeling results also generated topics that successfully captured key themes and content related to our investigation of COVID-19 diagnoses in YouTube vlogs. Conclusion: By leveraging NLP techniques on YouTube vlogs public health practitioners can enhance their ability to mitigate the effects of pandemics and effectively respond to public health challenges.

We present the data release and data reduction process for the Epoch 1 NIRCam observations for the Cosmic Evolution Early Release Science Survey (CEERS). These data consist of NIRCam imaging in six broadband filters (F115W, F150W, F200W, F277W, F356W and F444W) and one medium band filter (F410M) over four pointings, obtained in parallel with primary CEERS MIRI observations (Yang et al. in prep). We reduced the NIRCam imaging with the JWST Calibration Pipeline, with custom modifications and reduction steps designed to address additional features and challenges with the data. Here we provide a detailed description of each step in our reduction and a discussion of future expected improvements. Our reduction process includes corrections for known pre-launch issues such as 1/f noise, as well as in-flight issues including snowballs, wisps, and astrometric alignment. Many of our custom reduction processes were first developed with pre-launch simulated NIRCam imaging over the full 10 CEERS NIRCam pointings. We present a description of the creation and reduction of this simulated dataset in the Appendix. We provide mosaics of the real images in a public release, as well as our reduction scripts with detailed explanations to allow users to reproduce our final data products. These represent one of the first official public datasets released from the Directors Discretionary Early Release Science (DD-ERS) program.

Social isolation and loneliness, which have been increasing in recent years strongly contribute toward suicide rates. Although social isolation and loneliness are not currently recorded within the US National Violent Death Reporting System's (NVDRS) structured variables, natural language processing (NLP) techniques can be used to identify these constructs in law enforcement and coroner medical examiner narratives. Using topic modeling to generate lexicon development and supervised learning classifiers, we developed high-quality classifiers (average F1: .86, accuracy: .82). Evaluating over 300,000 suicides from 2002 to 2020, we identified 1,198 mentioning chronic social isolation. Decedents had higher odds of chronic social isolation classification if they were men (OR = 1.44; CI: 1.24, 1.69, p<.0001), gay (OR = 3.68; 1.97, 6.33, p<.0001), or were divorced (OR = 3.34; 2.68, 4.19, p<.0001). We found significant predictors for other social isolation topics of recent or impending divorce, child custody loss, eviction or recent move, and break-up. Our methods can improve surveillance and prevention of social isolation and loneliness in the United States.

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

Conventional surveillance systems for monitoring infectious diseases, such as influenza, face challenges due to shortage of skilled healthcare professionals, remoteness of communities and absence of communication infrastructures. Internet-based approaches for surveillance are appealing logistically as well as economically. Search engine queries and Twitter have been the primarily used data sources in such approaches. The aim of this study is to assess the predictive power of an alternative data source, Instagram. By using 317 weeks of publicly available data from Instagram, we trained several machine learning algorithms to both nowcast and forecast the number of official influenza-like illness incidents in Finland where population-wide official statistics about the weekly incidents are available. In addition to date and hashtag count features of online posts, we were able to utilize also the visual content of the posted images with the help of deep convolutional neural networks. Our best nowcasting model reached a mean absolute error of 11.33 incidents per week and a correlation coefficient of 0.963 on the test data. Forecasting models for predicting 1 week and 2 weeks ahead showed statistical significance as well by reaching correlation coefficients of 0.903 and 0.862, respectively. This study demonstrates how social media and in particular, digital photographs shared in them, can be a valuable source of information for the field of infodemiology.

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

Cancer is a complex disease, the understanding and treatment of which are being aided through increases in the volume of collected data and in the scale of deployed computing power. Consequently, there is a growing need for the development of data-driven and, in particular, deep learning methods for various tasks such as cancer diagnosis, detection, prognosis, and prediction. Despite recent successes, however, designing high-performing deep learning models for nonimage and nontext cancer data is a time-consuming, trial-and-error, manual task that requires both cancer domain and deep learning expertise. To that end, we develop a reinforcement-learning-based neural architecture search to automate deep-learning-based predictive model development for a class of representative cancer data. We develop custom building blocks that allow domain experts to incorporate the cancer-data-specific characteristics. We show that our approach discovers deep neural network architectures that have significantly fewer trainable parameters, shorter training time, and accuracy similar to or higher than those of manually designed architectures. We study and demonstrate the scalability of our approach on up to 1,024 Intel Knights Landing nodes of the Theta supercomputer at the Argonne Leadership Computing Facility.

Purpose: Medical imaging has become increasingly important in diagnosing and treating oncological patients, particularly in radiotherapy. Recent advances in synthetic computed tomography (sCT) generation have increased interest in public challenges to provide data and evaluation metrics for comparing different approaches openly. This paper describes a dataset of brain and pelvis computed tomography (CT) images with rigidly registered CBCT and MRI images to facilitate the development and evaluation of sCT generation for radiotherapy planning. Acquisition and validation methods: The dataset consists of CT, CBCT, and MRI of 540 brains and 540 pelvic radiotherapy patients from three Dutch university medical centers. Subjects' ages ranged from 3 to 93 years, with a mean age of 60. Various scanner models and acquisition settings were used across patients from the three data-providing centers. Details are available in CSV files provided with the datasets. Data format and usage notes: The data is available on Zenodo (https://doi.org/10.5281/zenodo.7260705) under the SynthRAD2023 collection. The images for each subject are available in nifti format. Potential applications: This dataset will enable the evaluation and development of image synthesis algorithms for radiotherapy purposes on a realistic multi-center dataset with varying acquisition protocols. Synthetic CT generation has numerous applications in radiation therapy, including diagnosis, treatment planning, treatment monitoring, and surgical planning.

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

Purpose: In radiology, large language models (LLMs), including ChatGPT, have recently gained attention, and their utility is being rapidly evaluated. However, concerns have emerged regarding their reliability in clinical applications due to limitations such as hallucinations and insufficient referencing. To address these issues, we focus on the latest technology, retrieval-augmented generation (RAG), which enables LLMs to reference reliable external knowledge (REK). Specifically, this study examines the utility and reliability of a recently released RAG-equipped LLM (RAG-LLM), NotebookLM, for staging lung cancer. Materials and methods: We summarized the current lung cancer staging guideline in Japan and provided this as REK to NotebookLM. We then tasked NotebookLM with staging 100 fictional lung cancer cases based on CT findings and evaluated its accuracy. For comparison, we performed the same task using a gold-standard LLM, GPT-4 Omni (GPT-4o), both with and without the REK. Results: NotebookLM achieved 86% diagnostic accuracy in the lung cancer staging experiment, outperforming GPT-4o, which recorded 39% accuracy with the REK and 25% without it. Moreover, NotebookLM demonstrated 95% accuracy in searching reference locations within the REK. Conclusion: NotebookLM successfully performed lung cancer staging by utilizing the REK, demonstrating superior performance compared to GPT-4o. Additionally, it provided highly accurate reference locations within the REK, allowing radiologists to efficiently evaluate the reliability of NotebookLM's responses and detect possible hallucinations. Overall, this study highlights the potential of NotebookLM, a RAG-LLM, in image diagnosis.

Whole-Slide Image (WSI) is an important tool for evaluating the prognosis of cancer patients. Present WSI-based prognosis studies generally follow a conventional paradigm -- cancer-specific model development -- where one cancer disease corresponds to one model and this model cannot make use of the prognostic knowledge from others. Despite its notable success in recent years, this paradigm has inherent limitations and has always been struggling with practical requirements: (i) scaling to the rare tumor diseases with very limited samples and (ii) benefiting from the generalizable prognostic knowledge in other cancers. To this end, this paper presents the first systematic study on Prognostic Knowledge Transfer in Pathology, called Path-PKT. It comprises three main parts. (1) We curate a large dataset (UNI2-h-DSS) with 13 cancers and use it to evaluate the transferability of prognostic knowledge between different cancers computationally. (2) We design experiments to understand what factors affect knowledge transfer and what causes positive transfers. (3) Motivated by empirical findings, we propose a new baseline approach (MoE-PKT) with a routing mechanism to utilize the generalizable prognostic knowledge in other cancers. Finally, we show the transferability of source models to rare tumor diseases. This study could lay solid foundations for the study of knowledge transfer in WSI-based cancer prognosis. Source code is available at https://github.com/liupei101/Path-PKT.

Purpose: To evaluate the performance of an automated deep learning method in detecting ascites and subsequently quantifying its volume in patients with liver cirrhosis and ovarian cancer. Materials and Methods: This retrospective study included contrast-enhanced and non-contrast abdominal-pelvic CT scans of patients with cirrhotic ascites and patients with ovarian cancer from two institutions, National Institutes of Health (NIH) and University of Wisconsin (UofW). The model, trained on The Cancer Genome Atlas Ovarian Cancer dataset (mean age, 60 years +/- 11 [s.d.]; 143 female), was tested on two internal (NIH-LC and NIH-OV) and one external dataset (UofW-LC). Its performance was measured by the Dice coefficient, standard deviations, and 95% confidence intervals, focusing on ascites volume in the peritoneal cavity. Results: On NIH-LC (25 patients; mean age, 59 years +/- 14 [s.d.]; 14 male) and NIH-OV (166 patients; mean age, 65 years +/- 9 [s.d.]; all female), the model achieved Dice scores of 0.855 +/- 0.061 (CI: 0.831-0.878) and 0.826 +/- 0.153 (CI: 0.764-0.887), with median volume estimation errors of 19.6% (IQR: 13.2-29.0) and 5.3% (IQR: 2.4-9.7) respectively. On UofW-LC (124 patients; mean age, 46 years +/- 12 [s.d.]; 73 female), the model had a Dice score of 0.830 +/- 0.107 (CI: 0.798-0.863) and median volume estimation error of 9.7% (IQR: 4.5-15.1). The model showed strong agreement with expert assessments, with r^2 values of 0.79, 0.98, and 0.97 across the test sets. Conclusion: The proposed deep learning method performed well in segmenting and quantifying the volume of ascites in concordance with expert radiologist assessments.

With the increasing availability of wearable devices, photoplethysmography (PPG) has emerged as a promising non-invasive tool for monitoring human hemodynamics. We propose a deep learning framework to estimate vascular age (AI-vascular age) from PPG signals, incorporating a distribution-aware loss to address biases caused by imbalanced data. The model was developed using data from the UK Biobank (UKB), with 98,672 participants in the development cohort and 113,559 participants (144,683 data pairs) for clinical evaluation. After adjusting for key confounders, individuals with a vascular age gap (AI-vascular age minus calendar age) exceeding 9 years had a significantly higher risk of major adverse cardiovascular and cerebrovascular events (MACCE) (HR = 2.37, p < 0.005) and secondary outcomes, including diabetes (HR = 2.69, p < 0.005), hypertension (HR = 2.88, p < 0.005), coronary heart disease (HR = 2.20, p < 0.005), heart failure (HR = 2.15, p < 0.005), myocardial infarction (HR = 2.51, p < 0.005), stroke (HR = 2.55, p < 0.005), and all-cause mortality (HR = 2.51, p < 0.005). Conversely, participants with a vascular age gap below -9 years exhibited a significantly lower incidence of these outcomes. We further evaluated the longitudinal applicability of AI-vascular age using serial PPG data from the UKB, demonstrating its value in risk stratification by leveraging AI-vascular age at two distinct time points to predict future MACCE incidence. External validation was performed on a MIMIC-III-derived cohort (n = 2,343), where each one-year increase in vascular age gap was significantly associated with elevated in-hospital mortality risk (OR = 1.02, p < 0.005). In conclusion, our study establishes AI-vascular age as a novel, non-invasive digital biomarker for cardiovascular health assessment.

Global comparisons of wellbeing increasingly rely on survey questions that ask respondents to evaluate their lives, most commonly in the form of "life satisfaction" and "Cantril ladder" items. These measures underpin international rankings such as the World Happiness Report and inform policy initiatives worldwide, yet their comparability has not been established with contemporary global data. Using the Gallup World Poll, Global Flourishing Study, and World Values Survey, I show that the two question formats yield divergent distributions, rankings, and response patterns that vary across countries and surveys, defying simple explanations. To explore differences in respondents' cognitive interpretations, I compare regression coefficients from the Global Flourishing Study, analyzing how each question wording relates to life circumstances. While international rankings of wellbeing are unstable, the scientific study of the determinants of life evaluations appears more robust. Together, the findings underscore the need for a renewed research agenda on critical limitations to cross-country comparability of wellbeing.

Machine learning (ML) approaches have demonstrated promising results in a wide range of healthcare applications. Data plays a crucial role in developing ML-based healthcare systems that directly affect people's lives. Many of the ethical issues surrounding the use of ML in healthcare stem from structural inequalities underlying the way we collect, use, and handle data. Developing guidelines to improve documentation practices regarding the creation, use, and maintenance of ML healthcare datasets is therefore of critical importance. In this work, we introduce Healthsheet, a contextualized adaptation of the original datasheet questionnaire ~gebru2018datasheets for health-specific applications. Through a series of semi-structured interviews, we adapt the datasheets for healthcare data documentation. As part of the Healthsheet development process and to understand the obstacles researchers face in creating datasheets, we worked with three publicly-available healthcare datasets as our case studies, each with different types of structured data: Electronic health Records (EHR), clinical trial study data, and smartphone-based performance outcome measures. Our findings from the interviewee study and case studies show 1) that datasheets should be contextualized for healthcare, 2) that despite incentives to adopt accountability practices such as datasheets, there is a lack of consistency in the broader use of these practices 3) how the ML for health community views datasheets and particularly Healthsheets as diagnostic tool to surface the limitations and strength of datasets and 4) the relative importance of different fields in the datasheet to healthcare concerns.

Although the fairness community has recognized the importance of data, researchers in the area primarily rely on UCI Adult when it comes to tabular data. Derived from a 1994 US Census survey, this dataset has appeared in hundreds of research papers where it served as the basis for the development and comparison of many algorithmic fairness interventions. We reconstruct a superset of the UCI Adult data from available US Census sources and reveal idiosyncrasies of the UCI Adult dataset that limit its external validity. Our primary contribution is a suite of new datasets derived from US Census surveys that extend the existing data ecosystem for research on fair machine learning. We create prediction tasks relating to income, employment, health, transportation, and housing. The data span multiple years and all states of the United States, allowing researchers to study temporal shift and geographic variation. We highlight a broad initial sweep of new empirical insights relating to trade-offs between fairness criteria, performance of algorithmic interventions, and the role of distribution shift based on our new datasets. Our findings inform ongoing debates, challenge some existing narratives, and point to future research directions. Our datasets are available at https://github.com/zykls/folktables.

Social media has become a valuable resource for the study of suicidal ideation and the assessment of suicide risk. Among social media platforms, Reddit has emerged as the most promising one due to its anonymity and its focus on topic-based communities (subreddits) that can be indicative of someone's state of mind or interest regarding mental health disorders such as r/SuicideWatch, r/Anxiety, r/depression. A challenge for previous work on suicide risk assessment has been the small amount of labeled data. We propose an empirical investigation into several classes of weakly-supervised approaches, and show that using pseudo-labeling based on related issues around mental health (e.g., anxiety, depression) helps improve model performance for suicide risk assessment.

The approval success rate of drug candidates is very low with the majority of failure due to safety and efficacy. Increasingly available high dimensional information on targets, drug molecules and indications provides an opportunity for ML methods to integrate multiple data modalities and better predict clinically promising drug targets. Notably, drug targets with human genetics evidence are shown to have better odds to succeed. However, a recent tensor factorization-based approach found that additional information on targets and indications might not necessarily improve the predictive accuracy. Here we revisit this approach by integrating different types of human genetics evidence collated from publicly available sources to support each target-indication pair. We use Bayesian tensor factorization to show that models incorporating all available human genetics evidence (rare disease, gene burden, common disease) modestly improves the clinical outcome prediction over models using single line of genetics evidence. We provide additional insight into the relative predictive power of different types of human genetics evidence for predicting the success of clinical outcomes.

The COVID-19 pandemic has escalated mental health crises worldwide, with social isolation and economic instability contributing to a rise in suicidal behavior. Suicide can result from social factors such as shame, abuse, abandonment, and mental health conditions like depression, Post-Traumatic Stress Disorder (PTSD), Attention-Deficit/Hyperactivity Disorder (ADHD), anxiety disorders, and bipolar disorders. As these conditions develop, signs of suicidal ideation may manifest in social media interactions. Analyzing social media data using artificial intelligence (AI) techniques can help identify patterns of suicidal behavior, providing invaluable insights for suicide prevention agencies, professionals, and broader community awareness initiatives. Machine learning algorithms for this purpose require large volumes of accurately labeled data. Previous research has not fully explored the potential of incorporating explanations in analyzing and labeling longitudinal social media data. In this study, we employed a model explanation method, Layer Integrated Gradients, on top of a fine-tuned state-of-the-art language model, to assign each token from Reddit users' posts an attribution score for predicting suicidal ideation. By extracting and analyzing attributions of tokens from the data, we propose a methodology for preliminary screening of social media posts for suicidal ideation without using large language models during inference.

Data driven activism attempts to collect, analyze and visualize data to foster social change. However, during media censorship it is often impossible to collect such data. Here we demonstrate that data from personal stories can also help us to gain insights about protests and activism which can work as a voice for the activists. We analyze protest story data by extracting location network from the stories and perform emotion mining to get insight about the protest.

Recruiting patients to participate in clinical trials can be challenging and time-consuming. Usually, participation in a clinical trial is initiated by a healthcare professional and proposed to the patient. Promoting clinical trials directly to patients via online recruitment might help to reach them more efficiently. In this study, we address the case where a patient is initiating their own recruitment process and wants to determine whether they are eligible for a given clinical trial, using their own language to describe their medical profile. To study whether this creates difficulties in the patient trial matching process, we design a new dataset and task, Natural Language Inference for Patient Recruitment (NLI4PR), in which patient language profiles must be matched to clinical trials. We create it by adapting the TREC 2022 Clinical Trial Track dataset, which provides patients' medical profiles, and rephrasing them manually using patient language. We also use the associated clinical trial reports where the patients are either eligible or excluded. We prompt several open-source Large Language Models on our task and achieve from 56.5 to 71.8 of F1 score using patient language, against 64.7 to 73.1 for the same task using medical language. When using patient language, we observe only a small loss in performance for the best model, suggesting that having the patient as a starting point could be adopted to help recruit patients for clinical trials. The corpus and code bases are all freely available on our Github and HuggingFace repositories.

Polyps in the colon are widely known cancer precursors identified by colonoscopy. Whilst most polyps are benign, the polyp's number, size and surface structure are linked to the risk of colon cancer. Several methods have been developed to automate polyp detection and segmentation. However, the main issue is that they are not tested rigorously on a large multicentre purpose-built dataset, one reason being the lack of a comprehensive public dataset. As a result, the developed methods may not generalise to different population datasets. To this extent, we have curated a dataset from six unique centres incorporating more than 300 patients. The dataset includes both single frame and sequence data with 3762 annotated polyp labels with precise delineation of polyp boundaries verified by six senior gastroenterologists. To our knowledge, this is the most comprehensive detection and pixel-level segmentation dataset (referred to as PolypGen) curated by a team of computational scientists and expert gastroenterologists. The paper provides insight into data construction and annotation strategies, quality assurance, and technical validation. Our dataset can be downloaded from https://doi.org/10.7303/syn26376615.

We here summarize our experience running a challenge with open data for musical genre recognition. Those notes motivate the task and the challenge design, show some statistics about the submissions, and present the results.

Social and behavioral determinants of health (SDOH) play a significant role in shaping health outcomes, and extracting these determinants from clinical notes is a first step to help healthcare providers systematically identify opportunities to provide appropriate care and address disparities. Progress on using NLP methods for this task has been hindered by the lack of high-quality publicly available labeled data, largely due to the privacy and regulatory constraints on the use of real patients' information. This paper introduces a new dataset, SDOH-NLI, that is based on publicly available notes and which we release publicly. We formulate SDOH extraction as a natural language inference (NLI) task, and provide binary textual entailment labels obtained from human raters for a cross product of a set of social history snippets as premises and SDOH factors as hypotheses. Our dataset differs from standard NLI benchmarks in that our premises and hypotheses are obtained independently. We evaluate both "off-the-shelf" entailment models as well as models fine-tuned on our data, and highlight the ways in which our dataset appears more challenging than commonly used NLI datasets.

As the production of and reliance on datasets to produce automated decision-making systems (ADS) increases, so does the need for processes for evaluating and interrogating the underlying data. After launching the Dataset Nutrition Label in 2018, the Data Nutrition Project has made significant updates to the design and purpose of the Label, and is launching an updated Label in late 2020, which is previewed in this paper. The new Label includes context-specific Use Cases &Alerts presented through an updated design and user interface targeted towards the data scientist profile. This paper discusses the harm and bias from underlying training data that the Label is intended to mitigate, the current state of the work including new datasets being labeled, new and existing challenges, and further directions of the work, as well as Figures previewing the new label.

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

Machine learning is now used in many applications thanks to its ability to predict, generate, or discover patterns from large quantities of data. However, the process of collecting and transforming data for practical use is intricate. Even in today's digital era, where substantial data is generated daily, it is uncommon for it to be readily usable; most often, it necessitates meticulous manual data preparation. The haste in developing new models can frequently result in various shortcomings, potentially posing risks when deployed in real-world scenarios (eg social discrimination, critical failures), leading to the failure or substantial escalation of costs in AI-based projects. This chapter provides a comprehensive overview of established methodological tools, enriched by our practical experience, in the development of datasets for machine learning. Initially, we develop the tasks involved in dataset development and offer insights into their effective management (including requirements, design, implementation, evaluation, distribution, and maintenance). Then, we provide more details about the implementation process which includes data collection, transformation, and quality evaluation. Finally, we address practical considerations regarding dataset distribution and maintenance.

Hypertension, defined as blood pressure (BP) that is above normal, holds paramount significance in the realm of public health, as it serves as a critical precursor to various cardiovascular diseases (CVDs) and significantly contributes to elevated mortality rates worldwide. However, many existing BP measurement technologies and standards might be biased because they do not consider clinical outcomes, comorbidities, or demographic factors, making them inconclusive for diagnostic purposes. There is limited data-driven research focused on studying the variance in BP measurements across these variables. In this work, we employed GPT-35-turbo, a large language model (LLM), to automatically extract the mean and standard deviation values of BP for both males and females from a dataset comprising 25 million abstracts sourced from PubMed. 993 article abstracts met our predefined inclusion criteria (i.e., presence of references to blood pressure, units of blood pressure such as mmHg, and mention of biological sex). Based on the automatically-extracted information from these articles, we conducted an analysis of the variations of BP values across biological sex. Our results showed the viability of utilizing LLMs to study the BP variations across different demographic factors.

Objective: We develop a deep learning framework based on the pre-trained Bidirectional Encoder Representations from Transformers (BERT) model using unstructured clinical notes from electronic health records (EHRs) to predict the risk of disease progression from Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD). Materials and Methods: We identified 3657 patients diagnosed with MCI together with their progress notes from Northwestern Medicine Enterprise Data Warehouse (NMEDW) between 2000-2020. The progress notes no later than the first MCI diagnosis were used for the prediction. We first preprocessed the notes by deidentification, cleaning and splitting, and then pretrained a BERT model for AD (AD-BERT) based on the publicly available Bio+Clinical BERT on the preprocessed notes. The embeddings of all the sections of a patient's notes processed by AD-BERT were combined by MaxPooling to compute the probability of MCI-to-AD progression. For replication, we conducted a similar set of experiments on 2563 MCI patients identified at Weill Cornell Medicine (WCM) during the same timeframe. Results: Compared with the 7 baseline models, the AD-BERT model achieved the best performance on both datasets, with Area Under receiver operating characteristic Curve (AUC) of 0.8170 and F1 score of 0.4178 on NMEDW dataset and AUC of 0.8830 and F1 score of 0.6836 on WCM dataset. Conclusion: We developed a deep learning framework using BERT models which provide an effective solution for prediction of MCI-to-AD progression using clinical note analysis.

Millions of users share their experiences on social media sites, such as Twitter, which in turn generate valuable data for public health monitoring, digital epidemiology, and other analyses of population health at global scale. The first, critical, task for these applications is classifying whether a personal health event was mentioned, which we call the (PHM) problem. This task is challenging for many reasons, including typically short length of social media posts, inventive spelling and lexicons, and figurative language, including hyperbole using diseases like "heart attack" or "cancer" for emphasis, and not as a health self-report. This problem is even more challenging for rarely reported, or frequent but ambiguously expressed conditions, such as "stroke". To address this problem, we propose a general, robust method for detecting PHMs in social media, which we call WESPAD, that combines lexical, syntactic, word embedding-based, and context-based features. WESPAD is able to generalize from few examples by automatically distorting the word embedding space to most effectively detect the true health mentions. Unlike previously proposed state-of-the-art supervised and deep-learning techniques, WESPAD requires relatively little training data, which makes it possible to adapt, with minimal effort, to each new disease and condition. We evaluate WESPAD on both an established publicly available Flu detection benchmark, and on a new dataset that we have constructed with mentions of multiple health conditions. Our experiments show that WESPAD outperforms the baselines and state-of-the-art methods, especially in cases when the number and proportion of true health mentions in the training data is small.

In recent years, the intersection of Natural Language Processing (NLP) and public health has opened innovative pathways for investigating various domains, including chronic pain in textual datasets. Despite the promise of NLP in chronic pain, the literature is dispersed across various disciplines, and there is a need to consolidate existing knowledge, identify knowledge gaps in the literature, and inform future research directions in this emerging field. This review aims to investigate the state of the research on NLP-based interventions designed for chronic pain research. A search strategy was formulated and executed across PubMed, Web of Science, IEEE Xplore, Scopus, and ACL Anthology to find studies published in English between 2014 and 2024. After screening 132 papers, 26 studies were included in the final review. Key findings from this review underscore the significant potential of NLP techniques to address pressing challenges in chronic pain research. The past 10 years in this field have showcased the utilization of advanced methods (transformers like RoBERTa and BERT) achieving high-performance metrics (e.g., F1>0.8) in classification tasks, while unsupervised approaches like Latent Dirichlet Allocation (LDA) and k-means clustering have proven effective for exploratory analyses. Results also reveal persistent challenges such as limited dataset diversity, inadequate sample sizes, and insufficient representation of underrepresented populations. Future research studies should explore multimodal data validation systems, context-aware mechanistic modeling, and the development of standardized evaluation metrics to enhance reproducibility and equity in chronic pain research.

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.

Epidemiologists aiming to model the dynamics of global events face a significant challenge in identifying the factors linked with anomalies such as disease outbreaks. In this paper, we present a novel method for identifying the most important development sectors sensitive to disease outbreaks by using global development indicators as markers. We use statistical methods to assess the causative linkages between these indicators and disease outbreaks, as well as to find the most often ranked indicators. We used data imputation techniques in addition to statistical analysis to convert raw real-world data sets into meaningful data for causal inference. The application of various algorithms for the detection of causal linkages between the indicators is the subject of this research. Despite the fact that disparities in governmental policies between countries account for differences in causal linkages, several indicators emerge as important determinants sensitive to disease outbreaks over the world in the 21st Century.

In medical applications, deep learning methods are built to automate diagnostic tasks. However, a clinically relevant question that practitioners usually face, is how to predict the future trajectory of a disease (prognosis). Current methods for such a problem often require domain knowledge, and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many forecasting problem from multimodal data. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner, we model a prognosis prediction problem with two transformer-based components that share information between each other. The first block in this model aims to analyze the imaging data, and the second block leverages the internal representations of the first one as inputs, also fusing them with auxiliary patient data. We show the effectiveness of our method in predicting the development of structural knee osteoarthritis changes over time. Our results show that the proposed method outperforms the state-of-the-art baselines in terms of various performance metrics. In addition, we empirically show that the existence of the multi-agent transformers with depths of 2 is sufficient to achieve good performances. Our code is publicly available at https://github.com/MIPT-Oulu/CLIMAT.

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on clinical trial data. The proposed challenges require multi-hop biomedical and numerical reasoning, which are of significant importance to the development of systems capable of large-scale interpretation and retrieval of medical evidence, to provide personalized evidence-based care. Task 1, the entailment task, received 643 submissions from 40 participants, and Task 2, the evidence selection task, received 364 submissions from 23 participants. The tasks are challenging, with the majority of submitted systems failing to significantly outperform the majority class baseline on the entailment task, and we observe significantly better performance on the evidence selection task than on the entailment task. Increasing the number of model parameters leads to a direct increase in performance, far more significant than the effect of biomedical pre-training. Future works could explore the limitations of large models for generalization and numerical inference, and investigate methods to augment clinical datasets to allow for more rigorous testing and to facilitate fine-tuning. We envisage that the dataset, models, and results of this task will be useful to the biomedical NLI and evidence retrieval communities. The dataset, competition leaderboard, and website are publicly available.

Artificial intelligence (AI) systems built on incomplete or biased data will often exhibit problematic outcomes. Current methods of data analysis, particularly before model development, are costly and not standardized. The Dataset Nutrition Label (the Label) is a diagnostic framework that lowers the barrier to standardized data analysis by providing a distilled yet comprehensive overview of dataset "ingredients" before AI model development. Building a Label that can be applied across domains and data types requires that the framework itself be flexible and adaptable; as such, the Label is comprised of diverse qualitative and quantitative modules generated through multiple statistical and probabilistic modelling backends, but displayed in a standardized format. To demonstrate and advance this concept, we generated and published an open source prototype with seven sample modules on the ProPublica Dollars for Docs dataset. The benefits of the Label are manyfold. For data specialists, the Label will drive more robust data analysis practices, provide an efficient way to select the best dataset for their purposes, and increase the overall quality of AI models as a result of more robust training datasets and the ability to check for issues at the time of model development. For those building and publishing datasets, the Label creates an expectation of explanation, which will drive better data collection practices. We also explore the limitations of the Label, including the challenges of generalizing across diverse datasets, and the risk of using "ground truth" data as a comparison dataset. We discuss ways to move forward given the limitations identified. Lastly, we lay out future directions for the Dataset Nutrition Label project, including research and public policy agendas to further advance consideration of the concept.

The work of this paper presents a dataset that contains the data of 4011 videos about the ongoing outbreak of measles published on 264 websites on the internet between January 1, 2024, and May 31, 2024. The dataset is available at https://dx.doi.org/10.21227/40s8-xf63. These websites primarily include YouTube and TikTok, which account for 48.6% and 15.2% of the videos, respectively. The remainder of the websites include Instagram and Facebook as well as the websites of various global and local news organizations. For each of these videos, the URL of the video, title of the post, description of the post, and the date of publication of the video are presented as separate attributes in the dataset. After developing this dataset, sentiment analysis (using VADER), subjectivity analysis (using TextBlob), and fine-grain sentiment analysis (using DistilRoBERTa-base) of the video titles and video descriptions were performed. This included classifying each video title and video description into (i) one of the sentiment classes i.e. positive, negative, or neutral, (ii) one of the subjectivity classes i.e. highly opinionated, neutral opinionated, or least opinionated, and (iii) one of the fine-grain sentiment classes i.e. fear, surprise, joy, sadness, anger, disgust, or neutral. These results are presented as separate attributes in the dataset for the training and testing of machine learning algorithms for performing sentiment analysis or subjectivity analysis in this field as well as for other applications. Finally, this paper also presents a list of open research questions that may be investigated using this dataset.

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

A major factor in the recent success of large language models is the use of enormous and ever-growing text datasets for unsupervised pre-training. However, naively training a model on all available data may not be optimal (or feasible), as the quality of available text data can vary. Filtering out data can also decrease the carbon footprint and financial costs of training models by reducing the amount of training required. Data selection methods aim to determine which candidate data points to include in the training dataset and how to appropriately sample from the selected data points. The promise of improved data selection methods has caused the volume of research in the area to rapidly expand. However, because deep learning is mostly driven by empirical evidence and experimentation on large-scale data is expensive, few organizations have the resources for extensive data selection research. Consequently, knowledge of effective data selection practices has become concentrated within a few organizations, many of which do not openly share their findings and methodologies. To narrow this gap in knowledge, we present a comprehensive review of existing literature on data selection methods and related research areas, providing a taxonomy of existing approaches. By describing the current landscape of research, this work aims to accelerate progress in data selection by establishing an entry point for new and established researchers. Additionally, throughout this review we draw attention to noticeable holes in the literature and conclude the paper by proposing promising avenues for future research.

We present CovidQA, the beginnings of a question answering dataset specifically designed for COVID-19, built by hand from knowledge gathered from Kaggle's COVID-19 Open Research Dataset Challenge. To our knowledge, this is the first publicly available resource of its type, and intended as a stopgap measure for guiding research until more substantial evaluation resources become available. While this dataset, comprising 124 question-article pairs as of the present version 0.1 release, does not have sufficient examples for supervised machine learning, we believe that it can be helpful for evaluating the zero-shot or transfer capabilities of existing models on topics specifically related to COVID-19. This paper describes our methodology for constructing the dataset and presents the effectiveness of a number of baselines, including term-based techniques and various transformer-based models. The dataset is available at http://covidqa.ai/

The COVID-19 pandemic caused great losses worldwide, efforts are taken place to prevent but many countries have failed. In Vietnam, the traceability, localization, and quarantine of people who contact with patients contribute to effective disease prevention. However, this is done by hand, and take a lot of work. In this research, we describe a named-entity recognition (NER) study that assists in the prevention of COVID-19 pandemic in Vietnam. We also present our manually annotated COVID-19 dataset with nested named entity recognition task for Vietnamese which be defined new entity types using for our system.

In recent years, there is strong emphasis on mining medical data using machine learning techniques. A common problem is to obtain a noiseless set of textual documents, with a relevant content for the research question, and developing a Question Answering (QA) model for a specific medical field. The purpose of this paper is to present a new methodology for building a medical dataset and obtain a QA model for analysis of symptoms and impact on daily life for a specific disease domain. The ``Mental Health'' forum was used, a forum dedicated to people suffering from schizophrenia and different mental disorders. Relevant posts of active users, who regularly participate, were extrapolated providing a new method of obtaining low-bias content and without privacy issues. Furthermore, it is shown how to pre-process the dataset to convert it into a QA dataset. The Bidirectional Encoder Representations from Transformers (BERT), DistilBERT, RoBERTa, and BioBERT models were fine-tuned and evaluated via F1-Score, Exact Match, Precision and Recall. Accurate empirical experiments demonstrated the effectiveness of the proposed method for obtaining an accurate dataset for QA model implementation. By fine-tuning the BioBERT QA model, we achieved an F1 score of 0.885, showing a considerable improvement and outperforming the state-of-the-art model for mental disorders domain.

The digitization of medical records ushered in a new era of big data to clinical science, and with it the possibility that data could be shared, to multiply insights beyond what investigators could abstract from paper records. The need to share individual-level medical data to accelerate innovation in precision medicine continues to grow, and has never been more urgent, as scientists grapple with the COVID-19 pandemic. However, enthusiasm for the use of big data has been tempered by a fully appropriate concern for patient autonomy and privacy. That is, the ability to extract private or confidential information about an individual, in practice, renders it difficult to share data, since significant infrastructure and data governance must be established before data can be shared. Although HIPAA provided de-identification as an approved mechanism for data sharing, linkage attacks were identified as a major vulnerability. A variety of mechanisms have been established to avoid leaking private information, such as field suppression or abstraction, strictly limiting the amount of information that can be shared, or employing mathematical techniques such as differential privacy. Another approach, which we focus on here, is creating synthetic data that mimics the underlying data. For synthetic data to be a useful mechanism in support of medical innovation and a proxy for real-world evidence, one must demonstrate two properties of the synthetic dataset: (1) any analysis on the real data must be matched by analysis of the synthetic data (statistical fidelity) and (2) the synthetic data must preserve privacy, with minimal risk of re-identification (privacy guarantee). In this paper we propose a framework for quantifying the statistical fidelity and privacy preservation properties of synthetic datasets and demonstrate these metrics for synthetic data generated by Syntegra technology.

Despite decades of clinical research, sepsis remains a global public health crisis with high mortality, and morbidity. Currently, when sepsis is detected and the underlying pathogen is identified, organ damage may have already progressed to irreversible stages. Effective sepsis management is therefore highly time-sensitive. By systematically analysing trends in the plethora of clinical data available in the intensive care unit (ICU), an early prediction of sepsis could lead to earlier pathogen identification, resistance testing, and effective antibiotic and supportive treatment, and thereby become a life-saving measure. Here, we developed and validated a machine learning (ML) system for the prediction of sepsis in the ICU. Our analysis represents the largest multi-national, multi-centre in-ICU study for sepsis prediction using ML to date. Our dataset contains 156,309 unique ICU admissions, which represent a refined and harmonised subset of five large ICU databases originating from three countries. Using the international consensus definition Sepsis-3, we derived hourly-resolved sepsis label annotations, amounting to 26,734 (17.1%) septic stays. We compared our approach, a deep self-attention model, to several clinical baselines as well as ML baselines and performed an extensive internal and external validation within and across databases. On average, our model was able to predict sepsis with an AUROC of 0.847 pm 0.050 (internal out-of sample validation) and 0.761 pm 0.052 (external validation). For a harmonised prevalence of 17%, at 80% recall our model detects septic patients with 39% precision 3.7 hours in advance.

Reducing traffic accidents is an important public safety challenge. However, the majority of studies on traffic accident analysis and prediction have used small-scale datasets with limited coverage, which limits their impact and applicability; and existing large-scale datasets are either private, old, or do not include important contextual information such as environmental stimuli (weather, points-of-interest, etc.). In order to help the research community address these shortcomings we have - through a comprehensive process of data collection, integration, and augmentation - created a large-scale publicly available database of accident information named US-Accidents. US-Accidents currently contains data about 2.25 million instances of traffic accidents that took place within the contiguous United States, and over the last three years. Each accident record consists of a variety of intrinsic and contextual attributes such as location, time, natural language description, weather, period-of-day, and points-of-interest. We present this dataset in this paper, along with a wide range of insights gleaned from this dataset with respect to the spatiotemporal characteristics of accidents. The dataset is publicly available at https://smoosavi.org/datasets/us_accidents.

Medical applications of machine learning (ML) have experienced a surge in popularity in recent years. The intensive care unit (ICU) is a natural habitat for ML given the abundance of available data from electronic health records. Models have been proposed to address numerous ICU prediction tasks like the early detection of complications. While authors frequently report state-of-the-art performance, it is challenging to verify claims of superiority. Datasets and code are not always published, and cohort definitions, preprocessing pipelines, and training setups are difficult to reproduce. This work introduces Yet Another ICU Benchmark (YAIB), a modular framework that allows researchers to define reproducible and comparable clinical ML experiments; we offer an end-to-end solution from cohort definition to model evaluation. The framework natively supports most open-access ICU datasets (MIMIC III/IV, eICU, HiRID, AUMCdb) and is easily adaptable to future ICU datasets. Combined with a transparent preprocessing pipeline and extensible training code for multiple ML and deep learning models, YAIB enables unified model development. Our benchmark comes with five predefined established prediction tasks (mortality, acute kidney injury, sepsis, kidney function, and length of stay) developed in collaboration with clinicians. Adding further tasks is straightforward by design. Using YAIB, we demonstrate that the choice of dataset, cohort definition, and preprocessing have a major impact on the prediction performance - often more so than model class - indicating an urgent need for YAIB as a holistic benchmarking tool. We provide our work to the clinical ML community to accelerate method development and enable real-world clinical implementations. Software Repository: https://github.com/rvandewater/YAIB.

A compartmental deterministic model that allows (1) immunity from two stages of infection and carriage, and (2) disease induced death, is used in studying the dynamics of meningitis epidemic process in a closed population. It allows for difference in the transmission rate of infection to a susceptible by a carrier and an infective. It is generalized to allow a proportion ({\phi}) of those susceptibles infected to progress directly to infectives in stage I. Both models are used in this study. The threshold conditions for the spread of carrier and infectives in stage I are derived for the two models. Sensitivity analysis is performed on the reproductive number derived from the next generation matrix. The case-carrier ratio profile for various parameters and threshold values are shown. So also are the graphs of the total number ever infected as influenced by {\epsilon} and {\phi}. The infection transmission rate (eta), the odds in favor of a carrier, over an infective, in transmitting an infection to a susceptible ({\epsilon}) and the carrier conversion rate ({\phi}) to an infective in stage I, are identified as key parameters that should be subject of attention for any control intervention strategy. The case-carrier ratio profiles provide evidence of a critical case-carrier ratio attained before the number of reported cases grows to an epidemic level. They also provide visual evidence of epidemiological context, in this case, epidemic incidence (in later part of dry season) and endemic incidence (during rainy season). Results from total proportion ever infected suggest that the model, in which {\phi}=0 obtained, can adequately represent, in essence, the generalized model for this study.

Meta-analyses statistically aggregate the findings of different randomized controlled trials (RCTs) to assess treatment effectiveness. Because this yields robust estimates of treatment effectiveness, results from meta-analyses are considered the strongest form of evidence. However, rigorous evidence syntheses are time-consuming and labor-intensive, requiring manual extraction of data from individual trials to be synthesized. Ideally, language technologies would permit fully automatic meta-analysis, on demand. This requires accurately extracting numerical results from individual trials, which has been beyond the capabilities of natural language processing (NLP) models to date. In this work, we evaluate whether modern large language models (LLMs) can reliably perform this task. We annotate (and release) a modest but granular evaluation dataset of clinical trial reports with numerical findings attached to interventions, comparators, and outcomes. Using this dataset, we evaluate the performance of seven LLMs applied zero-shot for the task of conditionally extracting numerical findings from trial reports. We find that massive LLMs that can accommodate lengthy inputs are tantalizingly close to realizing fully automatic meta-analysis, especially for dichotomous (binary) outcomes (e.g., mortality). However, LLMs -- including ones trained on biomedical texts -- perform poorly when the outcome measures are complex and tallying the results requires inference. This work charts a path toward fully automatic meta-analysis of RCTs via LLMs, while also highlighting the limitations of existing models for this aim.

Lower-Limb Fractures (LLF) are a major health concern for older adults, often leading to reduced mobility and prolonged recovery, potentially impairing daily activities and independence. During recovery, older adults frequently face social isolation and functional decline, complicating rehabilitation and adversely affecting physical and mental health. Multi-modal sensor platforms that continuously collect data and analyze it using machine-learning algorithms can remotely monitor this population and infer health outcomes. They can also alert clinicians to individuals at risk of isolation and decline. This paper presents a new publicly available multi-modal sensor dataset, MAISON-LLF, collected from older adults recovering from LLF in community settings. The dataset includes data from smartphone and smartwatch sensors, motion detectors, sleep-tracking mattresses, and clinical questionnaires on isolation and decline. The dataset was collected from ten older adults living alone at home for eight weeks each, totaling 560 days of 24-hour sensor data. For technical validation, supervised machine-learning and deep-learning models were developed using the sensor and clinical questionnaire data, providing a foundational comparison for the research community.

We present ReXGradient-160K, representing the largest publicly available chest X-ray dataset to date in terms of the number of patients. This dataset contains 160,000 chest X-ray studies with paired radiological reports from 109,487 unique patients across 3 U.S. health systems (79 medical sites). This comprehensive dataset includes multiple images per study and detailed radiology reports, making it particularly valuable for the development and evaluation of AI systems for medical imaging and automated report generation models. The dataset is divided into training (140,000 studies), validation (10,000 studies), and public test (10,000 studies) sets, with an additional private test set (10,000 studies) reserved for model evaluation on the ReXrank benchmark. By providing this extensive dataset, we aim to accelerate research in medical imaging AI and advance the state-of-the-art in automated radiological analysis. Our dataset will be open-sourced at https://huggingface.co/datasets/rajpurkarlab/ReXGradient-160K.

Databases of electronic health records (EHRs) are increasingly used to inform clinical decisions. Machine learning methods can find patterns in EHRs that are predictive of future adverse outcomes. However, statistical models may be built upon patterns of health-seeking behavior that vary across patient subpopulations, leading to poor predictive performance when training on one patient population and predicting on another. This note proposes two tests to better measure and understand model generalization. We use these tests to compare models derived from two data sources: (i) historical medical records, and (ii) electrocardiogram (EKG) waveforms. In a predictive task, we show that EKG-based models can be more stable than EHR-based models across different patient populations.

Epidemiologists often wish to estimate quantities that are easy to communicate and correspond to the results of realistic public health scenarios. Methods from causal inference can answer these questions. We adopt the language of potential outcomes under Rubin's original Bayesian framework and show that the parametric g-formula is easily amenable to a Bayesian approach. We show that the frequentist properties of the Bayesian g-formula suggest it improves the accuracy of estimates of causal effects in small samples or when data may be sparse. We demonstrate our approach to estimate the effect of environmental tobacco smoke on body mass index z-scores among children aged 4-9 years who were enrolled in a longitudinal birth cohort in New York, USA. We give a general algorithm and supply SAS and Stan code that can be adopted to implement our computational approach in both time-fixed and longitudinal data.

Large participatory biomedical studies, studies that recruit individuals to join a dataset, are gaining popularity and investment, especially for analysis by modern AI methods. Because they purposively recruit participants, these studies are uniquely able to address a lack of historical representation, an issue that has affected many biomedical datasets. In this work, we define representativeness as the similarity to a target population distribution of a set of attributes and our goal is to mirror the U.S. population across distributions of age, gender, race, and ethnicity. Many participatory studies recruit at several institutions, so we introduce a computational approach to adaptively allocate recruitment resources among sites to improve representativeness. In simulated recruitment of 10,000-participant cohorts from medical centers in the STAR Clinical Research Network, we show that our approach yields a more representative cohort than existing baselines. Thus, we highlight the value of computational modeling in guiding recruitment efforts.

The timely identification of socio-economic sectors vulnerable to a disease outbreak presents an important challenge to the civic authorities and healthcare workers interested in outbreak mitigation measures. This problem was traditionally solved by studying the aberrances in small-scale healthcare data. In this paper, we leverage data driven models to determine the relationship between the trends of World Development Indicators and occurrence of disease outbreaks using worldwide historical data from 2000-2019, and treat it as a classic supervised classification problem. CART based feature selection was employed in an unorthodox fashion to determine the covariates getting affected by the disease outbreak, thus giving the most vulnerable sectors. The result involves a comprehensive analysis of different classification algorithms and is indicative of the relationship between the disease outbreak occurrence and the magnitudes of various development indicators.

Clinical notes contain rich data, which is unexploited in predictive modeling compared to structured data. In this work, we developed a new text representation Clinical XLNet for clinical notes which also leverages the temporal information of the sequence of the notes. We evaluated our models on prolonged mechanical ventilation prediction problem and our experiments demonstrated that Clinical XLNet outperforms the best baselines consistently.

We study the problem of learning mixtures of Gaussians with censored data. Statistical learning with censored data is a classical problem, with numerous practical applications, however, finite-sample guarantees for even simple latent variable models such as Gaussian mixtures are missing. Formally, we are given censored data from a mixture of univariate Gaussians $sum_{i=1}^k w_i N(mu_i,sigma^2), i.e. the sample is observed only if it lies inside a set S. The goal is to learn the weights w_i and the means \mu_i. We propose an algorithm that takes only 1{\varepsilon^{O(k)}} samples to estimate the weights w_i and the means \mu_i within \varepsilon$ error.

The existing search tools for exploring the NASA Astrophysics Data System (ADS) can be quite rich and empowering (e.g., similar and trending operators), but researchers are not yet allowed to fully leverage semantic search. For example, a query for "results from the Planck mission" should be able to distinguish between all the various meanings of Planck (person, mission, constant, institutions and more) without further clarification from the user. At ADS, we are applying modern machine learning and natural language processing techniques to our dataset of recent astronomy publications to train astroBERT, a deeply contextual language model based on research at Google. Using astroBERT, we aim to enrich the ADS dataset and improve its discoverability, and in particular we are developing our own named entity recognition tool. We present here our preliminary results and lessons learned.

Mental health research through data-driven methods has been hindered by a lack of standard typology and scarcity of adequate data. In this study, we leverage the clinical articulation of depression to build a typology for social media texts for detecting the severity of depression. It emulates the standard clinical assessment procedure Diagnostic and Statistical Manual of Mental Disorders (DSM-5) and Patient Health Questionnaire (PHQ-9) to encompass subtle indications of depressive disorders from tweets. Along with the typology, we present a new dataset of 40191 tweets labeled by expert annotators. Each tweet is labeled as 'non-depressed' or 'depressed'. Moreover, three severity levels are considered for 'depressed' tweets: (1) mild, (2) moderate, and (3) severe. An associated confidence score is provided with each label to validate the quality of annotation. We examine the quality of the dataset via representing summary statistics while setting strong baseline results using attention-based models like BERT and DistilBERT. Finally, we extensively address the limitations of the study to provide directions for further research.

Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over 10 years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved F_1 scores of 88.6, 95.0, and 55.8 per cent in the mention extraction of procedures, drugs, and diseases, respectively.

Objective: To improve prediction of Chronic Kidney Disease (CKD) progression to End Stage Renal Disease (ESRD) using machine learning (ML) and deep learning (DL) models applied to an integrated clinical and claims dataset of varying observation windows, supported by explainable AI (XAI) to enhance interpretability and reduce bias. Materials and Methods: We utilized data about 10,326 CKD patients, combining their clinical and claims information from 2009 to 2018. Following data preprocessing, cohort identification, and feature engineering, we evaluated multiple statistical, ML and DL models using data extracted from five distinct observation windows. Feature importance and Shapley value analysis were employed to understand key predictors. Models were tested for robustness, clinical relevance, misclassification errors and bias issues. Results: Integrated data models outperformed those using single data sources, with the Long Short-Term Memory (LSTM) model achieving the highest AUC (0.93) and F1 score (0.65). A 24-month observation window was identified as optimal for balancing early detection and prediction accuracy. The 2021 eGFR equation improved prediction accuracy and reduced racial bias, notably for African American patients. Discussion: Improved ESRD prediction accuracy, results interpretability and bias mitigation strategies presented in this study have the potential to significantly enhance CKD and ESRD management, support targeted early interventions and reduce healthcare disparities. Conclusion: This study presents a robust framework for predicting ESRD outcomes in CKD patients, improving clinical decision-making and patient care through multi-sourced, integrated data and AI/ML methods. Future research will expand data integration and explore the application of this framework to other chronic diseases.

Organizations cannot address demographic disparities that they cannot see. Recent research on machine learning and fairness has emphasized that awareness of sensitive attributes, such as race and sex, is critical to the development of interventions. However, on the ground, the existence of these data cannot be taken for granted. This paper uses the domains of employment, credit, and healthcare in the United States to surface conditions that have shaped the availability of sensitive attribute data. For each domain, we describe how and when private companies collect or infer sensitive attribute data for antidiscrimination purposes. An inconsistent story emerges: Some companies are required by law to collect sensitive attribute data, while others are prohibited from doing so. Still others, in the absence of legal mandates, have determined that collection and imputation of these data are appropriate to address disparities. This story has important implications for fairness research and its future applications. If companies that mediate access to life opportunities are unable or hesitant to collect or infer sensitive attribute data, then proposed techniques to detect and mitigate bias in machine learning models might never be implemented outside the lab. We conclude that today's legal requirements and corporate practices, while highly inconsistent across domains, offer lessons for how to approach the collection and inference of sensitive data in appropriate circumstances. We urge stakeholders, including machine learning practitioners, to actively help chart a path forward that takes both policy goals and technical needs into account.

Automating radiology report generation can significantly alleviate radiologists' workloads. Previous research has primarily focused on realizing highly concise observations while neglecting the precise attributes that determine the severity of diseases (e.g., small pleural effusion). Since incorrect attributes will lead to imprecise radiology reports, strengthening the generation process with precise attribute modeling becomes necessary. Additionally, the temporal information contained in the historical records, which is crucial in evaluating a patient's current condition (e.g., heart size is unchanged), has also been largely disregarded. To address these issues, we propose RECAP, which generates precise and accurate radiology reports via dynamic disease progression reasoning. Specifically, RECAP first predicts the observations and progressions (i.e., spatiotemporal information) given two consecutive radiographs. It then combines the historical records, spatiotemporal information, and radiographs for report generation, where a disease progression graph and dynamic progression reasoning mechanism are devised to accurately select the attributes of each observation and progression. Extensive experiments on two publicly available datasets demonstrate the effectiveness of our model.

Healthcare is an important aspect of human life. Use of technologies in healthcare has increased manifolds after the pandemic. Internet of Things based systems and devices proposed in literature can help elders, children and adults facing/experiencing health problems. This paper exhaustively reviews thirty-nine wearable based datasets which can be used for evaluating the system to recognize Activities of Daily Living and Falls. A comparative analysis on the SisFall dataset using five machine learning methods i.e., Logistic Regression, Linear Discriminant Analysis, K-Nearest Neighbor, Decision Tree and Naive Bayes is performed in python. The dataset is modified in two ways, in first all the attributes present in dataset are used as it is and labelled in binary form. In second, magnitude of three axes(x,y,z) for three sensors value are computed and then used in experiment with label attribute. The experiments are performed on one subject, ten subjects and all the subjects and compared in terms of accuracy, precision and recall. The results obtained from this study proves that KNN outperforms other machine learning methods in terms of accuracy, precision and recall. It is also concluded that personalization of data improves accuracy.

Text data can pose a risk of harm. However, the risks are not fully understood, and how to handle, present, and discuss harmful text in a safe way remains an unresolved issue in the NLP community. We provide an analytical framework categorising harms on three axes: (1) the harm type (e.g., misinformation, hate speech or racial stereotypes); (2) whether a harm is sought as a feature of the research design if explicitly studying harmful content (e.g., training a hate speech classifier), versus unsought if harmful content is encountered when working on unrelated problems (e.g., language generation or part-of-speech tagging); and (3) who it affects, from people (mis)represented in the data to those handling the data and those publishing on the data. We provide advice for practitioners, with concrete steps for mitigating harm in research and in publication. To assist implementation we introduce HarmCheck -- a documentation standard for handling and presenting harmful text in research.

We describe a Magnetic Resonance Imaging (MRI) dataset from individuals from the African nation of Nigeria. The dataset contains pseudonymized structural MRI (T1w, T2w, FLAIR) data of clinical quality. The dataset contains data from 36 images from healthy control subjects, 32 images from individuals diagnosed with age-related dementia and 20 from individuals with Parkinson's disease. There is currently a paucity of data from the African continent. Given the potential for Africa to contribute to the global neuroscience community, this first MRI dataset represents both an opportunity and benchmark for future studies to share data from the African continent.

The way people respond to messaging from public health organizations on social media can provide insight into public perceptions on critical health issues, especially during a global crisis such as COVID-19. It could be valuable for high-impact organizations such as the US Centers for Disease Control and Prevention (CDC) or the World Health Organization (WHO) to understand how these perceptions impact reception of messaging on health policy recommendations. We collect two datasets of public health messages and their responses from Twitter relating to COVID-19 and Vaccines, and introduce a predictive method which can be used to explore the potential reception of such messages. Specifically, we harness a generative model (GPT-2) to directly predict probable future responses and demonstrate how it can be used to optimize expected reception of important health guidance. Finally, we introduce a novel evaluation scheme with extensive statistical testing which allows us to conclude that our models capture the semantics and sentiment found in actual public health responses.

There has been growing interest in utilizing occupational data mining and analysis. In today's job market, occupational data mining and analysis is growing in importance as it enables companies to predict employee turnover, model career trajectories, screen through resumes and perform other human resource tasks. A key requirement to facilitate these tasks is the need for an occupation-related dataset. However, most research use proprietary datasets or do not make their dataset publicly available, thus impeding development in this area. To solve this issue, we present the Industrial and Professional Occupation Dataset (IPOD), which comprises 192k job titles belonging to 56k LinkedIn users. In addition to making IPOD publicly available, we also: (i) manually annotate each job title with its associated level of seniority, domain of work and location; and (ii) provide embedding for job titles and discuss various use cases. This dataset is publicly available at https://github.com/junhua/ipod.

Along with COVID-19 pandemic we are also fighting an `infodemic'. Fake news and rumors are rampant on social media. Believing in rumors can cause significant harm. This is further exacerbated at the time of a pandemic. To tackle this, we curate and release a manually annotated dataset of 10,700 social media posts and articles of real and fake news on COVID-19. We benchmark the annotated dataset with four machine learning baselines - Decision Tree, Logistic Regression, Gradient Boost, and Support Vector Machine (SVM). We obtain the best performance of 93.46% F1-score with SVM. The data and code is available at: https://github.com/parthpatwa/covid19-fake-news-dectection

The lack of freely available standardized datasets represents an aggravating factor during the development and testing the performance of novel computational techniques in exposure assessment and dosimetry research. This hinders progress as researchers are required to generate numerical data (field, power and temperature distribution) anew using simulation software for each exposure scenario. Other than being time consuming, this approach is highly susceptible to errors that occur during the configuration of the electromagnetic model. To address this issue, in this paper, the limited available data on the incident power density and resultant maximum temperature rise on the skin surface considering various steady-state exposure scenarios at 10-90 GHz have been statistically modeled. The synthetic data have been sampled from the fitted statistical multivariate distribution with respect to predetermined dosimetric constraints. We thus present a comprehensive and open-source dataset compiled of the high-fidelity numerical data considering various exposures to a realistic source. Furthermore, different surrogate models for predicting maximum temperature rise on the skin surface were fitted based on the synthetic dataset. All surrogate models were tested on the originally available data where satisfactory predictive performance has been demonstrated. A simple technique of combining quadratic polynomial and tensor-product spline surrogates, each operating on its own cluster of data, has achieved the lowest mean absolute error of 0.058 {\deg}C. Therefore, overall experimental results indicate the validity of the proposed synthetic dataset.

Convincing people to get vaccinated against COVID-19 is a key societal challenge in the present times. As a first step towards this goal, many prior works have relied on social media analysis to understand the specific concerns that people have towards these vaccines, such as potential side-effects, ineffectiveness, political factors, and so on. Though there are datasets that broadly classify social media posts into Anti-vax and Pro-Vax labels, there is no dataset (to our knowledge) that labels social media posts according to the specific anti-vaccine concerns mentioned in the posts. In this paper, we have curated CAVES, the first large-scale dataset containing about 10k COVID-19 anti-vaccine tweets labelled into various specific anti-vaccine concerns in a multi-label setting. This is also the first multi-label classification dataset that provides explanations for each of the labels. Additionally, the dataset also provides class-wise summaries of all the tweets. We also perform preliminary experiments on the dataset and show that this is a very challenging dataset for multi-label explainable classification and tweet summarization, as is evident by the moderate scores achieved by some state-of-the-art models. Our dataset and codes are available at: https://github.com/sohampoddar26/caves-data

Temporally dense single-person "small data" have become widely available thanks to mobile apps and wearable sensors. Many caregivers and self-trackers want to use these data to help a specific person change their behavior to achieve desired health outcomes. Ideally, this involves discerning possible causes from correlations using that person's own observational time series data. In this paper, we estimate within-individual average treatment effects of physical activity on sleep duration, and vice-versa. We introduce the model twin randomization (MoTR; "motor") method for analyzing an individual's intensive longitudinal data. Formally, MoTR is an application of the g-formula (i.e., standardization, back-door adjustment) under serial interference. It estimates stable recurring effects, as is done in n-of-1 trials and single case experimental designs. We compare our approach to standard methods (with possible confounding) to show how to use causal inference to make better personalized recommendations for health behavior change, and analyze 222 days of Fitbit sleep and steps data for one of the authors.

Neonatal death is still a concerning reality for underdeveloped and even some developed countries. Worldwide data indicate that 26.693 babies out of 1,000 births die, according to Macro Trades. To reduce this number, early prediction of endangered babies is crucial. Such prediction enables the opportunity to take ample care of the child and mother so that early child death can be avoided. In this context, machine learning was used to determine whether a newborn baby is at risk. To train the predictive model, historical data of 1.4 million newborns was used. Machine learning and deep learning techniques such as logical regression, K-nearest neighbor, random forest classifier, extreme gradient boosting (XGBoost), convolutional neural network, and long short-term memory (LSTM) were implemented using the dataset to identify the most accurate model for predicting neonatal mortality. Among the machine learning algorithms, XGBoost and random forest classifier achieved the best accuracy with 94%, while among the deep learning models, LSTM delivered the highest accuracy with 99%. Therefore, using LSTM appears to be the most suitable approach to predict whether precautionary measures for a child are necessary.

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

Modern machine learning relies on datasets to develop and validate research ideas. Given the growth of publicly available data, finding the right dataset to use is increasingly difficult. Any research question imposes explicit and implicit constraints on how well a given dataset will enable researchers to answer this question, such as dataset size, modality, and domain. We operationalize the task of recommending datasets given a short natural language description of a research idea, to help people find relevant datasets for their needs. Dataset recommendation poses unique challenges as an information retrieval problem; datasets are hard to directly index for search and there are no corpora readily available for this task. To facilitate this task, we build the DataFinder Dataset which consists of a larger automatically-constructed training set (17.5K queries) and a smaller expert-annotated evaluation set (392 queries). Using this data, we compare various information retrieval algorithms on our test set and present a superior bi-encoder retriever for text-based dataset recommendation. This system, trained on the DataFinder Dataset, finds more relevant search results than existing third-party dataset search engines. To encourage progress on dataset recommendation, we release our dataset and models to the public.

The article presents a new multi-label comprehensive image dataset from flexible endoscopy, colonoscopy and capsule endoscopy, named ERS. The collection has been labeled according to the full medical specification of 'Minimum Standard Terminology 3.0' (MST 3.0), describing all possible findings in the gastrointestinal tract (104 possible labels), extended with an additional 19 labels useful in common machine learning applications. The dataset contains around 6000 precisely and 115,000 approximately labeled frames from endoscopy videos, 3600 precise and 22,600 approximate segmentation masks, and 1.23 million unlabeled frames from flexible and capsule endoscopy videos. The labeled data cover almost entirely the MST 3.0 standard. The data came from 1520 videos of 1135 patients. Additionally, this paper proposes and describes four exemplary experiments in gastrointestinal image classification task performed using the created dataset. The obtained results indicate the high usefulness and flexibility of the dataset in training and testing machine learning algorithms in the field of endoscopic data analysis.

Developing artificial intelligence (AI) for vertical domains requires a solid data foundation for both training and evaluation. In this work, we introduce TrialPanorama, a large-scale, structured database comprising 1,657,476 clinical trial records aggregated from 15 global sources. The database captures key aspects of trial design and execution, including trial setups, interventions, conditions, biomarkers, and outcomes, and links them to standard biomedical ontologies such as DrugBank and MedDRA. This structured and ontology-grounded design enables TrialPanorama to serve as a unified, extensible resource for a wide range of clinical trial tasks, including trial planning, design, and summarization. To demonstrate its utility, we derive a suite of benchmark tasks directly from the TrialPanorama database. The benchmark spans eight tasks across two categories: three for systematic review (study search, study screening, and evidence summarization) and five for trial design (arm design, eligibility criteria, endpoint selection, sample size estimation, and trial completion assessment). The experiments using five state-of-the-art large language models (LLMs) show that while general-purpose LLMs exhibit some zero-shot capability, their performance is still inadequate for high-stakes clinical trial workflows. We release TrialPanorama database and the benchmark to facilitate further research on AI for clinical trials.

The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert-level scientific software whose goal is to maximize a quality metric. The system uses a Large Language Model (LLM) and Tree Search (TS) to systematically improve the quality metric and intelligently navigate the large space of possible solutions. The system achieves expert-level results when it explores and integrates complex research ideas from external sources. The effectiveness of tree search is demonstrated across a wide range of benchmarks. In bioinformatics, it discovered 40 novel methods for single-cell data analysis that outperformed the top human-developed methods on a public leaderboard. In epidemiology, it generated 14 models that outperformed the CDC ensemble and all other individual models for forecasting COVID-19 hospitalizations. Our method also produced state-of-the-art software for geospatial analysis, neural activity prediction in zebrafish, time series forecasting and numerical solution of integrals. By devising and implementing novel solutions to diverse tasks, the system represents a significant step towards accelerating scientific progress.

A great deal of effort has been devoted to reducing the risk of spurious scientific discoveries, from the use of sophisticated validation techniques, to deep statistical methods for controlling the false discovery rate in multiple hypothesis testing. However, there is a fundamental disconnect between the theoretical results and the practice of data analysis: the theory of statistical inference assumes a fixed collection of hypotheses to be tested, or learning algorithms to be applied, selected non-adaptively before the data are gathered, whereas in practice data is shared and reused with hypotheses and new analyses being generated on the basis of data exploration and the outcomes of previous analyses. In this work we initiate a principled study of how to guarantee the validity of statistical inference in adaptive data analysis. As an instance of this problem, we propose and investigate the question of estimating the expectations of m adaptively chosen functions on an unknown distribution given n random samples. We show that, surprisingly, there is a way to estimate an exponential in n number of expectations accurately even if the functions are chosen adaptively. This gives an exponential improvement over standard empirical estimators that are limited to a linear number of estimates. Our result follows from a general technique that counter-intuitively involves actively perturbing and coordinating the estimates, using techniques developed for privacy preservation. We give additional applications of this technique to our question.

The UCR Time Series Archive - introduced in 2002, has become an important resource in the time series data mining community, with at least one thousand published papers making use of at least one data set from the archive. The original incarnation of the archive had sixteen data sets but since that time, it has gone through periodic expansions. The last expansion took place in the summer of 2015 when the archive grew from 45 to 85 data sets. This paper introduces and will focus on the new data expansion from 85 to 128 data sets. Beyond expanding this valuable resource, this paper offers pragmatic advice to anyone who may wish to evaluate a new algorithm on the archive. Finally, this paper makes a novel and yet actionable claim: of the hundreds of papers that show an improvement over the standard baseline (1-nearest neighbor classification), a large fraction may be mis-attributing the reasons for their improvement. Moreover, they may have been able to achieve the same improvement with a much simpler modification, requiring just a single line of code.

Online web communities often face bans for violating platform policies, encouraging their migration to alternative platforms. This migration, however, can result in increased toxicity and unforeseen consequences on the new platform. In recent years, researchers have collected data from many alternative platforms, indicating coordinated efforts leading to offline events, conspiracy movements, hate speech propagation, and harassment. Thus, it becomes crucial to characterize and understand these alternative platforms. To advance research in this direction, we collect and release a large-scale dataset from Scored -- an alternative Reddit platform that sheltered banned fringe communities, for example, c/TheDonald (a prominent right-wing community) and c/GreatAwakening (a conspiratorial community). Over four years, we collected approximately 57M posts from Scored, with at least 58 communities identified as migrating from Reddit and over 950 communities created since the platform's inception. Furthermore, we provide sentence embeddings of all posts in our dataset, generated through a state-of-the-art model, to further advance the field in characterizing the discussions within these communities. We aim to provide these resources to facilitate their investigations without the need for extensive data collection and processing efforts.

With the course of progress in the field of medicine, most of the patients lives can be saved. The only thing required is the proper attention at the proper time. Our wearable solution tries to solve this issue by taking the patients vitals and transmitting them to the server for live monitoring using the mobile app along with the patients current location. In case of an emergency, that is if any vitals show any abnormalities, an SMS is sent to the caregiver of the patient with the patients location so that he can reach there on time.

Ocean scientists have been collecting visual data to study marine organisms for decades. These images and videos are extremely valuable both for basic science and environmental monitoring tasks. There are tools for automatically processing these data, but none that are capable of handling the extreme variability in sample populations, image quality, and habitat characteristics that are common in visual sampling of the ocean. Such distribution shifts can occur over very short physical distances and in narrow time windows. Creating models that are able to recognize when an image or video sequence contains a new organism, an unusual collection of animals, or is otherwise out-of-sample is critical to fully leverage visual data in the ocean. The FathomNet2023 competition dataset presents a realistic scenario where the set of animals in the target data differs from the training data. The challenge is both to identify the organisms in a target image and assess whether it is out-of-sample.

Accurately forecasting patient arrivals at Urgent Care Clinics (UCCs) and Emergency Departments (EDs) is important for effective resourcing and patient care. However, correctly estimating patient flows is not straightforward since it depends on many drivers. The predictability of patient arrivals has recently been further complicated by the COVID-19 pandemic conditions and the resulting lockdowns. This study investigates how a suite of novel quasi-real-time variables like Google search terms, pedestrian traffic, the prevailing incidence levels of influenza, as well as the COVID-19 Alert Level indicators can both generally improve the forecasting models of patient flows and effectively adapt the models to the unfolding disruptions of pandemic conditions. This research also uniquely contributes to the body of work in this domain by employing tools from the eXplainable AI field to investigate more deeply the internal mechanics of the models than has previously been done. The Voting ensemble-based method combining machine learning and statistical techniques was the most reliable in our experiments. Our study showed that the prevailing COVID-19 Alert Level feature together with Google search terms and pedestrian traffic were effective at producing generalisable forecasts. The implications of this study are that proxy variables can effectively augment standard autoregressive features to ensure accurate forecasting of patient flows. The experiments showed that the proposed features are potentially effective model inputs for preserving forecast accuracies in the event of future pandemic outbreaks.

Background: This study aimed to evaluate and compare the performance of classical machine learning models (CMLs) and large language models (LLMs) in predicting mortality associated with COVID-19 by utilizing a high-dimensional tabular dataset. Materials and Methods: We analyzed data from 9,134 COVID-19 patients collected across four hospitals. Seven CML models, including XGBoost and random forest (RF), were trained and evaluated. The structured data was converted into text for zero-shot classification by eight LLMs, including GPT-4 and Mistral-7b. Additionally, Mistral-7b was fine-tuned using the QLoRA approach to enhance its predictive capabilities. Results: Among the CML models, XGBoost and RF achieved the highest accuracy, with F1 scores of 0.87 for internal validation and 0.83 for external validation. In the LLM category, GPT-4 was the top performer with an F1 score of 0.43. Fine-tuning Mistral-7b significantly improved its recall from 1% to 79%, resulting in an F1 score of 0.74, which was stable during external validation. Conclusion: While LLMs show moderate performance in zero-shot classification, fine-tuning can significantly enhance their effectiveness, potentially aligning them closer to CML models. However, CMLs still outperform LLMs in high-dimensional tabular data tasks.

Data plays a fundamental role in the training of Large Language Models (LLMs). Effective data management, particularly in the formulation of a well-suited training dataset, holds significance for enhancing model performance and improving training efficiency during pretraining and supervised fine-tuning phases. Despite the considerable importance of data management, the current research community still falls short in providing a systematic analysis of the rationale behind management strategy selection, its consequential effects, methodologies for evaluating curated datasets, and the ongoing pursuit of improved strategies. Consequently, the exploration of data management has attracted more and more attention among the research community. This survey provides a comprehensive overview of current research in data management within both the pretraining and supervised fine-tuning stages of LLMs, covering various noteworthy aspects of data management strategy design: data quantity, data quality, domain/task composition, etc. Looking toward the future, we extrapolate existing challenges and outline promising directions for development in this field. Therefore, this survey serves as a guiding resource for practitioners aspiring to construct powerful LLMs through effective data management practices. The collection of the latest papers is available at https://github.com/ZigeW/data_management_LLM.

Large language models are increasingly trained on all the data ever produced by humans. Many have raised concerns about the trustworthiness of public benchmarks due to potential contamination in pre-training or fine-tuning datasets. While most data decontamination efforts apply string matching (e.g., n-gram overlap) to remove benchmark data, we show that these methods are insufficient, and simple variations of test data (e.g., paraphrasing, translation) can easily bypass these decontamination measures. Furthermore, we demonstrate that if such variation of test data is not eliminated, a 13B model can easily overfit a test benchmark and achieve drastically high performance, on par with GPT-4. We validate such observations in widely used benchmarks such as MMLU, GSK8k, and HumanEval. To address this growing risk, we propose a stronger LLM-based decontamination method and apply it to widely used pre-training and fine-tuning datasets, revealing significant previously unknown test overlap. For example, in pre-training sets such as RedPajama-Data-1T and StarCoder-Data, we identified that 8-18\% of the HumanEval benchmark overlaps. Interestingly, we also find such contamination in synthetic dataset generated by GPT-3.5/4, suggesting a potential risk of unintentional contamination. We urge the community to adopt stronger decontamination approaches when using public benchmarks. Moreover, we call for the community to actively develop fresh one-time exams to evaluate models accurately. Our decontamination tool is publicly available at https://github.com/lm-sys/llm-decontaminator.

Large Language Models (LLMs) have been extensively evaluated for general summarization tasks as well as medical research assistance, but they have not been specifically evaluated for the task of summarizing real-world evidence (RWE) from structured output of RWE studies. We introduce RWESummary, a proposed addition to the MedHELM framework (Bedi, Cui, Fuentes, Unell et al., 2025) to enable benchmarking of LLMs for this task. RWESummary includes one scenario and three evaluations covering major types of errors observed in summarization of medical research studies and was developed using Atropos Health proprietary data. Additionally, we use RWESummary to compare the performance of different LLMs in our internal RWE summarization tool. At the time of publication, with 13 distinct RWE studies, we found the Gemini 2.5 models performed best overall (both Flash and Pro). We suggest RWESummary as a novel and useful foundation model benchmark for real-world evidence study summarization.

Time series research has gathered lots of interests in the last decade, especially for Time Series Classification (TSC) and Time Series Forecasting (TSF). Research in TSC has greatly benefited from the University of California Riverside and University of East Anglia (UCR/UEA) Time Series Archives. On the other hand, the advancement in Time Series Forecasting relies on time series forecasting competitions such as the Makridakis competitions, NN3 and NN5 Neural Network competitions, and a few Kaggle competitions. Each year, thousands of papers proposing new algorithms for TSC and TSF have utilized these benchmarking archives. These algorithms are designed for these specific problems, but may not be useful for tasks such as predicting the heart rate of a person using photoplethysmogram (PPG) and accelerometer data. We refer to this problem as Time Series Extrinsic Regression (TSER), where we are interested in a more general methodology of predicting a single continuous value, from univariate or multivariate time series. This prediction can be from the same time series or not directly related to the predictor time series and does not necessarily need to be a future value or depend heavily on recent values. To the best of our knowledge, research into TSER has received much less attention in the time series research community and there are no models developed for general time series extrinsic regression problems. Most models are developed for a specific problem. Therefore, we aim to motivate and support the research into TSER by introducing the first TSER benchmarking archive. This archive contains 19 datasets from different domains, with varying number of dimensions, unequal length dimensions, and missing values. In this paper, we introduce the datasets in this archive and did an initial benchmark on existing models.

We present xBD, a new, large-scale dataset for the advancement of change detection and building damage assessment for humanitarian assistance and disaster recovery research. Natural disaster response requires an accurate understanding of damaged buildings in an affected region. Current response strategies require in-person damage assessments within 24-48 hours of a disaster. Massive potential exists for using aerial imagery combined with computer vision algorithms to assess damage and reduce the potential danger to human life. In collaboration with multiple disaster response agencies, xBD provides pre- and post-event satellite imagery across a variety of disaster events with building polygons, ordinal labels of damage level, and corresponding satellite metadata. Furthermore, the dataset contains bounding boxes and labels for environmental factors such as fire, water, and smoke. xBD is the largest building damage assessment dataset to date, containing 850,736 building annotations across 45,362 km2 of imagery.

Tracking biosignals is crucial for monitoring wellness and preempting the development of severe medical conditions. Today, wearable devices can conveniently record various biosignals, creating the opportunity to monitor health status without disruption to one's daily routine. Despite widespread use of wearable devices and existing digital biomarkers, the absence of curated data with annotated medical labels hinders the development of new biomarkers to measure common health conditions. In fact, medical datasets are usually small in comparison to other domains, which is an obstacle for developing neural network models for biosignals. To address this challenge, we have employed self-supervised learning using the unlabeled sensor data collected under informed consent from the large longitudinal Apple Heart and Movement Study (AHMS) to train foundation models for two common biosignals: photoplethysmography (PPG) and electrocardiogram (ECG) recorded on Apple Watch. We curated PPG and ECG datasets from AHMS that include data from ~141K participants spanning ~3 years. Our self-supervised learning framework includes participant level positive pair selection, stochastic augmentation module and a regularized contrastive loss optimized with momentum training, and generalizes well to both PPG and ECG modalities. We show that the pre-trained foundation models readily encode information regarding participants' demographics and health conditions. To the best of our knowledge, this is the first study that builds foundation models using large-scale PPG and ECG data collected via wearable consumer devices x2013 prior works have commonly used smaller-size datasets collected in clinical and experimental settings. We believe PPG and ECG foundation models can enhance future wearable devices by reducing the reliance on labeled data and hold the potential to help the users improve their health.

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

With a 676% growth rate in HIV incidence between 2010 and 2021, the HIV/AIDS epidemic in the Philippines is the one that is spreading the quickest in the western Pacific. Although the full effects of COVID-19 on HIV services and development are still unknown, it is predicted that such disruptions could lead to a significant increase in HIV casualties. Therefore, the nation needs some modeling and forecasting techniques to foresee the spread pattern and enhance the governments prevention, treatment, testing, and care program. In this study, the researcher uses Multilayer Perceptron Neural Network to forecast time series during the period when the COVID-19 pandemic strikes the nation, using statistics taken from the HIV/AIDS and ART Registry of the Philippines. After training, validation, and testing of data, the study finds that the predicted cumulative cases in the nation by 2030 will reach 145,273. Additionally, there is very little difference between observed and anticipated HIV epidemic levels, as evidenced by reduced RMSE, MAE, and MAPE values as well as a greater coefficient of determination. Further research revealed that the Philippines seems far from achieving Sustainable Development Goal 3 of Project 2030 due to an increase in the nations rate of new HIV infections. Despite the detrimental effects of COVID-19 spread on HIV/AIDS efforts nationwide, the Philippine government, under the Marcos administration, must continue to adhere to the United Nations 90-90-90 targets by enhancing its ART program and ensuring that all vital health services are readily accessible and available.

Developing clinical prediction models (e.g., mortality prediction) based on electronic health records (EHRs) typically relies on expert opinion for feature selection and adjusting observation window size. This burdens experts and creates a bottleneck in the development process. We propose Retrieval-Enhanced Medical prediction model (REMed) to address such challenges. REMed can essentially evaluate an unlimited number of clinical events, select the relevant ones, and make predictions. This approach effectively eliminates the need for manual feature selection and enables an unrestricted observation window. We verified these properties through experiments on 27 clinical tasks and two independent cohorts from publicly available EHR datasets, where REMed outperformed other contemporary architectures that aim to handle as many events as possible. Notably, we found that the preferences of REMed align closely with those of medical experts. We expect our approach to significantly expedite the development of EHR prediction models by minimizing clinicians' need for manual involvement.

Air pollution constitutes a global problem of paramount importance that affects not only human health, but also the environment. The existence of spatial and temporal data regarding the concentrations of pollutants is crucial for performing air pollution studies and monitor emissions. However, although observation data presents great temporal coverage, the number of stations is very limited and they are usually built in more populated areas. The main objective of this work is to create models capable of inferring pollutant concentrations in locations where no observation data exists. A machine learning model, more specifically the random forest model, was developed for predicting concentrations in the Iberian Peninsula in 2019 for five selected pollutants: NO_2, O_3 SO_2, PM10, and PM2.5. Model features include satellite measurements, meteorological variables, land use classification, temporal variables (month, day of year), and spatial variables (latitude, longitude, altitude). The models were evaluated using various methods, including station 10-fold cross-validation, in which in each fold observations from 10\% of the stations are used as testing data and the rest as training data. The R^2, RMSE and mean bias were determined for each model. The NO_2 and O_3 models presented good values of R^2, 0.5524 and 0.7462, respectively. However, the SO_2, PM10, and PM2.5 models performed very poorly in this regard, with R^2 values of -0.0231, 0.3722, and 0.3303, respectively. All models slightly overestimated the ground concentrations, except the O_3 model. All models presented acceptable cross-validation RMSE, except the O_3 and PM10 models where the mean value was a little higher (12.5934 mu g/m^3 and 10.4737 mu g/m^3, respectively).

The 1st Workshop on Data Contamination (CONDA 2024) focuses on all relevant aspects of data contamination in natural language processing, where data contamination is understood as situations where evaluation data is included in pre-training corpora used to train large scale models, compromising evaluation results. The workshop fostered a shared task to collect evidence on data contamination in current available datasets and models. The goal of the shared task and associated database is to assist the community in understanding the extent of the problem and to assist researchers in avoiding reporting evaluation results on known contaminated resources. The shared task provides a structured, centralized public database for the collection of contamination evidence, open to contributions from the community via GitHub pool requests. This first compilation paper is based on 566 reported entries over 91 contaminated sources from a total of 23 contributors. The details of the individual contamination events are available in the platform. The platform continues to be online, open to contributions from the community.

We introduce MentalChat16K, an English benchmark dataset combining a synthetic mental health counseling dataset and a dataset of anonymized transcripts from interventions between Behavioral Health Coaches and Caregivers of patients in palliative or hospice care. Covering a diverse range of conditions like depression, anxiety, and grief, this curated dataset is designed to facilitate the development and evaluation of large language models for conversational mental health assistance. By providing a high-quality resource tailored to this critical domain, MentalChat16K aims to advance research on empathetic, personalized AI solutions to improve access to mental health support services. The dataset prioritizes patient privacy, ethical considerations, and responsible data usage. MentalChat16K presents a valuable opportunity for the research community to innovate AI technologies that can positively impact mental well-being. The dataset is available at https://huggingface.co/datasets/ShenLab/MentalChat16K and the code and documentation are hosted on GitHub at https://github.com/ChiaPatricia/MentalChat16K.

Open-source large language models are becoming increasingly available and popular among researchers and practitioners. While significant progress has been made on open-weight models, open training data is a practice yet to be adopted by the leading open-weight models creators. At the same time, there researchers are working to make language models safer. We propose a data curation pipeline to reduce harmful outputs by models trained on public domain data. There are unique challenges to working with public domain data, as these sources differ from web text in both form and content. Many sources are historical documents and are the result of Optical Character Recognition (OCR). Consequently, current state-of-the-art approaches to toxicity filtering are often infeasible or inappropriate for open data models. In this paper, we introduce a new fully open-source pipeline for open-data toxicity filtering. Our contributions are threefold. We create a custom training dataset, ToxicCommons, which is composed of texts which have been classified across five different dimensions (racial/origin-based, gender/sex-based, religious, ability-based discrimination, and violence). We use this dataset to train a custom classifier, Celadon, that can be used to detect toxic content in open data more efficiently at a larger scale. Finally, we describe the balanced approach to content filtration that optimizes safety filtering with respect to the filtered data available for training.

Gun violence is a pressing and growing human rights issue that affects nearly every dimension of the social fabric, from healthcare and education to psychology and the economy. Reliable data on firearm events is paramount to developing more effective public policy and emergency responses. However, the lack of comprehensive databases and the risks of in-person surveys prevent human rights organizations from collecting needed data in most countries. Here, we partner with a Brazilian human rights organization to conduct a systematic evaluation of language models to assist with monitoring real-world firearm events from social media data. We propose a fine-tuned BERT-based model trained on Twitter (now X) texts to distinguish gun violence reports from ordinary Portuguese texts. Our model achieves a high AUC score of 0.97. We then incorporate our model into a web application and test it in a live intervention. We study and interview Brazilian analysts who continuously fact-check social media texts to identify new gun violence events. Qualitative assessments show that our solution helped all analysts use their time more efficiently and expanded their search capacities. Quantitative assessments show that the use of our model was associated with more analysts' interactions with online users reporting gun violence. Taken together, our findings suggest that modern Natural Language Processing techniques can help support the work of human rights organizations.

The fire and crime incident datasets were requested and collected from two Philippine regional agencies (i.e., the Bureau of Fire Protection and the Philippine National Police). The datasets were used to initially analyze and map both fire and crime incidents within the province of Pampanga for a specific time frame. Several data preparation, normalization, and data cleaning steps were implemented to properly map and identify patterns within the datasets. The initial results also indicate the leading causes of fire and crimes are rubbish and acts against property. Fires mostly occur during the dry season in the province. Crime is particularly high during December, and most of the fire and crime incidents occur during the time when people are most active. The dataset was able to present the temporal characteristics of the fire and crime incidents that occurred in the province of Pampanga. Merge the existing dataset with the other datasets from other related agencies to get a bigger picture and produce more objective results that could be used for decision-making.

Respiratory viral infections pose a global health burden, yet the cellular immune responses driving protection or pathology remain unclear. Natural infection cohorts often lack pre-exposure baseline data and structured temporal sampling. In contrast, inoculation and vaccination trials generate insightful longitudinal transcriptomic data. However, the scattering of these datasets across platforms, along with inconsistent metadata and preprocessing procedure, hinders AI-driven discovery. To address these challenges, we developed the Human Respiratory Viral Immunization LongitudinAl Gene Expression (HR-VILAGE-3K3M) repository: an AI-ready, rigorously curated dataset that integrates 14,136 RNA-seq profiles from 3,178 subjects across 66 studies encompassing over 2.56 million cells. Spanning vaccination, inoculation, and mixed exposures, the dataset includes microarray, bulk RNA-seq, and single-cell RNA-seq from whole blood, PBMCs, and nasal swabs, sourced from GEO, ImmPort, and ArrayExpress. We harmonized subject-level metadata, standardized outcome measures, applied unified preprocessing pipelines with rigorous quality control, and aligned all data to official gene symbols. To demonstrate the utility of HR-VILAGE-3K3M, we performed predictive modeling of vaccine responders and evaluated batch-effect correction methods. Beyond these initial demonstrations, it supports diverse systems immunology applications and benchmarking of feature selection and transfer learning algorithms. Its scale and heterogeneity also make it ideal for pretraining foundation models of the human immune response and for advancing multimodal learning frameworks. As the largest longitudinal transcriptomic resource for human respiratory viral immunization, it provides an accessible platform for reproducible AI-driven research, accelerating systems immunology and vaccine development against emerging viral threats.

Machine learning models trained on Earth observation data, such as satellite imagery, have demonstrated significant promise in predicting household-level wealth indices, enabling the creation of high-resolution wealth maps that can be leveraged across multiple causal trials. However, because standard training objectives prioritize overall predictive accuracy, these predictions inherently suffer from shrinkage toward the mean, leading to attenuated estimates of causal treatment effects and limiting their utility in policy. Existing debiasing methods, such as Prediction-Powered Inference, can handle this attenuation bias but require additional fresh ground-truth data at the downstream stage of causal inference, which restricts their applicability in data-scarce environments. Here, we introduce and evaluate two correction methods -- linear calibration correction and Tweedie's correction -- that substantially reduce prediction bias without relying on newly collected labeled data. Linear calibration corrects bias through a straightforward linear transformation derived from held-out calibration data, whereas Tweedie's correction leverages empirical Bayes principles to directly address shrinkage-induced biases by exploiting score functions derived from the model's learning patterns. Through analytical exercises and experiments using Demographic and Health Survey data, we demonstrate that the proposed methods meet or outperform existing approaches that either require (a) adjustments to training pipelines or (b) additional labeled data. These approaches may represent a promising avenue for improving the reliability of causal inference when direct outcome measures are limited or unavailable, enabling a "one map, many trials" paradigm where a single upstream data creation team produces predictions usable by many downstream teams across diverse ML pipelines.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Biomedical data is inherently multimodal, consisting of electronic health records, medical imaging, digital pathology, genome sequencing, wearable sensors, and more. The application of artificial intelligence tools to these multifaceted sensing technologies has the potential to revolutionize the prognosis, diagnosis, and management of human health and disease. However, current approaches to biomedical AI typically only train and evaluate with one or a small set of medical modalities and tasks. This limitation hampers the development of comprehensive tools that can leverage the rich interconnected information across many heterogeneous biomedical sensors. To address this challenge, we present MultiMed, a benchmark designed to evaluate and enable large-scale learning across a wide spectrum of medical modalities and tasks. MultiMed consists of 2.56 million samples across ten medical modalities such as medical reports, pathology, genomics, and protein data, and is structured into eleven challenging tasks, including disease prognosis, protein structure prediction, and medical question answering. Using MultiMed, we conduct comprehensive experiments benchmarking state-of-the-art unimodal, multimodal, and multitask models. Our analysis highlights the advantages of training large-scale medical models across many related modalities and tasks. Moreover, MultiMed enables studies of generalization across related medical concepts, robustness to real-world noisy data and distribution shifts, and novel modality combinations to improve prediction performance. MultiMed will be publicly available and regularly updated and welcomes inputs from the community.

When deploying machine learning models in high-stakes real-world environments such as health care, it is crucial to accurately assess the uncertainty concerning a model's prediction on abnormal inputs. However, there is a scarcity of literature analyzing this problem on medical data, especially on mixed-type tabular data such as Electronic Health Records. We close this gap by presenting a series of tests including a large variety of contemporary uncertainty estimation techniques, in order to determine whether they are able to identify out-of-distribution (OOD) patients. In contrast to previous work, we design tests on realistic and clinically relevant OOD groups, and run experiments on real-world medical data. We find that almost all techniques fail to achieve convincing results, partly disagreeing with earlier findings.

Continuity of care is crucial to ensuring positive health outcomes for patients discharged from an inpatient hospital setting, and improved information sharing can help. To share information, caregivers write discharge notes containing action items to share with patients and their future caregivers, but these action items are easily lost due to the lengthiness of the documents. In this work, we describe our creation of a dataset of clinical action items annotated over MIMIC-III, the largest publicly available dataset of real clinical notes. This dataset, which we call CLIP, is annotated by physicians and covers 718 documents representing 100K sentences. We describe the task of extracting the action items from these documents as multi-aspect extractive summarization, with each aspect representing a type of action to be taken. We evaluate several machine learning models on this task, and show that the best models exploit in-domain language model pre-training on 59K unannotated documents, and incorporate context from neighboring sentences. We also propose an approach to pre-training data selection that allows us to explore the trade-off between size and domain-specificity of pre-training datasets for this task.

With the rapid evolution of large language models (LLMs), new and hard-to-predict harmful capabilities are emerging. This requires developers to be able to identify risks through the evaluation of "dangerous capabilities" in order to responsibly deploy LLMs. In this work, we collect the first open-source dataset to evaluate safeguards in LLMs, and deploy safer open-source LLMs at a low cost. Our dataset is curated and filtered to consist only of instructions that responsible language models should not follow. We annotate and assess the responses of six popular LLMs to these instructions. Based on our annotation, we proceed to train several BERT-like classifiers, and find that these small classifiers can achieve results that are comparable with GPT-4 on automatic safety evaluation. Warning: this paper contains example data that may be offensive, harmful, or biased.

Objective: To transform heterogeneous clinical data from electronic health records into clinically meaningful constructed features using data driven method that rely, in part, on temporal relations among data. Materials and Methods: The clinically meaningful representations of medical concepts and patients are the key for health analytic applications. Most of existing approaches directly construct features mapped to raw data (e.g., ICD or CPT codes), or utilize some ontology mapping such as SNOMED codes. However, none of the existing approaches leverage EHR data directly for learning such concept representation. We propose a new way to represent heterogeneous medical concepts (e.g., diagnoses, medications and procedures) based on co-occurrence patterns in longitudinal electronic health records. The intuition behind the method is to map medical concepts that are co-occuring closely in time to similar concept vectors so that their distance will be small. We also derive a simple method to construct patient vectors from the related medical concept vectors. Results: For qualitative evaluation, we study similar medical concepts across diagnosis, medication and procedure. In quantitative evaluation, our proposed representation significantly improves the predictive modeling performance for onset of heart failure (HF), where classification methods (e.g. logistic regression, neural network, support vector machine and K-nearest neighbors) achieve up to 23% improvement in area under the ROC curve (AUC) using this proposed representation. Conclusion: We proposed an effective method for patient and medical concept representation learning. The resulting representation can map relevant concepts together and also improves predictive modeling performance.

Adherence to prescribed treatments is crucial for individuals with chronic conditions to avoid costly or adverse health outcomes. For certain patient groups, intensive lifestyle interventions are vital for enhancing medication adherence. Accurate forecasting of treatment adherence can open pathways to developing an on-demand intervention tool, enabling timely and personalized support. With the increasing popularity of smartphones and wearables, it is now easier than ever to develop and deploy smart activity monitoring systems. However, effective forecasting systems for treatment adherence based on wearable sensors are still not widely available. We close this gap by proposing Adherence Forecasting and Intervention with Machine Intelligence (AIMI). AIMI is a knowledge-guided adherence forecasting system that leverages smartphone sensors and previous medication history to estimate the likelihood of forgetting to take a prescribed medication. A user study was conducted with 27 participants who took daily medications to manage their cardiovascular diseases. We designed and developed CNN and LSTM-based forecasting models with various combinations of input features and found that LSTM models can forecast medication adherence with an accuracy of 0.932 and an F-1 score of 0.936. Moreover, through a series of ablation studies involving convolutional and recurrent neural network architectures, we demonstrate that leveraging known knowledge about future and personalized training enhances the accuracy of medication adherence forecasting. Code available: https://github.com/ab9mamun/AIMI.

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

Clinical trials drive improvements in cancer treatments and outcomes. However, most adults with cancer do not participate in trials, and trials often fail to enroll enough patients to answer their scientific questions. Artificial intelligence could accelerate matching of patients to appropriate clinical trials. Here, we describe the development and evaluation of the MatchMiner-AI pipeline for clinical trial searching and ranking. MatchMiner-AI focuses on matching patients to potential trials based on core criteria describing clinical "spaces," or disease contexts, targeted by a trial. It aims to accelerate the human work of identifying potential matches, not to fully automate trial screening. The pipeline includes modules for extraction of key information from a patient's longitudinal electronic health record; rapid ranking of candidate trial-patient matches based on embeddings in vector space; and classification of whether a candidate match represents a reasonable clinical consideration. Code and synthetic data are available at https://huggingface.co/ksg-dfci/MatchMiner-AI . Model weights based on synthetic data are available at https://huggingface.co/ksg-dfci/TrialSpace and https://huggingface.co/ksg-dfci/TrialChecker . A simple cancer clinical trial search engine to demonstrate pipeline components is available at https://huggingface.co/spaces/ksg-dfci/trial_search_alpha .

We present a foundation model-derived method to identify highly informative tokens and events in electronic health records. Our approach considers incoming data in the entire context of a patient's hospitalization and so can flag anomalous events that rule-based approaches would consider within a normal range. We demonstrate that the events our model flags are significant for predicting downstream patient outcomes and that a fraction of events identified as carrying little information can safely be dropped. Additionally, we show how informativeness can help interpret the predictions of prognostic models trained on foundation model-derived representations.

Self-supervision may boost model performance in downstream tasks. However, there is no principled way of selecting the self-supervised objectives that yield the most adaptable models. Here, we study this problem on daily time-series data generated from wearable sensors used to detect onset of influenza-like illness (ILI). We first show that using self-supervised learning to predict next-day time-series values allows us to learn rich representations which can be adapted to perform accurate ILI prediction. Second, we perform an empirical analysis of three different self-supervised objectives to assess their adaptability to ILI prediction. Our results show that predicting the next day's resting heart rate or time-in-bed during sleep provides better representations for ILI prediction. These findings add to previous work demonstrating the practical application of self-supervised learning from activity data to improve health predictions.

The COVID-19 pandemic has accentuated socioeconomic disparities across various racial and ethnic groups in the United States. While previous studies have utilized traditional survey methods like the Household Pulse Survey (HPS) to elucidate these disparities, this paper explores the role of social media platforms in both highlighting and addressing these challenges. Drawing from real-time data sourced from Twitter, we analyzed language patterns related to four major types of adverse experiences: loss of employment income (LI), food scarcity (FS), housing insecurity (HI), and unmet needs for mental health services (UM). We first formulate a sparsity optimization problem that extracts low-level language features from social media data sources. Second, we propose novel constraints on feature similarity exploiting prior knowledge about the similarity of the language patterns among the adverse experiences. The proposed problem is challenging to solve due to the non-convexity objective and non-smoothness penalties. We develop an algorithm based on the alternating direction method of multipliers (ADMM) framework to solve the proposed formulation. Extensive experiments and comparisons to other models on real-world social media and the detection of adverse experiences justify the efficacy of our model.

"IMDb" as a user-regulating and one the most-visited portal has provided an opportunity to create an enormous database. Analysis of the information on Internet Movie Database - IMDb, either those related to the movie or provided by users would help to reveal the determinative factors in the route of success for each movie. As the lack of a comprehensive dataset was felt, we determined to do create a compendious dataset for the later analysis using the statistical methods and machine learning models; It comprises of various information provided on IMDb such as rating data, genre, cast and crew, MPAA rating certificate, parental guide details, related movie information, posters, etc, for over 79k titles which is the largest dataset by this date. The present paper is the first paper in a series of papers aiming at the mentioned goals, by a description of the created dataset and a preliminary analysis including some trend in data, demographic analysis of IMDb scores and their relation of genre MPAA rating certificate has been investigated.

The COVID-19 Open Research Dataset (CORD-19) is a growing resource of scientific papers on COVID-19 and related historical coronavirus research. CORD-19 is designed to facilitate the development of text mining and information retrieval systems over its rich collection of metadata and structured full text papers. Since its release, CORD-19 has been downloaded over 200K times and has served as the basis of many COVID-19 text mining and discovery systems. In this article, we describe the mechanics of dataset construction, highlighting challenges and key design decisions, provide an overview of how CORD-19 has been used, and describe several shared tasks built around the dataset. We hope this resource will continue to bring together the computing community, biomedical experts, and policy makers in the search for effective treatments and management policies for COVID-19.

We present a large real-world dataset obtained from monitoring a smart company facility over the course of six years, from 2018 to 2023. The dataset includes energy consumption data from various facility areas and components, energy production data from a photovoltaic system and a combined heat and power plant, operational data from heating and cooling systems, and weather data from an on-site weather station. The measurement sensors installed throughout the facility are organized in a hierarchical metering structure with multiple sub-metering levels, which is reflected in the dataset. The dataset contains measurement data from 72 energy meters, 9 heat meters and a weather station. Both raw and processed data at different processing levels, including labeled issues, is available. In this paper, we describe the data acquisition and post-processing employed to create the dataset. The dataset enables the application of a wide range of methods in the domain of energy management, including optimization, modeling, and machine learning to optimize building operations and reduce costs and carbon emissions.

The rapid evolution of artificial intelligence (AI), together with the increased availability of social media and news for epidemiological surveillance, are marking a pivotal moment in epidemiology and public health research. Leveraging the power of generative AI, we use an ensemble approach which incorporates multiple Large Language Models (LLMs) to extract valuable actionable epidemiological information from the World Health Organization (WHO) Disease Outbreak News (DONs). DONs is a collection of regular reports on global outbreaks curated by the WHO and the adopted decision-making processes to respond to them. The extracted information is made available in a daily-updated dataset and a knowledge graph, referred to as eKG, derived to provide a nuanced representation of the public health domain knowledge. We provide an overview of this new dataset and describe the structure of eKG, along with the services and tools used to access and utilize the data that we are building on top. These innovative data resources open altogether new opportunities for epidemiological research, and the analysis and surveillance of disease outbreaks.

Electronic medical records (EMR) contain sensitive personal information. For example, they may include details about infectious diseases, such as human immunodeficiency virus (HIV), or they may contain information about a mental illness. They may also contain other sensitive information such as medical details related to fertility treatments. Because EMRs are subject to confidentiality requirements, accessing and analyzing EMR databases is a privilege given to only a small number of individuals. Individuals who work at institutions that do not have access to EMR systems have no opportunity to gain hands-on experience with this valuable resource. Simulated medical databases are currently available; however, they are difficult to configure and are limited in their resemblance to real clinical databases. Generating highly accessible repositories of virtual patient EMRs while relying only minimally on real patient data is expected to serve as a valuable resource to a broader audience of medical personnel, including those who reside in underdeveloped countries.

Clinical notes contain information about patients that goes beyond structured data like lab values and medications. However, clinical notes have been underused relative to structured data, because notes are high-dimensional and sparse. This work develops and evaluates representations of clinical notes using bidirectional transformers (ClinicalBERT). ClinicalBERT uncovers high-quality relationships between medical concepts as judged by humans. ClinicalBert outperforms baselines on 30-day hospital readmission prediction using both discharge summaries and the first few days of notes in the intensive care unit. Code and model parameters are available.

The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have access to a vast amount of clinical data, which allows us to develop predictive models and decision support systems to address these challenges. To date, however, there are no widely accepted benchmark ED triage prediction models based on large-scale public EHR data. An open-source benchmarking platform would streamline research workflows by eliminating cumbersome data preprocessing, and facilitate comparisons among different studies and methodologies. In this paper, based on the Medical Information Mart for Intensive Care IV Emergency Department (MIMIC-IV-ED) database, we developed a publicly available benchmark suite for ED triage predictive models and created a benchmark dataset that contains over 400,000 ED visits from 2011 to 2019. We introduced three ED-based outcomes (hospitalization, critical outcomes, and 72-hour ED reattendance) and implemented a variety of popular methodologies, ranging from machine learning methods to clinical scoring systems. We evaluated and compared the performance of these methods against benchmark tasks. Our codes are open-source, allowing anyone with MIMIC-IV-ED data access to perform the same steps in data processing, benchmark model building, and experiments. This study provides future researchers with insights, suggestions, and protocols for managing raw data and developing risk triaging tools for emergency care.

Background: Recent advancements in large language models (LLMs) offer potential benefits in healthcare, particularly in processing extensive patient records. However, existing benchmarks do not fully assess LLMs' capability in handling real-world, lengthy clinical data. Methods: We present the LongHealth benchmark, comprising 20 detailed fictional patient cases across various diseases, with each case containing 5,090 to 6,754 words. The benchmark challenges LLMs with 400 multiple-choice questions in three categories: information extraction, negation, and sorting, challenging LLMs to extract and interpret information from large clinical documents. Results: We evaluated nine open-source LLMs with a minimum of 16,000 tokens and also included OpenAI's proprietary and cost-efficient GPT-3.5 Turbo for comparison. The highest accuracy was observed for Mixtral-8x7B-Instruct-v0.1, particularly in tasks focused on information retrieval from single and multiple patient documents. However, all models struggled significantly in tasks requiring the identification of missing information, highlighting a critical area for improvement in clinical data interpretation. Conclusion: While LLMs show considerable potential for processing long clinical documents, their current accuracy levels are insufficient for reliable clinical use, especially in scenarios requiring the identification of missing information. The LongHealth benchmark provides a more realistic assessment of LLMs in a healthcare setting and highlights the need for further model refinement for safe and effective clinical application. We make the benchmark and evaluation code publicly available.

After being collected for patient care, Observational Health Data (OHD) can further benefit patient well-being by sustaining the development of health informatics and medical research. Vast potential is unexploited because of the fiercely private nature of patient-related data and regulations to protect it. Generative Adversarial Networks (GANs) have recently emerged as a groundbreaking way to learn generative models that produce realistic synthetic data. They have revolutionized practices in multiple domains such as self-driving cars, fraud detection, digital twin simulations in industrial sectors, and medical imaging. The digital twin concept could readily apply to modelling and quantifying disease progression. In addition, GANs posses many capabilities relevant to common problems in healthcare: lack of data, class imbalance, rare diseases, and preserving privacy. Unlocking open access to privacy-preserving OHD could be transformative for scientific research. In the midst of COVID-19, the healthcare system is facing unprecedented challenges, many of which of are data related for the reasons stated above. Considering these facts, publications concerning GAN applied to OHD seemed to be severely lacking. To uncover the reasons for this slow adoption, we broadly reviewed the published literature on the subject. Our findings show that the properties of OHD were initially challenging for the existing GAN algorithms (unlike medical imaging, for which state-of-the-art model were directly transferable) and the evaluation synthetic data lacked clear metrics. We find more publications on the subject than expected, starting slowly in 2017, and since then at an increasing rate. The difficulties of OHD remain, and we discuss issues relating to evaluation, consistency, benchmarking, data modelling, and reproducibility.

We present the first smart phone tool that is capable of self-compilation, mutation and viral spreading. Our autonomous app does not require a host computer to alter its functionality, change its appearance and lacks the normal necessity of a central app store to spread among hosts. We pioneered survival skills for mobile software in order to overcome disrupted Internet access due to natural disasters and human made interference, like Internet kill switches or censored networks. Internet kill switches have proven to be an effective tool to eradicate open Internet access and all forms of digital communication within an hour on a country-wide basis. We present the first operational tool that is capable of surviving such digital eradication.

As of writing this paper, COVID-19 (Coronavirus disease 2019) has spread to more than 220 countries and territories. Following the outbreak, the pandemic's seriousness has made people more active on social media, especially on the microblogging platforms such as Twitter and Weibo. The pandemic-specific discourse has remained on-trend on these platforms for months now. Previous studies have confirmed the contributions of such socially generated conversations towards situational awareness of crisis events. The early forecasts of cases are essential to authorities to estimate the requirements of resources needed to cope with the outgrowths of the virus. Therefore, this study attempts to incorporate the public discourse in the design of forecasting models particularly targeted for the steep-hill region of an ongoing wave. We propose a sentiment-involved topic-based latent variables search methodology for designing forecasting models from publicly available Twitter conversations. As a use case, we implement the proposed methodology on Australian COVID-19 daily cases and Twitter conversations generated within the country. Experimental results: (i) show the presence of latent social media variables that Granger-cause the daily COVID-19 confirmed cases, and (ii) confirm that those variables offer additional prediction capability to forecasting models. Further, the results show that the inclusion of social media variables introduces 48.83--51.38% improvements on RMSE over the baseline models. We also release the large-scale COVID-19 specific geotagged global tweets dataset, MegaGeoCOV, to the public anticipating that the geotagged data of this scale would aid in understanding the conversational dynamics of the pandemic through other spatial and temporal contexts.

Machine learning (ML) holds great potential for accurately forecasting treatment outcomes over time, which could ultimately enable the adoption of more individualized treatment strategies in many practical applications. However, a significant challenge that has been largely overlooked by the ML literature on this topic is the presence of informative sampling in observational data. When instances are observed irregularly over time, sampling times are typically not random, but rather informative -- depending on the instance's characteristics, past outcomes, and administered treatments. In this work, we formalize informative sampling as a covariate shift problem and show that it can prohibit accurate estimation of treatment outcomes if not properly accounted for. To overcome this challenge, we present a general framework for learning treatment outcomes in the presence of informative sampling using inverse intensity-weighting, and propose a novel method, TESAR-CDE, that instantiates this framework using Neural CDEs. Using a simulation environment based on a clinical use case, we demonstrate the effectiveness of our approach in learning under informative sampling.

Natural disasters, such as floods, tornadoes, or wildfires, are increasingly pervasive as the Earth undergoes global warming. It is difficult to predict when and where an incident will occur, so timely emergency response is critical to saving the lives of those endangered by destructive events. Fortunately, technology can play a role in these situations. Social media posts can be used as a low-latency data source to understand the progression and aftermath of a disaster, yet parsing this data is tedious without automated methods. Prior work has mostly focused on text-based filtering, yet image and video-based filtering remains largely unexplored. In this work, we present the Incidents1M Dataset, a large-scale multi-label dataset which contains 977,088 images, with 43 incident and 49 place categories. We provide details of the dataset construction, statistics and potential biases; introduce and train a model for incident detection; and perform image-filtering experiments on millions of images on Flickr and Twitter. We also present some applications on incident analysis to encourage and enable future work in computer vision for humanitarian aid. Code, data, and models are available at http://incidentsdataset.csail.mit.edu.