Daily Papers

Recent advancements in language models (LMs) have notably enhanced their ability to reason with tabular data, primarily through program-aided mechanisms that manipulate and analyze tables. However, these methods often require the entire table as input, leading to scalability challenges due to the positional bias or context length constraints. In response to these challenges, we introduce TableRAG, a Retrieval-Augmented Generation (RAG) framework specifically designed for LM-based table understanding. TableRAG leverages query expansion combined with schema and cell retrieval to pinpoint crucial information before providing it to the LMs. This enables more efficient data encoding and precise retrieval, significantly reducing prompt lengths and mitigating information loss. We have developed two new million-token benchmarks from the Arcade and BIRD-SQL datasets to thoroughly evaluate TableRAG's effectiveness at scale. Our results demonstrate that TableRAG's retrieval design achieves the highest retrieval quality, leading to the new state-of-the-art performance on large-scale table understanding.

Existing Text-to-SQL generators require the entire schema to be encoded with the user text. This is expensive or impractical for large databases with tens of thousands of columns. Standard dense retrieval techniques are inadequate for schema subsetting of a large structured database, where the correct semantics of retrieval demands that we rank sets of schema elements rather than individual elements. In response, we propose a two-stage process for effective coverage during retrieval. First, we instruct an LLM to hallucinate a minimal DB schema deemed adequate to answer the query. We use the hallucinated schema to retrieve a subset of the actual schema, by composing the results from multiple dense retrievals. Remarkably, hallucination x2013 generally considered a nuisance x2013 turns out to be actually useful as a bridging mechanism. Since no existing benchmarks exist for schema subsetting on large databases, we introduce three benchmarks. Two semi-synthetic datasets are derived from the union of schemas in two well-known datasets, SPIDER and BIRD, resulting in 4502 and 798 schema elements respectively. A real-life benchmark called SocialDB is sourced from an actual large data warehouse comprising 17844 schema elements. We show that our method1 leads to significantly higher recall than SOTA retrieval-based augmentation methods.

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

Schema linking -- the process of aligning natural language questions with database schema elements -- is a critical yet underexplored component of Text-to-SQL systems. While recent methods have focused primarily on improving SQL generation, they often neglect the retrieval of relevant schema elements, which can lead to hallucinations and execution failures. In this work, we propose a context-aware bidirectional schema retrieval framework that treats schema linking as a standalone problem. Our approach combines two complementary strategies: table-first retrieval followed by column selection, and column-first retrieval followed by table selection. It is further augmented with techniques such as question decomposition, keyword extraction, and keyphrase extraction. Through comprehensive evaluations on challenging benchmarks such as BIRD and Spider, we demonstrate that our method significantly improves schema recall while reducing false positives. Moreover, SQL generation using our retrieved schema consistently outperforms full-schema baselines and closely approaches oracle performance, all without requiring query refinement. Notably, our method narrows the performance gap between full and perfect schema settings by 50\%. Our findings highlight schema linking as a powerful lever for enhancing Text-to-SQL accuracy and efficiency.

Recent advances in language models opened new opportunities to address complex schema matching tasks. Schema matching approaches have been proposed that demonstrate the usefulness of language models, but they have also uncovered important limitations: Small language models (SLMs) require training data (which can be both expensive and challenging to obtain), and large language models (LLMs) often incur high computational costs and must deal with constraints imposed by context windows. We present Magneto, a cost-effective and accurate solution for schema matching that combines the advantages of SLMs and LLMs to address their limitations. By structuring the schema matching pipeline in two phases, retrieval and reranking, Magneto can use computationally efficient SLM-based strategies to derive candidate matches which can then be reranked by LLMs, thus making it possible to reduce runtime without compromising matching accuracy. We propose a self-supervised approach to fine-tune SLMs which uses LLMs to generate syntactically diverse training data, and prompting strategies that are effective for reranking. We also introduce a new benchmark, developed in collaboration with domain experts, which includes real biomedical datasets and presents new challenges to schema matching methods. Through a detailed experimental evaluation, using both our new and existing benchmarks, we show that Magneto is scalable and attains high accuracy for datasets from different domains.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Tables have gained significant attention in large language models (LLMs) and multimodal large language models (MLLMs) due to their complex and flexible structure. Unlike linear text inputs, tables are two-dimensional, encompassing formats that range from well-structured database tables to complex, multi-layered spreadsheets, each with different purposes. This diversity in format and purpose has led to the development of specialized methods and tasks, instead of universal approaches, making navigation of table understanding tasks challenging. To address these challenges, this paper introduces key concepts through a taxonomy of tabular input representations and an introduction of table understanding tasks. We highlight several critical gaps in the field that indicate the need for further research: (1) the predominance of retrieval-focused tasks that require minimal reasoning beyond mathematical and logical operations; (2) significant challenges faced by models when processing complex table structures, large-scale tables, length context, or multi-table scenarios; and (3) the limited generalization of models across different tabular representations and formats.

Schemata are structured representations of complex tasks that can aid artificial intelligence by allowing models to break down complex tasks into intermediate steps. We propose a novel system that induces schemata from web videos and generalizes them to capture unseen tasks with the goal of improving video retrieval performance. Our system proceeds in three major phases: (1) Given a task with related videos, we construct an initial schema for a task using a joint video-text model to match video segments with text representing steps from wikiHow; (2) We generalize schemata to unseen tasks by leveraging language models to edit the text within existing schemata. Through generalization, we can allow our schemata to cover a more extensive range of tasks with a small amount of learning data; (3) We conduct zero-shot instructional video retrieval with the unseen task names as the queries. Our schema-guided approach outperforms existing methods for video retrieval, and we demonstrate that the schemata induced by our system are better than those generated by other models.

Several approaches are proposed to deal with the problem of the Automatic Schema Matching (ASM). The challenges and difficulties caused by the complexity and uncertainty characterizing both the process and the outcome of Schema Matching motivated us to investigate how bio-inspired emerging paradigm can help with understanding, managing, and ultimately overcoming those challenges. In this paper, we explain how we approached Automatic Schema Matching as a systemic and Complex Adaptive System (CAS) and how we modeled it using the approach of Agent-Based Modeling and Simulation (ABMS). This effort gives birth to a tool (prototype) for schema matching called Reflex-SMAS. A set of experiments demonstrates the viability of our approach on two main aspects: (i) effectiveness (increasing the quality of the found matchings) and (ii) efficiency (reducing the effort required for this efficiency). Our approach represents a significant paradigm-shift, in the field of Automatic Schema Matching.

The question-answering system for Life science research, which is characterized by the rapid pace of discovery, evolving insights, and complex interactions among knowledge entities, presents unique challenges in maintaining a comprehensive knowledge warehouse and accurate information retrieval. To address these issues, we introduce BioRAG, a novel Retrieval-Augmented Generation (RAG) with the Large Language Models (LLMs) framework. Our approach starts with parsing, indexing, and segmenting an extensive collection of 22 million scientific papers as the basic knowledge, followed by training a specialized embedding model tailored to this domain. Additionally, we enhance the vector retrieval process by incorporating a domain-specific knowledge hierarchy, which aids in modeling the intricate interrelationships among each query and context. For queries requiring the most current information, BioRAG deconstructs the question and employs an iterative retrieval process incorporated with the search engine for step-by-step reasoning. Rigorous experiments have demonstrated that our model outperforms fine-tuned LLM, LLM with search engines, and other scientific RAG frameworks across multiple life science question-answering tasks.

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

With the recent addition of Retrieval-Augmented Generation (RAG), the scope and importance of Information Retrieval (IR) has expanded. As a result, the importance of a deeper understanding of IR models also increases. However, interpretability in IR remains under-explored, especially when it comes to the models' inner mechanisms. In this paper, we explore the possibility of adapting Integrated Gradient-based methods in an IR context to identify the role of individual neurons within the model. In particular, we provide new insights into the role of what we call "relevance" neurons, as well as how they deal with unseen data. Finally, we carry out an in-depth pruning study to validate our findings.

Utilizing large language models (LLMs) for transforming natural language questions into SQL queries (text-to-SQL) is a promising yet challenging approach, particularly when applied to real-world databases with complex and extensive schemas. In particular, effectively incorporating data catalogs and database values for SQL generation remains an obstacle, leading to suboptimal solutions. We address this problem by proposing a new pipeline that effectively retrieves relevant data and context, selects an efficient schema, and synthesizes correct and efficient SQL queries. To increase retrieval precision, our pipeline introduces a hierarchical retrieval method leveraging model-generated keywords, locality-sensitive hashing indexing, and vector databases. Additionally, we have developed an adaptive schema pruning technique that adjusts based on the complexity of the problem and the model's context size. Our approach generalizes to both frontier proprietary models like GPT-4 and open-source models such as Llama-3-70B. Through a series of ablation studies, we demonstrate the effectiveness of each component of our pipeline and its impact on the end-to-end performance. Our method achieves new state-of-the-art performance on the cross-domain challenging BIRD dataset.

Schema matching -- the task of finding matches between attributes across disparate data sources with different tables and hierarchies -- is critical for creating interoperable machine learning (ML)-ready data. Addressing this fundamental data-centric problem has wide implications, especially in domains like healthcare, finance and e-commerce -- but also has the potential to benefit ML models more generally, by increasing the data available for ML model training. However, schema matching is a challenging ML task due to structural/hierarchical and semantic heterogeneity between different schemas. Previous ML approaches to automate schema matching have either required significant labeled data for model training, which is often unrealistic or suffer from poor zero-shot performance. To this end, we propose Matchmaker - a compositional language model program for schema matching, comprised of candidate generation, refinement and confidence scoring. Matchmaker also self-improves in a zero-shot manner without the need for labeled demonstrations via a novel optimization approach, which constructs synthetic in-context demonstrations to guide the language model's reasoning process. Empirically, we demonstrate on real-world medical schema matching benchmarks that Matchmaker outperforms previous ML-based approaches, highlighting its potential to accelerate data integration and interoperability of ML-ready data.

Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular biology", capturing intricate gene expression patterns at the single-cell level. However, interacting with this "language" through conventional tools is often inefficient and unintuitive, posing challenges for researchers. To address these limitations, we present InstructCell, a multi-modal AI copilot that leverages natural language as a medium for more direct and flexible single-cell analysis. We construct a comprehensive multi-modal instruction dataset that pairs text-based instructions with scRNA-seq profiles from diverse tissues and species. Building on this, we develop a multi-modal cell language architecture capable of simultaneously interpreting and processing both modalities. InstructCell empowers researchers to accomplish critical tasks-such as cell type annotation, conditional pseudo-cell generation, and drug sensitivity prediction-using straightforward natural language commands. Extensive evaluations demonstrate that InstructCell consistently meets or exceeds the performance of existing single-cell foundation models, while adapting to diverse experimental conditions. More importantly, InstructCell provides an accessible and intuitive tool for exploring complex single-cell data, lowering technical barriers and enabling deeper biological insights.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ranging from multiple-choice questions to long-form generations. To address challenges that still cannot be handled with the encoded knowledge of LLMs, various retrieval-augmented generation (RAG) methods have been developed by searching documents from the knowledge corpus and appending them unconditionally or selectively to the input of LLMs for generation. However, when applying existing methods to different domain-specific problems, poor generalization becomes apparent, leading to fetching incorrect documents or making inaccurate judgments. In this paper, we introduce Self-BioRAG, a framework reliable for biomedical text that specializes in generating explanations, retrieving domain-specific documents, and self-reflecting generated responses. We utilize 84k filtered biomedical instruction sets to train Self-BioRAG that can assess its generated explanations with customized reflective tokens. Our work proves that domain-specific components, such as a retriever, domain-related document corpus, and instruction sets are necessary for adhering to domain-related instructions. Using three major medical question-answering benchmark datasets, experimental results of Self-BioRAG demonstrate significant performance gains by achieving a 7.2% absolute improvement on average over the state-of-the-art open-foundation model with a parameter size of 7B or less. Overall, we analyze that Self-BioRAG finds the clues in the question, retrieves relevant documents if needed, and understands how to answer with information from retrieved documents and encoded knowledge as a medical expert does. We release our data and code for training our framework components and model weights (7B and 13B) to enhance capabilities in biomedical and clinical domains.

In-Context Learning (ICL) enables transformer-based language models to adapt to new tasks by conditioning on demonstration examples. However, traditional example-driven in-context learning lacks explicit modules for knowledge retrieval and transfer at the abstraction level. Inspired by cognitive science, specifically schema theory, which holds that humans interpret new information by activating pre-existing mental frameworks (schemas) to structure understanding, we introduce SCHEMA ACTIVATED IN CONTEXT LEARNING (SA-ICL). This framework extracts the representation of the building blocks of cognition for the reasoning process instilled from prior examples, creating an abstracted schema, a lightweight, structured template of key inferential steps and their relationships, which is then used to augment a model's reasoning process when presented with a novel question. We demonstrate that a broad range of large language models (LLMs) lack the capacity to form and utilize internal schema-based learning representations implicitly, but instead benefit significantly from explicit schema-based scaffolding. Across chemistry and physics questions from the GPQA dataset, our experiments show that SA-ICL consistently boosts performance, up to 36.19 percent, when the single demonstration example is of high quality, which simultaneously reduces reliance on the number of demonstrations and enhances interpretability. SCHEMA ACTIVATED IN CONTEXT LEARNING not only bridges disparate ICL strategies ranging from pattern priming to Chain-of-Thought prompting, but also paves a new path for enhancing human-like reasoning in LLMs.

In this paper, we explore the question of whether large language models can support cost-efficient information extraction from tables. We introduce schema-driven information extraction, a new task that transforms tabular data into structured records following a human-authored schema. To assess various LLM's capabilities on this task, we present a benchmark comprised of tables from four diverse domains: machine learning papers, chemistry literature, material science journals, and webpages. We use this collection of annotated tables to evaluate the ability of open-source and API-based language models to extract information from tables covering diverse domains and data formats. Our experiments demonstrate that surprisingly competitive performance can be achieved without requiring task-specific pipelines or labels, achieving F1 scores ranging from 74.2 to 96.1, while maintaining cost efficiency. Moreover, through detailed ablation studies and analyses, we investigate the factors contributing to model success and validate the practicality of distilling compact models to reduce API reliance.

Cell type annotation is a key task in analyzing the heterogeneity of single-cell RNA sequencing data. Although recent foundation models automate this process, they typically annotate cells independently, without considering batch-level cellular context or providing explanatory reasoning. In contrast, human experts often annotate distinct cell types for different cell clusters based on their domain knowledge. To mimic this workflow, we introduce the CellPuzzles task, where the objective is to assign unique cell types to a batch of cells. This benchmark spans diverse tissues, diseases, and donor conditions, and requires reasoning across the batch-level cellular context to ensure label uniqueness. We find that off-the-shelf large language models (LLMs) struggle on CellPuzzles, with the best baseline (OpenAI's o1) achieving only 19.0% batch-level accuracy. To fill this gap, we propose Cell-o1, a 7B LLM trained via supervised fine-tuning on distilled reasoning traces, followed by reinforcement learning with batch-level rewards. Cell-o1 achieves state-of-the-art performance, outperforming o1 by over 73% and generalizing well across contexts. Further analysis of training dynamics and reasoning behaviors provides insights into batch-level annotation performance and emergent expert-like reasoning. Code and data are available at https://github.com/ncbi-nlp/cell-o1.

We introduce Latent Meaning Cells, a deep latent variable model which learns contextualized representations of words by combining local lexical context and metadata. Metadata can refer to granular context, such as section type, or to more global context, such as unique document ids. Reliance on metadata for contextualized representation learning is apropos in the clinical domain where text is semi-structured and expresses high variation in topics. We evaluate the LMC model on the task of zero-shot clinical acronym expansion across three datasets. The LMC significantly outperforms a diverse set of baselines at a fraction of the pre-training cost and learns clinically coherent representations. We demonstrate that not only is metadata itself very helpful for the task, but that the LMC inference algorithm provides an additional large benefit.

Recent advancements in Text-to-SQL (Text2SQL) emphasize stimulating the large language models (LLM) on in-context learning, achieving significant results. Nevertheless, they face challenges when dealing with verbose database information and complex user intentions. This paper presents a two-stage framework to enhance the performance of current LLM-based natural language to SQL systems. We first introduce a novel prompt representation, called reference-enhanced representation, which includes schema information and randomly sampled cell values from tables to instruct LLMs in generating SQL queries. Then, in the first stage, question-SQL pairs are retrieved as few-shot demonstrations, prompting the LLM to generate a preliminary SQL (PreSQL). After that, the mentioned entities in PreSQL are parsed to conduct schema linking, which can significantly compact the useful information. In the second stage, with the linked schema, we simplify the prompt's schema information and instruct the LLM to produce the final SQL. Finally, as the post-refinement module, we propose using cross-consistency across different LLMs rather than self-consistency within a particular LLM. Our methods achieve new SOTA results on the Spider benchmark, with an execution accuracy of 87.6%.

JSON Schema is an important, evolving standard schema language for families of JSON documents. It is based on a complex combination of structural and Boolean assertions, and features negation and recursion. The static analysis of JSON Schema documents comprises practically relevant problems, including schema satisfiability, inclusion, and equivalence. These three problems can be reduced to witness generation: given a schema, generate an element of the schema, if it exists, and report failure otherwise. Schema satisfiability, inclusion, and equivalence have been shown to be decidable, by reduction to reachability in alternating tree automata. However, no witness generation algorithm has yet been formally described. We contribute a first, direct algorithm for JSON Schema witness generation. We study its effectiveness and efficiency, in experiments over several schema collections, including thousands of real-world schemas. Our focus is on the completeness of the language, where we only exclude the uniqueItems operator, and on the ability of the algorithm to run in a reasonable time on a large set of real-world examples, despite the exponential complexity of the underlying problem.

As Large Language Models (LLMs) rapidly evolve, their influence in science is becoming increasingly prominent. The emerging capabilities of LLMs in task generalization and free-form dialogue can significantly advance fields like chemistry and biology. However, the field of single-cell biology, which forms the foundational building blocks of living organisms, still faces several challenges. High knowledge barriers and limited scalability in current methods restrict the full exploitation of LLMs in mastering single-cell data, impeding direct accessibility and rapid iteration. To this end, we introduce ChatCell, which signifies a paradigm shift by facilitating single-cell analysis with natural language. Leveraging vocabulary adaptation and unified sequence generation, ChatCell has acquired profound expertise in single-cell biology and the capability to accommodate a diverse range of analysis tasks. Extensive experiments further demonstrate ChatCell's robust performance and potential to deepen single-cell insights, paving the way for more accessible and intuitive exploration in this pivotal field. Our project homepage is available at https://zjunlp.github.io/project/ChatCell.

Schema linking is a crucial step in Text-to-SQL pipelines, which translate natural language queries into SQL. The goal of schema linking is to retrieve relevant tables and columns (signal) while disregarding irrelevant ones (noise). However, imperfect schema linking can often exclude essential columns needed for accurate query generation. In this work, we revisit the need for schema linking when using the latest generation of large language models (LLMs). We find empirically that newer models are adept at identifying relevant schema elements during generation, without the need for explicit schema linking. This allows Text-to-SQL pipelines to bypass schema linking entirely and instead pass the full database schema to the LLM, eliminating the risk of excluding necessary information. Furthermore, as alternatives to schema linking, we propose techniques that improve Text-to-SQL accuracy without compromising on essential schema information. Our approach achieves 71.83\% execution accuracy on the BIRD benchmark, ranking first at the time of submission.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Large language models (LLMs) have grown in their usage to provide support for question answering across numerous disciplines. The models on their own have already shown promise for answering basic questions, however fail quickly where expert domain knowledge is required or the question is nuanced. Scientific research often involves searching for relevant literature, distilling pertinent information from that literature and analysing how the findings support or contradict one another. The information is often encapsulated in the full text body of research articles, rather than just in the abstracts. Statements within these articles frequently require the wider article context to be fully understood. We have built an LLM-based system that performs such search and distillation of information encapsulated in scientific literature, and we evaluate our keyword based search and information distillation system against a set of biology related questions from previously released literature benchmarks. We demonstrate sparse retrieval methods exhibit results close to state of the art without the need for dense retrieval, with its associated infrastructure and complexity overhead. We also show how to increase the coverage of relevant documents for literature review generation.

In the field of language modeling, models augmented with retrieval components have emerged as a promising solution to address several challenges faced in the natural language processing (NLP) field, including knowledge grounding, interpretability, and scalability. Despite the primary focus on NLP, we posit that the paradigm of retrieval-enhancement can be extended to a broader spectrum of machine learning (ML) such as computer vision, time series prediction, and computational biology. Therefore, this work introduces a formal framework of this paradigm, Retrieval-Enhanced Machine Learning (REML), by synthesizing the literature in various domains in ML with consistent notations which is missing from the current literature. Also, we found that while a number of studies employ retrieval components to augment their models, there is a lack of integration with foundational Information Retrieval (IR) research. We bridge this gap between the seminal IR research and contemporary REML studies by investigating each component that comprises the REML framework. Ultimately, the goal of this work is to equip researchers across various disciplines with a comprehensive, formally structured framework of retrieval-enhanced models, thereby fostering interdisciplinary future research.

Retrieval augmented generation (RAG) has shown great power in improving Large Language Models (LLMs). However, most existing RAG-based LLMs are dedicated to retrieving single modality information, mainly text; while for many real-world problems, such as healthcare, information relevant to queries can manifest in various modalities such as knowledge graph, text (clinical notes), and complex molecular structure. Thus, being able to retrieve relevant multi-modality domain-specific information, and reason and synthesize diverse knowledge to generate an accurate response is important. To address the gap, we present BioMol-MQA, a new question-answering (QA) dataset on polypharmacy, which is composed of two parts (i) a multimodal knowledge graph (KG) with text and molecular structure for information retrieval; and (ii) challenging questions that designed to test LLM capabilities in retrieving and reasoning over multimodal KG to answer questions. Our benchmarks indicate that existing LLMs struggle to answer these questions and do well only when given the necessary background data, signaling the necessity for strong RAG frameworks.

Traditional similarity-based schema matching methods are incapable of resolving semantic ambiguities and conflicts in domain-specific complex mapping scenarios due to missing commonsense and domain-specific knowledge. The hallucination problem of large language models (LLMs) also makes it challenging for LLM-based schema matching to address the above issues. Therefore, we propose a Knowledge Graph-based Retrieval-Augmented Generation model for Schema Matching, referred to as the KG-RAG4SM. In particular, KG-RAG4SM introduces novel vector-based, graph traversal-based, and query-based graph retrievals, as well as a hybrid approach and ranking schemes that identify the most relevant subgraphs from external large knowledge graphs (KGs). We showcase that KG-based retrieval-augmented LLMs are capable of generating more accurate results for complex matching cases without any re-training. Our experimental results show that KG-RAG4SM outperforms the LLM-based state-of-the-art (SOTA) methods (e.g., Jellyfish-8B) by 35.89% and 30.50% in terms of precision and F1 score on the MIMIC dataset, respectively; KG-RAG4SM with GPT-4o-mini outperforms the pre-trained language model (PLM)-based SOTA methods (e.g., SMAT) by 69.20% and 21.97% in terms of precision and F1 score on the Synthea dataset, respectively. The results also demonstrate that our approach is more efficient in end-to-end schema matching, and scales to retrieve from large KGs. Our case studies on the dataset from the real-world schema matching scenario exhibit that the hallucination problem of LLMs for schema matching is well mitigated by our solution.

Augmenting pretrained language models with retrievers to select the supporting documents has shown promise in effectively solving common NLP problems, including language modeling and question answering, in an interpretable way. In this paper, we first study the strengths and weaknesses of different retriever-augmented language models (REALM, kNN-LM, FiD coupled with DPR, and ATLAS and Flan-T5 coupled with Contriever) in reasoning over the retrieved statements in different tasks. We show how the retrieve-then-read models' limitations in reasoning are rooted both in the retriever module as well as the language model. Our experimental results demonstrate that the similarity metric used by the retrievers is generally insufficient for reasoning tasks. Additionally, we show that the language models in retriever-augmented models do not take the complicated relations between the statements into account, which leads to poor reasoning performance even when using the larger models. Moreover, we analyze the reasoning performance of large language models using multihop retrieval but we only observe minor improvements. Overall, this shows great room for further research in this area.

Scientific paper retrieval is essential for supporting literature discovery and research. While dense retrieval methods demonstrate effectiveness in general-purpose tasks, they often fail to capture fine-grained scientific concepts that are essential for accurate understanding of scientific queries. Recent studies also use large language models (LLMs) for query understanding; however, these methods often lack grounding in corpus-specific knowledge and may generate unreliable or unfaithful content. To overcome these limitations, we propose SemRank, an effective and efficient paper retrieval framework that combines LLM-guided query understanding with a concept-based semantic index. Each paper is indexed using multi-granular scientific concepts, including general research topics and detailed key phrases. At query time, an LLM identifies core concepts derived from the corpus to explicitly capture the query's information need. These identified concepts enable precise semantic matching, significantly enhancing retrieval accuracy. Experiments show that SemRank consistently improves the performance of various base retrievers, surpasses strong existing LLM-based baselines, and remains highly efficient.

In common law jurisdictions, legal practitioners rely on precedents to construct arguments, in line with the doctrine of stare decisis. As the number of cases grow over the years, prior case retrieval (PCR) has garnered significant attention. Besides lacking real-world scale, existing PCR datasets do not simulate a realistic setting, because their queries use complete case documents while only masking references to prior cases. The query is thereby exposed to legal reasoning not yet available when constructing an argument for an undecided case as well as spurious patterns left behind by citation masks, potentially short-circuiting a comprehensive understanding of case facts and legal principles. To address these limitations, we introduce a PCR dataset based on judgements from the European Court of Human Rights (ECtHR), which explicitly separate facts from arguments and exhibit precedential practices, aiding us to develop this PCR dataset to foster systems' comprehensive understanding. We benchmark different lexical and dense retrieval approaches with various negative sampling strategies, adapting them to deal with long text sequences using hierarchical variants. We found that difficulty-based negative sampling strategies were not effective for the PCR task, highlighting the need for investigation into domain-specific difficulty criteria. Furthermore, we observe performance of the dense models degrade with time and calls for further research into temporal adaptation of retrieval models. Additionally, we assess the influence of different views , Halsbury's and Goodhart's, in practice in ECtHR jurisdiction using PCR task.

Data scientists today search large data lakes to discover and integrate datasets. In order to bring together disparate data sources, dataset discovery methods rely on some form of schema matching: the process of establishing correspondences between datasets. Traditionally, schema matching has been used to find matching pairs of columns between a source and a target schema. However, the use of schema matching in dataset discovery methods differs from its original use. Nowadays schema matching serves as a building block for indicating and ranking inter-dataset relationships. Surprisingly, although a discovery method's success relies highly on the quality of the underlying matching algorithms, the latest discovery methods employ existing schema matching algorithms in an ad-hoc fashion due to the lack of openly-available datasets with ground truth, reference method implementations, and evaluation metrics. In this paper, we aim to rectify the problem of evaluating the effectiveness and efficiency of schema matching methods for the specific needs of dataset discovery. To this end, we propose Valentine, an extensible open-source experiment suite to execute and organize large-scale automated matching experiments on tabular data. Valentine includes implementations of seminal schema matching methods that we either implemented from scratch (due to absence of open source code) or imported from open repositories. The contributions of Valentine are: i) the definition of four schema matching scenarios as encountered in dataset discovery methods, ii) a principled dataset fabrication process tailored to the scope of dataset discovery methods and iii) the most comprehensive evaluation of schema matching techniques to date, offering insight on the strengths and weaknesses of existing techniques, that can serve as a guide for employing schema matching in future dataset discovery methods.

Current medical retrieval benchmarks primarily emphasize lexical or shallow semantic similarity, overlooking the reasoning-intensive demands that are central to clinical decision-making. In practice, physicians often retrieve authoritative medical evidence to support diagnostic hypotheses. Such evidence typically aligns with an inferred diagnosis rather than the surface form of a patient's symptoms, leading to low lexical or semantic overlap between queries and relevant documents. To address this gap, we introduce R2MED, the first benchmark explicitly designed for reasoning-driven medical retrieval. It comprises 876 queries spanning three tasks: Q&A reference retrieval, clinical evidence retrieval, and clinical case retrieval. These tasks are drawn from five representative medical scenarios and twelve body systems, capturing the complexity and diversity of real-world medical information needs. We evaluate 15 widely-used retrieval systems on R2MED and find that even the best model achieves only 31.4 nDCG@10, demonstrating the benchmark's difficulty. Classical re-ranking and generation-augmented retrieval methods offer only modest improvements. Although large reasoning models improve performance via intermediate inference generation, the best results still peak at 41.4 nDCG@10. These findings underscore a substantial gap between current retrieval techniques and the reasoning demands of real clinical tasks. We release R2MED as a challenging benchmark to foster the development of next-generation medical retrieval systems with enhanced reasoning capabilities. Data and code are available at https://github.com/R2MED/R2MED

Dense retrieval has become a prominent method to obtain relevant context or world knowledge in open-domain NLP tasks. When we use a learned dense retriever on a retrieval corpus at inference time, an often-overlooked design choice is the retrieval unit in which the corpus is indexed, e.g. document, passage, or sentence. We discover that the retrieval unit choice significantly impacts the performance of both retrieval and downstream tasks. Distinct from the typical approach of using passages or sentences, we introduce a novel retrieval unit, proposition, for dense retrieval. Propositions are defined as atomic expressions within text, each encapsulating a distinct factoid and presented in a concise, self-contained natural language format. We conduct an empirical comparison of different retrieval granularity. Our results reveal that proposition-based retrieval significantly outperforms traditional passage or sentence-based methods in dense retrieval. Moreover, retrieval by proposition also enhances the performance of downstream QA tasks, since the retrieved texts are more condensed with question-relevant information, reducing the need for lengthy input tokens and minimizing the inclusion of extraneous, irrelevant information.

Identifying patient cohorts is fundamental to numerous healthcare tasks, including clinical trial recruitment and retrospective studies. Current cohort retrieval methods in healthcare organizations rely on automated queries of structured data combined with manual curation, which are time-consuming, labor-intensive, and often yield low-quality results. Recent advancements in large language models (LLMs) and information retrieval (IR) offer promising avenues to revolutionize these systems. Major challenges include managing extensive eligibility criteria and handling the longitudinal nature of unstructured Electronic Medical Records (EMRs) while ensuring that the solution remains cost-effective for real-world application. This paper introduces a new task, Automatic Cohort Retrieval (ACR), and evaluates the performance of LLMs and commercial, domain-specific neuro-symbolic approaches. We provide a benchmark task, a query dataset, an EMR dataset, and an evaluation framework. Our findings underscore the necessity for efficient, high-quality ACR systems capable of longitudinal reasoning across extensive patient databases.

Extracting structured information from unstructured text is crucial for modeling real-world processes, but traditional schema mining relies on semi-structured data, limiting scalability. This paper introduces schema-miner, a novel tool that combines large language models with human feedback to automate and refine schema extraction. Through an iterative workflow, it organizes properties from text, incorporates expert input, and integrates domain-specific ontologies for semantic depth. Applied to materials science--specifically atomic layer deposition--schema-miner demonstrates that expert-guided LLMs generate semantically rich schemas suitable for diverse real-world applications.

Sparse autoencoders (SAEs) emerged as a promising tool for mechanistic interpretability of transformer-based foundation models. Very recently, SAEs were also adopted for the visual domain, enabling the discovery of visual concepts and their patch-wise attribution to tokens in the transformer model. While a growing number of foundation models emerged for medical imaging, tools for explaining their inferences are still lacking. In this work, we show the applicability of SAEs for hematology. We propose CytoSAE, a sparse autoencoder which is trained on over 40,000 peripheral blood single-cell images. CytoSAE generalizes to diverse and out-of-domain datasets, including bone marrow cytology, where it identifies morphologically relevant concepts which we validated with medical experts. Furthermore, we demonstrate scenarios in which CytoSAE can generate patient-specific and disease-specific concepts, enabling the detection of pathognomonic cells and localized cellular abnormalities at the patch level. We quantified the effect of concepts on a patient-level AML subtype classification task and show that CytoSAE concepts reach performance comparable to the state-of-the-art, while offering explainability on the sub-cellular level. Source code and model weights are available at https://github.com/dynamical-inference/cytosae.

Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multimodal data integration. However, progress remains fragmented across data modalities, architectures, and evaluation standards. LLM4Cell presents the first unified survey of 58 foundation and agentic models developed for single-cell research, spanning RNA, ATAC, multi-omic, and spatial modalities. We categorize these methods into five families-foundation, text-bridge, spatial, multimodal, epigenomic, and agentic-and map them to eight key analytical tasks including annotation, trajectory and perturbation modeling, and drug-response prediction. Drawing on over 40 public datasets, we analyze benchmark suitability, data diversity, and ethical or scalability constraints, and evaluate models across 10 domain dimensions covering biological grounding, multi-omics alignment, fairness, privacy, and explainability. By linking datasets, models, and evaluation domains, LLM4Cell provides the first integrated view of language-driven single-cell intelligence and outlines open challenges in interpretability, standardization, and trustworthy model development.

Large Reasoning Models (LRMs) have demonstrated remarkable capabilities in multi-step reasoning and calling search engines at appropriate steps. However, existing retrieval-augmented reasoning approaches rely on separate retrieval models, limiting the LRM's role in retrieval to deciding when to retrieve and how to query. This separation not only increases hardware and operational costs but also leads to errors in the retrieval process due to the representation bottleneck, a phenomenon where the retriever's embedding space is not expressive enough to meet the generator's requirements. To address this, we shift our perspective from sequence-to-sequence matching to locating the answer-containing paths within the corpus, and propose a novel framework called FREESON (Retriever-FREE Retrieval-Augmented ReaSONing). This framework enables LRMs to retrieve relevant knowledge on their own by acting as both a generator and retriever. To achieve this, we introduce a variant of the MCTS algorithm specialized for the retrieval task, which we call CT-MCTS (Corpus-Traversing Monte Carlo Tree Search). In this algorithm, LRMs traverse through the corpus toward answer-containing regions. Our results on five open-domain QA benchmarks, including single-hop and multi-hop questions, show that FREESON achieves an average improvement of 14.4% in EM and F1 over four multi-step reasoning models with a separate retriever, and it also performs comparably to the strongest baseline, surpassing it by 3% on PopQA and 2WikiMultihopQA.

Multi-document summarization (MDS) is a difficult task in Natural Language Processing, aiming to summarize information from several documents. However, the source documents are often insufficient to obtain a qualitative summary. We propose a retriever-guided model combined with non-parametric memory for summary generation. This model retrieves relevant candidates from a database and then generates the summary considering the candidates with a copy mechanism and the source documents. The retriever is implemented with Approximate Nearest Neighbor Search (ANN) to search large databases. Our method is evaluated on the MultiXScience dataset which includes scientific articles. Finally, we discuss our results and possible directions for future work.

Universal information extraction (UIE) primarily employs an extractive generation approach with large language models (LLMs), typically outputting structured information based on predefined schemas such as JSON or tables. UIE suffers from a lack of adaptability when selecting between predefined schemas and on-the-fly schema generation within the in-context learning paradigm, especially when there are numerous schemas to choose from. In this paper, we propose a unified adaptive text-to-structure generation framework, called Schema as Parameterized Tools (SPT), which reimagines the tool-calling capability of LLMs by treating predefined schemas as parameterized tools for tool selection and parameter filling. Specifically, our SPT method can be applied to unify closed, open, and on-demand IE tasks by adopting Schema Retrieval by fetching the relevant schemas from a predefined pool, Schema Filling by extracting information and filling slots as with tool parameters, or Schema Generation by synthesizing new schemas with uncovered cases. Experiments show that the SPT method can handle four distinct IE tasks adaptively, delivering robust schema retrieval and selection performance. SPT also achieves comparable extraction performance to LoRA baselines and current leading UIE systems with significantly fewer trainable parameters.

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called MedGraphRAG, aimed at enhancing Large Language Model (LLM) capabilities and generating evidence-based results, thereby improving safety and reliability when handling private medical data. Our comprehensive pipeline begins with a hybrid static-semantic approach to document chunking, significantly improving context capture over traditional methods. Extracted entities are used to create a three-tier hierarchical graph structure, linking entities to foundational medical knowledge sourced from medical papers and dictionaries. These entities are then interconnected to form meta-graphs, which are merged based on semantic similarities to develop a comprehensive global graph. This structure supports precise information retrieval and response generation. The retrieval process employs a U-retrieve method to balance global awareness and indexing efficiency of the LLM. Our approach is validated through a comprehensive ablation study comparing various methods for document chunking, graph construction, and information retrieval. The results not only demonstrate that our hierarchical graph construction method consistently outperforms state-of-the-art models on multiple medical Q\&A benchmarks, but also confirms that the responses generated include source documentation, significantly enhancing the reliability of medical LLMs in practical applications. Code will be at: https://github.com/MedicineToken/Medical-Graph-RAG/tree/main

Information retrieval (IR) is essential in biomedical knowledge acquisition and clinical decision support. While recent progress has shown that language model encoders perform better semantic retrieval, training such models requires abundant query-article annotations that are difficult to obtain in biomedicine. As a result, most biomedical IR systems only conduct lexical matching. In response, we introduce BioCPT, a first-of-its-kind Contrastively Pre-trained Transformer model for zero-shot biomedical IR. To train BioCPT, we collected an unprecedented scale of 255 million user click logs from PubMed. With such data, we use contrastive learning to train a pair of closely-integrated retriever and re-ranker. Experimental results show that BioCPT sets new state-of-the-art performance on five biomedical IR tasks, outperforming various baselines including much larger models such as GPT-3-sized cpt-text-XL. In addition, BioCPT also generates better biomedical article and sentence representations for semantic evaluations. As such, BioCPT can be readily applied to various real-world biomedical IR tasks. BioCPT API and code are publicly available at https://github.com/ncbi/BioCPT.

Biomedical text mining and question-answering are essential yet highly demanding tasks, particularly in the face of the exponential growth of biomedical literature. In this work, we present our participation in the 13th edition of the BioASQ challenge, which involves biomedical semantic question-answering for Task 13b and biomedical question-answering for developing topics for the Synergy task. We deploy a selection of open-source large language models (LLMs) as retrieval-augmented generators to answer biomedical questions. Various models are used to process the questions. A majority voting system combines their output to determine the final answer for Yes/No questions, while for list and factoid type questions, the union of their answers in used. We evaluated 13 state-of-the-art open source LLMs, exploring all possible model combinations to contribute to the final answer, resulting in tailored LLM pipelines for each question type. Our findings provide valuable insight into which combinations of LLMs consistently produce superior results for specific question types. In the four rounds of the 2025 BioASQ challenge, our system achieved notable results: in the Synergy task, we secured 1st place for ideal answers and 2nd place for exact answers in round 2, as well as two shared 1st places for exact answers in round 3 and 4.

We present a comprehensive evaluation of structured decoding for text-to-table generation with large language models (LLMs). While previous work has primarily focused on unconstrained generation of tables, the impact of enforcing structural constraints during generation remains underexplored. We systematically compare schema-guided (structured) decoding to standard one-shot prompting across three diverse benchmarks - E2E, Rotowire, and Livesum - using open-source LLMs of up to 32B parameters, assessing the performance of table generation approaches in resource-constrained settings. Our experiments cover a wide range of evaluation metrics at cell, row, and table levels. Results demonstrate that structured decoding significantly enhances the validity and alignment of generated tables, particularly in scenarios demanding precise numerical alignment (Rotowire), but may degrade performance in contexts involving densely packed textual information (E2E) or extensive aggregation over lengthy texts (Livesum). We further analyze the suitability of different evaluation metrics and discuss the influence of model size.

Vectors are universal mathematical objects that can represent text, images, speech, or a mix of these data modalities. That happens regardless of whether data is represented by hand-crafted features or learnt embeddings. Collect a large enough quantity of such vectors and the question of retrieval becomes urgently relevant: Finding vectors that are more similar to a query vector. This monograph is concerned with the question above and covers fundamental concepts along with advanced data structures and algorithms for vector retrieval. In doing so, it recaps this fascinating topic and lowers barriers of entry into this rich area of research.

Memory plays a pivotal role in enabling large language model~(LLM)-based agents to engage in complex and long-term interactions, such as question answering (QA) and dialogue systems. While various memory modules have been proposed for these tasks, the impact of different memory structures across tasks remains insufficiently explored. This paper investigates how memory structures and memory retrieval methods affect the performance of LLM-based agents. Specifically, we evaluate four types of memory structures, including chunks, knowledge triples, atomic facts, and summaries, along with mixed memory that combines these components. In addition, we evaluate three widely used memory retrieval methods: single-step retrieval, reranking, and iterative retrieval. Extensive experiments conducted across four tasks and six datasets yield the following key insights: (1) Different memory structures offer distinct advantages, enabling them to be tailored to specific tasks; (2) Mixed memory structures demonstrate remarkable resilience in noisy environments; (3) Iterative retrieval consistently outperforms other methods across various scenarios. Our investigation aims to inspire further research into the design of memory systems for LLM-based agents.

A key component of fact verification is thevevidence retrieval, often from multiple documents. Recent approaches use dense representations and condition the retrieval of each document on the previously retrieved ones. The latter step is performed over all the documents in the collection, requiring storing their dense representations in an index, thus incurring a high memory footprint. An alternative paradigm is retrieve-and-rerank, where documents are retrieved using methods such as BM25, their sentences are reranked, and further documents are retrieved conditioned on these sentences, reducing the memory requirements. However, such approaches can be brittle as they rely on heuristics and assume hyperlinks between documents. We propose a novel retrieve-and-rerank method for multi-hop retrieval, that consists of a retriever that jointly scores documents in the knowledge source and sentences from previously retrieved documents using an autoregressive formulation and is guided by a proof system based on natural logic that dynamically terminates the retrieval process if the evidence is deemed sufficient. This method is competitive with current state-of-the-art methods on FEVER, HoVer and FEVEROUS-S, while using 5 to 10 times less memory than competing systems. Evaluation on an adversarial dataset indicates improved stability of our approach compared to commonly deployed threshold-based methods. Finally, the proof system helps humans predict model decisions correctly more often than using the evidence alone.

Medical information retrieval (MIR) is essential for retrieving relevant medical knowledge from diverse sources, including electronic health records, scientific literature, and medical databases. However, achieving effective zero-shot dense retrieval in the medical domain poses substantial challenges due to the lack of relevance-labeled data. In this paper, we introduce a novel approach called Self-Learning Hypothetical Document Embeddings (SL-HyDE) to tackle this issue. SL-HyDE leverages large language models (LLMs) as generators to generate hypothetical documents based on a given query. These generated documents encapsulate key medical context, guiding a dense retriever in identifying the most relevant documents. The self-learning framework progressively refines both pseudo-document generation and retrieval, utilizing unlabeled medical corpora without requiring any relevance-labeled data. Additionally, we present the Chinese Medical Information Retrieval Benchmark (CMIRB), a comprehensive evaluation framework grounded in real-world medical scenarios, encompassing five tasks and ten datasets. By benchmarking ten models on CMIRB, we establish a rigorous standard for evaluating medical information retrieval systems. Experimental results demonstrate that SL-HyDE significantly surpasses existing methods in retrieval accuracy while showcasing strong generalization and scalability across various LLM and retriever configurations. CMIRB data and evaluation code are publicly available at: https://github.com/CMIRB-benchmark/CMIRB.

Retrieval-Augmented Generation (RAG) has become ubiquitous when deploying Large Language Models (LLMs), as it can address typical limitations such as generating hallucinated or outdated information. However, when building real-world RAG applications, practical issues arise. First, the retrieved information is generally domain-specific. Since it is computationally expensive to fine-tune LLMs, it is more feasible to fine-tune the retriever to improve the quality of the data included in the LLM input. Second, as more applications are deployed in the same real-world system, one cannot afford to deploy separate retrievers. Moreover, these RAG applications normally retrieve different kinds of data. Our solution is to instruction fine-tune a small retriever encoder on a variety of domain-specific tasks to allow us to deploy one encoder that can serve many use cases, thereby achieving low-cost, scalability, and speed. We show how this encoder generalizes to out-of-domain settings as well as to an unseen retrieval task on real-world enterprise use cases.

Document retrieval techniques form the foundation for the development of large-scale information systems. The prevailing methodology is to construct a bi-encoder and compute the semantic similarity. However, such scalar similarity is difficult to reflect enough information and impedes our comprehension of the retrieval results. In addition, this computational process mainly emphasizes the global semantics and ignores the fine-grained semantic relationship between the query and the complex text in the document. In this paper, we propose a new method called Generation Augmented Retrieval (GeAR) that incorporates well-designed fusion and decoding modules. This enables GeAR to generate the relevant text from documents based on the fused representation of the query and the document, thus learning to "focus on" the fine-grained information. Also when used as a retriever, GeAR does not add any computational burden over bi-encoders. To support the training of the new framework, we have introduced a pipeline to efficiently synthesize high-quality data by utilizing large language models. GeAR exhibits competitive retrieval and localization performance across diverse scenarios and datasets. Moreover, the qualitative analysis and the results generated by GeAR provide novel insights into the interpretation of retrieval results. The code, data, and models will be released after completing technical review to facilitate future research.

Many students struggle with math word problems (MWPs), often finding it difficult to identify key information and select the appropriate mathematical operations.Schema-based instruction (SBI) is an evidence-based strategy that helps students categorize problems based on their structure, improving problem-solving accuracy. Building on this, we propose a Schema-Based Instruction Retrieval-Augmented Generation (SBI-RAG) framework that incorporates a large language model (LLM).Our approach emphasizes step-by-step reasoning by leveraging schemas to guide solution generation. We evaluate its performance on the GSM8K dataset, comparing it with GPT-4 and GPT-3.5 Turbo, and introduce a "reasoning score" metric to assess solution quality. Our findings suggest that SBI-RAG enhances reasoning clarity and problem-solving accuracy, potentially providing educational benefits for students

Answering real-world user queries, such as product search, often requires accurate retrieval of information from semi-structured knowledge bases or databases that involve blend of unstructured (e.g., textual descriptions of products) and structured (e.g., entity relations of products) information. However, previous works have mostly studied textual and relational retrieval tasks as separate topics. To address the gap, we develop STARK, a large-scale Semi-structure retrieval benchmark on Textual and Relational Knowledge Bases. We design a novel pipeline to synthesize natural and realistic user queries that integrate diverse relational information and complex textual properties, as well as their ground-truth answers. Moreover, we rigorously conduct human evaluation to validate the quality of our benchmark, which covers a variety of practical applications, including product recommendations, academic paper searches, and precision medicine inquiries. Our benchmark serves as a comprehensive testbed for evaluating the performance of retrieval systems, with an emphasis on retrieval approaches driven by large language models (LLMs). Our experiments suggest that the STARK datasets present significant challenges to the current retrieval and LLM systems, indicating the demand for building more capable retrieval systems that can handle both textual and relational aspects.

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

Long-context language models (LCLM), characterized by their extensive context window, is becoming increasingly popular. Meanwhile, many long-context benchmarks present challenging tasks that even the most advanced LCLMs struggle to complete. However, the underlying sources of various challenging long-context tasks have seldom been studied. To bridge this gap, we conduct experiments to indicate their difficulty stems primarily from two basic issues: "multi-matching retrieval," which requires the simultaneous retrieval of multiple items, and "logic-based retrieval," which necessitates logical judgment within retrieval criteria. These two problems, while seemingly straightforward, actually exceed the capabilities of LCLMs because they are proven to be hyper-multi-step (demanding numerous steps to solve) in nature. This finding could explain why LLMs struggle with more advanced long-context tasks, providing a more accurate perspective for rethinking solutions for them.

Scientific researchers need intensive information about datasets to effectively evaluate and develop theories and methodologies. The information needs regarding datasets are implicitly embedded in particular research tasks, rather than explicitly expressed in search queries. However, existing scientific retrieval and question-answering (QA) datasets typically address straightforward questions, which do not align with the distribution of real-world research inquiries. To bridge this gap, we developed ScIRGen, a dataset generation framework for scientific QA \& retrieval that more accurately reflects the information needs of professional science researchers, and uses it to create a large-scale scientific retrieval-augmented generation (RAG) dataset with realistic queries, datasets and papers. Technically, we designed a dataset-oriented information extraction method that leverages academic papers to augment the dataset representation. We then proposed a question generation framework by employing cognitive taxonomy to ensure the quality of synthesized questions. We also design a method to automatically filter synthetic answers based on the perplexity shift of LLMs, which is highly aligned with human judgment of answers' validity. Collectively, these methodologies culminated in the creation of the 61k QA dataset, ScIRGen-Geo. We benchmarked representative methods on the ScIRGen-Geo dataset for their question-answering and retrieval capabilities, finding out that current methods still suffer from reasoning from complex questions. This work advances the development of more sophisticated tools to support the intricate information needs of the scientific community.

The data landscape is rich with structured data, often of high value to organizations, driving important applications in data analysis and machine learning. Recent progress in representation learning and generative models for such data has led to the development of natural language interfaces to structured data, including those leveraging text-to-SQL. Contextualizing interactions, either through conversational interfaces or agentic components, in structured data through retrieval-augmented generation can provide substantial benefits in the form of freshness, accuracy, and comprehensiveness of answers. The key question is: how do we retrieve the right table(s) for the analytical query or task at hand? To this end, we introduce TARGET: a benchmark for evaluating TAble Retrieval for GEnerative Tasks. With TARGET we analyze the retrieval performance of different retrievers in isolation, as well as their impact on downstream tasks. We find that dense embedding-based retrievers far outperform a BM25 baseline which is less effective than it is for retrieval over unstructured text. We also surface the sensitivity of retrievers across various metadata (e.g., missing table titles), and demonstrate a stark variation of retrieval performance across datasets and tasks. TARGET is available at https://target-benchmark.github.io.

Recent advances in sequencing technologies have enabled researchers to explore cellular heterogeneity at single-cell resolution. Meanwhile, interpretability has gained prominence parallel to the rapid increase in the complexity and performance of deep learning models. In recent years, topic models have been widely used for interpretable single-cell embedding learning and clustering analysis, which we refer to as single-cell embedded topic models. However, previous studies evaluated the interpretability of the models mainly through qualitative analysis, and these single-cell embedded topic models suffer from the potential problem of interpretation collapse. Furthermore, their neglect of external biological knowledge constrains analytical performance. Here, we present scE2TM, an external knowledge-guided single-cell embedded topic model that provides a high-quality cell embedding and strong interpretation, contributing to comprehensive scRNA-seq data analysis. Our comprehensive evaluation across 20 scRNA-seq datasets demonstrates that scE2TM achieves significant clustering performance gains compared to 7 state-of-the-art methods. In addition, we propose a new interpretability evaluation benchmark that introduces 10 metrics to quantitatively assess the interpretability of single-cell embedded topic models. The results show that the interpretation provided by scE2TM performs encouragingly in terms of diversity and consistency with the underlying biological signals, contributing to a better revealing of the underlying biological mechanisms.

When conducting literature reviews, scientists often create literature review tables - tables whose rows are publications and whose columns constitute a schema, a set of aspects used to compare and contrast the papers. Can we automatically generate these tables using language models (LMs)? In this work, we introduce a framework that leverages LMs to perform this task by decomposing it into separate schema and value generation steps. To enable experimentation, we address two main challenges: First, we overcome a lack of high-quality datasets to benchmark table generation by curating and releasing arxivDIGESTables, a new dataset of 2,228 literature review tables extracted from ArXiv papers that synthesize a total of 7,542 research papers. Second, to support scalable evaluation of model generations against human-authored reference tables, we develop DecontextEval, an automatic evaluation method that aligns elements of tables with the same underlying aspects despite differing surface forms. Given these tools, we evaluate LMs' abilities to reconstruct reference tables, finding this task benefits from additional context to ground the generation (e.g. table captions, in-text references). Finally, through a human evaluation study we find that even when LMs fail to fully reconstruct a reference table, their generated novel aspects can still be useful.

Software engineers are increasingly adding semantic search capabilities to applications using a strategy known as Retrieval Augmented Generation (RAG). A RAG system involves finding documents that semantically match a query and then passing the documents to a large language model (LLM) such as ChatGPT to extract the right answer using an LLM. RAG systems aim to: a) reduce the problem of hallucinated responses from LLMs, b) link sources/references to generated responses, and c) remove the need for annotating documents with meta-data. However, RAG systems suffer from limitations inherent to information retrieval systems and from reliance on LLMs. In this paper, we present an experience report on the failure points of RAG systems from three case studies from separate domains: research, education, and biomedical. We share the lessons learned and present 7 failure points to consider when designing a RAG system. The two key takeaways arising from our work are: 1) validation of a RAG system is only feasible during operation, and 2) the robustness of a RAG system evolves rather than designed in at the start. We conclude with a list of potential research directions on RAG systems for the software engineering community.

Document understanding is critical for applications from financial analysis to scientific discovery. Current approaches, whether OCR-based pipelines feeding Large Language Models (LLMs) or native Multimodal LLMs (MLLMs), face key limitations: the former loses structural detail, while the latter struggles with context modeling. Retrieval-Augmented Generation (RAG) helps ground models in external data, but documents' multimodal nature, i.e., combining text, tables, charts, and layout, demands a more advanced paradigm: Multimodal RAG. This approach enables holistic retrieval and reasoning across all modalities, unlocking comprehensive document intelligence. Recognizing its importance, this paper presents a systematic survey of Multimodal RAG for document understanding. We propose a taxonomy based on domain, retrieval modality, and granularity, and review advances involving graph structures and agentic frameworks. We also summarize key datasets, benchmarks, and applications, and highlight open challenges in efficiency, fine-grained representation, and robustness, providing a roadmap for future progress in document AI.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Large Language Models (LLMs), such as GPT3.5, have exhibited remarkable proficiency in comprehending and generating natural language. However, their unpersonalized generation paradigm may result in suboptimal user-specific outcomes. Typically, users converse differently based on their knowledge and preferences. This necessitates the task of enhancing user-oriented LLM which remains unexplored. While one can fully train an LLM for this objective, the resource consumption is unaffordable. Prior research has explored memory-based methods to store and retrieve knowledge to enhance generation without retraining for new queries. However, we contend that a mere memory module is inadequate to comprehend a user's preference, and fully training an LLM can be excessively costly. In this study, we propose a novel computational bionic memory mechanism, equipped with a parameter-efficient fine-tuning schema, to personalize LLMs. Our extensive experimental results demonstrate the effectiveness and superiority of the proposed approach. To encourage further research into this area, we are releasing a new conversation dataset generated entirely by LLM based on an open-source medical corpus, as well as our implementation code.

Recent studies show the growing significance of document retrieval in the generation of LLMs, i.e., RAG, within the scientific domain by bridging their knowledge gap. However, dense retrievers often struggle with domain-specific retrieval and complex query-document relationships, particularly when query segments correspond to various parts of a document. To alleviate such prevalent challenges, this paper introduces MixGR, which improves dense retrievers' awareness of query-document matching across various levels of granularity in queries and documents using a zero-shot approach. MixGR fuses various metrics based on these granularities to a united score that reflects a comprehensive query-document similarity. Our experiments demonstrate that MixGR outperforms previous document retrieval by 24.7%, 9.8%, and 6.9% on nDCG@5 with unsupervised, supervised, and LLM-based retrievers, respectively, averaged on queries containing multiple subqueries from five scientific retrieval datasets. Moreover, the efficacy of two downstream scientific question-answering tasks highlights the advantage of MixGR to boost the application of LLMs in the scientific domain. The code and experimental datasets are available.

Vision-language models in pathology enable multimodal case retrieval and automated report generation. Many of the models developed so far, however, have been trained on pathology reports that include information which cannot be inferred from paired whole slide images (e.g., patient history), potentially leading to hallucinated sentences in generated reports. To this end, we investigate how the selection of information from pathology reports for vision-language modeling affects the quality of the multimodal representations and generated reports. More concretely, we compare a model trained on full reports against a model trained on preprocessed reports that only include sentences describing the cell and tissue appearances based on the H&E-stained slides. For the experiments, we built upon the BLIP-2 framework and used a cutaneous melanocytic lesion dataset of 42,433 H&E-stained whole slide images and 19,636 corresponding pathology reports. Model performance was assessed using image-to-text and text-to-image retrieval, as well as qualitative evaluation of the generated reports by an expert pathologist. Our results demonstrate that text preprocessing prevents hallucination in report generation. Despite the improvement in the quality of the generated reports, training the vision-language model on full reports showed better cross-modal retrieval performance.

We present our submission to the Task 5 of SemEval-2025 that aims to aid librarians in assigning subject tags to the library records by producing a list of likely relevant tags for a given document. We frame the task as an information retrieval problem, where the document content is used to retrieve subject tags from a large subject taxonomy. We leverage two types of encoder models to build a two-stage information retrieval system -- a bi-encoder for coarse-grained candidate extraction at the first stage, and a cross-encoder for fine-grained re-ranking at the second stage. This approach proved effective, demonstrating significant improvements in recall compared to single-stage methods and showing competitive results according to qualitative evaluation.

In this work, we aim to connect two research areas: instruction models and retrieval-based models. While instruction-tuned Large Language Models (LLMs) excel at extracting information from text, they are not suitable for semantic retrieval. Similarity search over embedding vectors allows to index and query vectors, but the similarity reflected in the embedding is sub-optimal for many use cases. We identify the task of retrieving sentences based on abstract descriptions of their content. We demonstrate the inadequacy of current text embeddings and propose an alternative model that significantly improves when used in standard nearest neighbor search. The model is trained using positive and negative pairs sourced through prompting an a large language model (LLM). While it is easy to source the training material from an LLM, the retrieval task cannot be performed by the LLM directly. This demonstrates that data from LLMs can be used not only for distilling more efficient specialized models than the original LLM, but also for creating new capabilities not immediately possible using the original model.

We introduce MRMR, the first expert-level multidisciplinary multimodal retrieval benchmark requiring intensive reasoning. MRMR contains 1,502 queries spanning 23 domains, with positive documents carefully verified by human experts. Compared to prior benchmarks, MRMR introduces three key advancements. First, it challenges retrieval systems across diverse areas of expertise, enabling fine-grained model comparison across domains. Second, queries are reasoning-intensive, with images requiring deeper interpretation such as diagnosing microscopic slides. We further introduce Contradiction Retrieval, a novel task requiring models to identify conflicting concepts. Finally, queries and documents are constructed as image-text interleaved sequences. Unlike earlier benchmarks restricted to single images or unimodal documents, MRMR offers a realistic setting with multi-image queries and mixed-modality corpus documents. We conduct an extensive evaluation of 4 categories of multimodal retrieval systems and 14 frontier models on MRMR. The text embedding model Qwen3-Embedding with LLM-generated image captions achieves the highest performance, highlighting substantial room for improving multimodal retrieval models. Although latest multimodal models such as Ops-MM-Embedding perform competitively on expert-domain queries, they fall short on reasoning-intensive tasks. We believe that MRMR paves the way for advancing multimodal retrieval in more realistic and challenging scenarios.

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Segmenting cells and tracking their motion over time is a common task in biomedical applications. However, predicting accurate instance-wise segmentation and cell motions from microscopy imagery remains a challenging task. Using microstructured environments for analyzing single cells in a constant flow of media adds additional complexity. While large-scale labeled microscopy datasets are available, we are not aware of any large-scale dataset, including both cells and microstructures. In this paper, we introduce the trapped yeast cell (TYC) dataset, a novel dataset for understanding instance-level semantics and motions of cells in microstructures. We release 105 dense annotated high-resolution brightfield microscopy images, including about 19k instance masks. We also release 261 curated video clips composed of 1293 high-resolution microscopy images to facilitate unsupervised understanding of cell motions and morphology. TYC offers ten times more instance annotations than the previously largest dataset, including cells and microstructures. Our effort also exceeds previous attempts in terms of microstructure variability, resolution, complexity, and capturing device (microscopy) variability. We facilitate a unified comparison on our novel dataset by introducing a standardized evaluation strategy. TYC and evaluation code are publicly available under CC BY 4.0 license.

The challenge of information extraction (IE) lies in the diversity of label schemas and the heterogeneity of structures. Traditional methods require task-specific model design and rely heavily on expensive supervision, making them difficult to generalize to new schemas. In this paper, we decouple IE into two basic abilities, structuring and conceptualizing, which are shared by different tasks and schemas. Based on this paradigm, we propose to universally model various IE tasks with Unified Semantic Matching (USM) framework, which introduces three unified token linking operations to model the abilities of structuring and conceptualizing. In this way, USM can jointly encode schema and input text, uniformly extract substructures in parallel, and controllably decode target structures on demand. Empirical evaluation on 4 IE tasks shows that the proposed method achieves state-of-the-art performance under the supervised experiments and shows strong generalization ability in zero/few-shot transfer settings.

There has recently been considerable interest in incorporating information retrieval into large language models (LLMs). Retrieval from a dynamically expanding external corpus of text allows a model to incorporate current events and can be viewed as a form of episodic memory. Here we demonstrate that pre-processing the external corpus into semi-structured ''atomic facts'' makes retrieval more efficient. More specifically, we demonstrate that our particular form of atomic facts improves performance on various question answering tasks when the amount of retrieved text is limited. Limiting the amount of retrieval reduces the size of the context and improves inference efficiency.

Metadata extraction is essential for cataloging and preserving datasets, enabling effective research discovery and reproducibility, especially given the current exponential growth in scientific research. While Masader (Alyafeai et al.,2021) laid the groundwork for extracting a wide range of metadata attributes from Arabic NLP datasets' scholarly articles, it relies heavily on manual annotation. In this paper, we present MOLE, a framework that leverages Large Language Models (LLMs) to automatically extract metadata attributes from scientific papers covering datasets of languages other than Arabic. Our schema-driven methodology processes entire documents across multiple input formats and incorporates robust validation mechanisms for consistent output. Additionally, we introduce a new benchmark to evaluate the research progress on this task. Through systematic analysis of context length, few-shot learning, and web browsing integration, we demonstrate that modern LLMs show promising results in automating this task, highlighting the need for further future work improvements to ensure consistent and reliable performance. We release the code: https://github.com/IVUL-KAUST/MOLE and dataset: https://huggingface.co/datasets/IVUL-KAUST/MOLE for the research community.

When re-finding items, users who forget or are uncertain about identifying details often rely on creative strategies for expressing their information needs -- complex queries that describe content elements (e.g., book characters or events), information beyond the document text (e.g., descriptions of book covers), or personal context (e.g., when they read a book). This retrieval setting, called tip of the tongue (TOT), is especially challenging for models heavily reliant on lexical and semantic overlap between query and document text. In this work, we introduce a simple yet effective framework for handling such complex queries by decomposing the query into individual clues, routing those as sub-queries to specialized retrievers, and ensembling the results. This approach allows us to take advantage of off-the-shelf retrievers (e.g., CLIP for retrieving images of book covers) or incorporate retriever-specific logic (e.g., date constraints). We show that our framework incorportating query decompositions into retrievers can improve gold book recall up to 7% relative again for Recall@5 on a new collection of 14,441 real-world query-book pairs from an online community for resolving TOT inquiries.

We present Prompt Cache, an approach for accelerating inference for large language models (LLM) by reusing attention states across different LLM prompts. Many input prompts have overlapping text segments, such as system messages, prompt templates, and documents provided for context. Our key insight is that by precomputing and storing the attention states of these frequently occurring text segments on the inference server, we can efficiently reuse them when these segments appear in user prompts. Prompt Cache employs a schema to explicitly define such reusable text segments, called prompt modules. The schema ensures positional accuracy during attention state reuse and provides users with an interface to access cached states in their prompt. Using a prototype implementation, we evaluate Prompt Cache across several LLMs. We show that Prompt Cache significantly reduce latency in time-to-first-token, especially for longer prompts such as document-based question answering and recommendations. The improvements range from 8x for GPU-based inference to 60x for CPU-based inference, all while maintaining output accuracy and without the need for model parameter modifications.

Long-range tasks require reasoning over long inputs. Existing solutions either need large compute budgets, training data, access to model weights, or use complex, task-specific approaches. We present PRISM, which alleviates these concerns by processing information as a stream of chunks, maintaining a structured in-context memory specified by a typed hierarchy schema. This approach demonstrates superior performance to baselines on diverse tasks while using at least 4x smaller contexts than long-context models. Moreover, PRISM is token-efficient. By producing short outputs and efficiently leveraging key-value (KV) caches, it achieves up to 54% cost reduction when compared to alternative short-context approaches. The method also scales down to tiny information chunks (e.g., 500 tokens) without increasing the number of tokens encoded or sacrificing quality. Furthermore, we show that it is possible to generate schemas to generalize our approach to new tasks with minimal effort.

With recent advancements in Large Language Models (LLMs) and growing interest in retrieval-augmented generation (RAG), the ability to understand table structures has become increasingly important. This is especially critical in financial domains such as securities reports, where highly accurate question answering (QA) over tables is required. However, tables exist in various formats-including HTML, images, and plain text-making it difficult to preserve and extract structural information. Therefore, multimodal LLMs are essential for robust and general-purpose table understanding. Despite their promise, current Large Vision-Language Models (LVLMs), which are major representatives of multimodal LLMs, still face challenges in accurately understanding characters and their spatial relationships within documents. In this study, we propose a method to enhance LVLM-based table understanding by incorporating in-table textual content and layout features. Experimental results demonstrate that these auxiliary modalities significantly improve performance, enabling robust interpretation of complex document layouts without relying on explicitly structured input formats.

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.

Retrieval-Augmented Generation (RAG) systems are increasingly vital for navigating the ever-expanding body of scientific literature, particularly in high-stakes domains such as chemistry. Despite the promise of RAG, foundational design choices -- such as how documents are segmented and represented -- remain underexplored in domain-specific contexts. This study presents the first large-scale, systematic evaluation of chunking strategies and embedding models tailored to chemistry-focused RAG systems. We investigate 25 chunking configurations across five method families and evaluate 48 embedding models on three chemistry-specific benchmarks, including the newly introduced QuestChemRetrieval dataset. Our results reveal that recursive token-based chunking (specifically R100-0) consistently outperforms other approaches, offering strong performance with minimal resource overhead. We also find that retrieval-optimized embeddings -- such as Nomic and Intfloat E5 variants -- substantially outperform domain-specialized models like SciBERT. By releasing our datasets, evaluation framework, and empirical benchmarks, we provide actionable guidelines for building effective and efficient chemistry-aware RAG systems.

With the increasing use of RetrievalAugmented Generation (RAG), strong retrieval models have become more important than ever. In healthcare, multimodal retrieval models that combine information from both text and images offer major advantages for many downstream tasks such as question answering, cross-modal retrieval, and multimodal summarization, since medical data often includes both formats. However, there is currently no standard benchmark to evaluate how well these models perform in medical settings. To address this gap, we introduce M3Retrieve, a Multimodal Medical Retrieval Benchmark. M3Retrieve, spans 5 domains,16 medical fields, and 4 distinct tasks, with over 1.2 Million text documents and 164K multimodal queries, all collected under approved licenses. We evaluate leading multimodal retrieval models on this benchmark to explore the challenges specific to different medical specialities and to understand their impact on retrieval performance. By releasing M3Retrieve, we aim to enable systematic evaluation, foster model innovation, and accelerate research toward building more capable and reliable multimodal retrieval systems for medical applications. The dataset and the baselines code are available in this github page https://github.com/AkashGhosh/M3Retrieve.

With the advent of artificial intelligence (AI), many researchers are attempting to extract structured information from document-level biomedical literature by fine-tuning large language models (LLMs). However, they face significant challenges such as the need for expensive hardware, like high-performance GPUs and the high labor costs associated with annotating training datasets, especially in biomedical realm. Recent research on LLMs, such as GPT-4 and Llama3, has shown promising performance in zero-shot settings, inspiring us to explore a novel approach to achieve the same results from unannotated full documents using general LLMs with lower hardware and labor costs. Our approach combines two major stages: named entity recognition (NER) and relation extraction (RE). NER identifies chemical, disease and gene entities from the document with synonym and hypernym extraction using an LLM with a crafted prompt. RE extracts relations between entities based on predefined relation schemas and prompts. To enhance the effectiveness of prompt, we propose a five-part template structure and a scenario-based prompt design principles, along with evaluation method to systematically assess the prompts. Finally, we evaluated our approach against fine-tuning and pre-trained models on two biomedical datasets: ChemDisGene and CDR. The experimental results indicate that our proposed method can achieve comparable accuracy levels to fine-tuning and pre-trained models but with reduced human and hardware expenses.

Medical open-domain question answering demands substantial access to specialized knowledge. Recent efforts have sought to decouple knowledge from model parameters, counteracting architectural scaling and allowing for training on common low-resource hardware. The retrieve-then-read paradigm has become ubiquitous, with model predictions grounded on relevant knowledge pieces from external repositories such as PubMed, textbooks, and UMLS. An alternative path, still under-explored but made possible by the advent of domain-specific large language models, entails constructing artificial contexts through prompting. As a result, "to generate or to retrieve" is the modern equivalent of Hamlet's dilemma. This paper presents MedGENIE, the first generate-then-read framework for multiple-choice question answering in medicine. We conduct extensive experiments on MedQA-USMLE, MedMCQA, and MMLU, incorporating a practical perspective by assuming a maximum of 24GB VRAM. MedGENIE sets a new state-of-the-art (SOTA) in the open-book setting of each testbed, even allowing a small-scale reader to outcompete zero-shot closed-book 175B baselines while using up to 706times fewer parameters. Overall, our findings reveal that generated passages are more effective than retrieved counterparts in attaining higher accuracy.

Classical models of memory in psychology and neuroscience rely on similarity-based retrieval of stored patterns, where similarity is a function of retrieval cues and the stored patterns. While parsimonious, these models do not allow distinct representations for storage and retrieval, despite their distinct computational demands. Key-value memory systems, in contrast, distinguish representations used for storage (values) and those used for retrieval (keys). This allows key-value memory systems to optimize simultaneously for fidelity in storage and discriminability in retrieval. We review the computational foundations of key-value memory, its role in modern machine learning systems, related ideas from psychology and neuroscience, applications to a number of empirical puzzles, and possible biological implementations.

We introduce SMUTF, a unique approach for large-scale tabular data schema matching (SM), which assumes that supervised learning does not affect performance in open-domain tasks, thereby enabling effective cross-domain matching. This system uniquely combines rule-based feature engineering, pre-trained language models, and generative large language models. In an innovative adaptation inspired by the Humanitarian Exchange Language, we deploy 'generative tags' for each data column, enhancing the effectiveness of SM. SMUTF exhibits extensive versatility, working seamlessly with any pre-existing pre-trained embeddings, classification methods, and generative models. Recognizing the lack of extensive, publicly available datasets for SM, we have created and open-sourced the HDXSM dataset from the public humanitarian data. We believe this to be the most exhaustive SM dataset currently available. In evaluations across various public datasets and the novel HDXSM dataset, SMUTF demonstrated exceptional performance, surpassing existing state-of-the-art models in terms of accuracy and efficiency, and} improving the F1 score by 11.84% and the AUC of ROC by 5.08%.

Efficiently processing and interpreting network data is critical for the operation of increasingly complex networks. Recent advances in Large Language Models (LLM) and Retrieval-Augmented Generation (RAG) techniques have improved data processing in network management. However, existing RAG methods like VectorRAG and GraphRAG struggle with the complexity and implicit nature of semi-structured technical data, leading to inefficiencies in time, cost, and retrieval. This paper introduces FastRAG, a novel RAG approach designed for semi-structured data. FastRAG employs schema learning and script learning to extract and structure data without needing to submit entire data sources to an LLM. It integrates text search with knowledge graph (KG) querying to improve accuracy in retrieving context-rich information. Evaluation results demonstrate that FastRAG provides accurate question answering, while improving up to 90% in time and 85% in cost compared to GraphRAG.

Large language models (LLMs) have recently shown strong progress on scientific reasoning, yet two major bottlenecks remain. First, explicit retrieval fragments reasoning, imposing a hidden "tool tax" of extra tokens and steps. Second, multi-agent pipelines often dilute strong solutions by averaging across all candidates. We address these challenges with a unified framework that combines implicit retrieval and structured collaboration. At its foundation, a Monitor-based retrieval module operates at the token level, integrating external knowledge with minimal disruption to reasoning. On top of this substrate, Hierarchical Solution Refinement (HSR) iteratively designates each candidate as an anchor to be repaired by its peers, while Quality-Aware Iterative Reasoning (QAIR) adapts refinement to solution quality. On Humanity's Last Exam (HLE) Bio/Chem Gold, our framework achieves 48.3\% accuracy -- the highest reported to date, surpassing the strongest agent baseline by 13.4 points and leading frontier LLMs by up to 18.1 points, while simultaneously reducing token usage by 53.5\% and agent steps by 43.7\%. Results on SuperGPQA and TRQA confirm robustness across domains. Error analysis shows that reasoning failures and knowledge gaps co-occur in over 85\% of cases, while diversity analysis reveals a clear dichotomy: retrieval tasks benefit from solution variety, whereas reasoning tasks favor consensus. Together, these findings demonstrate how implicit augmentation and structured refinement overcome the inefficiencies of explicit tool use and uniform aggregation. Code is available at: https://github.com/tangxiangru/Eigen-1.

Image Schemas are repetitive cognitive patterns that influence the way we conceptualize and reason about various concepts present in speech. These patterns are deeply embedded within our cognitive processes and are reflected in our bodily expressions including gestures. Particularly, metaphoric gestures possess essential characteristics and semantic meanings that align with Image Schemas, to visually represent abstract concepts. The shape and form of gestures can convey abstract concepts, such as extending the forearm and hand or tracing a line with hand movements to visually represent the image schema of PATH. Previous behavior generation models have primarily focused on utilizing speech (acoustic features and text) to drive the generation model of virtual agents. They have not considered key semantic information as those carried by Image Schemas to effectively generate metaphoric gestures. To address this limitation, we introduce META4, a deep learning approach that generates metaphoric gestures from both speech and Image Schemas. Our approach has two primary goals: computing Image Schemas from input text to capture the underlying semantic and metaphorical meaning, and generating metaphoric gestures driven by speech and the computed image schemas. Our approach is the first method for generating speech driven metaphoric gestures while leveraging the potential of Image Schemas. We demonstrate the effectiveness of our approach and highlight the importance of both speech and image schemas in modeling metaphoric gestures.

Retrieval-Augmented Generation (RAG) prevails in Large Language Models. It mainly consists of retrieval and generation. The retrieval modules (a.k.a. retrievers) aim to find useful information used to facilitate generation modules (a.k.a. generators). As such, generators' performance largely depends on the effectiveness and efficiency of retrievers. However, the retrieval paradigm that we design and use remains flat, which treats the retrieval procedures as a one-off deal with constant granularity. Despite effectiveness, we argue that they suffer from two limitations: (1) flat retrieval exerts a significant burden on one retriever; (2) constant granularity limits the ceiling of retrieval performance. In this work, we propose a progressive retrieval paradigm with coarse-to-fine granularity for RAG, termed FunnelRAG, so as to balance effectiveness and efficiency. Specifically, FunnelRAG establishes a progressive retrieval pipeline by collaborating coarse-to-fine granularity, large-to-small quantity, and low-to-high capacity, which can relieve the burden on one retriever and also promote the ceiling of retrieval performance. Extensive experiments manifest that FunnelRAG achieves comparable retrieval performance while the time overhead is reduced by nearly 40 percent.

Complex dialog systems often use retrieved evidence to facilitate factual responses. Such RAG (Retrieval Augmented Generation) systems retrieve from massive heterogeneous data stores that are usually architected as multiple indexes or APIs instead of a single monolithic source. For a given query, relevant evidence needs to be retrieved from one or a small subset of possible retrieval sources. Complex queries can even require multi-step retrieval. For example, a conversational agent on a retail site answering customer questions about past orders will need to retrieve the appropriate customer order first and then the evidence relevant to the customer's question in the context of the ordered product. Most RAG Agents handle such Chain-of-Thought (CoT) tasks by interleaving reasoning and retrieval steps. However, each reasoning step directly adds to the latency of the system. For large models (>100B parameters) this latency cost is significant -- in the order of multiple seconds. Multi-agent systems may classify the query to a single Agent associated with a retrieval source, though this means that a (small) classification model dictates the performance of a large language model. In this work we present REAPER (REAsoning-based PlannER) - an LLM based planner to generate retrieval plans in conversational systems. We show significant gains in latency over Agent-based systems and are able to scale easily to new and unseen use cases as compared to classification-based planning. Though our method can be applied to any RAG system, we show our results in the context of Rufus -- Amazon's conversational shopping assistant.

Semantic code search is the task of retrieving a code snippet given a textual description of its functionality. Recent work has been focused on using similarity metrics between neural embeddings of text and code. However, current language models are known to struggle with longer, compositional text, and multi-step reasoning. To overcome this limitation, we propose supplementing the query sentence with a layout of its semantic structure. The semantic layout is used to break down the final reasoning decision into a series of lower-level decisions. We use a Neural Module Network architecture to implement this idea. We compare our model - NS3 (Neuro-Symbolic Semantic Search) - to a number of baselines, including state-of-the-art semantic code retrieval methods, and evaluate on two datasets - CodeSearchNet and Code Search and Question Answering. We demonstrate that our approach results in more precise code retrieval, and we study the effectiveness of our modular design when handling compositional queries.

Recent advances in large language models have demonstrated considerable potential in scientific domains such as drug repositioning. However, their effectiveness remains constrained when reasoning extends beyond the knowledge acquired during pretraining. Conventional approaches, such as fine-tuning or retrieval-augmented generation, face limitations in either imposing high computational overhead or failing to fully exploit structured scientific data. To overcome these challenges, we propose DrugMCTS, a novel framework that synergistically integrates RAG, multi-agent collaboration, and Monte Carlo Tree Search for drug repositioning. The framework employs five specialized agents tasked with retrieving and analyzing molecular and protein information, thereby enabling structured and iterative reasoning. Extensive experiments on the DrugBank and KIBA datasets demonstrate that DrugMCTS achieves substantially higher recall and robustness compared to both general-purpose LLMs and deep learning baselines. Our results highlight the importance of structured reasoning, agent-based collaboration, and feedback-driven search mechanisms in advancing LLM applications for drug repositioning.

Text-to-SQL aims to map natural language questions to SQL queries. The sketch-based method combined with execution-guided (EG) decoding strategy has shown a strong performance on the WikiSQL benchmark. However, execution-guided decoding relies on database execution, which significantly slows down the inference process and is hence unsatisfactory for many real-world applications. In this paper, we present the Schema Dependency guided multi-task Text-to-SQL model (SDSQL) to guide the network to effectively capture the interactions between questions and schemas. The proposed model outperforms all existing methods in both the settings with or without EG. We show the schema dependency learning partially cover the benefit from EG and alleviates the need for it. SDSQL without EG significantly reduces time consumption during inference, sacrificing only a small amount of performance and provides more flexibility for downstream applications.

Retrieval-augmented generation (RAG) has emerged as a powerful framework for enhancing large language models (LLMs) with external knowledge, particularly in scientific domains that demand specialized and dynamic information. Despite its promise, the application of RAG in the chemistry domain remains underexplored, primarily due to the lack of high-quality, domain-specific corpora and well-curated evaluation benchmarks. In this work, we introduce ChemRAG-Bench, a comprehensive benchmark designed to systematically assess the effectiveness of RAG across a diverse set of chemistry-related tasks. The accompanying chemistry corpus integrates heterogeneous knowledge sources, including scientific literature, the PubChem database, PubMed abstracts, textbooks, and Wikipedia entries. In addition, we present ChemRAG-Toolkit, a modular and extensible RAG toolkit that supports five retrieval algorithms and eight LLMs. Using ChemRAG-Toolkit, we demonstrate that RAG yields a substantial performance gain -- achieving an average relative improvement of 17.4% over direct inference methods. We further conduct in-depth analyses on retriever architectures, corpus selection, and the number of retrieved passages, culminating in practical recommendations to guide future research and deployment of RAG systems in the chemistry domain. The code and data is available at https://chemrag.github.io.

Research on parsing language to SQL has largely ignored the structure of the database (DB) schema, either because the DB was very simple, or because it was observed at both training and test time. In Spider, a recently-released text-to-SQL dataset, new and complex DBs are given at test time, and so the structure of the DB schema can inform the predicted SQL query. In this paper, we present an encoder-decoder semantic parser, where the structure of the DB schema is encoded with a graph neural network, and this representation is later used at both encoding and decoding time. Evaluation shows that encoding the schema structure improves our parser accuracy from 33.8% to 39.4%, dramatically above the current state of the art, which is at 19.7%.

The task of Prior Case Retrieval (PCR) in the legal domain is about automatically citing relevant (based on facts and precedence) prior legal cases in a given query case. To further promote research in PCR, in this paper, we propose a new large benchmark (in English) for the PCR task: IL-PCR (Indian Legal Prior Case Retrieval) corpus. Given the complex nature of case relevance and the long size of legal documents, BM25 remains a strong baseline for ranking the cited prior documents. In this work, we explore the role of events in legal case retrieval and propose an unsupervised retrieval method-based pipeline U-CREAT (Unsupervised Case Retrieval using Events Extraction). We find that the proposed unsupervised retrieval method significantly increases performance compared to BM25 and makes retrieval faster by a considerable margin, making it applicable to real-time case retrieval systems. Our proposed system is generic, we show that it generalizes across two different legal systems (Indian and Canadian), and it shows state-of-the-art performance on the benchmarks for both the legal systems (IL-PCR and COLIEE corpora).

Table Structure Recognition (TSR) is vital for various downstream tasks like information retrieval, table reconstruction, and document understanding. While most state-of-the-art (SOTA) research predominantly focuses on TSR in English documents, the need for similar capabilities in other languages is evident, considering the global diversity of data. Moreover, creating substantial labeled data in non-English languages and training these SOTA models from scratch is costly and time-consuming. We propose TSR as a language-agnostic cell arrangement prediction and introduce SPRINT, Script-agnostic Structure Recognition in Tables. SPRINT uses recently introduced Optimized Table Structure Language (OTSL) sequences to predict table structures. We show that when coupled with a pre-trained table grid estimator, SPRINT can improve the overall tree edit distance-based similarity structure scores of tables even for non-English documents. We experimentally evaluate our performance across benchmark TSR datasets including PubTabNet, FinTabNet, and PubTables-1M. Our findings reveal that SPRINT not only matches SOTA models in performance on standard datasets but also demonstrates lower latency. Additionally, SPRINT excels in accurately identifying table structures in non-English documents, surpassing current leading models by showing an absolute average increase of 11.12%. We also present an algorithm for converting valid OTSL predictions into a widely used HTML-based table representation. To encourage further research, we release our code and Multilingual Scanned and Scene Table Structure Recognition Dataset, MUSTARD labeled with OTSL sequences for 1428 tables in thirteen languages encompassing several scripts at https://github.com/IITB-LEAP-OCR/SPRINT

When completing knowledge-intensive tasks, humans sometimes need not just an answer but also a corresponding reference passage for auxiliary reading. Previous methods required obtaining pre-segmented article chunks through additional retrieval models. This paper explores leveraging the parameterized knowledge stored during the pre-training phase of large language models (LLMs) to independently recall reference passage from any starting position. We propose a two-stage framework that simulates the scenario of humans recalling easily forgotten references. Initially, the LLM is prompted to recall document title identifiers to obtain a coarse-grained document set. Then, based on the acquired coarse-grained document set, it recalls fine-grained passage. In the two-stage recall process, we use constrained decoding to ensure that content outside of the stored documents is not generated. To increase speed, we only recall a short prefix in the second stage, then locate its position to retrieve a complete passage. Experiments on KILT knowledge-sensitive tasks have verified that LLMs can independently recall reference passage location in various task forms, and the obtained reference significantly assist downstream tasks.

In this work we study various Retrieval Augmented Regeneration (RAG) approaches to gain an understanding of the strengths and weaknesses of each approach in a question-answering analysis. To gain this understanding we use a case-study subset of the Global Database of Events, Language, and Tone (GDELT) dataset as well as a corpus of raw text scraped from the online news articles. To retrieve information from the text corpus we implement a traditional vector store RAG as well as state-of-the-art large language model (LLM) based approaches for automatically constructing KGs and retrieving the relevant subgraphs. In addition to these corpus approaches, we develop a novel ontology-based framework for constructing knowledge graphs (KGs) from GDELT directly which leverages the underlying schema of GDELT to create structured representations of global events. For retrieving relevant information from the ontology-based KGs we implement both direct graph queries and state-of-the-art graph retrieval approaches. We compare the performance of each method in a question-answering task. We find that while our ontology-based KGs are valuable for question-answering, automated extraction of the relevant subgraphs is challenging. Conversely, LLM-generated KGs, while capturing event summaries, often lack consistency and interpretability. Our findings suggest benefits of a synergistic approach between ontology and LLM-based KG construction, with proposed avenues toward that end.

Large language models (LLMs) are becoming attractive as few-shot reasoners to solve Natural Language (NL)-related tasks. However, the understanding of their capability to process structured data like tables remains an under-explored area. While tables can be serialized as input for LLMs, there is a lack of comprehensive studies on whether LLMs genuinely comprehend this data. In this paper, we try to understand this by designing a benchmark to evaluate the structural understanding capabilities of LLMs through seven distinct tasks, e.g., cell lookup, row retrieval and size detection. Specially, we perform a series of evaluations on the recent most advanced LLM models, GPT-3.5 and GPT-4 and observe that performance varied with different input choices, including table input format, content order, role prompting, and partition marks. Drawing from the insights gained through the benchmark evaluations, we propose self-augmentation for effective structural prompting, such as critical value / range identification using internal knowledge of LLMs. When combined with carefully chosen input choices, these structural prompting methods lead to promising improvements in LLM performance on a variety of tabular tasks, e.g., TabFact(uparrow2.31%), HybridQA(uparrow2.13%), SQA(uparrow2.72%), Feverous(uparrow0.84%), and ToTTo(uparrow5.68%). We believe that our open source benchmark and proposed prompting methods can serve as a simple yet generic selection for future research. The code and data of this paper will be temporality released at https://anonymous.4open.science/r/StructuredLLM-76F3/README.md and will be replaced with an official one at https://github.com/microsoft/TableProvider later.

The performance of Retrieval Augmented Generation (RAG) systems relies heavily on the retriever quality and the size of the retrieved context. A large enough context ensures that the relevant information is present in the input context for the LLM, but also incorporates irrelevant content that has been shown to confuse the models. On the other hand, a smaller context reduces the irrelevant information, but it often comes at the risk of losing important information necessary to answer the input question. This duality is especially challenging to manage for complex queries that contain little information to retrieve the relevant chunks from the full context. To address this, we present a novel framework, called FB-RAG, which enhances the RAG pipeline by relying on a combination of backward lookup (overlap with the query) and forward lookup (overlap with candidate reasons and answers) to retrieve specific context chunks that are the most relevant for answering the input query. Our evaluations on 9 datasets from two leading benchmarks show that FB-RAG consistently outperforms RAG and Long Context baselines developed recently for these benchmarks. We further show that FB-RAG can improve performance while reducing latency. We perform qualitative analysis of the strengths and shortcomings of our approach, providing specific insights to guide future work.

To tackle the challenges of large language model performance in natural language to SQL tasks, we introduce XiYan-SQL, an innovative framework that employs a multi-generator ensemble strategy to improve candidate generation. We introduce M-Schema, a semi-structured schema representation method designed to enhance the understanding of database structures. To enhance the quality and diversity of generated candidate SQL queries, XiYan-SQL integrates the significant potential of in-context learning (ICL) with the precise control of supervised fine-tuning. On one hand, we propose a series of training strategies to fine-tune models to generate high-quality candidates with diverse preferences. On the other hand, we implement the ICL approach with an example selection method based on named entity recognition to prevent overemphasis on entities. The refiner optimizes each candidate by correcting logical or syntactical errors. To address the challenge of identifying the best candidate, we fine-tune a selection model to distinguish nuances of candidate SQL queries. The experimental results on multiple dialect datasets demonstrate the robustness of XiYan-SQL in addressing challenges across different scenarios. Overall, our proposed XiYan-SQL achieves the state-of-the-art execution accuracy of 89.65% on the Spider test set, 69.86% on SQL-Eval, 41.20% on NL2GQL, and a competitive score of 72.23% on the Bird development benchmark. The proposed framework not only enhances the quality and diversity of SQL queries but also outperforms previous methods.

In medical scenarios, effectively retrieving external knowledge and leveraging it for rigorous logical reasoning is of significant importance. Despite their potential, existing work has predominantly focused on enhancing either retrieval or reasoning capabilities of the models in isolation, with little attention given to their joint optimization, which leads to limited coordination between the two processes. Additionally, current methods rely heavily on supervised fine-tuning (SFT), which can cause models to memorize existing problem-solving pathways, thereby restricting their generalization ability when confronted with novel problem contexts. Furthermore, while some studies have explored to improve retrieval-augmented reasoning in general domains via reinforcement learning, their reward function designs do not adequately capture the specific demands of the medical domain. To address these challenges, we introduce **Med-R^3**, a **Med**ical **R**etrieval-augmented **R**easoning framework driven by progressive **R**einforcement learning. In this framework, we first develop the model's ability to perform logical reasoning over medical problems. Subsequently, on the basis of this foundation, we adaptively optimize the retrieval capability to better align with the characteristics of knowledge corpus and external information utilization throughout the reasoning process. Finally, we conduct joint optimization of the model's retrieval and reasoning coordination. Extensive experiments indicate that **Med-R^3** could achieve state-of-the-art performances, with LLaMA3.1-8B-Instruct + Med-R^3 surpassing closed-sourced GPT-4o-mini by 3.93\% at a comparable parameter scale, while Qwen2.5-14B augmented with Med-R^3 shows a more substantial gain of 13.53\%.

In many use-cases, information is stored in text but not available in structured data. However, extracting data from natural language text to precisely fit a schema, and thus enable querying, is a challenging task. With the rise of pre-trained Large Language Models (LLMs), there is now an effective solution to store and use information extracted from massive corpora of text documents. Thus, we envision the use of SQL queries to cover a broad range of data that is not captured by traditional databases by tapping the information in LLMs. To ground this vision, we present Galois, a prototype based on a traditional database architecture, but with new physical operators for querying the underlying LLM. The main idea is to execute some operators of the the query plan with prompts that retrieve data from the LLM. For a large class of SQL queries, querying LLMs returns well structured relations, with encouraging qualitative results. Preliminary experimental results make pre-trained LLMs a promising addition to the field of database systems, introducing a new direction for hybrid query processing. However, we pinpoint several research challenges that must be addressed to build a DBMS that exploits LLMs. While some of these challenges necessitate integrating concepts from the NLP literature, others offer novel research avenues for the DB community.

When do machine learning systems fail to generalize, and what mechanisms could improve their generalization? Here, we draw inspiration from cognitive science to argue that one weakness of machine learning systems is their failure to exhibit latent learning -- learning information that is not relevant to the task at hand, but that might be useful in a future task. We show how this perspective links failures ranging from the reversal curse in language modeling to new findings on agent-based navigation. We then highlight how cognitive science points to episodic memory as a potential part of the solution to these issues. Correspondingly, we show that a system with an oracle retrieval mechanism can use learning experiences more flexibly to generalize better across many of these challenges. We also identify some of the essential components for effectively using retrieval, including the importance of within-example in-context learning for acquiring the ability to use information across retrieved examples. In summary, our results illustrate one possible contributor to the relative data inefficiency of current machine learning systems compared to natural intelligence, and help to understand how retrieval methods can complement parametric learning to improve generalization.

Image-based or morphological profiling is a rapidly expanding field wherein cells are "profiled" by extracting hundreds to thousands of unbiased, quantitative features from images of cells that have been perturbed by genetic or chemical perturbations. The Cell Painting assay is the most popular imaged-based profiling assay wherein six small-molecule dyes label eight cellular compartments and thousands of measurements are made, describing quantitative traits such as size, shape, intensity, and texture within the nucleus, cytoplasm, and whole cell (Cimini et al., 2023). We have created the Cell Painting Gallery, a publicly available collection of Cell Painting datasets, with granular dataset descriptions and access instructions. It is hosted by AWS on the Registry of Open Data (RODA). As of January 2024, the Cell Painting Gallery holds 656 terabytes (TB) of image and associated numerical data. It includes the largest publicly available Cell Painting dataset, in terms of perturbations tested (Joint Undertaking for Morphological Profiling or JUMP (Chandrasekaran et al., 2023)), along with many other canonical datasets using Cell Painting, close derivatives of Cell Painting (such as LipocyteProfiler (Laber et al., 2023) and Pooled Cell Painting (Ramezani et al., 2023)).

Recent studies have shown that large language models (LLMs) can assess relevance and support information retrieval (IR) tasks such as document ranking and relevance judgment generation. However, the internal mechanisms by which off-the-shelf LLMs understand and operationalize relevance remain largely unexplored. In this paper, we systematically investigate how different LLM modules contribute to relevance judgment through the lens of mechanistic interpretability. Using activation patching techniques, we analyze the roles of various model components and identify a multi-stage, progressive process in generating either pointwise or pairwise relevance judgment. Specifically, LLMs first extract query and document information in the early layers, then process relevance information according to instructions in the middle layers, and finally utilize specific attention heads in the later layers to generate relevance judgments in the required format. Our findings provide insights into the mechanisms underlying relevance assessment in LLMs, offering valuable implications for future research on leveraging LLMs for IR tasks.

With the rapid advancement of large language models (LLMs), Retrieval-Augmented Generation (RAG) effectively combines LLMs generative capabilities with external retrieval-based information. The Hybrid Document RAG task aims to integrate textual and hierarchical tabular data for more comprehensive retrieval and generation in complex scenarios. However, there is no existing dataset specifically designed for this task that includes both text and tabular data. Additionally, existing methods struggle to retrieve relevant tabular data and integrate it with text. Semantic similarity-based retrieval lacks accuracy, while table-specific methods fail to handle complex hierarchical structures effectively. Furthermore, the QA task requires complex reasoning and calculations, further complicating the challenge. In this paper, we propose a new large-scale dataset, DocRAGLib, specifically designed for the question answering (QA) task scenario under Hybrid Document RAG. To tackle these challenges, we introduce HD-RAG, a novel framework that incorporates a row-and-column level (RCL) table representation, employs a two-stage process combining ensemble and LLM-based retrieval, and integrates RECAP, which is designed for multi-step reasoning and complex calculations in Document-QA tasks. We conduct comprehensive experiments with DocRAGLib, showing that HD-RAG outperforms existing baselines in both retrieval accuracy and QA performance, demonstrating its effectiveness.

The output structure of database-like tables, consisting of values structured in horizontal rows and vertical columns identifiable by name, can cover a wide range of NLP tasks. Following this constatation, we propose a framework for text-to-table neural models applicable to problems such as extraction of line items, joint entity and relation extraction, or knowledge base population. The permutation-based decoder of our proposal is a generalized sequential method that comprehends information from all cells in the table. The training maximizes the expected log-likelihood for a table's content across all random permutations of the factorization order. During the content inference, we exploit the model's ability to generate cells in any order by searching over possible orderings to maximize the model's confidence and avoid substantial error accumulation, which other sequential models are prone to. Experiments demonstrate a high practical value of the framework, which establishes state-of-the-art results on several challenging datasets, outperforming previous solutions by up to 15%.

This article aims to provide the information retrieval community with some reflections on recent advances in retrieval learning by analyzing the reproducibility of image-text retrieval models. Due to the increase of multimodal data over the last decade, image-text retrieval has steadily become a major research direction in the field of information retrieval. Numerous researchers train and evaluate image-text retrieval algorithms using benchmark datasets such as MS-COCO and Flickr30k. Research in the past has mostly focused on performance, with multiple state-of-the-art methodologies being suggested in a variety of ways. According to their assertions, these techniques provide improved modality interactions and hence more precise multimodal representations. In contrast to previous works, we focus on the reproducibility of the approaches and the examination of the elements that lead to improved performance by pretrained and nonpretrained models in retrieving images and text. To be more specific, we first examine the related reproducibility concerns and explain why our focus is on image-text retrieval tasks. Second, we systematically summarize the current paradigm of image-text retrieval models and the stated contributions of those approaches. Third, we analyze various aspects of the reproduction of pretrained and nonpretrained retrieval models. To complete this, we conducted ablation experiments and obtained some influencing factors that affect retrieval recall more than the improvement claimed in the original paper. Finally, we present some reflections and challenges that the retrieval community should consider in the future. Our source code is publicly available at https://github.com/WangFei-2019/Image-text-Retrieval.

Schema linking is a critical bottleneck in applying existing Text-to-SQL models to real-world, large-scale, multi-database environments. Through error analysis, we identify two major challenges in schema linking: (1) Database Retrieval: accurately selecting the target database from a large schema pool, while effectively filtering out irrelevant ones; and (2) Schema Item Grounding: precisely identifying the relevant tables and columns within complex and often redundant schemas for SQL generation. Based on these, we introduce LinkAlign, a novel framework tailored for large-scale databases with thousands of fields. LinkAlign comprises three key steps: multi-round semantic enhanced retrieval and irrelevant information isolation for Challenge 1, and schema extraction enhancement for Challenge 2. Each stage supports both Agent and Pipeline execution modes, enabling balancing efficiency and performance via modular design. To enable more realistic evaluation, we construct AmbiDB, a synthetic dataset designed to reflect the ambiguity of real-world schema linking. Experiments on widely-used Text-to-SQL benchmarks demonstrate that LinkAlign consistently outperforms existing baselines on all schema linking metrics. Notably, it improves the overall Text-to-SQL pipeline and achieves a new state-of-the-art score of 33.09% on the Spider 2.0-Lite benchmark using only open-source LLMs, ranking first on the leaderboard at the time of submission. The codes are available at https://github.com/Satissss/LinkAlign

Retrieval models are often evaluated on partially-annotated datasets. Each query is mapped to a few relevant texts and the remaining corpus is assumed to be irrelevant. As a result, models that successfully retrieve false negatives are punished in evaluation. Unfortunately, completely annotating all texts for every query is not resource efficient. In this work, we show that using partially-annotated datasets in evaluation can paint a distorted picture. We curate D-MERIT, a passage retrieval evaluation set from Wikipedia, aspiring to contain all relevant passages for each query. Queries describe a group (e.g., ``journals about linguistics'') and relevant passages are evidence that entities belong to the group (e.g., a passage indicating that Language is a journal about linguistics). We show that evaluating on a dataset containing annotations for only a subset of the relevant passages might result in misleading ranking of the retrieval systems and that as more relevant texts are included in the evaluation set, the rankings converge. We propose our dataset as a resource for evaluation and our study as a recommendation for balance between resource-efficiency and reliable evaluation when annotating evaluation sets for text retrieval.

Large language models (LLMs) are incredible and versatile tools for text-based tasks that have enabled countless, previously unimaginable, applications. Retrieval models, in contrast, have not yet seen such capable general-purpose models emerge. To achieve this goal, retrieval models must be able to perform complex retrieval tasks, where queries contain multiple parts, constraints, or requirements in natural language. These tasks represent a natural progression from the simple, single-aspect queries that are used in the vast majority of existing, commonly used evaluation sets. Complex queries naturally arise as people expect search systems to handle more specific and often ambitious information requests, as is demonstrated by how people use LLM-based information systems. Despite the growing desire for retrieval models to expand their capabilities in complex retrieval tasks, there exist limited resources to assess the ability of retrieval models on a comprehensive set of diverse complex tasks. The few resources that do exist feature a limited scope and often lack realistic settings making it hard to know the true capabilities of retrieval models on complex real-world retrieval tasks. To address this shortcoming and spur innovation in next-generation retrieval models, we construct a diverse and realistic set of complex retrieval tasks and benchmark a representative set of state-of-the-art retrieval models. Additionally, we explore the impact of LLM-based query expansion and rewriting on retrieval quality. Our results show that even the best models struggle to produce high-quality retrieval results with the highest average nDCG@10 of only 0.346 and R@100 of only 0.587 across all tasks. Although LLM augmentation can help weaker models, the strongest model has decreased performance across all metrics with all rewriting techniques.

Semantic textual similartiy (STS) and information retrieval tasks (IR) tasks have been the two major avenues to record the progress of embedding models in the past few years. Under the emerging Retrieval-augmented Generation (RAG) paradigm, we envision the need to evaluate next-level language understanding abilities of embedding models, and take a conscious look at the reasoning abilities stored in them. Addressing this, we pose the question: Can retrievers solve reasoning problems? By transforming reasoning tasks into retrieval tasks, we find that without specifically trained for reasoning-level language understanding, current state-of-the-art retriever models may still be far from being competent for playing the role of assisting LLMs, especially in reasoning-intensive tasks. Moreover, albeit trained to be aware of instructions, instruction-aware IR models are often better off without instructions in inference time for reasoning tasks, posing an overlooked retriever-LLM behavioral gap for the research community to align. However, recent decoder-based embedding models show great promise in narrowing the gap, highlighting the pathway for embedding models to achieve reasoning-level language understanding. We also show that, although current off-the-shelf re-ranker models fail on these tasks, injecting reasoning abilities into them through fine-tuning still appears easier than doing so to bi-encoders, and we are able to achieve state-of-the-art performance across all tasks by fine-tuning a reranking model. We release Reasoning as Retrieval Benchmark (RAR-b), a holistic suite of tasks and settings to evaluate the reasoning abilities stored in retriever models. RAR-b is available at https://github.com/gowitheflow-1998/RAR-b.

As an important component of intelligent legal systems, legal case retrieval plays a critical role in ensuring judicial justice and fairness. However, the development of legal case retrieval technologies in the Chinese legal system is restricted by three problems in existing datasets: limited data size, narrow definitions of legal relevance, and naive candidate pooling strategies used in data sampling. To alleviate these issues, we introduce LeCaRDv2, a large-scale Legal Case Retrieval Dataset (version 2). It consists of 800 queries and 55,192 candidates extracted from 4.3 million criminal case documents. To the best of our knowledge, LeCaRDv2 is one of the largest Chinese legal case retrieval datasets, providing extensive coverage of criminal charges. Additionally, we enrich the existing relevance criteria by considering three key aspects: characterization, penalty, procedure. This comprehensive criteria enriches the dataset and may provides a more holistic perspective. Furthermore, we propose a two-level candidate set pooling strategy that effectively identify potential candidates for each query case. It's important to note that all cases in the dataset have been annotated by multiple legal experts specializing in criminal law. Their expertise ensures the accuracy and reliability of the annotations. We evaluate several state-of-the-art retrieval models at LeCaRDv2, demonstrating that there is still significant room for improvement in legal case retrieval. The details of LeCaRDv2 can be found at the anonymous website https://github.com/anonymous1113243/LeCaRDv2.

Task-oriented dialogue (TOD) systems are required to identify key information from conversations for the completion of given tasks. Such information is conventionally specified in terms of intents and slots contained in task-specific ontology or schemata. Since these schemata are designed by system developers, the naming convention for slots and intents is not uniform across tasks, and may not convey their semantics effectively. This can lead to models memorizing arbitrary patterns in data, resulting in suboptimal performance and generalization. In this paper, we propose that schemata should be modified by replacing names or notations entirely with natural language descriptions. We show that a language description-driven system exhibits better understanding of task specifications, higher performance on state tracking, improved data efficiency, and effective zero-shot transfer to unseen tasks. Following this paradigm, we present a simple yet effective Description-Driven Dialog State Tracking (D3ST) model, which relies purely on schema descriptions and an "index-picking" mechanism. We demonstrate the superiority in quality, data efficiency and robustness of our approach as measured on the MultiWOZ (Budzianowski et al.,2018), SGD (Rastogi et al., 2020), and the recent SGD-X (Lee et al., 2021) benchmarks.

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt.

Semantic search for candidate retrieval is an important yet neglected problem in retrieval-based Chatbots, which aims to select a bunch of candidate responses efficiently from a large pool. The existing bottleneck is to ensure the model architecture having two points: 1) rich interactions between a query and a response to produce query-relevant responses; 2) ability of separately projecting the query and the response into latent spaces to apply efficiently in semantic search during online inference. To tackle this problem, we propose a novel approach, called Multitask-based Semantic Search Neural Network (MSSNN) for candidate retrieval, which accomplishes query-response interactions through multi-tasks. The method employs a Seq2Seq modeling task to learn a good query encoder, and then performs a word prediction task to build response embeddings, finally conducts a simple matching model to form the dot-product scorer. Experimental studies have demonstrated the potential of the proposed approach.

Retrieval-augmented generation has gained significant attention due to its ability to integrate relevant external knowledge, enhancing the accuracy and reliability of the LLMs' responses. Most of the existing methods apply a dynamic multiple retrieval-generating process, to address multi-hop complex questions by decomposing them into sub-problems. However, these methods rely on an unidirectional forward reasoning paradigm, where errors from insufficient reasoning steps or inherent flaws in current retrieval systems are irreversible, potentially derailing the entire reasoning chain. For the first time, this work introduces Retroactive Retrieval-Augmented Generation (RetroRAG), a novel framework to build a retroactive reasoning paradigm. RetroRAG revises and updates the evidence, redirecting the reasoning chain to the correct direction. RetroRAG constructs an evidence-collation-discovery framework to search, generate, and refine credible evidence. It synthesizes inferential evidence related to the key entities in the question from the existing source knowledge and formulates search queries to uncover additional information. As new evidence is found, RetroRAG continually updates and organizes this information, enhancing its ability to locate further necessary evidence. Paired with an Answerer to generate and evaluate outputs, RetroRAG is capable of refining its reasoning process iteratively until a reliable answer is obtained. Empirical evaluations show that RetroRAG significantly outperforms existing methods.

In this paper, we propose KnowCoder, a Large Language Model (LLM) to conduct Universal Information Extraction (UIE) via code generation. KnowCoder aims to develop a kind of unified schema representation that LLMs can easily understand and an effective learning framework that encourages LLMs to follow schemas and extract structured knowledge accurately. To achieve these, KnowCoder introduces a code-style schema representation method to uniformly transform different schemas into Python classes, with which complex schema information, such as constraints among tasks in UIE, can be captured in an LLM-friendly manner. We further construct a code-style schema library covering over 30,000 types of knowledge, which is the largest one for UIE, to the best of our knowledge. To ease the learning process of LLMs, KnowCoder contains a two-phase learning framework that enhances its schema understanding ability via code pretraining and its schema following ability via instruction tuning. After code pretraining on around 1.5B automatically constructed data, KnowCoder already attains remarkable generalization ability and achieves relative improvements by 49.8% F1, compared to LLaMA2, under the few-shot setting. After instruction tuning, KnowCoder further exhibits strong generalization ability on unseen schemas and achieves up to 12.5% and 21.9%, compared to sota baselines, under the zero-shot setting and the low resource setting, respectively. Additionally, based on our unified schema representations, various human-annotated datasets can simultaneously be utilized to refine KnowCoder, which achieves significant improvements up to 7.5% under the supervised setting.

Knowledge-intensive language tasks require NLP systems to both provide the correct answer and retrieve supporting evidence for it in a given corpus. Autoregressive language models are emerging as the de-facto standard for generating answers, with newer and more powerful systems emerging at an astonishing pace. In this paper we argue that all this (and future) progress can be directly applied to the retrieval problem with minimal intervention to the models' architecture. Previous work has explored ways to partition the search space into hierarchical structures and retrieve documents by autoregressively generating their unique identifier. In this work we propose an alternative that doesn't force any structure in the search space: using all ngrams in a passage as its possible identifiers. This setup allows us to use an autoregressive model to generate and score distinctive ngrams, that are then mapped to full passages through an efficient data structure. Empirically, we show this not only outperforms prior autoregressive approaches but also leads to an average improvement of at least 10 points over more established retrieval solutions for passage-level retrieval on the KILT benchmark, establishing new state-of-the-art downstream performance on some datasets, while using a considerably lighter memory footprint than competing systems. Code and pre-trained models at https://github.com/facebookresearch/SEAL.

Learned sparse retrieval (LSR) is a family of first-stage retrieval methods that are trained to generate sparse lexical representations of queries and documents for use with an inverted index. Many LSR methods have been recently introduced, with Splade models achieving state-of-the-art performance on MSMarco. Despite similarities in their model architectures, many LSR methods show substantial differences in effectiveness and efficiency. Differences in the experimental setups and configurations used make it difficult to compare the methods and derive insights. In this work, we analyze existing LSR methods and identify key components to establish an LSR framework that unifies all LSR methods under the same perspective. We then reproduce all prominent methods using a common codebase and re-train them in the same environment, which allows us to quantify how components of the framework affect effectiveness and efficiency. We find that (1) including document term weighting is most important for a method's effectiveness, (2) including query weighting has a small positive impact, and (3) document expansion and query expansion have a cancellation effect. As a result, we show how removing query expansion from a state-of-the-art model can reduce latency significantly while maintaining effectiveness on MSMarco and TripClick benchmarks. Our code is publicly available at https://github.com/thongnt99/learned-sparse-retrieval

This paper presents the development and application of a Large Language Model Retrieval-Augmented Generation (LLM-RAG) system tailored for nanotechnology research. The system leverages the capabilities of a sophisticated language model to serve as an intelligent research assistant, enhancing the efficiency and comprehensiveness of literature reviews in the nanotechnology domain. Central to this LLM-RAG system is its advanced query backend retrieval mechanism, which integrates data from multiple reputable sources. The system retrieves relevant literature by utilizing Google Scholar's advanced search, and scraping open-access papers from Elsevier, Springer Nature, and ACS Publications. This multifaceted approach ensures a broad and diverse collection of up-to-date scholarly articles and papers. The proposed system demonstrates significant potential in aiding researchers by providing a streamlined, accurate, and exhaustive literature retrieval process, thereby accelerating research advancements in nanotechnology. The effectiveness of the LLM-RAG system is validated through rigorous testing, illustrating its capability to significantly reduce the time and effort required for comprehensive literature reviews, while maintaining high accuracy, query relevance and outperforming standard, publicly available LLMS.

In order to thrive in hostile and ever-changing natural environments, mammalian brains evolved to store large amounts of knowledge about the world and continually integrate new information while avoiding catastrophic forgetting. Despite the impressive accomplishments, large language models (LLMs), even with retrieval-augmented generation (RAG), still struggle to efficiently and effectively integrate a large amount of new experiences after pre-training. In this work, we introduce HippoRAG, a novel retrieval framework inspired by the hippocampal indexing theory of human long-term memory to enable deeper and more efficient knowledge integration over new experiences. HippoRAG synergistically orchestrates LLMs, knowledge graphs, and the Personalized PageRank algorithm to mimic the different roles of neocortex and hippocampus in human memory. We compare HippoRAG with existing RAG methods on multi-hop question answering and show that our method outperforms the state-of-the-art methods remarkably, by up to 20%. Single-step retrieval with HippoRAG achieves comparable or better performance than iterative retrieval like IRCoT while being 10-30 times cheaper and 6-13 times faster, and integrating HippoRAG into IRCoT brings further substantial gains. Finally, we show that our method can tackle new types of scenarios that are out of reach of existing methods. Code and data are available at https://github.com/OSU-NLP-Group/HippoRAG.

Graph retrieval-augmented generation (GraphRAG) has effectively enhanced large language models in complex reasoning by organizing fragmented knowledge into explicitly structured graphs. Prior efforts have been made to improve either graph construction or graph retrieval in isolation, yielding suboptimal performance, especially when domain shifts occur. In this paper, we propose a vertically unified agentic paradigm, Youtu-GraphRAG, to jointly connect the entire framework as an intricate integration. Specifically, (i) a seed graph schema is introduced to bound the automatic extraction agent with targeted entity types, relations and attribute types, also continuously expanded for scalability over unseen domains; (ii) To obtain higher-level knowledge upon the schema, we develop novel dually-perceived community detection, fusing structural topology with subgraph semantics for comprehensive knowledge organization. This naturally yields a hierarchical knowledge tree that supports both top-down filtering and bottom-up reasoning with community summaries; (iii) An agentic retriever is designed to interpret the same graph schema to transform complex queries into tractable and parallel sub-queries. It iteratively performs reflection for more advanced reasoning; (iv) To alleviate the knowledge leaking problem in pre-trained LLM, we propose a tailored anonymous dataset and a novel 'Anonymity Reversion' task that deeply measures the real performance of the GraphRAG frameworks. Extensive experiments across six challenging benchmarks demonstrate the robustness of Youtu-GraphRAG, remarkably moving the Pareto frontier with up to 90.71% saving of token costs and 16.62% higher accuracy over state-of-the-art baselines. The results indicate our adaptability, allowing seamless domain transfer with minimal intervention on schema.

Retrieval-Augmented Generation (RAG) systems represent a significant advancement over traditional Large Language Models (LLMs). RAG systems enhance their generation ability by incorporating external data retrieved through an Information Retrieval (IR) phase, overcoming the limitations of standard LLMs, which are restricted to their pre-trained knowledge and limited context window. Most research in this area has predominantly concentrated on the generative aspect of LLMs within RAG systems. Our study fills this gap by thoroughly and critically analyzing the influence of IR components on RAG systems. This paper analyzes which characteristics a retriever should possess for an effective RAG's prompt formulation, focusing on the type of documents that should be retrieved. We evaluate various elements, such as the relevance of the documents to the prompt, their position, and the number included in the context. Our findings reveal, among other insights, that including irrelevant documents can unexpectedly enhance performance by more than 30% in accuracy, contradicting our initial assumption of diminished quality. These results underscore the need for developing specialized strategies to integrate retrieval with language generation models, thereby laying the groundwork for future research in this field.

Retrieval-Augmented Generation (RAG) systems often struggle with imperfect retrieval, as traditional retrievers focus on lexical or semantic similarity rather than logical relevance. To address this, we propose HopRAG, a novel RAG framework that augments retrieval with logical reasoning through graph-structured knowledge exploration. During indexing, HopRAG constructs a passage graph, with text chunks as vertices and logical connections established via LLM-generated pseudo-queries as edges. During retrieval, it employs a retrieve-reason-prune mechanism: starting with lexically or semantically similar passages, the system explores multi-hop neighbors guided by pseudo-queries and LLM reasoning to identify truly relevant ones. Experiments on multiple multi-hop benchmarks demonstrate that HopRAG's retrieve-reason-prune mechanism can expand the retrieval scope based on logical connections and improve final answer quality.

The increasing number of academic papers poses significant challenges for researchers to efficiently acquire key details. While retrieval augmented generation (RAG) shows great promise in large language model (LLM) based automated question answering, previous works often isolate neural and symbolic retrieval despite their complementary strengths. Moreover, conventional single-view chunking neglects the rich structure and layout of PDFs, e.g., sections and tables. In this work, we propose NeuSym-RAG, a hybrid neural symbolic retrieval framework which combines both paradigms in an interactive process. By leveraging multi-view chunking and schema-based parsing, NeuSym-RAG organizes semi-structured PDF content into both the relational database and vectorstore, enabling LLM agents to iteratively gather context until sufficient to generate answers. Experiments on three full PDF-based QA datasets, including a self-annotated one AIRQA-REAL, show that NeuSym-RAG stably defeats both the vector-based RAG and various structured baselines, highlighting its capacity to unify both retrieval schemes and utilize multiple views. Code and data are publicly available at https://github.com/X-LANCE/NeuSym-RAG.

Retrieval-Augmented Generation (RAG) has emerged as a promising framework to mitigate hallucinations in Large Language Models (LLMs), yet its overall performance is dependent on the underlying retrieval system. In the finance domain, documents such as 10-K reports pose distinct challenges due to domain-specific vocabulary and multi-hierarchical tabular data. In this work, we introduce an efficient, end-to-end RAG pipeline that enhances retrieval for financial documents through a three-phase approach: pre-retrieval, retrieval, and post-retrieval. In the pre-retrieval phase, various query and corpus preprocessing techniques are employed to enrich input data. During the retrieval phase, we fine-tuned state-of-the-art (SOTA) embedding models with domain-specific knowledge and implemented a hybrid retrieval strategy that combines dense and sparse representations. Finally, the post-retrieval phase leverages Direct Preference Optimization (DPO) training and document selection methods to further refine the results. Evaluations on seven financial question answering datasets-FinDER, FinQABench, FinanceBench, TATQA, FinQA, ConvFinQA, and MultiHiertt-demonstrate substantial improvements in retrieval performance, leading to more accurate and contextually appropriate generation. These findings highlight the critical role of tailored retrieval techniques in advancing the effectiveness of RAG systems for financial applications. A fully replicable pipeline is available on GitHub: https://github.com/seohyunwoo-0407/GAR.

We investigate the exploitation of both lexical and neural relevance signals for ad-hoc passage retrieval. Our exploration involves a large-scale training dataset in which dense neural representations of MS-MARCO queries and passages are complemented and integrated with 253 hand-crafted lexical features extracted from the same corpus. Blending of the relevance signals from the two different groups of features is learned by a classical Learning-to-Rank (LTR) model based on a forest of decision trees. To evaluate our solution, we employ a pipelined architecture where a dense neural retriever serves as the first stage and performs a nearest-neighbor search over the neural representations of the documents. Our LTR model acts instead as the second stage that re-ranks the set of candidates retrieved by the first stage to enhance effectiveness. The results of reproducible experiments conducted with state-of-the-art dense retrievers on publicly available resources show that the proposed solution significantly enhances the end-to-end ranking performance while relatively minimally impacting efficiency. Specifically, we achieve a boost in nDCG@10 of up to 11% with an increase in average query latency of only 4.3%. This confirms the advantage of seamlessly combining two distinct families of signals that mutually contribute to retrieval effectiveness.

We introduce Trove, an easy-to-use open-source retrieval toolkit that simplifies research experiments without sacrificing flexibility or speed. For the first time, we introduce efficient data management features that load and process (filter, select, transform, and combine) retrieval datasets on the fly, with just a few lines of code. This gives users the flexibility to easily experiment with different dataset configurations without the need to compute and store multiple copies of large datasets. Trove is highly customizable: in addition to many built-in options, it allows users to freely modify existing components or replace them entirely with user-defined objects. It also provides a low-code and unified pipeline for evaluation and hard negative mining, which supports multi-node execution without any code changes. Trove's data management features reduce memory consumption by a factor of 2.6. Moreover, Trove's easy-to-use inference pipeline incurs no overhead, and inference times decrease linearly with the number of available nodes. Most importantly, we demonstrate how Trove simplifies retrieval experiments and allows for arbitrary customizations, thus facilitating exploratory research.

Recent advancements in function calling and tool use have significantly enhanced the capabilities of large language models (LLMs) by enabling them to interact with external information sources and execute complex tasks. However, the limited context window of LLMs presents challenges when a large number of tools are available, necessitating efficient methods to manage prompt length and maintain accuracy. Existing approaches, such as fine-tuning LLMs or leveraging their reasoning capabilities, either require frequent retraining or incur significant latency overhead. A more efficient solution involves training smaller models to retrieve the most relevant tools for a given query, although this requires high quality, domain-specific data. To address those challenges, we present a novel framework for generating synthetic data for tool retrieval applications and an efficient data-driven tool retrieval strategy using small encoder models. Empowered by LLMs, we create ToolBank, a new tool retrieval dataset that reflects real human user usages. For tool retrieval methodologies, we propose novel approaches: (1) Tool2Vec: usage-driven tool embedding generation for tool retrieval, (2) ToolRefiner: a staged retrieval method that iteratively improves the quality of retrieved tools, and (3) MLC: framing tool retrieval as a multi-label classification problem. With these new methods, we achieve improvements of up to 27.28 in Recall@K on the ToolBench dataset and 30.5 in Recall@K on ToolBank. Additionally, we present further experimental results to rigorously validate our methods. Our code is available at https://github.com/SqueezeAILab/Tool2Vec

Language models pretrained on large collections of tabular data have demonstrated their effectiveness in several downstream tasks. However, many of these models do not take into account the row/column permutation invariances, hierarchical structure, etc. that exist in tabular data. To alleviate these limitations, we propose HYTREL, a tabular language model, that captures the permutation invariances and three more structural properties of tabular data by using hypergraphs - where the table cells make up the nodes and the cells occurring jointly together in each row, column, and the entire table are used to form three different types of hyperedges. We show that HYTREL is maximally invariant under certain conditions for tabular data, i.e., two tables obtain the same representations via HYTREL iff the two tables are identical up to permutations. Our empirical results demonstrate that HYTREL consistently outperforms other competitive baselines on four downstream tasks with minimal pretraining, illustrating the advantages of incorporating the inductive biases associated with tabular data into the representations. Finally, our qualitative analyses showcase that HYTREL can assimilate the table structures to generate robust representations for the cells, rows, columns, and the entire table.

Retrieval-augmented Generation (RAG) has markedly enhanced the capabilities of Large Language Models (LLMs) in tackling knowledge-intensive tasks. The increasing demands of application scenarios have driven the evolution of RAG, leading to the integration of advanced retrievers, LLMs and other complementary technologies, which in turn has amplified the intricacy of RAG systems. However, the rapid advancements are outpacing the foundational RAG paradigm, with many methods struggling to be unified under the process of "retrieve-then-generate". In this context, this paper examines the limitations of the existing RAG paradigm and introduces the modular RAG framework. By decomposing complex RAG systems into independent modules and specialized operators, it facilitates a highly reconfigurable framework. Modular RAG transcends the traditional linear architecture, embracing a more advanced design that integrates routing, scheduling, and fusion mechanisms. Drawing on extensive research, this paper further identifies prevalent RAG patterns-linear, conditional, branching, and looping-and offers a comprehensive analysis of their respective implementation nuances. Modular RAG presents innovative opportunities for the conceptualization and deployment of RAG systems. Finally, the paper explores the potential emergence of new operators and paradigms, establishing a solid theoretical foundation and a practical roadmap for the continued evolution and practical deployment of RAG technologies.

Scientific paper retrieval, particularly framed as document-to-document retrieval, aims to identify relevant papers in response to a long-form query paper, rather than a short query string. Previous approaches to this task have focused on abstracts, embedding them into dense vectors as surrogates for full documents and calculating similarity across them, although abstracts provide only sparse and high-level summaries. To address this, we propose PRISM, a novel document-to-document retrieval method that introduces multiple, fine-grained representations for both the query and candidate papers. In particular, each query paper is decomposed into multiple aspect-specific views and individually embedded, which are then matched against candidate papers similarity segmented to consider their multifaceted dimensions. Moreover, we present SciFullBench, a novel benchmark in which the complete and segmented context of full papers for both queries and candidates is available. Then, experimental results show that PRISM improves performance by an average of 4.3% over existing retrieval baselines.

Diffusion models enable high-quality and diverse visual content synthesis. However, they struggle to generate rare or unseen concepts. To address this challenge, we explore the usage of Retrieval-Augmented Generation (RAG) with image generation models. We propose ImageRAG, a method that dynamically retrieves relevant images based on a given text prompt, and uses them as context to guide the generation process. Prior approaches that used retrieved images to improve generation, trained models specifically for retrieval-based generation. In contrast, ImageRAG leverages the capabilities of existing image conditioning models, and does not require RAG-specific training. Our approach is highly adaptable and can be applied across different model types, showing significant improvement in generating rare and fine-grained concepts using different base models. Our project page is available at: https://rotem-shalev.github.io/ImageRAG

Retrieval-augmented generation (RAG) based large language models (LLMs) are widely used in finance for their excellent performance on knowledge-intensive tasks. However, standardized documents (e.g., SEC filing) share similar formats such as repetitive boilerplate texts, and similar table structures. This similarity forces traditional RAG methods to misidentify near-duplicate text, leading to duplicate retrieval that undermines accuracy and completeness. To address these issues, we propose the Hierarchical Retrieval with Evidence Curation (HiREC) framework. Our approach first performs hierarchical retrieval to reduce confusion among similar texts. It first retrieve related documents and then selects the most relevant passages from the documents. The evidence curation process removes irrelevant passages. When necessary, it automatically generates complementary queries to collect missing information. To evaluate our approach, we construct and release a Large-scale Open-domain Financial (LOFin) question answering benchmark that includes 145,897 SEC documents and 1,595 question-answer pairs. Our code and data are available at https://github.com/deep-over/LOFin-bench-HiREC.

Listeners of long-form talk-audio content, such as podcast episodes, often find it challenging to understand the overall structure and locate relevant sections. A practical solution is to divide episodes into chapters--semantically coherent segments labeled with titles and timestamps. Since most episodes on our platform at Spotify currently lack creator-provided chapters, automating the creation of chapters is essential. Scaling the chapterization of podcast episodes presents unique challenges. First, episodes tend to be less structured than written texts, featuring spontaneous discussions with nuanced transitions. Second, the transcripts are usually lengthy, averaging about 16,000 tokens, which necessitates efficient processing that can preserve context. To address these challenges, we introduce PODTILE, a fine-tuned encoder-decoder transformer to segment conversational data. The model simultaneously generates chapter transitions and titles for the input transcript. To preserve context, each input text is augmented with global context, including the episode's title, description, and previous chapter titles. In our intrinsic evaluation, PODTILE achieved an 11% improvement in ROUGE score over the strongest baseline. Additionally, we provide insights into the practical benefits of auto-generated chapters for listeners navigating episode content. Our findings indicate that auto-generated chapters serve as a useful tool for engaging with less popular podcasts. Finally, we present empirical evidence that using chapter titles can enhance effectiveness of sparse retrieval in search tasks.

Despite the recent progress in long-context language models, it remains elusive how transformer-based models exhibit the capability to retrieve relevant information from arbitrary locations within the long context. This paper aims to address this question. Our systematic investigation across a wide spectrum of models reveals that a special type of attention heads are largely responsible for retrieving information, which we dub retrieval heads. We identify intriguing properties of retrieval heads:(1) universal: all the explored models with long-context capability have a set of retrieval heads; (2) sparse: only a small portion (less than 5\%) of the attention heads are retrieval. (3) intrinsic: retrieval heads already exist in models pretrained with short context. When extending the context length by continual pretraining, it is still the same set of heads that perform information retrieval. (4) dynamically activated: take Llama-2 7B for example, 12 retrieval heads always attend to the required information no matter how the context is changed. The rest of the retrieval heads are activated in different contexts. (5) causal: completely pruning retrieval heads leads to failure in retrieving relevant information and results in hallucination, while pruning random non-retrieval heads does not affect the model's retrieval ability. We further show that retrieval heads strongly influence chain-of-thought (CoT) reasoning, where the model needs to frequently refer back the question and previously-generated context. Conversely, tasks where the model directly generates the answer using its intrinsic knowledge are less impacted by masking out retrieval heads. These observations collectively explain which internal part of the model seeks information from the input tokens. We believe our insights will foster future research on reducing hallucination, improving reasoning, and compressing the KV cache.

Many methods have been proposed for removing batch effects and aligning single-cell RNA (scRNA) datasets. However, performance is typically evaluated based on multiple parameters and few datasets, creating challenges in assessing which method is best for aligning data at scale. Here, we introduce the K-Neighbors Intersection (KNI) score, a single score that both penalizes batch effects and measures accuracy at cross-dataset cell-type label prediction alongside carefully curated small (scMARK) and large (scREF) benchmarks comprising 11 and 46 human scRNA studies respectively, where we have standardized author labels. Using the KNI score, we evaluate and optimize approaches for cross-dataset single-cell RNA integration. We introduce Batch Adversarial single-cell Variational Inference (BA-scVI), as a new variant of scVI that uses adversarial training to penalize batch-effects in the encoder and decoder, and show this approach outperforms other methods. In the resulting aligned space, we find that the granularity of cell-type groupings is conserved, supporting the notion that whole-organism cell-type maps can be created by a single model without loss of information.

This paper presents a comprehensive study of Retrieval-Augmented Generation (RAG), tracing its evolution from foundational concepts to the current state of the art. RAG combines retrieval mechanisms with generative language models to enhance the accuracy of outputs, addressing key limitations of LLMs. The study explores the basic architecture of RAG, focusing on how retrieval and generation are integrated to handle knowledge-intensive tasks. A detailed review of the significant technological advancements in RAG is provided, including key innovations in retrieval-augmented language models and applications across various domains such as question-answering, summarization, and knowledge-based tasks. Recent research breakthroughs are discussed, highlighting novel methods for improving retrieval efficiency. Furthermore, the paper examines ongoing challenges such as scalability, bias, and ethical concerns in deployment. Future research directions are proposed, focusing on improving the robustness of RAG models, expanding the scope of application of RAG models, and addressing societal implications. This survey aims to serve as a foundational resource for researchers and practitioners in understanding the potential of RAG and its trajectory in natural language processing.

Advancements in Large Language Models (LLMs) have extended their input context length, yet they still struggle with retrieval and reasoning in long-context inputs. Existing methods propose to utilize the prompt strategy and retrieval head to alleviate this limitation. However, they still face challenges in balancing retrieval precision and recall, impacting their efficacy in answering questions. To address this, we introduce CAFE, a two-stage coarse-to-fine method to enhance multi-document question-answering capacities. By gradually eliminating the negative impacts of background and distracting documents, CAFE makes the responses more reliant on the evidence documents. Initially, a coarse-grained filtering method leverages retrieval heads to identify and rank relevant documents. Then, a fine-grained steering method guides attention to the most relevant content. Experiments across benchmarks show CAFE outperforms baselines, achieving up to 22.1% and 13.7% SubEM improvement over SFT and RAG methods on the Mistral model, respectively.

When a language model is trained to predict natural language sequences, its prediction at each moment depends on a representation of prior context. What kind of information about the prior context can language models retrieve? We tested whether language models could retrieve the exact words that occurred previously in a text. In our paradigm, language models (transformers and an LSTM) processed English text in which a list of nouns occurred twice. We operationalized retrieval as the reduction in surprisal from the first to the second list. We found that the transformers retrieved both the identity and ordering of nouns from the first list. Further, the transformers' retrieval was markedly enhanced when they were trained on a larger corpus and with greater model depth. Lastly, their ability to index prior tokens was dependent on learned attention patterns. In contrast, the LSTM exhibited less precise retrieval, which was limited to list-initial tokens and to short intervening texts. The LSTM's retrieval was not sensitive to the order of nouns and it improved when the list was semantically coherent. We conclude that transformers implemented something akin to a working memory system that could flexibly retrieve individual token representations across arbitrary delays; conversely, the LSTM maintained a coarser and more rapidly-decaying semantic gist of prior tokens, weighted toward the earliest items.

Document retrieval is an important task for search and Retrieval-Augmented Generation (RAG) applications. Large Language Models (LLMs) have contributed to improving the accuracy of text-based document retrieval. However, documents with complex layout and visual elements like tables, charts and infographics are not perfectly represented in textual format. Recently, image-based document retrieval pipelines have become popular, which use visual large language models (VLMs) to retrieve relevant page images given a query. Current evaluation benchmarks on visual document retrieval are limited, as they primarily focus only English language, rely on synthetically generated questions and offer a small corpus size. Therefore, we introduce MIRACL-VISION, a multilingual visual document retrieval evaluation benchmark. MIRACL-VISION covers 18 languages, and is an extension of the MIRACL dataset, a popular benchmark to evaluate text-based multilingual retrieval pipelines. MIRACL was built using a human-intensive annotation process to generate high-quality questions. In order to reduce MIRACL-VISION corpus size to make evaluation more compute friendly while keeping the datasets challenging, we have designed a method for eliminating the "easy" negatives from the corpus. We conducted extensive experiments comparing MIRACL-VISION with other benchmarks, using popular public text and image models. We observe a gap in state-of-the-art VLM-based embedding models on multilingual capabilities, with up to 59.7% lower retrieval accuracy than a text-based retrieval models. Even for the English language, the visual models retrieval accuracy is 12.1% lower compared to text-based models. MIRACL-VISION is a challenging, representative, multilingual evaluation benchmark for visual retrieval pipelines and will help the community build robust models for document retrieval.

High-quality medical systematic reviews require comprehensive literature searches to ensure the recommendations and outcomes are sufficiently reliable. Indeed, searching for relevant medical literature is a key phase in constructing systematic reviews and often involves domain (medical researchers) and search (information specialists) experts in developing the search queries. Queries in this context are highly complex, based on Boolean logic, include free-text terms and index terms from standardised terminologies (e.g., MeSH), and are difficult and time-consuming to build. The use of MeSH terms, in particular, has been shown to improve the quality of the search results. However, identifying the correct MeSH terms to include in a query is difficult: information experts are often unfamiliar with the MeSH database and unsure about the appropriateness of MeSH terms for a query. Naturally, the full value of the MeSH terminology is often not fully exploited. This paper investigates methods to suggest MeSH terms based on an initial Boolean query that includes only free-text terms. These methods promise to automatically identify highly effective MeSH terms for inclusion in a systematic review query. Our study contributes an empirical evaluation of several MeSH term suggestion methods. We perform an extensive analysis of the retrieval, ranking, and refinement of MeSH term suggestions for each method and how these suggestions impact the effectiveness of Boolean queries.

In text-to-SQL task, seq-to-seq models often lead to sub-optimal performance due to limitations in their architecture. In this paper, we present a simple yet effective approach that adapts transformer-based seq-to-seq model to robust text-to-SQL generation. Instead of inducing constraint to decoder or reformat the task as slot-filling, we propose to train seq-to-seq model with Schema aware Denoising (SeaD), which consists of two denoising objectives that train model to either recover input or predict output from two novel erosion and shuffle noises. These denoising objectives acts as the auxiliary tasks for better modeling the structural data in S2S generation. In addition, we improve and propose a clause-sensitive execution guided (EG) decoding strategy to overcome the limitation of EG decoding for generative model. The experiments show that the proposed method improves the performance of seq-to-seq model in both schema linking and grammar correctness and establishes new state-of-the-art on WikiSQL benchmark. The results indicate that the capacity of vanilla seq-to-seq architecture for text-to-SQL may have been under-estimated.

Instance segmentation is critical in biomedical imaging to accurately distinguish individual objects like cells, which often overlap and vary in size. Recent query-based methods, where object queries guide segmentation, have shown strong performance. While U-Net has been a go-to architecture in medical image segmentation, its potential in query-based approaches remains largely unexplored. In this work, we present IAUNet, a novel query-based U-Net architecture. The core design features a full U-Net architecture, enhanced by a novel lightweight convolutional Pixel decoder, making the model more efficient and reducing the number of parameters. Additionally, we propose a Transformer decoder that refines object-specific features across multiple scales. Finally, we introduce the 2025 Revvity Full Cell Segmentation Dataset, a unique resource with detailed annotations of overlapping cell cytoplasm in brightfield images, setting a new benchmark for biomedical instance segmentation. Experiments on multiple public datasets and our own show that IAUNet outperforms most state-of-the-art fully convolutional, transformer-based, and query-based models and cell segmentation-specific models, setting a strong baseline for cell instance segmentation tasks. Code is available at https://github.com/SlavkoPrytula/IAUNet

Medical imaging analysis plays a critical role in the diagnosis and treatment of various medical conditions. This paper focuses on chest X-ray images and their corresponding radiological reports. It presents a new model that learns a joint X-ray image & report representation. The model is based on a novel alignment scheme between the visual data and the text, which takes into account both local and global information. Furthermore, the model integrates domain-specific information of two types -- lateral images and the consistent visual structure of chest images. Our representation is shown to benefit three types of retrieval tasks: text-image retrieval, class-based retrieval, and phrase-grounding.

Metadata plays a critical role in indexing, documenting, and analyzing scientific literature, yet extracting it accurately and efficiently remains a challenging task. Traditional approaches often rely on rule-based or task-specific models, which struggle to generalize across domains and schema variations. In this paper, we present MeXtract, a family of lightweight language models designed for metadata extraction from scientific papers. The models, ranging from 0.5B to 3B parameters, are built by fine-tuning Qwen 2.5 counterparts. In their size family, MeXtract achieves state-of-the-art performance on metadata extraction on the MOLE benchmark. To further support evaluation, we extend the MOLE benchmark to incorporate model-specific metadata, providing an out-of-domain challenging subset. Our experiments show that fine-tuning on a given schema not only yields high accuracy but also transfers effectively to unseen schemas, demonstrating the robustness and adaptability of our approach. We release all the code, datasets, and models openly for the research community.

Recent advancements in tool-equipped Agents (LLMs) have enabled complex tasks like secure database interactions and multi-agent code development. However, scaling tool capacity beyond agent reasoning or model limits remains a challenge. In this paper, we address these challenges by introducing Toolshed Knowledge Bases, a tool knowledge base (vector database) designed to store enhanced tool representations and optimize tool selection for large-scale tool-equipped Agents. Additionally, we propose Advanced RAG-Tool Fusion, a novel ensemble of tool-applied advanced retrieval-augmented generation (RAG) techniques across the pre-retrieval, intra-retrieval, and post-retrieval phases, without requiring model fine-tuning. During pre-retrieval, tool documents are enhanced with key information and stored in the Toolshed Knowledge Base. Intra-retrieval focuses on query planning and transformation to increase retrieval accuracy. Post-retrieval refines the retrieved tool documents and enables self-reflection. Furthermore, by varying both the total number of tools (tool-M) an Agent has access to and the tool selection threshold (top-k), we address trade-offs between retrieval accuracy, agent performance, and token cost. Our approach achieves 46%, 56%, and 47% absolute improvements on the ToolE single-tool, ToolE multi-tool and Seal-Tools benchmark datasets, respectively (Recall@5).

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

Extracting semantic representations from mobile user interfaces (UI) and using the representations for designers' decision-making processes have shown the potential to be effective computational design support tools. Current approaches rely on machine learning models trained on small-sized mobile UI datasets to extract semantic vectors and use screenshot-to-screenshot comparison to retrieve similar-looking UIs given query screenshots. However, the usability of these methods is limited because they are often not open-sourced and have complex training pipelines for practitioners to follow, and are unable to perform screenshot set-to-set (i.e., app-to-app) retrieval. To this end, we (1) employ visual models trained with large web-scale images and test whether they could extract a UI representation in a zero-shot way and outperform existing specialized models, and (2) use mathematically founded methods to enable app-to-app retrieval and design consistency analysis. Our experiments show that our methods not only improve upon previous retrieval models but also enable multiple new applications.

With the advent of Large Language Models (LLMs), the potential of Retrieval Augmented Generation (RAG) techniques have garnered considerable research attention. Numerous novel algorithms and models have been introduced to enhance various aspects of RAG systems. However, the absence of a standardized framework for implementation, coupled with the inherently intricate RAG process, makes it challenging and time-consuming for researchers to compare and evaluate these approaches in a consistent environment. Existing RAG toolkits like LangChain and LlamaIndex, while available, are often heavy and unwieldy, failing to meet the personalized needs of researchers. In response to this challenge, we propose FlashRAG, an efficient and modular open-source toolkit designed to assist researchers in reproducing existing RAG methods and in developing their own RAG algorithms within a unified framework. Our toolkit implements 12 advanced RAG methods and has gathered and organized 32 benchmark datasets. Our toolkit has various features, including customizable modular framework, rich collection of pre-implemented RAG works, comprehensive datasets, efficient auxiliary pre-processing scripts, and extensive and standard evaluation metrics. Our toolkit and resources are available at https://github.com/RUC-NLPIR/FlashRAG.

Spatial Transcriptomics (ST) technologies provide biologists with rich insights into single-cell biology by preserving spatial context of cells. Building foundational models for ST can significantly enhance the analysis of vast and complex data sources, unlocking new perspectives on the intricacies of biological tissues. However, modeling ST data is inherently challenging due to the need to extract multi-scale information from tissue slices containing vast numbers of cells. This process requires integrating macro-scale tissue morphology, micro-scale cellular microenvironment, and gene-scale gene expression profile. To address this challenge, we propose SToFM, a multi-scale Spatial Transcriptomics Foundation Model. SToFM first performs multi-scale information extraction on each ST slice, to construct a set of ST sub-slices that aggregate macro-, micro- and gene-scale information. Then an SE(2) Transformer is used to obtain high-quality cell representations from the sub-slices. Additionally, we construct SToCorpus-88M, the largest high-resolution spatial transcriptomics corpus for pretraining. SToFM achieves outstanding performance on a variety of downstream tasks, such as tissue region semantic segmentation and cell type annotation, demonstrating its comprehensive understanding of ST data through capturing and integrating multi-scale information.

Large-scale language models (LLMs) have achieved remarkable success across various language tasks but suffer from hallucinations and temporal misalignment. To mitigate these shortcomings, Retrieval-augmented generation (RAG) has been utilized to provide external knowledge to facilitate the answer generation. However, applying such models to the medical domain faces several challenges due to the lack of domain-specific knowledge and the intricacy of real-world scenarios. In this study, we explore LLMs with RAG framework for knowledge-intensive tasks in the medical field. To evaluate the capabilities of LLMs, we introduce MedicineQA, a multi-round dialogue benchmark that simulates the real-world medication consultation scenario and requires LLMs to answer with retrieved evidence from the medicine database. MedicineQA contains 300 multi-round question-answering pairs, each embedded within a detailed dialogue history, highlighting the challenge posed by this knowledge-intensive task to current LLMs. We further propose a new Distill-Retrieve-Read framework instead of the previous Retrieve-then-Read. Specifically, the distillation and retrieval process utilizes a tool calling mechanism to formulate search queries that emulate the keyword-based inquiries used by search engines. With experimental results, we show that our framework brings notable performance improvements and surpasses the previous counterparts in the evidence retrieval process in terms of evidence retrieval accuracy. This advancement sheds light on applying RAG to the medical domain.

The exponential growth of scientific literature has made it increasingly difficult for researchers to keep up with the literature. In an attempt to alleviate this problem, we propose CASPER, a sparse retrieval model for scientific search that utilizes tokens and keyphrases as representation units (i.e. dimensions in the sparse embedding space), enabling it to represent queries and documents with research concepts and match them at both granular and conceptual levels. To overcome the lack of suitable training data, we propose mining training data by leveraging scholarly references (i.e. signals that capture how research concepts of papers are expressed in different settings), including titles, citation contexts, author-assigned keyphrases, and co-citations. CASPER outperforms strong dense and sparse retrieval baselines on eight scientific retrieval benchmarks. Moreover, we demonstrate that through simple post-processing, CASPER can be effectively used for the keyphrase generation tasks, achieving competitive performance with the established CopyRNN while producing more diverse keyphrases and being nearly four times faster.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

Recent developments in representational learning for information retrieval can be organized in a conceptual framework that establishes two pairs of contrasts: sparse vs. dense representations and unsupervised vs. learned representations. Sparse learned representations can further be decomposed into expansion and term weighting components. This framework allows us to understand the relationship between recently proposed techniques such as DPR, ANCE, DeepCT, DeepImpact, and COIL, and furthermore, gaps revealed by our analysis point to "low hanging fruit" in terms of techniques that have yet to be explored. We present a novel technique dubbed "uniCOIL", a simple extension of COIL that achieves to our knowledge the current state-of-the-art in sparse retrieval on the popular MS MARCO passage ranking dataset. Our implementation using the Anserini IR toolkit is built on the Lucene search library and thus fully compatible with standard inverted indexes.

A widely used strategy to discover and understand language model mechanisms is circuit analysis. A circuit is a minimal subgraph of a model's computation graph that executes a specific task. We identify a gap in existing circuit discovery methods: they assume circuits are position-invariant, treating model components as equally relevant across input positions. This limits their ability to capture cross-positional interactions or mechanisms that vary across positions. To address this gap, we propose two improvements to incorporate positionality into circuits, even on tasks containing variable-length examples. First, we extend edge attribution patching, a gradient-based method for circuit discovery, to differentiate between token positions. Second, we introduce the concept of a dataset schema, which defines token spans with similar semantics across examples, enabling position-aware circuit discovery in datasets with variable length examples. We additionally develop an automated pipeline for schema generation and application using large language models. Our approach enables fully automated discovery of position-sensitive circuits, yielding better trade-offs between circuit size and faithfulness compared to prior work.

Semantic retrieval is crucial for modern applications yet remains underexplored in current research. Existing datasets are limited to single languages, single images, or singular retrieval conditions, often failing to fully exploit the expressive capacity of visual information as evidenced by maintained performance when images are replaced with captions. However, practical retrieval scenarios frequently involve interleaved multi-condition queries with multiple images. Hence, this paper introduces MERIT, the first multilingual dataset for interleaved multi-condition semantic retrieval, comprising 320,000 queries with 135,000 products in 5 languages, covering 7 distinct product categories. Extensive experiments on MERIT identify existing models's limitation: focusing solely on global semantic information while neglecting specific conditional elements in queries. Consequently, we propose Coral, a novel fine-tuning framework that adapts pre-trained MLLMs by integrating embedding reconstruction to preserve fine-grained conditional elements and contrastive learning to extract comprehensive global semantics. Experiments demonstrate that Coral achieves a 45.9% performance improvement over conventional approaches on MERIT, with strong generalization capabilities validated across 8 established retrieval benchmarks. Collectively, our contributions - a novel dataset, identification of critical limitations in existing approaches, and an innovative fine-tuning framework - establish a foundation for future research in interleaved multi-condition semantic retrieval.

With the increasing adoption of Large Language Models (LLMs) and Vision-Language Models (VLMs), rich document analysis technologies for applications like Retrieval-Augmented Generation (RAG) and visual RAG are gaining significant attention. Recent research indicates that using VLMs can achieve better RAG performance, but processing rich documents still remains a challenge since a single page contains large amounts of information. In this paper, we present SCAN (SemantiC Document Layout ANalysis), a novel approach enhancing both textual and visual Retrieval-Augmented Generation (RAG) systems working with visually rich documents. It is a VLM-friendly approach that identifies document components with appropriate semantic granularity, balancing context preservation with processing efficiency. SCAN uses a coarse-grained semantic approach that divides documents into coherent regions covering continuous components. We trained the SCAN model by fine-tuning object detection models with sophisticated annotation datasets. Our experimental results across English and Japanese datasets demonstrate that applying SCAN improves end-to-end textual RAG performance by up to 9.0\% and visual RAG performance by up to 6.4\%, outperforming conventional approaches and even commercial document processing solutions.

We present SymbioticRAG, a novel framework that fundamentally reimagines Retrieval-Augmented Generation~(RAG) systems by establishing a bidirectional learning relationship between humans and machines. Our approach addresses two critical challenges in current RAG systems: the inherently human-centered nature of relevance determination and users' progression from "unconscious incompetence" in query formulation. SymbioticRAG introduces a two-tier solution where Level 1 enables direct human curation of retrieved content through interactive source document exploration, while Level 2 aims to build personalized retrieval models based on captured user interactions. We implement Level 1 through three key components: (1)~a comprehensive document processing pipeline with specialized models for layout detection, OCR, and extraction of tables, formulas, and figures; (2)~an extensible retriever module supporting multiple retrieval strategies; and (3)~an interactive interface that facilitates both user engagement and interaction data logging. We experiment Level 2 implementation via a retriever strategy incorporated LLM summarized user intention from user interaction logs. To maintain high-quality data preparation, we develop a human-on-the-loop validation interface that improves pipeline output while advancing research in specialized extraction tasks. Evaluation across three scenarios (literature review, geological exploration, and education) demonstrates significant improvements in retrieval relevance and user satisfaction compared to traditional RAG approaches. To facilitate broader research and further advancement of SymbioticRAG Level 2 implementation, we will make our system openly accessible to the research community.

Large language models (LLMs) have become a disruptive force in the industry, introducing unprecedented capabilities in natural language processing, logical reasoning and so on. However, the challenges of knowledge updates and hallucination issues have limited the application of LLMs in medical scenarios, where retrieval-augmented generation (RAG) can offer significant assistance. Nevertheless, existing retrieve-then-read approaches generally digest the retrieved documents, without considering the timeliness, authoritativeness and commonality of retrieval. We argue that these approaches can be suboptimal, especially in real-world applications where information from different sources might conflict with each other and even information from the same source in different time scale might be different, and totally relying on this would deteriorate the performance of RAG approaches. We propose PolyRAG that carefully incorporate judges from different perspectives and finally integrate the polyviews for retrieval augmented generation in medical applications. Due to the scarcity of real-world benchmarks for evaluation, to bridge the gap we propose PolyEVAL, a benchmark consists of queries and documents collected from real-world medical scenarios (including medical policy, hospital & doctor inquiry and healthcare) with multiple tagging (e.g., timeliness, authoritativeness) on them. Extensive experiments and analysis on PolyEVAL have demonstrated the superiority of PolyRAG.