Daily Papers

Multi-subject fMRI studies are challenging due to the high variability of both brain anatomy and functional brain topographies across participants. An effective way of aggregating multi-subject fMRI data is to extract a shared representation that filters out unwanted variability among subjects. Some recent work has implemented probabilistic models to extract a shared representation in task fMRI. In the present work, we improve upon these models by incorporating temporal information in the common latent structures. We introduce a new model, Shared Gaussian Process Factor Analysis (S-GPFA), that discovers shared latent trajectories and subject-specific functional topographies, while modelling temporal correlation in fMRI data. We demonstrate the efficacy of our model in revealing ground truth latent structures using simulated data, and replicate experimental performance of time-segment matching and inter-subject similarity on the publicly available Raider and Sherlock datasets. We further test the utility of our model by analyzing its learned model parameters in the large multi-site SPINS dataset, on a social cognition task from participants with and without schizophrenia.

It is commonplace to encounter heterogeneous or nonstationary data, of which the underlying generating process changes across domains or over time. Such a distribution shift feature presents both challenges and opportunities for causal discovery. In this paper, we develop a framework for causal discovery from such data, called Constraint-based causal Discovery from heterogeneous/NOnstationary Data (CD-NOD), to find causal skeleton and directions and estimate the properties of mechanism changes. First, we propose an enhanced constraint-based procedure to detect variables whose local mechanisms change and recover the skeleton of the causal structure over observed variables. Second, we present a method to determine causal orientations by making use of independent changes in the data distribution implied by the underlying causal model, benefiting from information carried by changing distributions. After learning the causal structure, next, we investigate how to efficiently estimate the "driving force" of the nonstationarity of a causal mechanism. That is, we aim to extract from data a low-dimensional representation of changes. The proposed methods are nonparametric, with no hard restrictions on data distributions and causal mechanisms, and do not rely on window segmentation. Furthermore, we find that data heterogeneity benefits causal structure identification even with particular types of confounders. Finally, we show the connection between heterogeneity/nonstationarity and soft intervention in causal discovery. Experimental results on various synthetic and real-world data sets (task-fMRI and stock market data) are presented to demonstrate the efficacy of the proposed methods.

Due to the lack of paired samples and the low signal-to-noise ratio of functional MRI (fMRI) signals, reconstructing perceived natural images or decoding their semantic contents from fMRI data are challenging tasks. In this work, we propose, for the first time, a task-agnostic fMRI-based brain decoding model, BrainCLIP, which leverages CLIP's cross-modal generalization ability to bridge the modality gap between brain activity, image, and text. Our experiments demonstrate that CLIP can act as a pivot for generic brain decoding tasks, including zero-shot visual categories decoding, fMRI-image/text matching, and fMRI-to-image generation. Specifically, BrainCLIP aims to train a mapping network that transforms fMRI patterns into a well-aligned CLIP embedding space by combining visual and textual supervision. Our experiments show that this combination can boost the decoding model's performance on certain tasks like fMRI-text matching and fMRI-to-image generation. On the zero-shot visual category decoding task, BrainCLIP achieves significantly better performance than BraVL, a recently proposed multi-modal method specifically designed for this task. BrainCLIP can also reconstruct visual stimuli with high semantic fidelity and establishes a new state-of-the-art for fMRI-based natural image reconstruction in terms of high-level semantic features.

Reconstructing 3D visuals from functional Magnetic Resonance Imaging (fMRI) data, introduced as Recon3DMind in our conference work, is of significant interest to both cognitive neuroscience and computer vision. To advance this task, we present the fMRI-3D dataset, which includes data from 15 participants and showcases a total of 4768 3D objects. The dataset comprises two components: fMRI-Shape, previously introduced and accessible at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Shape, and fMRI-Objaverse, proposed in this paper and available at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Objaverse. fMRI-Objaverse includes data from 5 subjects, 4 of whom are also part of the Core set in fMRI-Shape, with each subject viewing 3142 3D objects across 117 categories, all accompanied by text captions. This significantly enhances the diversity and potential applications of the dataset. Additionally, we propose MinD-3D, a novel framework designed to decode 3D visual information from fMRI signals. The framework first extracts and aggregates features from fMRI data using a neuro-fusion encoder, then employs a feature-bridge diffusion model to generate visual features, and finally reconstructs the 3D object using a generative transformer decoder. We establish new benchmarks by designing metrics at both semantic and structural levels to evaluate model performance. Furthermore, we assess our model's effectiveness in an Out-of-Distribution setting and analyze the attribution of the extracted features and the visual ROIs in fMRI signals. Our experiments demonstrate that MinD-3D not only reconstructs 3D objects with high semantic and spatial accuracy but also deepens our understanding of how human brain processes 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

Functional magnetic resonance imaging (fMRI) is an indispensable tool in modern neuroscience, providing a non-invasive window into whole-brain dynamics at millimeter-scale spatial resolution. However, fMRI is constrained by issues such as high operation costs and immobility. With the rapid advancements in cross-modality synthesis and brain decoding, the use of deep neural networks has emerged as a promising solution for inferring whole-brain, high-resolution fMRI features directly from electroencephalography (EEG), a more widely accessible and portable neuroimaging modality. Nonetheless, the complex projection from neural activity to fMRI hemodynamic responses and the spatial ambiguity of EEG pose substantial challenges both in modeling and interpretability. Relatively few studies to date have developed approaches for EEG-fMRI translation, and although they have made significant strides, the inference of fMRI signals in a given study has been limited to a small set of brain areas and to a single condition (i.e., either resting-state or a specific task). The capability to predict fMRI signals in other brain areas, as well as to generalize across conditions, remain critical gaps in the field. To tackle these challenges, we introduce a novel and generalizable framework: NeuroBOLT, i.e., Neuro-to-BOLD Transformer, which leverages multi-dimensional representation learning from temporal, spatial, and spectral domains to translate raw EEG data to the corresponding fMRI activity signals across the brain. Our experiments demonstrate that NeuroBOLT effectively reconstructs unseen resting-state fMRI signals from primary sensory, high-level cognitive areas, and deep subcortical brain regions, achieving state-of-the-art accuracy with the potential to generalize across varying conditions and sites, which significantly advances the integration of these two modalities.

In this paper, we introduce Recon3DMind, an innovative task aimed at reconstructing 3D visuals from Functional Magnetic Resonance Imaging (fMRI) signals, marking a significant advancement in the fields of cognitive neuroscience and computer vision. To support this pioneering task, we present the fMRI-Shape dataset, which includes data from 14 participants and features 360-degree videos of 3D objects to enable comprehensive fMRI signal capture across various settings, thereby laying a foundation for future research. Furthermore, we propose MinD-3D, a novel and effective three-stage framework specifically designed to decode the brain's 3D visual information from fMRI signals, demonstrating the feasibility of this challenging task. The framework begins by extracting and aggregating features from fMRI frames through a neuro-fusion encoder, subsequently employs a feature bridge diffusion model to generate visual features, and ultimately recovers the 3D object via a generative transformer decoder. We assess the performance of MinD-3D using a suite of semantic and structural metrics and analyze the correlation between the features extracted by our model and the visual regions of interest (ROIs) in fMRI signals. Our findings indicate that MinD-3D not only reconstructs 3D objects with high semantic relevance and spatial similarity but also significantly enhances our understanding of the human brain's capabilities in processing 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.