Decoding Visual Experience and Mapping Semantics through Whole-Brain Analysis Using fMRI Foundation Models

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

SOE: SO(3)-Equivariant 3D MRI Encoding

Representation learning has become increasingly important, especially as powerful models have shifted towards learning latent representations before fine-tuning for downstream tasks. This approach is particularly valuable in leveraging the structural information within brain anatomy. However, a common limitation of recent models developed for MRIs is their tendency to ignore or remove geometric information, such as translation and rotation, thereby creating invariance with respect to geometric operations. We contend that incorporating knowledge about these geometric transformations into the model can significantly enhance its ability to learn more detailed anatomical information within brain structures. As a result, we propose a novel method for encoding 3D MRIs that enforces equivariance with respect to all rotations in 3D space, in other words, SO(3)-equivariance (SOE). By explicitly modeling this geometric equivariance in the representation space, we ensure that any rotational operation applied to the input image space is also reflected in the embedding representation space. This approach requires moving beyond traditional representation learning methods, as we need a representation vector space that allows for the application of the same SO(3) operation in that space. To facilitate this, we leverage the concept of vector neurons. The representation space formed by our method captures the brain's structural and anatomical information more effectively. We evaluate SOE pretrained on the structural MRIs of two public data sets with respect to the downstream task of predicting age and diagnosing Alzheimer's Disease from T1-weighted brain scans of the ADNI data set. We demonstrate that our approach not only outperforms other methods but is also robust against various degrees of rotation along different axes. The code is available at https://github.com/shizhehe/SOE-representation-learning.

GAMMA-PD: Graph-based Analysis of Multi-Modal Motor Impairment Assessments in Parkinson's Disease

The rapid advancement of medical technology has led to an exponential increase in multi-modal medical data, including imaging, genomics, and electronic health records (EHRs). Graph neural networks (GNNs) have been widely used to represent this data due to their prominent performance in capturing pairwise relationships. However, the heterogeneity and complexity of multi-modal medical data still pose significant challenges for standard GNNs, which struggle with learning higher-order, non-pairwise relationships. This paper proposes GAMMA-PD (Graph-based Analysis of Multi-modal Motor Impairment Assessments in Parkinson's Disease), a novel heterogeneous hypergraph fusion framework for multi-modal clinical data analysis. GAMMA-PD integrates imaging and non-imaging data into a "hypernetwork" (patient population graph) by preserving higher-order information and similarity between patient profiles and symptom subtypes. We also design a feature-based attention-weighted mechanism to interpret feature-level contributions towards downstream decision tasks. We evaluate our approach with clinical data from the Parkinson's Progression Markers Initiative (PPMI) and a private dataset. We demonstrate gains in predicting motor impairment symptoms in Parkinson's disease. Our end-to-end framework also learns associations between subsets of patient characteristics to generate clinically relevant explanations for disease and symptom profiles. The source code is available at https://github.com/favour-nerrise/GAMMA-PD.

Brain-Cognition Fingerprinting via Graph-GCCA with Contrastive Learning

Many longitudinal neuroimaging studies aim to improve the understanding of brain aging and diseases by studying the dynamic interactions between brain function and cognition. Doing so requires accurate encoding of their multidimensional relationship while accounting for individual variability over time. For this purpose, we propose an unsupervised learning model (called \underline{\textbf{Co}}ntrastive Learning-based \underline{\textbf{Gra}}ph Generalized \underline{\textbf{Ca}}nonical Correlation Analysis (CoGraCa)) that encodes their relationship via Graph Attention Networks and generalized Canonical Correlational Analysis. To create brain-cognition fingerprints reflecting unique neural and cognitive phenotype of each person, the model also relies on individualized and multimodal contrastive learning. We apply CoGraCa to longitudinal dataset of healthy individuals consisting of resting-state functional MRI and cognitive measures acquired at multiple visits for each participant. The generated fingerprints effectively capture significant individual differences and outperform current single-modal and CCA-based multimodal models in identifying sex and age. More importantly, our encoding provides interpretable interactions between those two modalities.

Latent 3D Brain MRI Counterfactual

The number of samples in structural brain MRI studies is often too small to properly train deep learning models. Generative models show promise in addressing this issue by effectively learning the data distribution and generating high-fidelity MRI. However, they struggle to produce diverse, high-quality data outside the distribution defined by the training data. One way to address the issue is using causal models developed for 3D volume counterfactuals. However, accurately modeling causality in high-dimensional spaces is a challenge so that these models generally generate 3D brain MRIS of lower quality. To address these challenges, we propose a two-stage method that constructs a Structural Causal Model (SCM) within the latent space. In the first stage, we employ a VQ-VAE to learn a compact embedding of the MRI volume. Subsequently, we integrate our causal model into this latent space and execute a three-step counterfactual procedure using a closed-form Generalized Linear Model (GLM). Our experiments conducted on real-world high-resolution MRI data (1mm) demonstrate that our method can generate high-quality 3D MRI counterfactuals.

OccFusion: Rendering Occluded Humans with Generative Diffusion Priors

Most existing human rendering methods require every part of the human to be fully visible throughout the input video. However, this assumption does not hold in real-life settings where obstructions are common, resulting in only partial visibility of the human. Considering this, we present OccFusion, an approach that utilizes efficient 3D Gaussian splatting supervised by pretrained 2D diffusion models for efficient and high-fidelity human rendering. We propose a pipeline consisting of three stages. In the Initialization stage, complete human masks are generated from partial visibility masks. In the Optimization stage, 3D human Gaussians are optimized with additional supervision by Score-Distillation Sampling (SDS) to create a complete geometry of the human. Finally, in the Refinement stage, in-context inpainting is designed to further improve rendering quality on the less observed human body parts. We evaluate OccFusion on ZJU-MoCap and challenging OcMotion sequences and find that it achieves state-of-the-art performance in the rendering of occluded humans.

Few-Shot Classification of Interactive Activities of Daily Living (InteractADL)

Understanding Activities of Daily Living (ADLs) is a crucial step for different applications including assistive robots, smart homes, and healthcare. However, to date, few benchmarks and methods have focused on complex ADLs, especially those involving multi-person interactions in home environments. In this paper, we propose a new dataset and benchmark, InteractADL, for understanding complex ADLs that involve interaction between humans (and objects). Furthermore, complex ADLs occurring in home environments comprise a challenging long-tailed distribution due to the rarity of multi-person interactions, and pose fine-grained visual recognition tasks due to the presence of semantically and visually similar classes. To address these issues, we propose a novel method for fine-grained few-shot video classification called Name Tuning that enables greater semantic separability by learning optimal class name vectors. We show that Name Tuning can be combined with existing prompt tuning strategies to learn the entire input text (rather than only learning the prompt or class names) and demonstrate improved performance for few-shot classification on InteractADL and 4 other fine-grained visual classification benchmarks. For transparency and reproducibility, we release our code at https://github.com/zanedurante/vlm_benchmark.

Enforcing Conditional Independence for Fair Representation Learning and Causal Image Generation

Conditional independence (CI) constraints are critical for defining and evaluating fairness in machine learning, as well as for learning unconfounded or causal representations. Traditional methods for ensuring fairness either blindly learn invariant features with respect to a protected variable (e.g., race when classifying sex from face images) or enforce CI relative to the protected attribute only on the model output (e.g., the sex label). Neither of these methods are effective in enforcing CI in high-dimensional feature spaces. In this paper, we focus on a nascent approach characterizing the CI constraint in terms of two Jensen-Shannon divergence terms, and we extend it to high-dimensional feature spaces using a novel dynamic sampling strategy. In doing so, we introduce a new training paradigm that can be applied to any encoder architecture. We are able to enforce conditional independence of the diffusion autoencoder latent representation with respect to any protected attribute under the equalized odds constraint and show that this approach enables causal image generation with controllable latent spaces. Our experimental results demonstrate that our approach can achieve high accuracy on downstream tasks while upholding equality of odds.

Towards Robust 3D Pose Transfer with Adversarial Learning

3D pose transfer that aims to transfer the desired pose to a target mesh is one of the most challenging 3D generation tasks. Previous attempts rely on well-defined parametric human models or skeletal joints as driving pose sources. However, to obtain those clean pose sources, cumbersome but necessary pre-processing pipelines are inevitable, hindering implementations of the real-time applications. This work is driven by the intuition that the robustness of the model can be enhanced by introducing adversarial samples into the training, leading to a more invulnerable model to the noisy inputs, which even can be further extended to directly handling the real-world data like raw point clouds/scans without intermediate processing. Furthermore, we propose a novel 3D pose Masked Autoencoder (3D-PoseMAE), a customized MAE that effectively learns 3D extrinsic presentations (i.e., pose). 3D-PoseMAE facilitates learning from the aspect of extrinsic attributes by simultaneously generating adversarial samples that perturb the model and learning the arbitrary raw noisy poses via a multi-scale masking strategy. Both qualitative and quantitative studies show that the transferred meshes given by our network result in much better quality. Besides, we demonstrate the strong generalizability of our method on various poses, different domains, and even raw scans. Experimental results also show meaningful insights that the intermediate adversarial samples generated in the training can successfully attack the existing pose transfer models.

An Interactive Agent Foundation Model

The development of artificial intelligence systems is transitioning from creating static, task-specific models to dynamic, agent-based systems capable of performing well in a wide range of applications. We propose an Interactive Agent Foundation Model that uses a novel multi-task agent training paradigm for training AI agents across a wide range of domains, datasets, and tasks. Our training paradigm unifies diverse pre-training strategies, including visual masked auto-encoders, language modeling, and next-action prediction, enabling a versatile and adaptable AI framework. We demonstrate the performance of our framework across three separate domains -- Robotics, Gaming AI, and Healthcare. Our model demonstrates its ability to generate meaningful and contextually relevant outputs in each area. The strength of our approach lies in its generality, leveraging a variety of data sources such as robotics sequences, gameplay data, large-scale video datasets, and textual information for effective multimodal and multi-task learning. Our approach provides a promising avenue for developing generalist, action-taking, multimodal systems.