Rethinking Functional Brain Connectome Analysis: Do Graph Deep Learning Models Help?

Functional brain connectome is crucial for deciphering the neural mechanisms underlying cognitive functions and neurological disorders. Graph deep learning models have recently gained tremendous popularity in this field. However, their actual effectiveness in modeling the brain connectome remains unclear. In this study, we re-examine graph deep learning models based on four large-scale neuroimaging studies encompassing diverse cognitive and clinical outcomes. Surprisingly, we find that the message aggregation mechanism, a hallmark of graph deep learning models, does not help with predictive performance as typically assumed, but rather consistently degrades it. To address this issue, we propose a hybrid model combining a linear model with a graph attention network through dual pathways, achieving robust predictions and enhanced interpretability by revealing both localized and global neural connectivity patterns. Our findings urge caution in adopting complex deep learning models for functional brain connectome analysis, emphasizing the need for rigorous experimental designs to establish tangible performance gains and perhaps more importantly, to pursue improvements in model interpretability.

ION-C: Integration of Overlapping Networks via Constraints

In many causal learning problems, variables of interest are often not all measured over the same observations, but are instead distributed across multiple datasets with overlapping variables. Tillman et al. (2008) presented the first algorithm for enumerating the minimal equivalence class of ground-truth DAGs consistent with all input graphs by exploiting local independence relations, called ION. In this paper, this problem is formulated as a more computationally efficient answer set programming (ASP) problem, which we call ION-C, and solved with the ASP system clingo. The ION-C algorithm was run on random synthetic graphs with varying sizes, densities, and degrees of overlap between subgraphs, with overlap having the largest impact on runtime, number of solution graphs, and agreement within the output set. To validate ION-C on real-world data, we ran the algorithm on overlapping graphs learned from data from two successive iterations of the European Social Survey (ESS), using a procedure for conducting joint independence tests to prevent inconsistencies in the input.

Unmasking Efficiency: Learning Salient Sparse Models in Non-IID Federated Learning

In this work, we propose Salient Sparse Federated Learning (SSFL), a streamlined approach for sparse federated learning with efficient communication. SSFL identifies a sparse subnetwork prior to training, leveraging parameter saliency scores computed separately on local client data in non-IID scenarios, and then aggregated, to determine a global mask. Only the sparse model weights are communicated each round between the clients and the server. We validate SSFL's effectiveness using standard non-IID benchmarks, noting marked improvements in the sparsity--accuracy trade-offs. Finally, we deploy our method in a real-world federated learning framework and report improvement in communication time.

DynaLay: An Introspective Approach to Dynamic Layer Selection for Deep Networks

Deep learning models have become increasingly computationally intensive, requiring extensive computational resources and time for both training and inference. A significant contributing factor to this challenge is the uniform computational effort expended on each input example, regardless of its complexity. We introduce \textbf{DynaLay}, an alternative architecture that features a decision-making agent to adaptively select the most suitable layers for processing each input, thereby endowing the model with a remarkable level of introspection. DynaLay reevaluates more complex inputs during inference, adjusting the computational effort to optimize both performance and efficiency. The core of the system is a main model equipped with Fixed-Point Iterative (FPI) layers, capable of accurately approximating complex functions, paired with an agent that chooses these layers or a direct action based on the introspection of the models inner state. The model invests more time in processing harder examples, while minimal computation is required for easier ones. This introspective approach is a step toward developing deep learning models that "think" and "ponder", rather than "ballistically'' produce answers. Our experiments demonstrate that DynaLay achieves accuracy comparable to conventional deep models while significantly reducing computational demands.

Brainchop: Next Generation Web-Based Neuroimaging Application

Performing volumetric image processing directly within the browser, particularly with medical data, presents unprecedented challenges compared to conventional backend tools. These challenges arise from limitations inherent in browser environments, such as constrained computational resources and the availability of frontend machine learning libraries. Consequently, there is a shortage of neuroimaging frontend tools capable of providing comprehensive end-to-end solutions for whole brain preprocessing and segmentation while preserving end-user data privacy and residency. In light of this context, we introduce Brainchop (http://www.brainchop.org) as a groundbreaking in-browser neuroimaging tool that enables volumetric analysis of structural MRI using pre-trained full-brain deep learning models, all without requiring technical expertise or intricate setup procedures. Beyond its commitment to data privacy, this frontend tool offers multiple features, including scalability, low latency, user-friendly operation, cross-platform compatibility, and enhanced accessibility. This paper outlines the processing pipeline of Brainchop and evaluates the performance of models across various software and hardware configurations. The results demonstrate the practicality of client-side processing for volumetric data, owing to the robust MeshNet architecture, even within the resource-constrained environment of web browsers.

Learning low-dimensional dynamics from whole-brain data improves task capture

The neural dynamics underlying brain activity are critical to understanding cognitive processes and mental disorders. However, current voxel-based whole-brain dimensionality reduction techniques fall short of capturing these dynamics, producing latent timeseries that inadequately relate to behavioral tasks. To address this issue, we introduce a novel approach to learning low-dimensional approximations of neural dynamics by using a sequential variational autoencoder (SVAE) that represents the latent dynamical system via a neural ordinary differential equation (NODE). Importantly, our method finds smooth dynamics that can predict cognitive processes with accuracy higher than classical methods. Our method also shows improved spatial localization to task-relevant brain regions and identifies well-known structures such as the motor homunculus from fMRI motor task recordings. We also find that non-linear projections to the latent space enhance performance for specific tasks, offering a promising direction for future research. We evaluate our approach on various task-fMRI datasets, including motor, working memory, and relational processing tasks, and demonstrate that it outperforms widely used dimensionality reduction techniques in how well the latent timeseries relates to behavioral sub-tasks, such as left-hand or right-hand tapping. Additionally, we replace the NODE with a recurrent neural network (RNN) and compare the two approaches to understand the importance of explicitly learning a dynamical system. Lastly, we analyze the robustness of the learned dynamical systems themselves and find that their fixed points are robust across seeds, highlighting our method's potential for the analysis of cognitive processes as dynamical systems.

SalientGrads: Sparse Models for Communication Efficient and Data Aware Distributed Federated Training

Federated learning (FL) enables the training of a model leveraging decentralized data in client sites while preserving privacy by not collecting data. However, one of the significant challenges of FL is limited computation and low communication bandwidth in resource limited edge client nodes. To address this, several solutions have been proposed in recent times including transmitting sparse models and learning dynamic masks iteratively, among others. However, many of these methods rely on transmitting the model weights throughout the entire training process as they are based on ad-hoc or random pruning criteria. In this work, we propose Salient Grads, which simplifies the process of sparse training by choosing a data aware subnetwork before training, based on the model-parameter's saliency scores, which is calculated from the local client data. Moreover only highly sparse gradients are transmitted between the server and client models during the training process unlike most methods that rely on sharing the entire dense model in each round. We also demonstrate the efficacy of our method in a real world federated learning application and report improvement in wall-clock communication time.

Self-Supervised Mental Disorder Classifiers via Time Reversal

Data scarcity is a notable problem, especially in the medical domain, due to patient data laws. Therefore, efficient Pre-Training techniques could help in combating this problem. In this paper, we demonstrate that a model trained on the time direction of functional neuro-imaging data could help in any downstream task, for example, classifying diseases from healthy controls in fMRI data. We train a Deep Neural Network on Independent components derived from fMRI data using the Independent component analysis (ICA) technique. It learns time direction in the ICA-based data. This pre-trained model is further trained to classify brain disorders in different datasets. Through various experiments, we have shown that learning time direction helps a model learn some causal relation in fMRI data that helps in faster convergence, and consequently, the model generalizes well in downstream classification tasks even with fewer data records.

Pipeline-Invariant Representation Learning for Neuroimaging

Deep learning has been widely applied in neuroimaging, including to predicting brain-phenotype relationships from magnetic resonance imaging (MRI) volumes. MRI data usually requires extensive preprocessing before it is ready for modeling, even via deep learning, in part due to its high dimensionality and heterogeneity. A growing array of MRI preprocessing pipelines have been developed each with its own strengths and limitations. Recent studies have shown that pipeline-related variation may lead to different scientific findings, even when using the identical data. Meanwhile, the machine learning community has emphasized the importance of shifting from model-centric to data-centric approaches given that data quality plays an essential role in deep learning applications. Motivated by this idea, we first evaluate how preprocessing pipeline selection can impact the downstream performance of a supervised learning model. We next propose two pipeline-invariant representation learning methodologies, MPSL and PXL, to improve consistency in classification performance and to capture similar neural network representations between pipeline pairs. Using 2000 human subjects from the UK Biobank dataset, we demonstrate that both models present unique advantages, in particular that MPSL can be used to improve out-of-sample generalization to new pipelines, while PXL can be used to improve predictive performance consistency and representational similarity within a closed pipeline set. These results suggest that our proposed models can be applied to overcome pipeline-related biases and to improve reproducibility in neuroimaging prediction tasks.

Geometrically Guided Integrated Gradients

Interpretability methods for deep neural networks mainly focus on the sensitivity of the class score with respect to the original or perturbed input, usually measured using actual or modified gradients. Some methods also use a model-agnostic approach to understanding the rationale behind every prediction. In this paper, we argue and demonstrate that local geometry of the model parameter space relative to the input can also be beneficial for improved post-hoc explanations. To achieve this goal, we introduce an interpretability method called "geometrically-guided integrated gradients" that builds on top of the gradient calculation along a linear path as traditionally used in integrated gradient methods. However, instead of integrating gradient information, our method explores the model's dynamic behavior from multiple scaled versions of the input and captures the best possible attribution for each input. We demonstrate through extensive experiments that the proposed approach outperforms vanilla and integrated gradients in subjective and quantitative assessment. We also propose a "model perturbation" sanity check to complement the traditionally used "model randomization" test.