Meenakshi Khosla

Meenakshi Khosla, Alex H. Williams

Common measures of neural representational (dis)similarity are designed to be insensitive to rotations and reflections of the neural activation space. Motivated by the premise that the tuning of individual units may be important, there has been recent interest in developing stricter notions of representational (dis)similarity that require neurons to be individually matched across networks. When two networks have the same size (i.e. same number of neurons), a distance metric can be formulated by optimizing over neuron index permutations to maximize tuning curve alignment. However, it is not clear how to generalize this metric to measure distances between networks with different sizes. Here, we leverage a connection to optimal transport theory to derive a natural generalization based on "soft" permutations. The resulting metric is symmetric, satisfies the triangle inequality, and can be interpreted as a Wasserstein distance between two empirical distributions. Further, our proposed metric avoids counter-intuitive outcomes suffered by alternative approaches, and captures complementary geometric insights into neural representations that are entirely missed by rotation-invariant metrics.

Nirmalendu Prakash, Narmeen Fatimah Oozeer, Xin Su et al.

CLIP retrieval is typically framed as a pointwise similarity problem in a shared embedding space. While CLIP achieves strong global cross-modal alignment, many retrieval failures arise from local geometric inconsistencies: nearby items are incorrectly ordered, leading to systematic confusions (e.g., pentagon vs. hexagon) and produces diffuse, weakly controlled result sets. Prior work largely optimizes for point wise relevance or finetuning to mitigate these problems. We instead view retrieval as a problem of neighborhood alignment. Our work introduces (1) neighborhood-level re-ranking via Hungarian matching, which rewards structural consistency; (2) query-conditioned local steering, where directions derived from contrastive neighborhoods around the query reshape retrieval. We show that these techniques improve retrieval performance on attribute-binding and compositional retrieval tasks. Together, these methods operate on local neighborhoods but serve different roles: re-ranking rewards alignment whereas local steering controls neighborhood structure. This shows that retrieval quality and controllability depend critically on local structure, which can be exploited at inference time without retraining.

Chaitanya Kapoor, Alex H. Williams, Meenakshi Khosla

Representational similarity metrics typically force all units to be matched, making them susceptible to noise and outliers common in neural representations. We extend the soft-matching distance to a partial optimal transport setting that allows some neurons to remain unmatched, yielding rotation-sensitive but robust correspondences. This partial soft-matching distance provides theoretical advantages -- relaxing strict mass conservation while maintaining interpretable transport costs -- and practical benefits through efficient neuron ranking in terms of cross-network alignment without costly iterative recomputation. In simulations, it preserves correct matches under outliers and reliably selects the correct model in noise-corrupted identification tasks. On fMRI data, it automatically excludes low-reliability voxels and produces voxel rankings by alignment quality that closely match computationally expensive brute-force approaches. It achieves higher alignment precision across homologous brain areas than standard soft-matching, which is forced to match all units regardless of quality. In deep networks, highly matched units exhibit similar maximally exciting images, while unmatched units show divergent patterns. This ability to partition by match quality enables focused analyses, e.g., testing whether networks have privileged axes even within their most aligned subpopulations. Overall, partial soft-matching provides a principled and practical method for representational comparison under partial correspondence.

Jenelle Feather, Meenakshi Khosla, N. Apurva Ratan Murty et al.

What makes an artificial system a good model of intelligence? The classical test proposed by Alan Turing focuses on behavior, requiring that an artificial agent's behavior be indistinguishable from that of a human. While behavioral similarity provides a strong starting point, two systems with very different internal representations can produce the same outputs. Thus, in modeling biological intelligence, the field of NeuroAI often aims to go beyond behavioral similarity and achieve representational convergence between a model's activations and the measured activity of a biological system. This position paper argues that the standard definition of the Turing Test is incomplete for NeuroAI, and proposes a stronger framework called the ``NeuroAI Turing Test'', a benchmark that extends beyond behavior alone and \emph{additionally} requires models to produce internal neural representations that are empirically indistinguishable from those of a brain up to measured individual variability, i.e. the differences between a computational model and the brain is no more than the difference between one brain and another brain. While the brain is not necessarily the ceiling of intelligence, it remains the only universally agreed-upon example, making it a natural reference point for evaluating computational models. By proposing this framework, we aim to shift the discourse from loosely defined notions of brain inspiration to a systematic and testable standard centered on both behavior and internal representations, providing a clear benchmark for neuroscientific modeling and AI development.

Yiqing Bo, Ansh Soni, Sudhanshu Srivastava et al.

Neuroscience and artificial intelligence (AI) both face the challenge of interpreting high-dimensional neural data, where the comparative analysis of such data is crucial for revealing shared mechanisms and differences between these complex systems. Despite the widespread use of representational comparisons and the abundance classes of comparison methods, a critical question remains: which metrics are most suitable for these comparisons? While some studies evaluate metrics based on their ability to differentiate models of different origins or constructions (e.g., various architectures), another approach is to assess how well they distinguish models that exhibit distinct behaviors. To investigate this, we examine the degree of alignment between various representational similarity measures and behavioral outcomes, employing group statistics and a comprehensive suite of behavioral metrics for comparison. In our evaluation of eight commonly used representational similarity metrics in the visual domain -- spanning alignment-based, Canonical Correlation Analysis (CCA)-based, inner product kernel-based, and nearest-neighbor methods -- we found that metrics like linear Centered Kernel Alignment (CKA) and Procrustes distance, which emphasize the overall geometric structure or shape of representations, excelled in differentiating trained from untrained models and aligning with behavioral measures, whereas metrics such as linear predictivity, commonly used in neuroscience, demonstrated only moderate alignment with behavior. These insights are crucial for selecting metrics that emphasize behaviorally meaningful comparisons in NeuroAI research.

Shreya Saha, Ishaan Chadha, Meenakshi Khosla

Over the past decade, predictive modeling of neural responses in the primate visual system has advanced significantly, largely driven by various DNN approaches. These include models optimized directly for visual recognition, cross-modal alignment through contrastive objectives, neural response prediction from scratch, and large language model embeddings.Likewise, different readout mechanisms, ranging from fully linear to spatial-feature factorized methods have been explored for mapping network activations to neural responses. Despite the diversity of these approaches, it remains unclear which method performs best across different visual regions. In this study, we systematically compare these approaches for modeling the human visual system and investigate alternative strategies to improve response predictions. Our findings reveal that for early to mid-level visual areas, response-optimized models with visual inputs offer superior prediction accuracy, while for higher visual regions, embeddings from LLMs based on detailed contextual descriptions of images and task-optimized models pretrained on large vision datasets provide the best fit. Through comparative analysis of these modeling approaches, we identified three distinct regions in the visual cortex: one sensitive primarily to perceptual features of the input that are not captured by linguistic descriptions, another attuned to fine-grained visual details representing semantic information, and a third responsive to abstract, global meanings aligned with linguistic content. We also highlight the critical role of readout mechanisms, proposing a novel scheme that modulates receptive fields and feature maps based on semantic content, resulting in an accuracy boost of 3-23% over existing SOTAs for all models and brain regions. Together, these findings offer key insights into building more precise models of the visual system.

Sunny Liu, Habon Issa, André Longon et al.

Comparing the internal representations of neural networks is a central goal in both neuroscience and machine learning. Standard alignment metrics operate on raw neural activations, implicitly assuming that similar representations produce similar activity patterns. However, neural systems frequently operate in superposition, encoding more features than they have neurons via linear compression. We derive closed-form expressions showing that superposition systematically deflates Representational Similarity Analysis, Centered Kernel Alignment, and linear regression, causing networks with identical feature content to appear dissimilar. The root cause is that these metrics are dependent on cross-similarity between two systems' respective superposition matrices, which under assumption of random projection usually differ significantly, not on the latent features themselves: alignment scores conflate what a system represents with how it represents it. Under partial feature overlap, this confound can invert the expected ordering, making systems sharing fewer features appear more aligned than systems sharing more. Crucially, the apparent misalignment need not reflect a loss of information; compressed sensing guarantees that the original features remain recoverable from the lower-dimensional activity, provided they are sparse. We therefore argue that comparing neural systems in superposition requires extracting and aligning the underlying features rather than comparing the raw neural mixtures.

Shreya Saha, Zoe Wanying He, Meenakshi Khosla

Comparing representations across neural networks is challenging because representations admit symmetries, such as arbitrary reordering of units or rotations of activation space, that obscure underlying equivalence between models. We introduce a barycentric alignment framework that quotients out these nuisance symmetries to construct a universal embedding space across many models. Unlike existing similarity measures, which summarize relationships over entire stimulus sets, this framework enables similarity to be defined at the level of individual stimuli, revealing inputs that elicit convergent versus divergent representations across models. Using this instance-level notion of similarity, we identify systematic input properties that predict representational convergence versus divergence across vision and language model families. We also construct universal embedding spaces for brain representations across individuals and cortical regions, enabling instance-level comparison of representational agreement across stages of the human visual hierarchy. Finally, we apply the same barycentric alignment framework to purely unimodal vision and language models and find that post-hoc alignment into a shared space yields image text similarity scores that closely track human cross-modal judgments and approach the performance of contrastively trained vision-language models. This strikingly suggests that independently learned representations already share sufficient geometric structure for human-aligned cross-modal comparison. Together, these results show that resolving representational similarity at the level of individual stimuli reveals phenomena that cannot be detected by set-level comparison metrics.

Jialin Wu, Shreya Saha, Yiqing Bo et al.

The extent to which different neural or artificial neural networks (models) rely on equivalent representations to support similar tasks remains a central question in neuroscience and machine learning. Prior work has typically compared systems using a single representational similarity metric, yet each captures only one facet of representational structure. To address this, we leverage a suite of representational similarity metrics-each capturing a distinct facet of representational correspondence, such as geometry, unit-level tuning, or linear decodability-and assess brain region or model separability using multiple complementary measures. Metrics that preserve geometric or tuning structure (e.g., RSA, Soft Matching) yield stronger region-based discrimination, whereas more flexible mappings such as Linear Predictivity show weaker separation. These findings suggest that geometry and tuning encode brain-region- or model-family-specific signatures, while linearly decodable information tends to be more globally shared across regions or models. To integrate these complementary representational facets, we adapt Similarity Network Fusion (SNF), a framework originally developed for multi-omics data integration. SNF produces substantially sharper regional and model family-level separation than any single metric and yields robust composite similarity profiles. Moreover, clustering cortical regions using SNF-derived similarity scores reveals a clearer hierarchical organization that aligns closely with established anatomical and functional hierarchies of the visual cortex-surpassing the correspondence achieved by individual metrics.

Ammar I Marvi, Nancy G Kanwisher, Meenakshi Khosla

The ventral, dorsal, and lateral streams in high-level human visual cortex are implicated in distinct functional processes. Yet, deep neural networks (DNNs) trained on a single task model the entire visual system surprisingly well, hinting at common computational principles across these pathways. To explore this inconsistency, we applied a novel sparse decomposition approach to identify the dominant components of visual representations within each stream. Consistent with traditional neuroscience research, we find a clear difference in component response profiles across the three visual streams -- identifying components selective for faces, places, bodies, text, and food in the ventral stream; social interactions, implied motion, and hand actions in the lateral stream; and some less interpretable components in the dorsal stream. Building on this, we introduce Sparse Component Alignment (SCA), a new method for measuring representational alignment between brains and machines that better captures the latent neural tuning of these two visual systems. Using SCA, we find that standard visual DNNs are more aligned with the ventral than either dorsal or lateral representations. SCA reveals these distinctions with greater resolution than conventional population-level geometry, offering a measure of representational alignment that is sensitive to a system's underlying axes of neural tuning.

André Longon, David Klindt, Meenakshi Khosla

The superposition hypothesis states that single neurons may participate in representing multiple features in order for the neural network to represent more features than it has neurons. In neuroscience and AI, representational alignment metrics measure the extent to which different deep neural networks (DNNs) or brains represent similar information. In this work, we explore a critical question: does superposition interact with alignment metrics in any undesirable way? We hypothesize that models which represent the same features in different superposition arrangements, i.e., their neurons have different linear combinations of the features, will interfere with predictive mapping metrics (semi-matching, soft-matching, linear regression), producing lower alignment than expected. We develop a theory for how permutation metrics are dependent on superposition arrangements. This is tested by training sparse autoencoders (SAEs) to disentangle superposition in toy models, where alignment scores are shown to typically increase when a model's base neurons are replaced with its sparse overcomplete latent codes. We find similar increases for DNN-DNN and DNN-brain linear regression alignment in the visual domain. Our results suggest that superposition disentanglement is necessary for mapping metrics to uncover the true representational alignment between neural networks.

Shaan Shah, Meenakshi Khosla

Standard representational similarity methods align each layer of a network to its best match in another independently, producing asymmetric results, lacking a global alignment score, and struggling with networks of different depths. These limitations arise from ignoring global activation structure and restricting mappings to rigid one-to-one layer correspondences. We propose Hierarchical Optimal Transport (HOT), a unified framework that jointly infers soft, globally consistent layer-to-layer couplings and neuron-level transport plans. HOT allows source neurons to distribute mass across multiple target layers while minimizing total transport cost under marginal constraints. This yields both a single alignment score for the entire network comparison and a soft transport plan that naturally handles depth mismatches through mass distribution. We evaluate HOT on vision models, large language models, and human visual cortex recordings. Across all domains, HOT matches or surpasses standard pairwise matching in alignment quality. Moreover, it reveals smooth, fine-grained hierarchical correspondences: early layers map to early layers, deeper layers maintain relative positions, and depth mismatches are resolved by distributing representations across multiple layers. These structured patterns emerge naturally from global optimization without being imposed, yet are absent in greedy layer-wise methods. HOT thus enables richer, more interpretable comparisons between representations, particularly when networks differ in architecture or depth.

Shreya Saha, Shurui Li, Greta Tuckute et al.

The human language system represents both linguistic forms and meanings, but the abstractness of the meaning representations remains debated. Here, we searched for abstract representations of meaning in the language cortex by modeling neural responses to sentences using representations from vision and language models. When we generate images corresponding to sentences and extract vision model embeddings, we find that aggregating across multiple generated images yields increasingly accurate predictions of language cortex responses, sometimes rivaling large language models. Similarly, averaging embeddings across multiple paraphrases of a sentence improves prediction accuracy compared to any single paraphrase. Enriching paraphrases with contextual details that may be implicit (e.g., augmenting "I had a pancake" to include details like "maple syrup") further increases prediction accuracy, even surpassing predictions based on the embedding of the original sentence, suggesting that the language system maintains richer and broader semantic representations than language models. Together, these results demonstrate the existence of highly abstract, form-independent meaning representations within the language cortex.

Jialin Wu, Shreya Saha, Yiqing Bo et al.

Large vision models differ widely in architecture and training paradigm, yet we lack principled methods to determine which aspects of their representations are shared across families and which reflect distinctive computational strategies. We leverage a suite of representational similarity metrics, each capturing a different facet-geometry, unit tuning, or linear decodability-and assess family separability using multiple complementary measures. Metrics preserving geometry or tuning (e.g., RSA, Soft Matching) yield strong family discrimination, whereas flexible mappings such as Linear Predictivity show weaker separation. These findings indicate that geometry and tuning carry family-specific signatures, while linearly decodable information is more broadly shared. To integrate these complementary facets, we adapt Similarity Network Fusion (SNF), a method inspired by multi-omics integration. SNF achieves substantially sharper family separation than any individual metric and produces robust composite signatures. Clustering of the fused similarity matrix recovers both expected and surprising patterns: supervised ResNets and ViTs form distinct clusters, yet all self-supervised models group together across architectural boundaries. Hybrid architectures (ConvNeXt, Swin) cluster with masked autoencoders, suggesting convergence between architectural modernization and reconstruction-based training. This biology-inspired framework provides a principled typology of vision models, showing that emergent computational strategies-shaped jointly by architecture and training objective-define representational structure beyond surface design categories.

Zoe Wanying He, Sean Trott, Meenakshi Khosla

Recent studies show that deep vision-only and language-only models--trained on disjoint modalities--nonetheless project their inputs into a partially aligned representational space. Yet we still lack a clear picture of where in each network this convergence emerges, what visual or linguistic cues support it, whether it captures human preferences in many-to-many image-text scenarios, and how aggregating exemplars of the same concept affects alignment. Here, we systematically investigate these questions. We find that alignment peaks in mid-to-late layers of both model types, reflecting a shift from modality-specific to conceptually shared representations. This alignment is robust to appearance-only changes but collapses when semantics are altered (e.g., object removal or word-order scrambling), highlighting that the shared code is truly semantic. Moving beyond the one-to-one image-caption paradigm, a forced-choice "Pick-a-Pic" task shows that human preferences for image-caption matches are mirrored in the embedding spaces across all vision-language model pairs. This pattern holds bidirectionally when multiple captions correspond to a single image, demonstrating that models capture fine-grained semantic distinctions akin to human judgments. Surprisingly, averaging embeddings across exemplars amplifies alignment rather than blurring detail. Together, our results demonstrate that unimodal networks converge on a shared semantic code that aligns with human judgments and strengthens with exemplar aggregation.

Jialin Wu, Shreya Saha, Yiqing Bo et al.

Representational similarity metrics are fundamental tools in neuroscience and AI, yet we lack systematic comparisons of their discriminative power across model families. We introduce a quantitative framework to evaluate representational similarity measures based on their ability to separate model families-across architectures (CNNs, Vision Transformers, Swin Transformers, ConvNeXt) and training regimes (supervised vs. self-supervised). Using three complementary separability measures-dprime from signal detection theory, silhouette coefficients and ROC-AUC, we systematically assess the discriminative capacity of commonly used metrics including RSA, linear predictivity, Procrustes, and soft matching. We show that separability systematically increases as metrics impose more stringent alignment constraints. Among mapping-based approaches, soft-matching achieves the highest separability, followed by Procrustes alignment and linear predictivity. Non-fitting methods such as RSA also yield strong separability across families. These results provide the first systematic comparison of similarity metrics through a separability lens, clarifying their relative sensitivity and guiding metric choice for large-scale model and brain comparisons.

Chaitanya Kapoor, Sudhanshu Srivastava, Meenakshi Khosla

Understanding convergent learning -- the degree to which independently trained neural systems -- whether multiple artificial networks or brains and models -- arrive at similar internal representations -- is crucial for both neuroscience and AI. Yet, the literature remains narrow in scope -- typically examining just a handful of models with one dataset, relying on one alignment metric, and evaluating networks at a single post-training checkpoint. We present a large-scale audit of convergent learning, spanning dozens of vision models and thousands of layer-pair comparisons, to close these long-standing gaps. First, we pit three alignment families against one another -- linear regression (affine-invariant), orthogonal Procrustes (rotation-/reflection-invariant), and permutation/soft-matching (unit-order-invariant). We find that orthogonal transformations align representations nearly as effectively as more flexible linear ones, and although permutation scores are lower, they significantly exceed chance, indicating a privileged representational basis. Tracking convergence throughout training further shows that nearly all eventual alignment crystallizes within the first epoch -- well before accuracy plateaus -- indicating it is largely driven by shared input statistics and architectural biases, not by the final task solution. Finally, when models are challenged with a battery of out-of-distribution images, early layers remain tightly aligned, whereas deeper layers diverge in proportion to the distribution shift. These findings fill critical gaps in our understanding of representational convergence, with implications for neuroscience and AI.

Zijin Gu, Keith W. Jamison, Meenakshi Khosla et al.

Functional MRI (fMRI) is a powerful technique that has allowed us to characterize visual cortex responses to stimuli, yet such experiments are by nature constructed based on a priori hypotheses, limited to the set of images presented to the individual while they are in the scanner, are subject to noise in the observed brain responses, and may vary widely across individuals. In this work, we propose a novel computational strategy, which we call NeuroGen, to overcome these limitations and develop a powerful tool for human vision neuroscience discovery. NeuroGen combines an fMRI-trained neural encoding model of human vision with a deep generative network to synthesize images predicted to achieve a target pattern of macro-scale brain activation. We demonstrate that the reduction of noise that the encoding model provides, coupled with the generative network's ability to produce images of high fidelity, results in a robust discovery architecture for visual neuroscience. By using only a small number of synthetic images created by NeuroGen, we demonstrate that we can detect and amplify differences in regional and individual human brain response patterns to visual stimuli. We then verify that these discoveries are reflected in the several thousand observed image responses measured with fMRI. We further demonstrate that NeuroGen can create synthetic images predicted to achieve regional response patterns not achievable by the best-matching natural images. The NeuroGen framework extends the utility of brain encoding models and opens up a new avenue for exploring, and possibly precisely controlling, the human visual system.

Meenakshi Khosla, Gia H. Ngo, Keith Jamison et al.

Visual perception is critically influenced by the focus of attention. Due to limited resources, it is well known that neural representations are biased in favor of attended locations. Using concurrent eye-tracking and functional Magnetic Resonance Imaging (fMRI) recordings from a large cohort of human subjects watching movies, we first demonstrate that leveraging gaze information, in the form of attentional masking, can significantly improve brain response prediction accuracy in a neural encoding model. Next, we propose a novel approach to neural encoding by including a trainable soft-attention module. Using our new approach, we demonstrate that it is possible to learn visual attention policies by end-to-end learning merely on fMRI response data, and without relying on any eye-tracking. Interestingly, we find that attention locations estimated by the model on independent data agree well with the corresponding eye fixation patterns, despite no explicit supervision to do so. Together, these findings suggest that attention modules can be instrumental in neural encoding models of visual stimuli.

Gia H. Ngo, Meenakshi Khosla, Keith Jamison et al.

Resting-state functional MRI (rsfMRI) yields functional connectomes that can serve as cognitive fingerprints of individuals. Connectomic fingerprints have proven useful in many machine learning tasks, such as predicting subject-specific behavioral traits or task-evoked activity. In this work, we propose a surface-based convolutional neural network (BrainSurfCNN) model to predict individual task contrasts from their resting-state fingerprints. We introduce a reconstructive-contrastive loss that enforces subject-specificity of model outputs while minimizing predictive error. The proposed approach significantly improves the accuracy of predicted contrasts over a well-established baseline. Furthermore, BrainSurfCNN's prediction also surpasses test-retest benchmark in a subject identification task.

Meenakshi Khosla, Gia H. Ngo, Keith Jamison et al.

The increasing popularity of naturalistic paradigms in fMRI (such as movie watching) demands novel strategies for multi-subject data analysis, such as use of neural encoding models. In the present study, we propose a shared convolutional neural encoding method that accounts for individual-level differences. Our method leverages multi-subject data to improve the prediction of subject-specific responses evoked by visual or auditory stimuli. We showcase our approach on high-resolution 7T fMRI data from the Human Connectome Project movie-watching protocol and demonstrate significant improvement over single-subject encoding models. We further demonstrate the ability of the shared encoding model to successfully capture meaningful individual differences in response to traditional task-based facial and scenes stimuli. Taken together, our findings suggest that inter-subject knowledge transfer can be beneficial to subject-specific predictive models.

Meenakshi Khosla, Keith Jamison, Amy Kuceyeski et al.

Resting-state functional MRI (rs-fMRI) is a rich imaging modality that captures spontaneous brain activity patterns, revealing clues about the connectomic organization of the human brain. While many rs-fMRI studies have focused on static measures of functional connectivity, there has been a recent surge in examining the temporal patterns in these data. In this paper, we explore two strategies for capturing the normal variability in resting-state activity across a healthy population: (a) an autoencoder approach on the rs-fMRI sequence, and (b) a next frame prediction strategy. We show that both approaches can learn useful representations of rs-fMRI data and demonstrate their novel application for abnormality detection in the context of discriminating autism patients from healthy controls.

Meenakshi Khosla, Keith Jamison, Gia H. Ngo et al.

Machine learning techniques have gained prominence for the analysis of resting-state functional Magnetic Resonance Imaging (rs-fMRI) data. Here, we present an overview of various unsupervised and supervised machine learning applications to rs-fMRI. We present a methodical taxonomy of machine learning methods in resting-state fMRI. We identify three major divisions of unsupervised learning methods with regard to their applications to rs-fMRI, based on whether they discover principal modes of variation across space, time or population. Next, we survey the algorithms and rs-fMRI feature representations that have driven the success of supervised subject-level predictions. The goal is to provide a high-level overview of the burgeoning field of rs-fMRI from the perspective of machine learning applications.

Meenakshi Khosla, Keith Jamison, Amy Kuceyeski et al.

The specificty and sensitivity of resting state functional MRI (rs-fMRI) measurements depend on pre-processing choices, such as the parcellation scheme used to define regions of interest (ROIs). In this study, we critically evaluate the effect of brain parcellations on machine learning models applied to rs-fMRI data. Our experiments reveal a remarkable trend: On average, models with stochastic parcellations consistently perform as well as models with widely used atlases at the same spatial scale. We thus propose an ensemble learning strategy to combine the predictions from models trained on connectivity data extracted using different (e.g., stochastic) parcellations. We further present an implementation of our ensemble learning strategy with a novel 3D Convolutional Neural Network (CNN) approach. The proposed CNN approach takes advantage of the full-resolution 3D spatial structure of rs-fMRI data and fits non-linear predictive models. Our ensemble CNN framework overcomes the limitations of traditional machine learning models for connectomes that often rely on region-based summary statistics and/or linear models. We showcase our approach on a classification (autism patients versus healthy controls) and a regression problem (prediction of subject's age), and report promising results.

Meenakshi Khosla, Keith Jamison, Amy Kuceyeski et al.

Resting-state functional MRI (rs-fMRI) scans hold the potential to serve as a diagnostic or prognostic tool for a wide variety of conditions, such as autism, Alzheimer's disease, and stroke. While a growing number of studies have demonstrated the promise of machine learning algorithms for rs-fMRI based clinical or behavioral prediction, most prior models have been limited in their capacity to exploit the richness of the data. For example, classification techniques applied to rs-fMRI often rely on region-based summary statistics and/or linear models. In this work, we propose a novel volumetric Convolutional Neural Network (CNN) framework that takes advantage of the full-resolution 3D spatial structure of rs-fMRI data and fits non-linear predictive models. We showcase our approach on a challenging large-scale dataset (ABIDE, with N > 2,000) and report state-of-the-art accuracy results on rs-fMRI-based discrimination of autism patients and healthy controls.