Comparing brain-like representations learned by vanilla, residual, and recurrent CNN architectures

Though it has been hypothesized that state-of-the art residual networks approximate the recurrent visual system, it is yet to be seen if the representations learned by these biologically inspired CNNs actually have closer representations to neural data. It is likely that CNNs and DNNs that are most functionally similar to the brain will contain mechanisms that are most like those used by the brain. In this thesis, we investigate how different CNN architectures approximate the representations learned through the ventral-object recognition and processing-stream of the brain. We specifically evaluate how recent approximations of biological neural recurrence-such as residual connections, dense residual connections, and a biologically-inspired implemen- tation of recurrence-affect the representations learned by each CNN. We first investigate the representations learned by layers throughout a few state-of-the-art CNNs-VGG-19 (vanilla CNN), ResNet-152 (CNN with residual connections), and DenseNet-161 (CNN with dense connections). To control for differences in model depth, we then extend this analysis to the CORnet family of biologically-inspired CNN models with matching high-level architectures. The CORnet family has three models: a vanilla CNN (CORnet-Z), a CNN with biologically-valid recurrent dynamics (CORnet-R), and a CNN with both recurrent and residual connections (CORnet-S). We compare the representations of these six models to functionally aligned (with hyperalignment) fMRI brain data acquired during a naturalistic visual task. We take two approaches to comparing these CNN and brain representations. We first use forward encoding, a predictive approach that uses CNN features to predict neural responses across the whole brain. We next use representational similarity analysis (RSA) and centered kernel alignment (CKA) to measure the similarities in representation within CNN layers and specific brain ROIs. We show that, compared to vanilla CNNs, CNNs with residual and recurrent connections exhibit representations that are even more similar to those learned by the human ventral visual stream. We also achieve state-of-the-art forward encoding and RSA performance with the residual and recurrent CNN models

Modeling Semantic Encoding in a Common Neural Representational Space

Encoding models for mapping voxelwise semantic tuning are typically estimated separately for each individual, limiting their generalizability. In the current report, we develop a method for estimating semantic encoding models that generalize across individuals. Functional MRI was used to measure brain responses while participants freely viewed a naturalistic audiovisual movie. Word embeddings capturing agent-, action-, object-, and scene-related semantic content were assigned to each imaging volume based on an annotation of the film. We constructed both conventional within-subject semantic encoding models and between-subject models where the model was trained on a subset of participants and validated on a left-out participant. Between-subject models were trained using cortical surface-based anatomical normalization or surface-based whole-cortex hyperalignment. We used hyperalignment to project group data into an individual’s unique anatomical space via a common representational space, thus leveraging a larger volume of data for out-of-sample prediction while preserving the individual’s fine-grained functional–anatomical idiosyncrasies. Our findings demonstrate that anatomical normalization degrades the spatial specificity of between-subject encoding models relative to within-subject models. Hyperalignment, on the other hand, recovers the spatial specificity of semantic tuning lost during anatomical normalization, and yields model performance exceeding that of within-subject models

Supervised Hyperalignment for multi-subject fMRI data alignment

Hyperalignment has been widely employed in Multivariate Pattern (MVP) analysis to discover the cognitive states in the human brains based on multi-subject functional Magnetic Resonance Imaging (fMRI) datasets. Most of the existing HA methods utilized unsupervised approaches, where they only maximized the correlation between the voxels with the same position in the time series. However, these unsupervised solutions may not be optimum for handling the functional alignment in the supervised MVP problems. This paper proposes a Supervised Hyperalignment (SHA) method to ensure better functional alignment for MVP analysis, where the proposed method provides a supervised shared space that can maximize the correlation among the stimuli belonging to the same category and minimize the correlation between distinct categories of stimuli. Further, SHA employs a generalized optimization solution, which generates the shared space and calculates the mapped features in a single iteration, hence with optimum time and space complexities for large datasets. Experiments on multi-subject datasets demonstrate that SHA method achieves up to 19% better performance for multi-class problems over the state-of-the-art HA algorithms

Modeling Semantic Encoding in a Common Neural Representational Space

Encoding models for mapping voxelwise semantic tuning are typically estimated separately for each individual, limiting their generalizability. In the current report, we develop a method for estimating semantic encoding models that generalize across individuals. Functional MRI was used to measure brain responses while participants freely viewed a naturalistic audiovisual movie. Word embeddings capturing agent-, action-, object-, and scene-related semantic content were assigned to each imaging volume based on an annotation of the film. We constructed both conventional within-subject semantic encoding models and between-subject models where the model was trained on a subset of participants and validated on a left-out participant. Between-subject models were trained using cortical surface-based anatomical normalization or surface-based whole-cortex hyperalignment. We used hyperalignment to project group data into an individual’s unique anatomical space via a common representational space, thus leveraging a larger volume of data for out-of-sample prediction while preserving the individual’s fine-grained functional–anatomical idiosyncrasies. Our findings demonstrate that anatomical normalization degrades the spatial specificity of between-subject encoding models relative to within-subject models. Hyperalignment, on the other hand, recovers the spatial specificity of semantic tuning lost during anatomical normalization, and yields model performance exceeding that of within-subject models

Inter-individual deep image reconstruction via hierarchical neural code conversion

The sensory cortex is characterized by general organizational principles such as topography and hierarchy. However, measured brain activity given identical input exhibits substantially different patterns across individuals. Although anatomical and functional alignment methods have been proposed in functional magnetic resonance imaging (fMRI) studies, it remains unclear whether and how hierarchical and fine-grained representations can be converted between individuals while preserving the encoded perceptual content. In this study, we trained a method of functional alignment called neural code converter that predicts a target subject’s brain activity pattern from a source subject given the same stimulus, and analyzed the converted patterns by decoding hierarchical visual features and reconstructing perceived images. The converters were trained on fMRI responses to identical sets of natural images presented to pairs of individuals, using the voxels on the visual cortex that covers from V1 through the ventral object areas without explicit labels of the visual areas. We decoded the converted brain activity patterns into the hierarchical visual features of a deep neural network using decoders pre-trained on the target subject and then reconstructed images via the decoded features. Without explicit information about the visual cortical hierarchy, the converters automatically learned the correspondence between visual areas of the same levels. Deep neural network feature decoding at each layer showed higher decoding accuracies from corresponding levels of visual areas, indicating that hierarchical representations were preserved after conversion. The visual images were reconstructed with recognizable silhouettes of objects even with relatively small numbers of data for converter training. The decoders trained on pooled data from multiple individuals through conversions led to a slight improvement over those trained on a single individual. These results demonstrate that the hierarchical and fine-grained representation can be converted by functional alignment, while preserving sufficient visual information to enable inter-individual visual image reconstruction

Improved fMRI-based Pain Prediction using Bayesian Group-wise Functional Registration

In recent years, neuroimaging has undergone a paradigm shift, moving away from the traditional brain mapping approach toward developing integrated, multivariate brain models that can predict categories of mental events. However, large interindividual differences in brain anatomy and functional localization after standard anatomical alignment remain a major limitation in performing this analysis, as it leads to feature misalignment across subjects in subsequent predictive models