A fine-grained account of functional selectivity in the cortex is essential for understanding how visual information is processed and represented in the brain. Classical studies using designed experiments have identified multiple category-selective regions; however, these approaches rely on preconceived hypotheses about categories. Subsequent data-driven discovery methods have sought to address this limitation but are often limited by simple, typically linear encoding models. We propose an in silico approach for data-driven discovery of novel category-selectivity hypotheses based on an encoder-decoder transformer model. The architecture incorporates a brain-region to image-feature cross-attention mechanism, enabling nonlinear mappings between high-dimensional deep network features and semantic patterns encoded in the brain activity. We further introduce a method to characterize the selectivity of individual parcels by leveraging diffusion-based image generative models and large-scale datasets to synthesize and select images that maximally activate each parcel. Our approach reveals regions with complex, compositional selectivity involving diverse semantic concepts, which we validate in silico both within and across subjects. Using a brain encoder as a "digital twin" offers a powerful, data-driven framework for generating and testing hypotheses about visual selectivity in the human brain--hypotheses that can guide future fMRI experiments.

Understanding functional representations within higher visual cortex is a fundamental question in computational neuroscience. While artificial neural networks pretrained on large-scale datasets exhibit striking representational alignment with human neural responses, learning image-computable models of visual cortex relies on individual-level, large-scale fMRI datasets. The necessity for expensive, time-intensive, and often impractical data acquisition limits the generalizability of encoders to new subjects and stimuli. BraInCoRL uses incontext learning to predict voxelwise neural responses from few-shot examples without any additional finetuning for novel subjects and stimuli.

The ability to extract oriented edges from visual input is a core computation across animal vision systems. Orientation maps, long associated with the layered architecture of the mammalian visual cortex, systematically organise neurons by their preferred edge orientation. Despite lacking cortical structures, the Drosophila melanogaster brain contains feature-selective neurons and exhibits complex visual detection capacity, raising the question of whether map-like vision representations can emerge without cortical infrastructure. We integrate a complete fruit fly brain connectome with biologically grounded spiking neuron models to simulate neuroprocessing in the fly visual system. By driving the network with oriented stimuli and analysing downstream responses, we show that coherent orientation maps can emerge from purely connectome-constrained dynamics. These results suggest that species of independent origin could evolve similar visual structures.

Deep neural networks trained to predict neural activity from visual input and behaviour have shown great potential to serve as digital twins of the visual cortex. Per-neuron embeddings derived from these models could potentially be used to map the functional landscape or identify cell types. However, state-of-the-art predictive models of mouse V1 do not generate functional embeddings that exhibit clear clustering patterns which would correspond to cell types. This raises the question whether the lack of clustered structure is due to limitations of current models or a true feature of the functional organization of mouse V1. In this work, we introduce DECEMber - Deep Embedding Clustering via Expectation Maximization-based refinement - an explicit inductive bias into predictive models that enhances clustering by adding an auxiliary t-distribution-inspired loss function that enforces structured organization among per-neuron embeddings.

Invariant object recognition-the ability to identify objects despite changes in appearance-is a hallmark of visual processing in the brain, yet its understanding remains a central challenge in systems neuroscience. Artificial neural networks trained to predict neural responses to visual stimuli ("digital twins") could provide a powerful framework for studying such complex computations in silico. However, while current models accurately capture single-neuron responses within individual visual areas, their ability to reproduce how populations of neurons represent object identity, and how these representations transform across the cortical hierarchy, remains largely unexplored. Here we examine key functional signatures observed experimentally and find that current models account for hierarchical changes in basic single-neuron properties, such as receptive field size, but fail to capture more complex population-level phenomena, particularly invariant object representations. To address this gap, we introduce a biologically inspired hierarchical readout scheme that mirrors cortical anatomy, modeling each visual area as a projection from a distinct depth within a shared core network. This approach significantly improves the prediction of population-level representational transformations, outperforming standard models that use only the final layer, as well as alternatives with modified architecture, regularization, and loss function. Our results suggest that incorporating anatomical information provides a strong inductive bias in digital twin models, enabling them to better capture general principles of brain function.

Biological and artificial vision systems both rely on hierarchical architectures, yet it remains unclear how their representational geometry evolves across processing stages, and what functional consequences may arise from potential differences. In this work, we systematically quantify and compare the linear and nonlinear dimensionality of human brain activity (fMRI) and artificial neural networks (ANNs) during natural image viewing. In the human ventral visual stream, both dimensionality measures increase along the visual hierarchy, supporting the emergence of semantic and abstract representations. For linear dimensionality, most ANNs show a similar increase, but only for pooled features, emphasizing the importance of appropriate feature readouts in brain-model comparisons. In contrast, nonlinear dimensionality shows a collapse in the later layers of ANNs, pointing at a mismatch in representational geometry between the human and artificial visual systems. This mismatch may have functional consequences: while high-dimensional brain representations support flexible generalization to abstract features, ANNs appear to lose this capacity in later layers, where their representations become overly compressed. Overall, our findings propose dimensionality alignment as a benchmark for building more flexible and biologically grounded vision models.

The neural activity in the visual processing is influenced by both external stimuli and internal brain states. Ideally, a neural predictive model should account for both of them. Currently, there are no dynamic encoding models that explicitly model a latent state and the entire neuronal response distribution. We address this gap by proposing a probabilistic model that predicts the joint distribution of the neuronal responses from video stimuli and stimulus-independent latent factors. After training and testing our model on mouse V1 neuronal responses, we find that it outperforms video-only models in terms of log-likelihood and achieves improvements in likelihood and correlation when conditioned on responses from other neurons. Furthermore, we find that the learned latent factors strongly correlate with mouse behavior and that they exhibit patterns related to the neurons' position on the visual cortex, although the model was trained without behavior and cortical coordinates. Our findings demonstrate that unsupervised learning of latent factors from population responses can reveal biologically meaningful structure that bridges sensory processing and behavior, without requiring explicit behavioral annotations during training.

In recent years, the alignment between artificial neural network (ANN) embeddings and blood oxygenation level dependent (BOLD) responses in functional magnetic resonance imaging (fMRI) via neural encoding models has significantly advanced research on neural representation mechanisms and interpretability in the brain. However, these approaches remain limited in characterizing the brain's inherently nonlinear response properties. To address this, we propose the Jacobianbased Nonlinearity Evaluation (JNE), an interpretability metric for nonlinear neural encoding models. JNE quantifies nonlinearity by statistically measuring the dispersion of local linear mappings (Jacobians) from model representations to predicted BOLD responses, thereby approximating the nonlinearity of BOLD signals. Centered on proposing JNE as a novel interpretability metric, we validated its effectiveness through controlled simulation experiments on various activation functions and network architectures, and further verified it on real fMRI data, demonstrating a hierarchical progression of nonlinear characteristics from primary to higher-order visual cortices, consistent with established cortical organization. We further extended JNE with Sample-Specificity (JNE-SS), revealing stimulus-selective nonlinear response patterns in functionally specialized brain regions. As the first interpretability metric for quantifying nonlinear responses, JNE provides new insights into brain information processing.

Encoding models have been used to assess how the human brain represents concepts in language and vision. While language and vision rely on similar concept representations, current encoding models are typically trained and tested on brain responses to each modality in isolation. Recent advances in multimodal pretraining have produced transformers that can extract aligned representations of concepts in language and vision. In this work, we used representations from multimodal transformers to train encoding models that can transfer across fMRI responses to stories and movies. We found that encoding models trained on brain responses to one modality can successfully predict brain responses to the other modality, particularly in cortical regions that represent conceptual meaning. Further analysis of these encoding models revealed shared semantic dimensions that underlie concept representations in language and vision. Comparing encoding models trained using representations from multimodal and unimodal transformers, we found that multimodal transformers learn more aligned representations of concepts in language and vision. Our results demonstrate how multimodal transformers can provide insights into the brain's capacity for multimodal processing.

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach - Brain Diffusion for Visual Exploration ("BrainDiVE") - builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.