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.

Visual search is a ubiquitous and often challenging daily task, exemplified by looking for the car keys at home or a friend in a crowd. An intriguing property of some classical search tasks is an asymmetry such that finding a target A among distractors B can be easier than finding B among A. To elucidate the mechanisms responsible for asymmetry in visual search, we propose a computational model that takes a target and a search image as inputs and produces a sequence of eye movements until the target is found.

A.1 Does our neural regression method work? To ensure our neural regression method works, we verify its efficacy on a known benchmark: the activity of 256 cells in the V4 and IT regions of two Rhesus macaque monkeys, a core component of BrainScore [4]. BrainScore's in-house method involves a combination of principal components analysis (for dimensionality reduction) and k-fold cross-validated partial least squares regression (for the linear mapping of model to brain activity). Here, we exchange principal components analysis for sparse random projection and partial least squares regression for ridge regression with generalized cross-validation. We compute the scores for each benchmark in the same fashion as BrainScore: as the Pearson correlation coefficient between the actual and predicted (cross-validated) activity of the biological neurons in the V4 and IT samples.

Traditionally convolutional neural network architectures have been designed by stacking layers on top of each other to form deeper hierarchical networks. The cortex in the brain however does not just stack layers as done in standard convolution neural networks, instead different regions are organized next to each other in a large single sheet of neurons. Biological neurons self organize to form topographic maps, where neurons encoding similar stimuli group together to form logical clusters. Here we propose new self-organization principles that allow for the formation of hierarchical cortical regions (i.e.