Despite their immense success as a model of macaque visual cortex, deep convolutional neural networks (CNNs) have struggled to predict activity in visual cortex of the mouse, which is thought to be strongly dependent on the animal's behavioral state. Furthermore, most computational models focus on predicting neural responses to static images presented under head fixation, which are dramatically different from the dynamic, continuous visual stimuli that arise during movement in the real world. Consequently, it is still unknown how natural visual input and different behavioral variables may integrate over time to generate responses in primary visual cortex (V1). To address this, we introduce a multimodal recurrent neural network that integrates gaze-contingent visual input with behavioral and temporal dynamics to explain V1 activity in freely moving mice. We show that the model achieves state-of-the-art predictions of V1 activity during free exploration and demonstrate the importance of each component in an extensive ablation study. Analyzing our model using maximally activating stimuli and saliency maps, we reveal new insights into cortical function, including the prevalence of mixed selectivity for behavioral variables in mouse V1. In summary, our model offers a comprehensive deep-learning framework for exploring the computational principles underlying V1 neurons in freely-moving animals engaged in natural behavior.

The full procedure of data collection and data preprocessing is described in detail in Ref. [ In addition, a top-down camera recorded the mouse in the arena at 60 Hz . Kernel size 7 performed best. We repeated the grid search for CNNs with different number of convolutional layers. We initially hypothesized that an autoencoder could provide regularization benefits over a "vanilla" CNN, because the reconstruction loss might encourage the model to learn visual features that are useful for decoding. After hyperparameter search, we settled on size 256 for the latent space vector, and the weight of the reconstruction loss relative to the Poisson loss was fixed at 0.5.

Analyzing our model using maximally activating stimuli and saliency maps, we reveal new insights into cortical function, including the prevalence of mixed selectivity for behavioral variables in mouse V1.

Contextual anomaly detection (CAD) aims to identify anomalies in a target (behavioral) variable conditioned on a set of contextual variables that influence the normalcy of the target variable but are not themselves indicators of anomaly. In many anomaly detection tasks, there exist contextual variables that influence the normalcy of the target variable but are not themselves indicators of anomaly. In this work, we propose a novel framework for CAD, normalcy score (NS), that explicitly models both the aleatoric and epistemic uncertainties. Built on heteroscedastic Gaussian process regression, our method regards the Z-score as a random variable, providing confidence intervals that reflect the reliability of the anomaly assessment. Through experiments on benchmark datasets and a real-world application in cardiology, we demonstrate that NS outperforms state-of-the-art CAD methods in both detection accuracy and interpretability. Moreover, confidence intervals enable an adaptive, uncertainty-driven decision-making process, which may be very important in domains such as healthcare.

Despite their immense success as a model of macaque visual cortex, deep convolutional neural networks (CNNs) have struggled to predict activity in visual cortex of the mouse, which is thought to be strongly dependent on the animal's behavioral state. Furthermore, most computational models focus on predicting neural responses to static images presented under head fixation, which are dramatically different from the dynamic, continuous visual stimuli that arise during movement in the real world. Consequently, it is still unknown how natural visual input and different behavioral variables may integrate over time to generate responses in primary visual cortex (V1). To address this, we introduce a multimodal recurrent neural network that integrates gaze-contingent visual input with behavioral and temporal dynamics to explain V1 activity in freely moving mice. We show that the model achieves state-of-the-art predictions of V1 activity during free exploration and demonstrate the importance of each component in an extensive ablation study. Analyzing our model using maximally activating stimuli and saliency maps, we reveal new insights into cortical function, including the prevalence of mixed selectivity for behavioral variables in mouse V1.

Recent advances in recording technology have allowed neuroscientists to monitor activity from thousands of neurons simultaneously. Latent variable models are increasingly valuable for distilling these recordings into compact and interpretable representations. Here we propose a new approach to neural data analysis that leverages advances in conditional generative modeling to enable the unsupervised inference of disentangled behavioral variables from recorded neural activity. Our approach builds on InfoDiffusion, which augments diffusion models with a set of latent variables that capture important factors of variation in the data. We apply our model, called Generating Neural Observations Conditioned on Codes with High Information (GNOCCHI), to time series neural data and test its application to synthetic and biological recordings of neural activity during reaching. In comparison to a VAE-based sequential autoencoder, GNOCCHI learns higher-quality latent spaces that are more clearly structured and more disentangled with respect to key behavioral variables. These properties enable accurate generation of novel samples (unseen behavioral conditions) through simple linear traversal of the latent spaces produced by GNOCCHI. Our work demonstrates the potential of unsupervised, information-based models for the discovery of interpretable latent spaces from neural data, enabling researchers to generate high-quality samples from unseen conditions.

Accurate predictive models of the visual cortex neural response to natural visual stimuli remain a challenge in computational neuroscience. In this work, we introduce V1T, a novel Vision Transformer based architecture that learns a shared visual and behavioral representation across animals. We evaluate our model on two large datasets recorded from mouse primary visual cortex and outperform previous convolution-based models by more than 12.7% in prediction performance. Moreover, we show that the self-attention weights learned by the Transformer correlate with the population receptive fields. Our model thus sets a new benchmark for neural response prediction and can be used jointly with behavioral and neural recordings to reveal meaningful characteristic features of the visual cortex.