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The ability to record activities from hundreds of neurons simultaneously in the brain has placed an increasing demand for developing appropriate statistical techniques to analyze such data. Recently, deep generative models have been proposed to fit neural population responses. While these methods are flexible and expressive, the downside is that they can be difficult to interpret and identify. To address this problem, we propose a method that integrates key ingredients from latent models and traditional neural encoding models. Our method, pi-VAE, is inspired by recent progress on identifiable variational auto-encoder, which we adapt to make appropriate for neuroscience applications. Specifically, we propose to construct latent variable models of neural activity while simultaneously modeling the relation between the latent and task variables (non-neural variables, e.g. sensory, motor, and other externally observable states). The incorporation of task variables results in models that are not only more constrained, but also show qualitative improvements in interpretability and identifiability. We validate pi-VAE using synthetic data, and apply it to analyze neurophysiological datasets from rat hippocampus and macaque motor cortex. We demonstrate that pi-VAE not only fits the data better, but also provides unexpected novel insights into the structure of the neural codes.

Understanding how grid cells perform path integration calculations remains a fundamental problem. In this paper, we conduct theoretical analysis of a general representation model of path integration by grid cells, where the 2D self-position is encoded as a higher dimensional vector, and the 2D self-motion is represented by a general transformation of the vector. We identify two conditions on the transformation. One is a group representation condition that is necessary for path integration. The other is an isotropic scaling condition that ensures locally conformal embedding, so that the error in the vector representation translates conformally to the error in the 2D self-position. Then we investigate the simplest transformation, i.e., the linear transformation, uncover its explicit algebraic and geometric structure as matrix Lie group of rotation, and explore the connection between the isotropic scaling condition and a special class of hexagon grid patterns. Finally, with our optimization-based approach, we manage to learn hexagon grid patterns that share similar properties of the grid cells in the rodent brain. The learned model is capable of accurate long distance path integration. Code is available at https://github.com/ruiqigao/grid-cell-path.

Calcium imaging is a critical tool for measuring the activity of large neural populations. Much effort has been devoted to developing "pre-processing" tools for calcium video data, addressing the important issues of e.g., motion correction, denoising, compression, demixing, and deconvolution. However, statistical modeling of deconvolved calcium signals (i.e., the estimated activity extracted by a pre-processing pipeline) is just as critical for interpreting calcium measurements, and for incorporating these observations into downstream probabilistic encoding and decoding models. Surprisingly, these issues have to date received significantly less attention. In this work we examine the statistical properties of the deconvolved activity estimates, and compare probabilistic models for these random signals. In particular, we propose a zero-inflated gamma (ZIG) model, which characterizes the calcium responses as a mixture of a gamma distribution and a point mass that serves to model zero responses. We apply the resulting models to neural encoding and decoding problems. We find that the ZIG model outperforms simpler models (e.g., Poisson or Bernoulli models) in the context of both simulated and real neural data, and can therefore play a useful role in bridging calcium imaging analysis methods with tools for analyzing activity in large neural populations., Comment: Accepted for publication in Neurons, Behavior, Data analysis, and Theory

Recent work suggests goal-driven training of neural networks can be used to model neural activity in the brain. While response properties of neurons in artificial neural networks bear similarities to those in the brain, the network architectures are often constrained to be different. Here we ask if a neural network can recover both neural representations and, if the architecture is unconstrained and optimized, the anatomical properties of neural circuits. We demonstrate this in a system where the connectivity and the functional organization have been characterized, namely, the head direction circuits of the rodent and fruit fly. We trained recurrent neural networks (RNNs) to estimate head direction through integration of angular velocity. We found that the two distinct classes of neurons observed in the head direction system, the Compass neurons and the Shifter neurons, emerged naturally in artificial neural networks as a result of training. Furthermore, connectivity analysis and in-silico neurophysiology revealed structural and mechanistic similarities between artificial networks and the head direction system. Overall, our results show that optimization of RNNs in a goal-driven task can recapitulate the structure and function of biological circuits, suggesting that artificial neural networks can be used to study the brain at the level of both neural activity and anatomical organization., Comment: International Conference on Learning Representations (ICLR) 2020