Population activity measurement by calcium imaging can be combined with cellular resolution optogenetic activity perturbations to enable the mapping of neural connectivity in vivo. This requires accurate inference of perturbed and unperturbed neural activity from calcium imaging measurements, which are noisy and indirect, and can also be contaminated by photostimulation artifacts. We have developed a new fully Bayesian approach to jointly inferring spiking activity and neural connectivity from in vivo all-optical perturbation experiments. In contrast to standard approaches that perform spike inference and analysis in two separate maximum-likelihood phases, our joint model is able to propagate uncertainty in spike inference to the inference of connectivity and vice versa. We use the framework of variational autoencoders to model spiking activity using discrete latent variables, low-dimensional latent common input, and sparse spike-and-slab generalized linear coupling between neurons.

Naive Bayes algorithms are a set of supervised machine learning algorithms based on the Bayes probability theorem, which we'll discuss in this article. Naive Bayes algorithms assume that there's no correlation between features in a dataset used to train the model. In spite of this oversimplified assumption, naive Bayes classifiers work very well in many complex real-world problems. A big advantage of naive Bayes classifiers is that they only require a relatively small number of training data samples to perform classification efficiently, compared to other algorithms like logistic regression, decision trees, and support vector machines. Before we dive into the implementation, let's first cover some key terms related to naive Bayes.

A fundamental goal of systems neuroscience is to understand the relationship between neural activity and behavior. Behavior has traditionally been characterized by low-dimensional, task-related variables such as movement speed or response times. More recently, there has been a growing interest in automated analysis of high-dimensional video data collected during experiments. Here we introduce a probabilistic framework for the analysis of behavioral video and neural activity. This framework provides tools for compression, segmentation, generation, and decoding of behavioral videos.

Estimating graphical model structure from high-dimensional and undersampled data is a fundamental problem in many scientific fields. Existing approaches, such as GLASSO, latent variable GLASSO, and latent tree models, suffer from high computational complexity and may impose unrealistic sparsity priors in some cases. We introduce a novel method that leverages a newly discovered connection between information-theoretic measures and structured latent factor models to derive an optimization objective which encourages modular structures where each observed variable has a single latent parent. The proposed method has linear stepwise computational complexity w.r.t. the number of observed variables. Our experiments on synthetic data demonstrate that our approach is the only method that recovers modular structure better as the dimensionality increases.

The vertices represent the RVs, and the edges signify the conditional dependencies among the RVs. Structure learning is the process of inferring the edges by observing realizations of the RVs, and it has applications in a wide range of technological, social, and biological networks. Learning the structure of graphs when the vertices are treated in isolation from inferential information known about them is well-investigated. In a wide range of domains, however, often there exist additional inferred knowledge about the structure, which can serve as valuable side information. For instance, the gene networks that represent different subtypes of the same cancer share similar edges across all subtypes and also have exclusive edges corresponding to each subtype, rendering partially similar graphical models for gene expression in different cancer subtypes.

We consider constraint-based methods for causal structure learning, such as the PC algorithm or any PC-derived algorithms whose first step consists in pruning a complete graph to obtain an undirected graph skeleton, which is subsequently oriented. All constraint-based methods perform this first step of removing dispensable edges, iteratively, whenever a separating set and corresponding conditional independence can be found. Yet, constraint-based methods lack robustness over sampling noise and are prone to uncover spurious conditional independences in finite datasets. In particular, there is no guarantee that the separating sets identified during the iterative pruning step remain consistent with the final graph. In this paper, we propose a simple modification of PC and PC-derived algorithms so as to ensure that all separating sets identified to remove dispensable edges are consistent with the final graph,thus enhancing the explainability of constraint-basedmethods. It is achieved by repeating the constraint-based causal structure learning scheme, iteratively, while searching for separating sets that are consistent with the graph obtained at the previous iteration.

This manuscript contributes a general and practical framework for casting a Markov process model of a system at equilibrium as a structural causal model, and carrying out counterfactual inference. Markov processes mathematically describe the mechanisms in the system, and predict the system's equilibrium behavior upon intervention, but do not support counterfactual inference. In contrast, structural causal models support counterfactual inference, but do not identify the mechanisms. We define the structural causal models in terms of the parameters and the equilibrium dynamics of the Markov process models, and counterfactual inference flows from these settings. The proposed approach alleviates the identifiability drawback of the structural causal models, in that the counterfactual inference is consistent with the counterfactual trajectories simulated from the Markov process model. We illustrate that, in presence of Markov process model misspecification, counterfactual inference leverages prior data, and therefore estimates the outcome of an intervention more accurately than a direct simulation.

Many decision-making problems naturally exhibit pronounced structures inherited from the characteristics of the underlying environment. In a Markov decision process model, for example, two distinct states can have inherently related semantics or encode resembling physical state configurations. This often implies locally correlated transition dynamics among the states. In order to complete a certain task in such environments, the operating agent usually needs to execute a series of temporally and spatially correlated actions. Though there exists a variety of approaches to capture these correlations in continuous state-action domains, a principled solution for discrete environments is missing.

A graphical model is a structured representation of the data generating process. The traditional method to reason over random variables is to perform inference in this graphical model. However, in many cases the generating process is only a poor approximation of the much more complex true data generating process, leading to suboptimal estimation. The subtleties of the generative process are however captured in the data itself and we can learn to infer'', that is, learn a direct mapping from observations to explanatory latent variables. In this work we propose a hybrid model that combines graphical inference with a learned inverse model, which we structure as in a graph neural network, while the iterative algorithm as a whole is formulated as a recurrent neural network.

We study the problem of learning the transition matrices of a set of Markov chains from a single stream of observations on each chain. We assume that the Markov chains are ergodic but otherwise unknown. The learner can sample Markov chains sequentially to observe their states. The goal of the learner is to sequentially select various chains to learn transition matrices uniformly well with respect to some loss function. We introduce a notion of loss that naturally extends the squared loss for learning distributions to the case of Markov chains, and further characterize the notion of being \emph{uniformly good} in all problem instances.