This factorization enables closed-form updates during optimization (see below).

Latent variable models are ubiquitous in the exploratory analysis of neural population recordings, where they allow researchers to summarize the activity of large populations of neurons in lower dimensional'latent' spaces. Existing methods can generally be categorized into (i) Bayesian methods that facilitate flexible incorporation of prior knowledge and uncertainty estimation, but which typically do not scale to large datasets; and (ii) highly parameterized methods without explicit priors that scale better but often struggle in the low-data regime. Here, we bridge this gap by developing a fully Bayesian yet scalable version of Gaussian process factor analysis (bGPFA), which models neural data as arising from a set of inferred latent processes with a prior that encourages smoothness over time. Additionally, bGPFA uses automatic relevance determination to infer the dimensionality of neural activity directly from the training data during optimization. To enable the analysis of continuous recordings without trial structure, we introduce a novel variational inference strategy that scales near-linearly in time and also allows for non-Gaussian noise models appropriate for electrophysiological recordings.

Taken together, these results further validate the utility of bGPFA on both synthetic and biological data with non-conjugate noise models.

Taken together, these results further validate the utility of bGPFA on both synthetic and biological data with non-conjugate noise models.

We propose Network Automatic Relevance Determination (NARD), an extension of ARD for linearly probabilistic models, to simultaneously model sparse relationships between inputs $X \in \mathbb R^{d \times N}$ and outputs $Y \in \mathbb R^{m \times N}$, while capturing the correlation structure among the $Y$. NARD employs a matrix normal prior which contains a sparsity-inducing parameter to identify and discard irrelevant features, thereby promoting sparsity in the model. Algorithmically, it iteratively updates both the precision matrix and the relationship between $Y$ and the refined inputs. To mitigate the computational inefficiencies of the $\mathcal O(m^3 + d^3)$ cost per iteration, we introduce Sequential NARD, which evaluates features sequentially, and a Surrogate Function Method, leveraging an efficient approximation of the marginal likelihood and simplifying the calculation of determinant and inverse of an intermediate matrix. Combining the Sequential update with the Surrogate Function method further reduces computational costs. The computational complexity per iteration for these three methods is reduced to $\mathcal O(m^3+p^3)$, $\mathcal O(m^3 + d^2)$, $\mathcal O(m^3+p^2)$, respectively, where $p \ll d$ is the final number of features in the model. Our methods demonstrate significant improvements in computational efficiency with comparable performance on both synthetic and real-world datasets.

Latent variable models are ubiquitous in the exploratory analysis of neural population recordings, where they allow researchers to summarize the activity of large populations of neurons in lower dimensional'latent' spaces. Existing methods can generally be categorized into (i) Bayesian methods that facilitate flexible incorporation of prior knowledge and uncertainty estimation, but which typically do not scale to large datasets; and (ii) highly parameterized methods without explicit priors that scale better but often struggle in the low-data regime. Here, we bridge this gap by developing a fully Bayesian yet scalable version of Gaussian process factor analysis (bGPFA), which models neural data as arising from a set of inferred latent processes with a prior that encourages smoothness over time. Additionally, bGPFA uses automatic relevance determination to infer the dimensionality of neural activity directly from the training data during optimization. To enable the analysis of continuous recordings without trial structure, we introduce a novel variational inference strategy that scales near-linearly in time and also allows for non-Gaussian noise models appropriate for electrophysiological recordings.

Tensors or multi-way arrays naturally occur in practically all areas of science including psychology (i.e., human responses to questionnaire data according to scoring criteria of different objects), chemometrics (i.e., excitation and emission spectra across samples), biology (i.e., genetic expression of cell proles across time and experimental conditions), and knowledge representations (i.e., entity-entity relationships across predicates), see also [1] and references therein. To analyze these multi-way arrays accounting for their higher order structure tensor decompositions have become important tools to characterize and discover structure in these data, see [2, 1] for details. Tensor decompositions have historically focused on maximum likelihood estimation methods to obtain a point estimate to decompose the data, most predominately based on Gaussian likelihood (least squares estimation). Recently, there has been a rise in the development of Bayesian inference for tensor data, initially focusing on binary or count data, but now applied more broadly to various types of data, for an overview see [3, 4]. The benets of a Bayesian approach are that it characterizes the decomposition solution as a distribution, the so-called posterior distribution, which allows characterization of the uncertainty whereas priors acts as regularizers adding robustness and preventing issues of degeneracy. Additionally, it provides a principled way to incorporate a priori information. For a review on maximum likelihood based and Bayesian tensor decomposition, see [2] and [3], respectively. The two most common tensor decomposition methods are the Canonical Polyadic Decomposition/PARAFAC (CPD) and Tucker model. The CPD model represents the data through a sum of outer product rank-1 terms (i.e., separate multi-linear structures), whereas Tucker uses a multi-linear rank decomposition (i.e., with "connected" multi-linear structures).