We implement gradient-based variational inference routines for Wishart and inverse Wishart processes, which we apply as Bayesian models for the dynamic, heteroskedastic covariance matrix ofamultivariate timeseries.

The signaling capacity of a neural population depends on the scale and orientation of its covariance across trials. Estimating this noise covariance is challenging and is thought to require a large number of stereotyped trials. New approaches are therefore needed to interrogate the structure of neural noise across rich, naturalistic behaviors and sensory experiences, with few trials per condition. Here, we exploit the fact that conditions are smoothly parameterized in many experiments and leverage Wishart process models to pool statistical power from trials in neighboring conditions. We demonstrate that these models perform favorably on experimental data from the mouse visual cortex and monkey motor cortex relative to standard covariance estimators. Moreover, they produce smooth estimates of covariance as a function of stimulus parameters, enabling estimates of noise correlations in entirely unseen conditions as well as continuous estimates of Fisher information--a commonly used measure of signal fidelity. Together, our results suggest that Wishart processes are broadly applicable tools for quantification and uncertainty estimation of noise correlations in trial-limited regimes, paving the way toward understanding the role of noise in complex neural computations and behavior.

Recent work introduced deep kernel processes as an entirely kernel-based alternative to NNs (Aitchison et al. 2020).

They are themselves constructed from i.i.d. Gaussian processes, in analogy to the construction of Wishart or inverse Wishart random variables from i.i.d.

We develop a model by choosing the maximum entropy distribution from the set of models satisfying certain smoothness and independence criteria; we show that inference on this model generalizes local kernel estimation to the context of Bayesian inference on stochastic processes. Our model enables Bayesian inference in contexts when standard techniques like Gaussian process inference are too expensive to apply. Exact inference on our model is possible for any likelihood function from the exponential family. Inference is then highly efficient, requiring only O (log N) time and O (N) space at run time. We demonstrate our algorithm on several problems and show quantifiable improvement in both speed and performance relative to models based on the Gaussian process.

The signaling capacity of a neural population depends on the scale and orientation of its covariance across trials. Estimating this "noise" covariance is challenging and is thought to require a large number of stereotyped trials. New approaches are therefore needed to interrogate the structure of neural noise across rich, naturalistic behaviors and sensory experiences, with few trials per condition. Here, we exploit the fact that conditions are smoothly parameterized in many experiments and leverage Wishart process models to pool statistical power from trials in neighboring conditions. We demonstrate that these models perform favorably on experimental data from the mouse visual cortex and monkey motor cortex relative to standard covariance estimators.

A Bayesian nonparametric model known as the Wishart process has been shown to be effective in this situation, but its inference remains highly challenging. In this work, we introduce a Sequential Monte Carlo (SMC) sampler for the Wishart process, and show how it compares to conventional inference approaches, namely MCMC and variational inference. Using simulations we show that SMC sampling results in the most robust estimates and out-of-sample predictions of dynamic covariance. SMC especially outperforms the alternative approaches when using composite covariance functions with correlated parameters. We demonstrate the practical applicability of our proposed approach on a dataset of clinical depression (n = 1), and show how using an accurate representation of the posterior distribution can be used to test for dynamics on covariance.

We develop a model by choosing the maximum entropy distribution from the set of models satisfying certain smoothness and independence criteria; we show that inference on this model generalizes local kernel estimation to the context of Bayesian inference on stochastic processes. Our model enables Bayesian inference in contexts when standard techniques like Gaussian process inference are too expensive to apply. Exact inference on our model is possible for any likelihood function from the exponential family. Inference is then highly efficient, requiring only O (log N) time and O (N) space at run time. We demonstrate our algorithm on several problems and show quantifiable improvement in both speed and performance relative to models based on the Gaussian process.

Deep kernel processes are a recently introduced class of deep Bayesian models that have the flexibility of neural networks, but work entirely with Gram matrices. They operate by alternately sampling a Gram matrix from a distribution over positive semi-definite matrices, and applying a deterministic transformation. When the distribution is chosen to be Wishart, the model is called a deep Wishart process (DWP). This particular model is of interest because its prior is equivalent to a deep Gaussian process (DGP) prior, but at the same time it is invariant to rotational symmetries, leading to a simpler posterior distribution. Practical inference in the DWP was made possible in recent work ("A variational approximate posterior for the deep Wishart process" Ober and Aitchison 2021a) where the authors used a generalisation of the Bartlett decomposition of the Wishart distribution as the variational approximate posterior. However, predictive performance in that paper was less impressive than one might expect, with the DWP only beating a DGP on a few of the UCI datasets used for comparison. In this paper, we show that further generalising their distribution to allow linear combinations of rows and columns in the Bartlett decomposition results in better predictive performance, while incurring negligible additional computation cost.