Systems neuroscience aims to understand how networks of neurons distributed throughout the brain mediate computational tasks. One popular approach to identify those networks is to first calculate measures of neural activity (e.g. power spectra) from multiple brain regions, and then apply a linear factor model to those measures. Critically, despite the established role of directed communication between brain regions in neural computation, measures of directed communication have been rarely utilized in network estimation because they are incompatible with the implicit assumptions of the linear factor model approach. Here, we develop a novel spectral measure of directed communication called the Directed Spectrum (DS). We prove that it is compatible with the implicit assumptions of linear factor models, and we provide a method to estimate the DS. We demonstrate that latent linear factor models of DS measures better capture underlying brain networks in both simulated and real neural recording data compared to available alternatives. Thus, linear factor models of the Directed Spectrum offer neuroscientists a simple and effective way to explicitly model directed communication in networks of neural populations.

In neuropsychiatric disorders such as schizophrenia or depression, there is often a disruption in the way that regions of the brain synchronize with one another. To facilitate understanding of network-level synchronization between brain regions, we introduce a novel model of multisite low-frequency neural recordings, such as local field potentials (LFPs) and electroencephalograms (EEGs). The proposed model, named Cross-Spectral Factor Analysis (CSFA), breaks the observed signal into factors defined by unique spatio-spectral properties. These properties are granted to the factors via a Gaussian process formulation in a multiple kernel learning framework. In this way, the LFP signals can be mapped to a lower dimensional space in a way that retains information of relevance to neuroscientists. Critically, the factors are interpretable. The proposed approach empirically allows similar performance in classifying mouse genotype and behavioral context when compared to commonly used approaches that lack the interpretability of CSFA. We also introduce a semi-supervised approach, termed discriminative CSFA (dCSFA). CSFA and dCSFA provide useful tools for understanding neural dynamics, particularly by aiding in the design of causal follow-up experiments.

We consider the analysis of Electroencephalography (EEG) and Local Field Potential (LFP) datasets, which are “big” in terms of the size of recorded data but rarely have sufficient labels required to train complex models (e.g., conventional deep learning methods). Furthermore, in many scientific applications, the goal is to be able to understand the underlying features related to the classification, which prohibits the blind application of deep networks. This motivates the development of a new model based on {\em parameterized} convolutional filters guided by previous neuroscience research; the filters learn relevant frequency bands while targeting synchrony, which are frequency-specific power and phase correlations between electrodes. This results in a highly expressive convolutional neural network with only a few hundred parameters, applicable to smaller datasets. The proposed approach is demonstrated to yield competitive (often state-of-the-art) predictive performance during our empirical tests while yielding interpretable features. Furthermore, a Gaussian process adapter is developed to combine analysis over distinct electrode layouts, allowing the joint processing of multiple datasets to address overfitting and improve generalizability. Finally, it is demonstrated that the proposed framework effectively tracks neural dynamics on children in a clinical trial on Autism Spectrum Disorder.

Multi-output Gaussian processes provide a convenient framework for multi-task problems. An illustrative and motivating example of a multi-task problem is multi-region electrophysiological time-series data, where experimentalists are interested in both power and phase coherence between channels. Recently, Wilson and Adams (2013) proposed the spectral mixture (SM) kernel to model the spectral density of a single task in a Gaussian process framework. In this paper, we develop a novel covariance kernel for multiple outputs, called the cross-spectral mixture (CSM) kernel. This new, flexible kernel represents both the power and phase relationship between multiple observation channels. We demonstrate the expressive capabilities of the CSM kernel through implementation of a Bayesian hidden Markov model, where the emission distribution is a multi-output Gaussian process with a CSM covariance kernel. Results are presented for measured multi-region electrophysiological data.