Han-Lin Hsieh

Han-Lin Hsieh, Maryam M. Shanechi

Dimensionality reduction is critical across various domains of science including neuroscience. Probabilistic Principal Component Analysis (PPCA) is a prominent dimensionality reduction method that provides a probabilistic approach unlike the deterministic approach of PCA and serves as a connection between PCA and Factor Analysis (FA). Despite their power, PPCA and its extensions are mainly based on linear models and can only describe the data in a Euclidean coordinate system. However, in many neuroscience applications, data may be distributed around a nonlinear geometry (i.e., manifold) rather than lying in the Euclidean space. We develop Probabilistic Geometric Principal Component Analysis (PGPCA) for such datasets as a new dimensionality reduction algorithm that can explicitly incorporate knowledge about a given nonlinear manifold that is first fitted from these data. Further, we show how in addition to the Euclidean coordinate system, a geometric coordinate system can be derived for the manifold to capture the deviations of data from the manifold and noise. We also derive a data-driven EM algorithm for learning the PGPCA model parameters. As such, PGPCA generalizes PPCA to better describe data distributions by incorporating a nonlinear manifold geometry. In simulations and brain data analyses, we show that PGPCA can effectively model the data distribution around various given manifolds and outperforms PPCA for such data. Moreover, PGPCA provides the capability to test whether the new geometric coordinate system better describes the data than the Euclidean one. Finally, PGPCA can perform dimensionality reduction and learn the data distribution both around and on the manifold. These capabilities make PGPCA valuable for enhancing the efficacy of dimensionality reduction for analysis of high-dimensional data that exhibit noise and are distributed around a nonlinear manifold.

DongKyu Kim, Han-Lin Hsieh, Maryam M. Shanechi

Neural population activity often exhibits regime-dependent non-stationarity in the form of switching dynamics. Learning accurate switching dynamical system models can reveal how behavior is encoded in neural activity. Existing switching approaches have primarily focused on learning models from a single neural modality, either continuous Gaussian signals or discrete Poisson signals. However, multiple neural modalities are often recorded simultaneously to measure different spatiotemporal scales of brain activity, and all these modalities can encode behavior. Moreover, regime labels are typically unavailable in training data, posing a significant challenge for learning models of regime-dependent switching dynamics. To address these challenges, we develop a novel unsupervised learning algorithm that learns the parameters of switching multiscale dynamical system models using only multiscale neural observations. We demonstrate our method using both simulations and two distinct experimental datasets with multimodal spike-LFP observations during different motor tasks. We find that our switching multiscale dynamical system models more accurately decode behavior than switching single-scale dynamical models, showing the success of multiscale neural fusion. Further, our models outperform stationary multiscale models, illustrating the importance of tracking regime-dependent non-stationarity in multimodal neural data. The developed unsupervised learning framework enables more accurate modeling of complex multiscale neural dynamics by leveraging information in multimodal recordings while incorporating regime switches. This approach holds promise for improving the performance and robustness of brain-computer interfaces over time and for advancing our understanding of the neural basis of behavior.