Mikio Aoi

Zhanqi Zhang, Shun Li, Bernardo L. Sabatini et al.

Intracortical brain-computer interfaces (BCIs) can decode speech from neural activity with high accuracy when trained on data pooled across recording sessions. In realistic deployment, however, models must generalize to new sessions without labeled data, and performance often degrades due to cross-session nonstationarities (e.g., electrode shifts, neural turnover, and changes in user strategy). In this paper, we propose ALIGN, a session-invariant learning framework based on multi-domain adversarial neural networks for semi-supervised cross-session adaptation. ALIGN trains a feature encoder jointly with a phoneme classifier and a domain classifier operating on the latent representation. Through adversarial optimization, the encoder is encouraged to preserve task-relevant information while suppressing session-specific cues. We evaluate ALIGN on intracortical speech decoding and find that it generalizes consistently better to previously unseen sessions, improving both phoneme error rate and word error rate relative to baselines. These results indicate that adversarial domain alignment is an effective approach for mitigating session-level distribution shift and enabling robust longitudinal BCI decoding.

Rabia Gondur, Usama Bin Sikandar, Evan Schaffer et al.

Characterizing the relationship between neural population activity and behavioral data is a central goal of neuroscience. While latent variable models (LVMs) are successful in describing high-dimensional time-series data, they are typically only designed for a single type of data, making it difficult to identify structure shared across different experimental data modalities. Here, we address this shortcoming by proposing an unsupervised LVM which extracts temporally evolving shared and independent latents for distinct, simultaneously recorded experimental modalities. We do this by combining Gaussian Process Factor Analysis (GPFA), an interpretable LVM for neural spiking data with temporally smooth latent space, with Gaussian Process Variational Autoencoders (GP-VAEs), which similarly use a GP prior to characterize correlations in a latent space, but admit rich expressivity due to a deep neural network mapping to observations. We achieve interpretability in our model by partitioning latent variability into components that are either shared between or independent to each modality. We parameterize the latents of our model in the Fourier domain, and show improved latent identification using this approach over standard GP-VAE methods. We validate our model on simulated multi-modal data consisting of Poisson spike counts and MNIST images that scale and rotate smoothly over time. We show that the multi-modal GP-VAE (MM-GPVAE) is able to not only identify the shared and independent latent structure across modalities accurately, but provides good reconstructions of both images and neural rates on held-out trials. Finally, we demonstrate our framework on two real world multi-modal experimental settings: Drosophila whole-brain calcium imaging alongside tracked limb positions, and Manduca sexta spike train measurements from ten wing muscles as the animal tracks a visual stimulus.

Michael Shvartsman, Narayanan Sundaram, Mikio C. Aoi et al.

Multivariate analysis of fMRI data has benefited substantially from advances in machine learning. Most recently, a range of probabilistic latent variable models applied to fMRI data have been successful in a variety of tasks, including identifying similarity patterns in neural data (Representational Similarity Analysis and its empirical Bayes variant, RSA and BRSA; Intersubject Functional Connectivity, ISFC), combining multi-subject datasets (Shared Response Mapping; SRM), and mapping between brain and behavior (Joint Modeling). Although these methods share some underpinnings, they have been developed as distinct methods, with distinct algorithms and software tools. We show how the matrix-variate normal (MN) formalism can unify some of these methods into a single framework. In doing so, we gain the ability to reuse noise modeling assumptions, algorithms, and code across models. Our primary theoretical contribution shows how some of these methods can be written as instantiations of the same model, allowing us to generalize them to flexibly modeling structured noise covariances. Our formalism permits novel model variants and improved estimation strategies: in contrast to SRM, the number of parameters for MN-SRM does not scale with the number of voxels or subjects; in contrast to BRSA, the number of parameters for MN-RSA scales additively rather than multiplicatively in the number of voxels. We empirically demonstrate advantages of two new methods derived in the formalism: for MN-RSA, we show up to 10x improvement in runtime, up to 6x improvement in RMSE, and more conservative behavior under the null. For MN-SRM, our method grants a modest improvement to out-of-sample reconstruction while relaxing an orthonormality constraint of SRM. We also provide a software prototyping tool for MN models that can flexibly reuse noise covariance assumptions and algorithms across models.

Anqi Wu, Mikio C. Aoi, Jonathan W. Pillow

An exciting branch of machine learning research focuses on methods for learning, optimizing, and integrating unknown functions that are difficult or costly to evaluate. A popular Bayesian approach to this problem uses a Gaussian process (GP) to construct a posterior distribution over the function of interest given a set of observed measurements, and selects new points to evaluate using the statistics of this posterior. Here we extend these methods to exploit derivative information from the unknown function. We describe methods for Bayesian optimization (BO) and Bayesian quadrature (BQ) in settings where first and second derivatives may be evaluated along with the function itself. We perform sampling-based inference in order to incorporate uncertainty over hyperparameters, and show that both hyperparameter and function uncertainty decrease much more rapidly when using derivative information. Moreover, we introduce techniques for overcoming ill-conditioning issues that have plagued earlier methods for gradient-enhanced Gaussian processes and kriging. We illustrate the efficacy of these methods using applications to real and simulated Bayesian optimization and quadrature problems, and show that exploting derivatives can provide substantial gains over standard methods.