arXiv subjects

John Magnotti

Publications and source records attributed to John Magnotti.

3 recordsLinked to original sources

arXiv2023

A Comparison of Neuroelectrophysiology Databases

As data sharing has become more prevalent, three pillars - archives, standards, and analysis tools - have emerged as critical components in facilitating effective data sharing and collaboration. This paper compares four freely available intracranial neuroelectrophysiology data repositories: Data Archive for the BRAIN Initiative (DABI), Distributed Archives for Neurophysiology Data Integration (DANDI), OpenNeuro, and Brain-CODE. The aim of this review is to describe archives that provide researchers with tools to store, share, and reanalyze both human and non-human neurophysiology data based on criteria that are of interest to the neuroscientific community. The Brain Imaging Data Structure (BIDS) and Neurodata Without Borders (NWB) are utilized by these archives to make data more accessible to researchers by implementing a common standard. As the necessity for integrating large-scale analysis into data repository platforms continues to grow within the neuroscientific community, this article will highlight the various analytical and customizable tools developed within the chosen archives that may advance the field of neuroinformatics.

q-bio.QM↗

arXiv2020

Interpretable Visualization and Higher-Order Dimension Reduction for ECoG Data

ElectroCOrticoGraphy (ECoG) technology measures electrical activity in the human brain via electrodes placed directly on the cortical surface during neurosurgery. Through its capability to record activity at a fast temporal resolution, ECoG experiments have allowed scientists to better understand how the human brain processes speech. By its nature, ECoG data is difficult for neuroscientists to directly interpret for two major reasons. Firstly, ECoG data tends to be large in size, as each individual experiment yields data up to several gigabytes. Secondly, ECoG data has a complex, higher-order nature. After signal processing, this type of data may be organized as a 4-way tensor with dimensions representing trials, electrodes, frequency, and time. In this paper, we develop an interpretable dimension reduction approach called Regularized Higher Order Principal Components Analysis, as well as an extension to Regularized Higher Order Partial Least Squares, that allows neuroscientists to explore and visualize ECoG data. Our approach employs a sparse and functional Candecomp-Parafac (CP) decomposition that incorporates sparsity to select relevant electrodes and frequency bands, as well as smoothness over time and frequency, yielding directly interpretable factors. We demonstrate the performance and interpretability of our method with an ECoG case study on audio and visual processing of human speech.

physics.med-ph↗

arXiv2020

Functional Group Bridge for Simultaneous Regression and Support Estimation

This article is motivated by studying multisensory effects on brain activities in intracranial electroencephalography (iEEG) experiments. Differential brain activities to multisensory stimulus presentations are zero in most regions and non-zero in some local regions, yielding locally sparse functions. Such studies are essentially a function-on-scalar regression problem, with interest being focused not only on estimating nonparametric functions but also on recovering the function supports. We propose a weighted group bridge approach for simultaneous function estimation and support recovery in function-on-scalar mixed effect models, while accounting for heterogeneity present in functional data. We use B-splines to transform sparsity of functions to its sparse vector counterpart of increasing dimension, and propose a fast non-convex optimization algorithm using nested alternative direction method of multipliers (ADMM) for estimation. Large sample properties are established. In particular, we show that the estimated coefficient functions are rate optimal in the minimax sense under the $L_2$ norm and resemble a phase transition phenomenon. For support estimation, we derive a convergence rate under the $L_{\infty}$ norm that leads to a sparsistency property under $\delta$-sparsity, and provide a simple sufficient regularity condition under which a strict sparsistency property is established. An adjusted extended Bayesian information criterion is proposed for parameter tuning. The developed method is illustrated through simulation and an application to a novel iEEG dataset to study multisensory integration. We integrate the proposed method into RAVE, an R package that gains increasing popularity in the iEEG community.

stat.ME↗