eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity …

A Anguita-Ruiz, A Segura-Delgado… - PLoS computational …, 2020 - journals.plos.org
Until date, several machine learning approaches have been proposed for the dynamic
modeling of temporal omics data. Although they have yielded impressive results in terms of …

Causal connectivity measures for pulse-output network reconstruction: Analysis and applications

ZK Tian, K Chen, S Li… - Proceedings of the …, 2024 - National Acad Sciences
The causal connectivity of a network is often inferred to understand network function. It is
arguably acknowledged that the inferred causal connectivity relies on the causality measure …

Causal inference in nonlinear systems: Granger causality versus time-delayed mutual information

S Li, Y Xiao, D Zhou, D Cai - Physical Review E, 2018 - APS
The Granger causality (GC) analysis has been extensively applied to infer causal
interactions in dynamical systems arising from economy and finance, physics …

Statistically inferred neuronal connections in subsampled neural networks strongly correlate with spike train covariances

T Liang, BAW Brinkman - Physical Review E, 2024 - APS
Statistically inferred neuronal connections from observed spike train data are often skewed
from ground truth by factors such as model mismatch, unobserved neurons, and limited data …

Hierarchy of neural organization in the embryonic spinal cord: Granger-causality graph analysis of in vivo calcium imaging data

FDV Fallani, M Corazzol, JR Sternberg… - … on Neural Systems …, 2014 - ieeexplore.ieee.org
The recent development of genetically encoded calcium indicators enables monitoring in
vivo the activity of neuronal populations. Most analysis of these calcium transients relies on …

Distributed network reconstruction based on binary compressed sensing via ADMM

Y Liu, K Huang, C Yang, Z Wang - IEEE Transactions on …, 2023 - ieeexplore.ieee.org
At present, network model is a general framework for the representation of complex system,
and its structure is the fundamental and prerequisite for control and other applications of …

Designing patient-specific optimal neurostimulation patterns for seizure suppression

RA Sandler, K Geng, D Song, RE Hampson… - Neural …, 2018 - direct.mit.edu
Neurostimulation is a promising therapy for abating epileptic seizures. However, it is
extremely difficult to identify optimal stimulation patterns experimentally. In this study, human …

Distributed evidence accumulation across macaque large-scale neocortical networks during perceptual decision making

L Zou, N Palomero-Gallagher, D Zhou, S Li, JF Mejias - bioRxiv, 2023 - biorxiv.org
Despite the traditional view of parietal cortex as an important region for perceptual decision-
making, recent evidence suggests that sensory accumulation occurs simultaneously across …

Compressive sensing inference of neuronal network connectivity in balanced neuronal dynamics

VJ Barranca, D Zhou - Frontiers in neuroscience, 2019 - frontiersin.org
Determining the structure of a network is of central importance to understanding its function
in both neuroscience and applied mathematics. However, recovering the structural …

Analysis of sampling artifacts on the Granger causality analysis for topology extraction of neuronal dynamics

D Zhou, Y Zhang, Y Xiao, D Cai - Frontiers in computational …, 2014 - frontiersin.org
Granger causality (GC) is a powerful method for causal inference for time series. In general,
the GC value is computed using discrete time series sampled from continuous-time …