Biology subjects

Bahrami, M.

Publications and source records attributed to Bahrami, M..

2 recordsLinked to original sources

bioRxiv2021

A Mixed-Modeling Framework for Whole-Brain Dynamic Network Analysis

The emerging area of dynamic brain network analysis has gained considerable attraction in recent years. While current tools have proven useful in providing insight into dynamic patterns of brain networks, development of multivariate statistical frameworks that allow for examining the associations between phenotypic traits and dynamic patterns of system-level properties of the brain, and drawing statistical inference about such associations, has largely lagged behind. To address this need we developed a mixed-modeling framework that allows for assessing the relationship between any desired phenotype and dynamic patterns of whole-brain connectivity and topology. Unlike current tools which largely use data-driven methods, our model-based method enables aligning neuroscientific hypotheses with the analytic approach. We demonstrate the utility of this model in identifying the relationship between fluid intelligence and dynamic brain networks using resting-state fMRI (rfMRI) data from 200 subjects in the Human Connectome Project (HCP) study. To our knowledge, this approach provides the first model-based statistical method for examining dynamic patterns of system-level properties of the brain and their relationships to phenotypic traits.

neuroscience↗

bioRxiv2020

Deep feature extraction of single-cell transcriptomes by generative adversarial network

MotivationSingle-cell RNA-sequencing (scRNA-seq) has opened the opportunities to dissect the heterogeneous cellular composition and interrogate the cell-type-specific gene expression patterns across diverse conditions. However, batch effects such as laboratory conditions and individual-variability hinder their usage in cross-condition design. ResultsWe present single-cell Generative Adversarial Network (scGAN). Our main contribution is to introduce an adversarial network to predict batch effects using the embeddings from the variational autoencoder network, which does not only need to maximize the Negative Binomial data likelihood of the raw scRNA-seq counts but also minimize the correlation between the latent embeddings and the batch effects. We demonstrate scGAN on three public scRNA-seq datasets and show that our method confers superior performance over the state-of-the-art methods in forming clusters of known cell types and identifying known psychiatric genes that are associated with major depressive disorder. AvailabilityThe code is available at https://github.com/li-lab-mcgill/singlecell-deepfeature Contactyueli@cs.mcgill.ca

bioinformatics↗