LIMO-GCN: a linear model-integrated graph convolutional network for predicting Alzheimer disease genes

CX Lin, HD Li, J Wang - Briefings in Bioinformatics, 2025 - academic.oup.com
Alzheimer's disease (AD) is a complex disease with its genetic etiology not fully understood.
Gene network-based methods have been proven promising in predicting AD genes …

Prediction of Lung Adenocarcinoma Driver Genes Through Protein–Protein Interaction Networks Utilizing GenePlexus

F Yuan, YH Zhang, FM Huang, X Cao, L Chen… - …, 2024 - Wiley Online Library
Lung adenocarcinoma, a subtype of lung cancer, is produced by uncontrolled proliferation of
somatic cells affected by some tumorigenic factors. The origin of this disease can be …

Open Biomedical Network Benchmark: A Python Toolkit for Benchmarking Datasets with Biomedical Networks

R Liu, A Krishnan - Machine Learning in Computational …, 2024 - proceedings.mlr.press
Over the past decades, network biology has been a major driver of computational methods
developed to better understand the functional roles of each gene in the human genome in …

Joint representation of molecular networks from multiple species improves gene classification

CA Mancuso, KA Johnson, R Liu… - PLOS Computational …, 2024 - journals.plos.org
Network-based machine learning (ML) has the potential for predicting novel genes
associated with nearly any health and disease context. However, this approach often uses …

ProteinWeaver: A Webtool to Visualize Ontology-Annotated Protein Networks

O Anderson, A Barelvi, A O'Brien, A Norman, I Jan… - bioRxiv, 2024 - biorxiv.org
Molecular interaction networks are a vital tool for studying biological systems. While many
tools exist that visualize a protein or a pathway within a network, no tool provides the ability …

nleval: A Python Toolkit for Generating Benchmarking Datasets for Machine Learning with Biological Networks

R Liu, A Krishnan - bioRxiv, 2023 - biorxiv.org
Recent breakthroughs in graph representation learning (GRL) methods have vastly
advanced many real-world applications where graph structures naturally arise, such as drug …

Network Biology Powered by Graph Deep Learning: Understanding the Molecular Basis of Human Genetics

R Liu - 2024 - search.proquest.com
Graph learning is revolutionizing the 25-year-old field of network biology by advancing our
ability to gain novel molecular insights into biological functions and complex diseases using …

Data-Driven Computational Approaches to Unravel and Interpret the Polygenic Architecture of Human Complex Traits and Diseases

AP McKim - 2024 - search.proquest.com
The genetics and mechanisms underlying most human traits and diseases can be very
complex, where the number of true gene associations can number in the many hundreds …

[PDF][PDF] Open Biomedical Network Benchmark

R Liu, A Krishnan - biorxiv.org
Over the past decades, network biology has been a major driver of computational methods
developed to better understand the functional roles of each gene in the human genome in …