AIMC Topic: Gene Regulatory Networks

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Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer.

Genome medicine
BACKGROUND: Contemporary deep learning approaches show cutting-edge performance in a variety of complex prediction tasks. Nonetheless, the application of deep learning in healthcare remains limited since deep learning methods are often considered as ...

PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks.

PloS one
Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as eff...

Single Cell RNA-Seq and Machine Learning Reveal Novel Subpopulations in Low-Grade Inflammatory Monocytes With Unique Regulatory Circuits.

Frontiers in immunology
Subclinical doses of LPS (SD-LPS) are known to cause low-grade inflammatory activation of monocytes, which could lead to inflammatory diseases including atherosclerosis and metabolic syndrome. Sodium 4-phenylbutyrate is a potential therapeutic compou...

Discriminating the single-cell gene regulatory networks of human pancreatic islets: A novel deep learning application.

Computers in biology and medicine
Analysis of single-cell pancreatic data can play an important role in understanding various metabolic diseases and health conditions. Due to the sparsity and noise present in such single-cell gene expression data, inference of single-cell gene regula...

Integrated analysis of multiple microarray studies to identify novel gene signatures in preeclampsia.

Placenta
INTRODUCTION: Preeclampsia (PE) is one of the major causes of maternal and fetal morbidity and mortality in pregnancy worldwide. However, the intrinsic molecular mechanisms underlying the pathogenesis of PE have not yet been fully elucidated.

On transformative adaptive activation functions in neural networks for gene expression inference.

PloS one
Gene expression profiling was made more cost-effective by the NIH LINCS program that profiles only ∼1, 000 selected landmark genes and uses them to reconstruct the whole profile. The D-GEX method employs neural networks to infer the entire profile. H...

Network-based drug sensitivity prediction.

BMC medical genomics
BACKGROUND: Drug sensitivity prediction and drug responsive biomarker selection on high-throughput genomic data is a critical step in drug discovery. Many computational methods have been developed to serve this purpose including several deep neural n...

Systems Approach to Pathogenic Mechanism of Type 2 Diabetes and Drug Discovery Design Based on Deep Learning and Drug Design Specifications.

International journal of molecular sciences
In this study, we proposed a systems biology approach to investigate the pathogenic mechanism for identifying significant biomarkers as drug targets and a systematic drug discovery strategy to design a potential multiple-molecule targeting drug for t...