Biological network analysis with deep learning

G Muzio, L O'Bray, K Borgwardt - Briefings in bioinformatics, 2021 - academic.oup.com
Recent advancements in experimental high-throughput technologies have expanded the
availability and quantity of molecular data in biology. Given the importance of interactions in …

Deep learning in omics: a survey and guideline

Z Zhang, Y Zhao, X Liao, W Shi, K Li… - Briefings in functional …, 2019 - academic.oup.com
Omics, such as genomics, transcriptome and proteomics, has been affected by the era of big
data. A huge amount of high dimensional and complex structured data has made it no …

Repository and mutation based particle swarm optimization (RMPSO): A new PSO variant applied to reconstruction of gene regulatory network

B Jana, S Mitra, S Acharyya - Applied Soft Computing, 2019 - Elsevier
Abstract Particle Swarm Optimization (PSO) is a meta-heuristic approach based on swarm
intelligence, which is inspired by the social behaviour of bird flocking or fish schooling. The …

A machine learning approach to simulate gene expression and infer gene regulatory networks

F Zito, V Cutello, M Pavone - Entropy, 2023 - mdpi.com
The ability to simulate gene expression and infer gene regulatory networks has vast
potential applications in various fields, including medicine, agriculture, and environmental …

Fuzzy logic based approaches for gene regulatory network inference

K Raza - Artificial intelligence in medicine, 2019 - Elsevier
The rapid advancements in high-throughput techniques have fueled large-scale production
of biological data at very affordable costs. Some of these techniques are microarrays and …

Integrative approaches to reconstruct regulatory networks from multi-omics data: a review of state-of-the-art methods

N Wani, K Raza - Computational biology and chemistry, 2019 - Elsevier
Data generation using high throughput technologies has led to the accumulation of diverse
types of molecular data. These data have different types (discrete, real, string, etc.) and …

Consequential innovations in nature-inspired intelligent computing techniques for biomarkers and potential therapeutics identification

K Sheikh, S Sayeed, A Asif, MF Siddiqui… - … computing techniques in …, 2022 - Springer
Computational biology has changed how healthcare systems and biomedical engineering
work. Nature-inspired intelligent computing (NIIC) approaches in predicting potential …

A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints

S Barbosa, B Niebel, S Wolf, K Mauch, R Takors - Biosystems, 2018 - Elsevier
The study of biological systems at a system level has become a reality due to the increasing
powerful computational approaches able to handle increasingly larger datasets. Uncovering …

Diesel engine modeling based on recurrent neural networks for a hardware-in-the-loop simulation system of diesel generator sets

M Yu, X Tang, Y Lin, X Wang - Neurocomputing, 2018 - Elsevier
The electronic speed governors are widely used in diesel generator sets (DGS). To develop
and debug electronic speed governor, the best option is to build a hardware-in-the-loop …

Inference of gene regulatory networks based on the Light Gradient Boosting Machine

Z Du, X Zhong, F Wang, VN Uversky - Computational Biology and …, 2022 - Elsevier
Inference of gene regulatory networks (GRNs) is one of the major challenges in molecular
biology, understanding of which can reveal the regulatory relationship between transcription …