Regularized non-negative matrix factorization for identifying differentially expressed genes and clustering samples: A survey

JX Liu, D Wang, YL Gao, CH Zheng… - … /ACM transactions on …, 2017 - ieeexplore.ieee.org
Non-negative Matrix Factorization (NMF), a classical method for dimensionality reduction,
has been applied in many fields. It is based on the idea that negative numbers are physically …

Two-stage hybrid gene selection using mutual information and genetic algorithm for cancer data classification

M Jansi Rani, D Devaraj - Journal of medical systems, 2019 - Springer
Cancer is a deadly disease which requires a very complex and costly treatment. Microarray
data classification plays an important role in cancer treatment. An efficient gene selection …

High dimensionality reduction by matrix factorization for systems pharmacology

A Mehrpooya, F Saberi-Movahed… - Briefings in …, 2022 - academic.oup.com
The extraction of predictive features from the complex high-dimensional multi-omic data is
necessary for decoding and overcoming the therapeutic responses in systems …

A big data driven distributed density based hesitant fuzzy clustering using Apache spark with application to gene expression microarray

B Hosseini, K Kiani - Engineering Applications of Artificial Intelligence, 2019 - Elsevier
This paper introduces a distributed density based clustering approach that benefits from the
hesitant fuzzy weighted correlation coefficient as its similarity measure. All the proposed …

Characteristic gene selection based on robust graph regularized non-negative matrix factorization

D Wang, JX Liu, YL Gao, CH Zheng… - IEEE/ACM transactions …, 2015 - ieeexplore.ieee.org
Many methods have been considered for gene selection and analysis of gene expression
data. Nonetheless, there still exists the considerable space for improving the explicitness …

Biomarker identification for cancer disease using biclustering approach: An empirical study

K Mandal, R Sarmah… - IEEE/ACM transactions …, 2018 - ieeexplore.ieee.org
This paper presents an exhaustive empirical study to identify biomarkers using two
approaches: frequency-based and network-based, over 17 different biclustering algorithms …

Biclustering of human cancer microarray data using co-similarity based co-clustering

SF Hussain, M Ramazan - Expert Systems with Applications, 2016 - Elsevier
Biclustering of gene expression data aims at finding localized patterns in a subspace. A
bicluster (sometimes called a co-cluster), in the context of gene expression data, is a set of …

Bi-EB: Empirical Bayesian Biclustering for Multi-Omics Data Integration Pattern Identification among Species

A Yazdanparast, L Li, C Zhang, L Cheng - Genes, 2022 - mdpi.com
Although several biclustering algorithms have been studied, few are used for cross-pattern
identification across species using multi-omics data mining. A fast empirical Bayesian …

Branching evolution for unknown objective optimization in biclustering

Q Huang, H Xu, H Li - Applied Soft Computing, 2024 - Elsevier
Biclusters hold significant importance in microarray analysis. Given the EA algorithm's
efficacy in tackling nonlinear problems, it has become a prevalent choice for evolutionary …

Biclustering using venus flytrap optimization algorithm

R Gowri, S Sivabalan, R Rathipriya - … Conference on CIDM, 5-6 December …, 2016 - Springer
Digging up the coregulated gene biclusters using a novel Nature-inspired Meta-Heuristic
algorithm named Venus Flytrap Optimization (VFO). This optimized biclustering approach …