NDLI: RUBic: rapid unsupervised biclustering

Content Provider	Springer Nature : BioMed Central
Author	Sriwastava, Brijesh K. Halder, Anup Kumar Basu, Subhadip Chakraborti, Tapabrata
Abstract	Biclustering of biologically meaningful binary information is essential in many applications related to drug discovery, like protein–protein interactions and gene expressions. However, for robust performance in recently emerging large health datasets, it is important for new biclustering algorithms to be scalable and fast. We present a rapid unsupervised biclustering (RUBic) algorithm that achieves this objective with a novel encoding and search strategy. RUBic significantly reduces the computational overhead on both synthetic and experimental datasets shows significant computational benefits, with respect to several state-of-the-art biclustering algorithms. In 100 synthetic binary datasets, our method took $\sim 71.1$ s to extract 494,872 biclusters. In the human PPI database of size $4085\times 4085$ , our method generates 1840 biclusters in $\sim 48.6$ s. On a central nervous system embryonic tumor gene expression dataset of size 712,940, our algorithm takes 101 min to produce 747,069 biclusters, while the recent competing algorithms take significantly more time to produce the same result. RUBic is also evaluated on five different gene expression datasets and shows significant speed-up in execution time with respect to existing approaches to extract significant KEGG-enriched bi-clustering. RUBic can operate on two modes, base and flex, where base mode generates maximal biclusters and flex mode generates less number of clusters and faster based on their biological significance with respect to KEGG pathways. The code is available at ( https://github.com/CMATERJU-BIOINFO/RUBic ) for academic use only.
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05534-3.pdf
Ending Page	16
Page Count	16
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/s12859-023-05534-3
Journal	BMC Bioinformatics
Issue Number	1
Volume Number	24
Language	English
Publisher	BioMed Central
Publisher Date	2023-11-16
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Data mining Algorithm design and analysis Biclustering algorithms Computational complexity Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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