NDLI: P-Biblio-MetReS, a parallel data mining tool for the reconstruction of molecular networks

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P-Biblio-MetReS, a parallel data mining tool for the reconstruction of molecular networks

Content Provider	ACM Digital Library
Author	Solsona, Francesc Torres, Nestor Karathia, Hiren Alves, Rui Lérida, Josep Ll. Teixidó, Ivan Comas, Jorge Usié, Anabel
Abstract	Biblio-MetReS is a single-thread data mining application that facilitates the reconstruction of molecular networks based on automated text mining analysis of published scientific literature. This application is very CPU-intensive, requiring High Performace Computing (HPC). Due to the amount of execution tasks, it can be quite slow. Those tasks are repetitive and consist in mining the information from large sets of scientific documents, a process where the time-cost of the application could be improved through paralellization. This paper presents a parallel version of Biblio-MetReS. The multithreading application P(arallel)-Biblio-MetReS distributes the work among copies of the same Java class, each mining a collection of documents obtained in a previous search phase from different literature sources of Internet. In this article, we compare performances between the parallel and non-parallel versions of the application and discuss scalability issues on multi-threading systems in the context of this application. Furthermore, we also optimize memory management and reutilization of document parsing results. Our experimental results corroborate the good performance of P-Biblio-MetReS, pinpointing specific aspects that still need to be improved.
Starting Page	247
Ending Page	252
Page Count	6
File Format	PDF
ISBN	9781450319034
DOI	10.1145/2488551.2488586
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2013-09-15
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Data/text mining Multithreading Parallel programming Scalability Molecular network reconstruction Parallelization
Content Type	Text
Resource Type	Article

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
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
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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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