NDLI: AdaBoost Based Multi-Instance Transfer Learning for Predicting Proteome-Wide Interactions between Salmonella and Human Proteins

Content Provider	PubMed Central
Author	Mei, Suyu Zhu, Hao
Editor	Hensel, Michael
Copyright Year	2014
Abstract	Pathogen-host protein-protein interaction (PPI) plays an important role in revealing the underlying pathogenesis of viruses and bacteria. The need of rapidly mapping proteome-wide pathogen-host interactome opens avenues for and imposes burdens on computational modeling. For Salmonella typhimurium, only 62 interactions with human proteins are reported to date, and the computational modeling based on such a small training data is prone to yield model overfitting. In this work, we propose a multi-instance transfer learning method to reconstruct the proteome-wide Salmonella-human PPI networks, wherein the training data is augmented by homolog knowledge transfer in the form of independent homolog instances. We use AdaBoost instance reweighting to counteract the noise from homolog instances, and deliberately design three experimental settings to validate the assumption that the homolog instances are effective to address the problems of data scarcity and data unavailability. The experimental results show that the proposed method outperforms the existing models and some predictions are validated by the findings from recent literature. Lastly, we conduct gene ontology based clustering analysis of the predicted networks to provide insights into the pathogenesis of Salmonella.
Related Links	http://dx.doi.org/10.1371/journal.pone.0110488
Starting Page	110488
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	10
Volume Number	9
Language	English
Publisher	Public Library of Science
Publisher Date	2014-10-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Probability Weighted Ensemble Transfer Learning for Predicting Interactions between HIV-1 and Human Proteins

3D Profile-Based Approach to Proteome-Wide Discovery of Novel Human Chemokines

Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome

Weak Interactions between Salmonella enterica FlhB and Other Flagellar Export Apparatus Proteins Govern Type III Secretion Dynamics

Chromosome Conformation Capture Uncovers Potential Genome-Wide Interactions between Human Conserved Non-Coding Sequences

Using Multi-Instance Hierarchical Clustering Learning System to Predict Yeast Gene Function

The Core Proteome and Pan Proteome of Salmonella Paratyphi A Epidemic Strains

Proteome-Wide Identification of Lysine Succinylation in the Proteins of Tomato (Solanum lycopersicum)

Predicting Biological Functions of Compounds Based on Chemical-Chemical Interactions

AdaBoost Based Multi-Instance Transfer Learning for Predicting Proteome-Wide Interactions between Salmonella and Human Proteins

Similar Documents

Probability Weighted Ensemble Transfer Learning for Predicting Interactions between HIV-1 and Human Proteins

3D Profile-Based Approach to Proteome-Wide Discovery of Novel Human Chemokines

Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome

Weak Interactions between Salmonella enterica FlhB and Other Flagellar Export Apparatus Proteins Govern Type III Secretion Dynamics

Chromosome Conformation Capture Uncovers Potential Genome-Wide Interactions between Human Conserved Non-Coding Sequences

Using Multi-Instance Hierarchical Clustering Learning System to Predict Yeast Gene Function

The Core Proteome and Pan Proteome of Salmonella Paratyphi A Epidemic Strains

Proteome-Wide Identification of Lysine Succinylation in the Proteins of Tomato (Solanum lycopersicum)

Predicting Biological Functions of Compounds Based on Chemical-Chemical Interactions

AdaBoost Based Multi-Instance Transfer Learning for Predicting Proteome-Wide Interactions between Salmonella and Human Proteins