IEEE Transactions on Computational Biology and Bioinformatics (TCBB) will move to the OnlinePlus publication model starting with 2015 issues!
From the September/October 2014 Issue
Network-Based Drug-Target Interaction Prediction with Probabilistic Soft Logic
By Shobeir Fakhraei, Bert Huang, Louiqa Raschid, and Lise Getoor
Drug-target interaction studies are important because they can predict drugs' unexpected therapeutic or adverse side effects. In silico predictions of potential interactions are valuable and can focus effort on in vitro experiments. We propose a prediction framework that represents the problem using a bipartite graph of drug-target interactions augmented with drug-drug and target-target similarity measures and makes predictions using probabilistic soft logic (PSL). Using probabilistic rules in PSL, we predict interactions with models based on triad and tetrad structures. We apply (blocking) techniques that make link prediction in PSL more efficient for drug-target interaction prediction. We then perform extensive experimental studies to highlight different aspects of the model and the domain, first comparing the models with different structures and then measuring the effect of the proposed blocking on the prediction performance and efficiency. We demonstrate the importance of rule weight learning in the proposed PSL model and then show that PSL can effectively make use of a variety of similarity measures. We perform an experiment to validate the importance of collective inference and using multiple similarity measures for accurate predictions in contrast to non-collective and single similarity assumptions. Finally, we illustrate that our PSL model achieves state-of-the-art performance with simple, interpretable rules and evaluate our novel predictions using online data sets.
Editorials and Announcements
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- TCBB celebrates its 10th Anniversary. Editor-in-Chief Ying Xu says, "The emergence and maturation of increasingly more and powerful molecular measurement technologies such as next generation sequencing and chromosome conformation capture allow scientists to tackle biological problems at the depth and breadth that we have never seen before. At the same time the enormity and complexity of the data generated using these technologies raised tremendous challenges to computational scientists to develop more effective techniques to store, transmit, organize, process, analyze and mine the data, and to construct models to assist interpreting the data. Since its creation ten years ago, TCBB has been playing a major role in bridging the world of computing and the world of biology. I want to congratulate what the journal has done in providing biologists with the most powerful computational tools to help address their data and modeling needs. I fully expect that TCBB will continue to play increasingly significant roles in attracting more computational scientists to address the ever increasing needs for new and more powerful computational techniques and to introduce to new comers the important and challenging computational biology problems in a timely fashion."
- eBooks of issues of TCBB can now be downloaded from the Computer Society Digital Library
- Subscribe to TCBB in 2014. Click for more information. (PDF)
- Reviewer Appreciation Editorial by Y. Xu (July/August 2014)
- EIC Editorial by M.-F. Sagot (March/April 2011)
- EIC Editorial by M.-F. Sagot (January/February 2011)
- Special Section on BIOKDD2013 (Sept/Oct 2014)
- 12th Asia Pacific Bioinformatics Conference (July/August 2014)
- Pattern Recognition in Bioinformatics (May/June 2014)
- Special Section on Bioinformatics Research and Applications (May/June 2014)
- Bioinformatics and Computational Systems Biology (July/August 2012)
- High Performance Computational Systems Biology (May/June 2012)
- Special Section on Bioinformatics Research and Applications (July/August 2011)
- Special Focus on Bioinformatics and Systems Biology (March/April 2011)
- Special Section on Bioinformatics Research and Applications (Oct-Dec 2010)
Call for Papers
- Special Section on Semantic-Based Approaches for Analysis of Biological Data (PDF)
Submission Deadline: March 20, 2015
- Special Issue on Big Data Processing in Computational Biology and Bioinformatics (PDF)
Submission Deadline: March 31, 2015
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TCBB is a joint publication of the IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.
Published in cooperation with: IEEE Control Systems Society
Indexed in MEDLINE®/PubMed® & ISI
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) is a bimonthly journal that publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology.
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