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AIC Seminar Series

Issues in Reasoning about Interaction Networks in Cells: Necessity of Event Ordering Knowledge

Nam TranInformatics Center for Neurogenetics & Neurogenomics, Semel Institute, UCLA

Notice:  Hosted by Vinay Chaudhri.

Date:  2012-07-02 at 16:00

Location:  EJ228 (SRI E building)  (Directions)


Molecular interactions within the cell determines its functions, thus reasoning about molecular interactions is important from various perspectives such as predicting side effects of drugs, explaining unusual cellular behaviors and drug and therapy design. The interaction networks involve thousands of interacting molecules, thus a typical biologist can only focus on a very small sub-network. For large scale and automated reasoning about interaction networks, we propose to use action language - a knowledge representation formalism - to represent the interaction networks in a knowledge base. In this approach, an interaction between molecule can be modeled as an action that transform the cell from one state to another state. Such an action (or molecular interaction) is usually triggered or inhibited in the cell. We shall first introduce a new action language A^0_T for representing and reasoning about triggered actions. Then we discuss several representation issues we came across while modelling real biological networks. One of the issues is that the triggering of molecular actions is not necessarily immediate, leading to multiple evolution models in the absence of additional information. Second, often an action or a triggering mechanism at one level of granularity of representation can be elaborated and refined. We show that an adequate solution is to extend the language A^0_T with event ordering knowledge.

   Bio for Nam Tran

Nam Tran obtained a PhD in Computer Science from Arizona State University then joined Yale School of Medicine as a postdoc in Biomedical Informatics. He currently works as a lead bioinformatician in the Informatics Center for Neurogenetics and Neurogenomics at UCLA. His research interests include knowledge representation and discovery, large scale data mining and analysis. He has published works in the major journals Bioinformatics, BMC Medical Genomics, PLoS ONE, J. Applied Logic, Annals of Mathematics and AI, ACM Transactions on Computational Logic as well as the leading conferences AAAI, KRR, ECCB, ISMB, AMIA, CMSB. He also has significant interdisciplinary research experience from close collaboration with researchers in various biomedical and clinical fields (brain oncology, plant biology, translational skin oncology, clinical practice guidelines, neurogenetics, neurology).

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