Batyr Charyyev

Gene Relation Network Constructed by Mining Biomedical Literature Abstracts. As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Gene Relation Network Constructed by Mining Biomedical Literature Abstracts. As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Gene Relation Network Constructed by Mining Biomedical Literature Abstracts. Amount of data Unstructured format As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Gene Relation Network Constructed by Mining Biomedical Literature Abstracts. Amount of data Unstructured format Why it is important? Easy analyze and interpret data. Provide full data. Comprehensive view. As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Gene Relation Network Constructed by Mining Biomedical Literature Abstracts. Information retrieval Information extraction Generating relation network Three main components As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Information retrieval Source: PubMed-NCBI Technique: Number of co-occurences of phrases Challenges: Irrelevant papers. As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Information extraction Source: Abstracts Techniques: Rule based extraction, structure and semantics of sentence Challenges: Greek letters and acronyms As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Generating relation network Source: Output of our second component Relation: Activation, suppressing. Challenges: Verification of results. As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Related works “Text Mining Biomedical Literature for Constructing Gene Regulatory Networks” by Young Ling Song and Su Shing Chen “Context-rich biological network constructed by mining PubMed abstracts” by Hao Chen and Burt Sharp “How to infer gene networks from expression profiles” by Mukesh Bansal, Vincenzo Belcastro, Alberto Ambesimpiobato, Diego di Bernardo As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Text mining Biomedical Literature for Constructing Gene Regulatory Networks Goal: Automatically mine the data to extract gene regulatory information and construct gene regulatory network. Components: Text Mining Biomedical literature, Online tools, Analysis tools Source: Full-text paper Techniques: Rule-based Result: Precision and Recall As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Text mining Biomedical Literature for Constructing Gene Regulatory Networks As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Content-rich biological network constructed by mining PubMed abstracts Goal: Construct content-rich relationship networks between genes, proteins, drugs and biological concepts. Source: Abstracts of paper Techniques: Synonyms of user entered queries As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Content-rich biological network constructed by mining PubMed abstracts As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

How to infer gene networks from expression profiles Goal: Compare different algorithms and show they are indeed able to infer regulatory interactions among genes. Algorithms: Coexpression networks and clustering, Bayesian networks, Information theoretic approach. As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Coexpression networks and clustering Idea: Grouping genes with similar expression profiles in cluster As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Bayesian network Idea: Describe relationship among random genes with joint probability distribution. As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

Information-theoretic approach Idea: Compute Mutual Information(MI) for each pairs of genes and put edge between them if it is greater than threshold. MI is symmetric As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

What is next? Focus on relation network component Start basic proceed incrementally Information theory model Small sample As the largest man-made complex network, the Internet grows with no central authority. Thousands of small and medium size Autonomous Systems connect individuals, businesses, universities, and agencies while focusing on optimizing their own communication efficiency and economic objectives make it challenging to maintain and control the growth

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