1. Batyr Charyyev

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. Questions