1. CSE 591 (99689) Application of AI to molecular Biology (5:15 – 6: 30 PM, PSA 309) Instructor: Chitta Baral Office hours: Tuesday 2 to 5 PM

2. Meaning of the word: ``intelligence'' 1 (a) The capacity to acquire and apply knowledge. (b) The faculty of thought and reason. (c) Superior powers of mind. See Synonyms at mind. Source: The American Heritage® Dictionary of the English Language, Fourth Edition Copyright © 2000 by Houghton Mifflin Company.Published by Houghton Mifflin Company. All rights reserved. n 1: the ability to comprehend; to understand and profit from experience [ant: stupidity] –Source: WordNet ® 1.6, © 1997 Princeton University

3. AI: Artificial Intelligence Based on the above, `artificial intelligence' is about the science and engineering necessary to create artifacts that can – acquire knowledge, i.e., can learn and extract knowledge; and –reason with knowledge (leading to doing tasks such as planning, explaining, diagnosing, acting rationally, etc.)

4. AI and molecular biology This course is about the application of the above science and engineering (referred to as AI) to molecular biology.

5. Molecular Biology molecular biology n. –The branch of biology that deals with the formation, structure, and function of macromolecules essential to life, such as nucleic acids and proteins, and especially with their role in cell replication and the transmission of genetic information. –The branch of biology that deals with the manipulation of DNA so that it can be sequenced or mutated. If mutated, the DNA is often inserted into the genome of an organism to study the biological effects of the mutation. –Source: The American Heritage® Dictionary of the English Language, Fourth Edition Copyright © 2000 by Houghton Mifflin Company. Published by Houghton Mifflin Company. All rights reserved. n : the branch of biology that studies the structure and activity of macromolecules essential to life (and especially with their genetic role) –Source: WordNet ® 1.6, © 1997 Princeton University

6. Main themes of the course How to acquire molecular biology knowledge? How to do various kinds of reasoning with such knowledge? Acquiring biological knowledge: – Extracting from articles and abstracts. – Learning from experimental data – Using existing databases and ontology (and building new ones) to help in the previous two steps. Various kinds of reasoning with such knowledge: – Prediction – Explanation and diagnosis – Planning and drug design

7. Tentative topics to be covered Text Mining and Ontologies –Biological Wordnet Learning gene networks –Boolean networks, –probabilistic boolean networks, –Bayes nets, etc.) Representation and reasoning with biological knowledge More on Hidden Markov Models Use of decision trees, inductive Logic programming (Progol), etc. –for classification and prediction.

8. Grading and Modus Operandi project + paper + class presentations 80% –Expected to be of publication quality Class Test (Nov 17th) 20% Modus Operandi: –There will be 8-9 groups each of 1-2 students –Groups select project asap (in two weeks) –First 5 classes (Aug 25 th, 27 th, Sept 3 rd,8 th and 10 th ) I will present –After that each group will present 6 presentations (4 if the group consists of a single student) each, lasting 30 minutes each. –Groups need to meet me one day before the class with their slides. –We will have some guest lectures.

9. Projects Each project is of research interest to ASU and TGen researchers Students will work closely with ASU and TGen researchers

10. Tentative list of projects - 1 Extracting pathway knowledge from abstracts and articles Extracting ontologies (gene and protein names, etc.) from abstracts and articles Creating a knowledge base of available resources and developing a guiding system based on this knowledge base Learning gene interactions (as Bayes nets or a similar structure) from time series micro-array data Learning causal connection between genes from micro- array data, and developing a gene interaction model

11. Tentative list of projects - 2 Representation of signal networks and doing various kinds of reasoning with it (*571) Developing a knowledge base that represents AP level biological knowledge and can answer (with explanations) AP questions (*571) Using Hidden Markov Models for tasks such as classification and prediction Developing a system that helps find genes in a genome. You may suggest and discuss a topic, but need to do it asap