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 This
course covers some basic problems in bioinformatics and related natural
language processing (NLP) techniques, e.g. bio/medical text mining,
information extraction, clustering/classification, bio information
retrieval, bio ontology processing and some of the system design issues.
The course conisists of two parts: the first part will review some basic
knowledge in bioinformatics field and NLP techniques, and the second part
will study more indepth on-going research problems in bioNLP community.
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No
particular requirements. No background knowledge for NLP is assumed, so
all bioinformatics students are welcome.
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 midterm
40%
paper presentation 50%
class participation 10%
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Lecture
part: David W. Mount, Bioinformatics: sequence and genome analysis, cold
spring harbor laboratory press, 2001
Presentation part: Literature in BioNLP, lecture note edited by Gary G.
Lee (provided)
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[L] Lecture [S] student
presentation
1st week: [L]introduction to bioinformatics
2nd week: [L]sequence alignment/ multiple sequence alignment
3rd week: [L]RNA secondary structure [S]review bioNLP
4th week: [L]Terminology and ontology [S]review bioNLP
5th week: [L]Micro array clustering and classification [S]named-entity
tagging
6th week: [L]Hidden Markov Models and bio application [S]named-entity
tagging
7th week: [L]genetic networks & Systems biology
[S]relation/interaction extraction
8th week: [L]Gene structure and gene finding [S]relation/interaction
extraction
9th week: [L]Bio natural language processing and information retrieval
[S]bio IE system (midterm exam)
10th week: [L]future opportunities in bioinformatics [S]bio IE system
11th week: [S]bio ontology/knowledge respresentation
12th week: [S]clustering/classification
13th week: [S]medical informatics
14th week: [S]visulalization/bio IR
15th week: [S]automatic annotation
16th week: review and course wrap up
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English is the
language for teaching and for all the student presentation. However,
discussion can be in Korean.
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