Large Conference Room (Room 470)
Institute for Research in Cognitive Science
3401 Walnut Street, Suite 400A Philadelphia, PA 19104

Sunday, February 25, 2001
8:30 a.m. - 9:00 a.m.	Continental Breakfast
9:00 a.m. - 10:30 a.m.	Introduction and Topic I Topic I:Structure of Genes and Genomes Key Issues: How much do strongly model-based, "syntactic" algorithms enhance gene identification and genome characterization? Can general-purpose or domain-specific parsing methods find application in genome analysis? Background Speaker: Chris Burge Commentary: Richard Durbin, Ian Holmes, Bjarne Knudsen, Rune Lyngso, Eric Brill, Steve Pulman, Chris Mellish, Michael Brent, Andrey Rzhetsky Session Chair: Ken Dill
10:30 a.m. - 10:45 a.m.	Break
10:45 a.m. - 12:30 p.m.	Topic I Continued
12:30 p.m. - 2:00 p.m.	Lunch (provided)
2:00 p.m. - 3:00 p.m.	Topic II and Topic VI Topic II: Structure of Macromolecules Key Issues: What is the practical utility of non-regular stochastic grammars in recognizing RNA secondary structures? Can stronger (as compared to CFG) formal systems be useful in protein structural studies? Background Speaker: Sean Eddy Commentary: Ken Dill, David Searls, Richard Hughey, Elena Rivas, Yasuo Uemura, Kevin Knight, Satoshi Kobayashi, Aravind Joshi Session Chair: Richard Durbin Topic VI: Strong Models of Grammars (Grammars with structured primitives) Key Issues: What are some of the structural linguistic aspects motivating the strong models? Computational and stochastic implications. Relevance to topological structures in CB. Are there technologies that could be successfully adopted, patterned after the success of HMMs in biology? Background Speaker: David Searls/Aravind Joshi Commentary: Michael Brent, Giorgio Satta, Satoshi Kobayashi, Jinichi Tsujii, Fernando Pereira,Sean Eddy, Elena Rivas Session Chair: Giorgio Satta
3:15 p.m. - 3:30 p.m.	Break
3:30 p.m. - 5:30 p.m.	Topic II and Topic VI Continued
6:00 p.m. - 8:00 p.m.	Cocktail Reception Arthur Ross Gallery Furness Building 220 South 34th Street
Monday, February 26, 2001
8:30 a.m. - 9:00 a.m.	Continental Breakfast
9:00 a.m. - 10:30 a.m.	Topic IV Topic IV:Inferences from Genomes Key Issues: Are there lessons from comparative linguistics for comparative genomics? How does phylogenetic reconstruction resemble classical linguistics? How can multiple genomes be used to infer phylogenetic relationships, protein interactions, etc? Are there techniques from linguistics and/or machine learning that might bear on the analysis of gene expression? Background Speaker: Edward Marcotte Commentary: David Searls, Robert Berwick, Mark Liberman, Satoshi Kobayashi/Yasuo Uemura, Don Ringe, Fernando Pereira Session Chair: Robin Clark
10:30 a.m. - 10:45 a.m.	Break
10:45 a.m. - 12:30 p.m.	Topic IV Continued
12:30 p.m. - 2:00p.m.	Lunch (provided)
2:00 p.m. - 3:00 p.m.	Topic III and Free Time Topic III: Pattern Search and Analysis Key Issues: What do stochastic methods add to sequence search and analysis? Are there uses for recent statistical linguistic methods? Do linguistic methods apply to the analysis of regulatory regions? Background Speaker: Richard Durbin Commentary: William Grundy, John Lafferty, Fernando Pereira, Giorgio Satta, Mike Collins, Mitch Marcus Session Chair: Ian Holmes
3:15 p.m. - 3:30 p.m.	Break
3:30 p.m. - 5:30 p.m.	Topic III and Topic V continued
6:30 p.m. - 9:00 p.m.	Cocktail Hour and Dinner Institute for Contemporary Art (ICA) 36th and Sansom Streets
Tuesday, February 27, 2001
8:30 a.m. - 9:00 a.m.	Continental Breakfast
9:00-10:30	Topic V and Free Time Topic V: Developments in Parsing Key Issues: What are some of the recent developments in statistical parsing in computational linguistics that may be of relevance to CB. Background Speaker: Mike Collins Commentary: Giorgio Satta, B. Srinivas, Sean Eddy E, Steve Pulman, Partha Mitra Session Chair: Steve Pulman
10:30 a.m.-10:45 a.m.	Break
10:45 a.m. - 12:00 p.m.	Topic V and Free Time Continued
12:00 p.m. - 1:15 p.m.	Lunch (provided) Session VII may begin during lunch.
1:15 p.m. - 2:30 p.m.	Topic VII Topic VII: Wrap-Up
3:00 p.m.	End of Workshop