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IMA Annual Program Year Workshop

Applications in Biology, Dynamics, and Statistics

March 5-9, 2007
Organizers:
Serkan Hosten Mathematics, San Francisco State University
Lior Pachter Mathematics, University of California - Berkeley
Seth Sullivant Mathematics, Harvard University

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Abstracts and Talk Materials Dining Guide
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Description:

Advances in computational algebra in the past few years have led to the use of algebraic geometry to study problems in biology, dynamics, and statistics. Some highlights of these new applications include: algebraic techniques for studying and solving the likelihood equations for discrete random variables in statistics; Groebner basis techniques to generate random walks on high dimensional contingency tables and their applications in disclosure limitation; the use of toric geometry to study the dynamics of chemical systems; the algebraic tools for producing invariants of Markov models in phylogeny and their applications in phylogenetic tree recovery; and the application of tropical geometry for parametric sequence alignment in genomics.

The focus of this workshop is on these relatively new applications of algebraic geometry where the full scope of the techniques are still developing. We hope to bring together a broad range of researchers in both algebraic geometry and applied science. A key aim is to establish a bridge between mathematicians wishing to learn more about these applications and to expose new algebraic tools to researchers in industry and academia.

Schedule
Monday | Tuesday | Wednesday | Thursday | Friday
  Monday, March 5
8:15am-9:00am Registration and coffee   EE/CS 3-176
9:00am-9:15am Welcome and introduction Douglas N. Arnold (University of Minnesota) EE/CS 3-180
9:15am-10:05am Open problems in algebraic statistics Bernd Sturmfels (University of California, Berkeley)
(Cancelled)
EE/CS 3-180
10:05am-10:40am Coffee   EE/CS 3-176
10:40am-11:30am Likelihood ratio tests and singularities Mathias Drton (University of Chicago) EE/CS 3-180
11:30am-1:30pm Lunch    
1:30pm-2:20pm Stability and instability in polynomial equations arising from complex chemical reaction networks: the big picture Martin Feinberg (Ohio State University) EE/CS 3-180
2:20pm-2:50pm Coffee   EE/CS 3-176
2:50pm-3:40pm Stability and instability in polynomial equations arising from complex chemical reaction networks: some underlying mathematics Gheorghe Craciun (University of Wisconsin) EE/CS 3-180
3:40pm-4:10pm Second Chances   EE/CS 3-180
4:10pm-4:30pm Group Photos   EE/CS 3-180
4:30pm-6:30pm IMA Tea and Poster Session
Lind Hall 400
A flow that computes the best positive semi-definite approximation of a symmetric matrix Kenneth R. Driessel (Iowa State University)
Multiple solutions to the likelihood equations in the Behrens-Fisher problem Mathias Drton (University of Chicago)
Metric learning for phylogenetic invariants Nicholas Eriksson (Stanford University)
Geometry of rank tests Jason Morton (University of California, Berkeley)
Supervised learning artifical neural network algorithms for optimizing mechanical properties of elastin-like polypeptide hydrogels for cartilage repair Sarah Olson (North Carolina State University)
Toric ideals of phylogenetic invariants for the general group-based model on claw trees Sonja Petrovic (University of Kentucky)
Conditional independence for Gaussian random variables is not finitely axiomatizable Seth Sullivant (Harvard University)
Linkage problems and real algebraic geometry Thorsten Theobald (Johann Wolfgang Goethe-Universität Frankfurt)
Classifying disease models using regular polyhedral subdivisions Debbie Yuster (Columbia University)
Maximum likelihood estimation in latent class Yi Zhou (Carnegie Mellon University)
  Tuesday, March 6
8:30am-9:00am Coffee   EE/CS 3-176
9:00am-9:50am Phylogenetic models: algebra and evolution Elizabeth S. Allman (University of Alaska) EE/CS 3-180
9:50am-10:30am Coffee   EE/CS 3-176
10:30am-11:20am Generalized maximum likelihood estimates for exponential families František Matúš (Czech Academy of Sciences (AVČR)) EE/CS 3-180
11:20am-1:30pm Lunch    
1:30pm-2:20pm Bifurcations in coupled systems Martin Golubitsky (University of Houston) EE/CS 3-180
2:20pm-3:00pm Coffee   EE/CS 3-176
3:00pm-3:50pm Application of algebraic statistics for statistical disclosure limitation Aleksandra B. Slavković (Pennsylvania State University) EE/CS 3-180
4:00pm-4:30pm Second Chances   EE/CS 3-180
  Wednesday, March 7
8:30am-9:00am Coffee   EE/CS 3-176
9:00am-9:50am Polynomial dynamical systems over finite fields, with applications to modeling and simulation of biological networks Reinhard Laubenbacher (Virginia Polytechnic Institute and State University) EE/CS 3-180
9:50am-10:30am Coffee    
10:30am-11:20am Gene interactions and the geometry of fitness landscapes Niko Beerenwinkel (Harvard University) EE/CS 3-180
11:30am-12:00pm Second Chances   EE/CS 3-180
5:00pm-6:30pm Reception   Lind Hall 400
7:00pm-8:00pm Math Matters - IMA Public Lecture: Patterns Patterns Everywhere Martin Golubitsky (University of Houston) Willey Hall 125
  Thursday, March 8
8:30am-9:00am Coffee   EE/CS 3-176
9:00am-9:50am Gaussian path diagrams Thomas S. Richardson (University of Washington) EE/CS 3-180
9:50am-10:30am Coffee    
10:30am-11:20am Using algebraic geometry for phylogenetic reconstruction Marta Casanellas (Polytechnical University of Cataluña (Barcelona)) EE/CS 3-180
11:20am-1:30pm Lunch    
1:30pm-2:20pm Modelling with mass-action kinetics and beyond Markus Kirkilionis (University of Warwick) EE/CS 3-180
2:20pm-3:00pm Coffee   EE/CS 3-176
3:00pm-3:50pm Information geometry and algebraic statistics Giovanni Pistone (Politecnico di Torino) EE/CS 3-180
4:00pm-4:30pm Second Chances    
6:30pm-8:00pm Dinner: Caspian Bistro Restaurant   2418 University Ave SE
612-623-1133 
  Friday, March 9
8:30am-9:00am Coffee   EE/CS 3-176
9:00am-9:50am On phylogenetic trees – a geometer's view Jaroslaw Wisniewski (University of Warsaw) EE/CS 3-180
9:50am-10:30am Coffee    
10:30am-11:20am A combinatorial test for significant codivergence between cool-season grasses and their symbiotic fungal endophytes Ruriko Yoshida (University of Kentucky) EE/CS 3-180
11:20am-1:30pm Lunch    
1:30pm-2:20pm Subspace arrangements in theory and practice Robert M. Fossum (University of Illinois at Urbana-Champaign) EE/CS 3-180
2:20pm-3:00pm Coffee   EE/CS 3-176
3:00pm-3:50pm Algebraic statistics and the analysis of contingency tables: Old wine in new bottles? Stephen E. Fienberg (Carnegie Mellon University) EE/CS 3-180
4:00pm-4:30pm Second Chances and closing remarks.    

LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
Elizabeth S. Allman Department of Mathematics and Statistics University of Alaska
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
Donald G. Aronson Institute for Mathematics and its Applications University of Minnesota
Hélène Barcelo Department of Mathematics and Statistics Arizona State University
Brandon Barker   University of Kentucky
Daniel J. Bates Institute for Mathematics and its Applications University of Minnesota
Niko Beerenwinkel Program for Evolutionary Dynamics Harvard University
Jeremy Bellay School of Mathematics University of Minnesota
Wicher Bergsma   London School of Economics and Political Science
Víctor Blanco Izquierdo Department of Statistics and Operational Research University of Sevilla
Cristiano Bocci Department of Mathematics Università di Milano
Tristram Bogart Department of Mathematics University of Washington
Joseph P. Brennan Department of Mathematics University of Central Florida
Marta Casanellas Departament de Matematica Aplicada I Polytechnical University of Cataluña (Barcelona)
Hegang Chen School of Medicine, Division of Biostatistics and Bioinformatics University of Maryland at Baltimore
Vera Cherepinsky Department of Mathematics and Computer Science Fairfield University
Ionut Ciocan-Fontanine Institute for Mathematics and its Applications University of Minnesota
Barry Cipra    
Eduardo Corel Laboratoire Statistique et Génome Centre National de la Recherche Scientifique (CNRS)
Gheorghe Craciun Department of Mathematics and Department of Biomolecular Chemistry University of Wisconsin
Alicia Dickenstein Departamento de Matematica - FCEyN University of Buenos Aires
Kequan Ding   Chinese Academy of Sciences
Jianping Dong Department of Mathematical Sciences Michigan Technological University
Kenneth R. Driessel Department of Mathematics Iowa State University
Mathias Drton Department of Statistics University of Chicago
Vanja Dukic Department of Health Studies (Biostatistics) University of Chicago
Ryan S. Elliott   University of Michigan
Nicholas Eriksson Department of Statistics Stanford University
Makan Fardad Department of Electrical and Computer Engineering University of Minnesota
Martin Feinberg Department of Chemical and Biomolecular Engineering Ohio State University
David Fernández-Baca Department of Computer Science Iowa State University
Stephen E. Fienberg Department of Statistics Carnegie Mellon University
Robert M. Fossum Department of Mathematics University of Illinois at Urbana-Champaign
Surya Ganguli Sloan-Swartz Center for Theoretical Neurobiology University of San Francisco
Martin Golubitsky Department of Mathematics University of Houston
Jason E. Gower Institute for Mathematics and its Applications University of Minnesota
Mansoor Haider Department of Mathematics North Carolina State University
Michael Hardy School of Mathematics University of Minnesota
Gloria Haro Ortega   University of Minnesota
Christine E. Heitsch School of Mathematics Georgia Institute of Technology
J. William Helton Department of Mathematics University of California, San Diego
Milena Hering Institute for Mathematics and its Applications University of Minnesota
Patricia Hersh Department of Mathematics Indiana University
Benjamin J. Howard   University of Minnesota
Evelyne Hubert Project CAFE Institut National de Recherche en Informatique Automatique (INRIA)
Peter Huggins Department of Mathematics University of California
Satish Iyengar Department of Statistics University of Pittsburgh
Farhad Jafari Department of Mathematics University of Wyoming
Abdul Salam Jarrah Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
Anders Nedergaard Jensen Institut for Matematiske Fag Aarhus University
Renfang Jiang Department of Mathematical Sciences Michigan Technological University
Ben Jordan Department of Mathematics University of Minnesota
Steve Kaliszewski Department of Mathematics and Statistics Arizona State University
Mordechai Katzman Department of Pure Mathematics University of Sheffield
Michael Kerber   Universität Kaiserslautern
Markus Kirkilionis Department of Mathematics University of Warwick
Elizabeth Kleiman Department of Mathematics Iowa State University
Song-Hwa Kwon   University of Minnesota
Batool Labibi Department of Electrical and Computer Engineering University of Alberta
Reinhard Laubenbacher Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
Niels Lauritzen Institut for Matematiske Fag Aarhus University
Reiner Lauterbach Fachbereich Mathematik Universität Hamburg
Juyoun Lee Department of Statistics Pennsylvania State University
Namyong Lee Department of Mathematics Minnesota State University
Anton Leykin Institute for Mathematics and its Applications University of Minnesota
Hstau Y Liao   University of Minnesota
Gennady Lyubeznik School of Mathematics University of Minnesota
James Madden Department of Mathematics Louisiana State University
Thomas Markwig Department of Mathematics Universität Kaiserslautern
František Matúš Institute of Information Theory and Automation Czech Academy of Sciences (AVČR)
Richard B. Moeckel School of Mathematics University of Minnesota
Jason Morton Department of Mathematics University of California
Anca Mustata Department of Mathematics University of Illinois at Urbana-Champaign
Uwe Nagel Department of Mathematics University of Kentucky
Yuval Nardi Department of Statistics Carnegie Mellon University
Jiawang Nie   University of Minnesota
Ignacio Ojeda Martinez de Castilla Departamento de Matemáticas University of Extremadura
Sarah Olson Department of Biomathematical Sciences North Carolina State University
Michael E. O'Sullivan Department of Mathematics and Statistics San Diego State University
Lior Pachter Department of Mathematics University of California
Casian Pantea Department of Mathematics University of Wisconsin
Sonja Petrovic Department of Mathematics University of Kentucky
Giovanni Pistone Dipartimento di Matematica Politecnico di Torino
Mihai Putinar Department of Mathematics University of California
Kristian Ranestad Department of Mathematics University of Oslo
Victor Reiner School of Mathematics University of Minnesota
John A. Rhodes Department of Mathematics and Statistics University of Alaska
Eva Riccomagno Dipartimento di Matematica Università di Genova
Donald Richards Department of Statistics Pennsylvania State University
Thomas S. Richardson Department of Statistics University of Washington
Alessandro Rinaldo Department of Statistics Carnegie Mellon University
Joel Roberts School of Mathematics University of Minnesota
Daniel Robertz Lehrstuhl B fur Mathematik RWTH Aachen
Marie Rognes   University of Oslo
Bjarke Hammersholt Roune Department of Mathematics Aarhus University
Arnd Scheel Institute for Mathematics and its Applications University of Minnesota
Chehrzad Shakiban Institute of Mathematics and its Application University of Minnesota
Anne Shiu Department of Mathematics University of California
Aleksandra B. Slavković Department of Statistics Pennsylvania State University
Jim Smith Department of Statistics University of Warwick
Frank Sottile Department of Mathematics Texas A & M University
Steven Sperber School of Mathematics University of Minnesota
David Speyer Department of Mathematics University of Michigan
Sundararajan Srinivasan Sr. Department of Electrical Mississippi State University
Dumitru Stamate School of Mathematics University of Minnesota
Russell Steele Department of Mathematics and Statistics McGill University
Brandilyn Stigler Mathematical Biosciences Institute Ohio State University
Michael E. Stillman Department of Mathematics Cornell University
Bernd Sturmfels Department of Mathematics University of California
Seth Sullivant Department of Mathematics Harvard University
Rebecca Swanson Department of Mathematics Indiana University
Berhanu Tameru Center for Computational Epidemiology, Bioinformatics & Risk Analysis (CCEBRA) Tuskegee University
Amelia Taylor   Colorado College
Glenn Tesler Department of Mathematics University of California, San Diego
Thorsten Theobald Department of Computer Science and Mathematics Johann Wolfgang Goethe-Universität Frankfurt
Rekha R. Thomas Department of Mathematics University of Washington
Carl Toews   University of Minnesota
Ya-lun Tsai Department of Mathematics University of Minnesota
Caroline Uhler Department of Mathematics Universität Zürich
Jose Vargas CIIDIR-Oaxaca Instituto Politecnico Nacional, Mexico
Martha Paola Vera-Licona Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
Alberto Vigneron-Tenorio Facultad de Ciencias Sociales y de la Comunicacion University of Cádiz
John Voight   University of Minnesota
Jaroslaw Wisniewski Department of Mathematics University of Warsaw
Matthias Wolfrum   Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS)
Seongho Wu Department of Statistics University of Minnesota
Alexander Yong Department of Mathematics University of Minnesota
Ruriko Yoshida Department of Statistics University of Kentucky
Josephine Yu Department of Mathematics University of California
Cornelia Yuen Department of Mathematics University of Kentucky
Debbie Yuster Department of Mathematics Columbia University
Hongchao Zhang Institute for Mathematics and its Applications University of Minnesota
Mengyuan Zhao Department of Statistics University of Pittsburgh
Yi Zhou Department of Machine Learning Carnegie Mellon University