SorinFest: Phase Transitions in Computer Science and Computational Biology








Brown University's Department of Computer Science and Center for Computational Molecular Biology present a conference upon the occasion of Sorin Istrail’s seventieth birthday:




SorinFest: Phase Transitions in Computer Science and Computational Biology

Friday, October 6, and Saturday, October 7, 2023
Room 368, The Thomas J. Watson Sr. Center for Information Technology (115 Waterman Street, Providence, RI 02906)

Click here for a complete set of videos of the event. Sorin's new website is here and a new short bio written especially for SorinFest is available here.

Distinguished Lectures

Introductory Remarks

Opening Keynote: Craig Venter (CEO of Celera Genomics and the J. Craig Venter Institute, and winner of the US National Medal of Science), a John von Neumann Distinguished Lecture: "The past, the present and the future of genomics

Bonnie Berger (Simons Professor of Mathematics, Massachusetts Institute of Technology), a John von Neumann Distinguished Lecture): "21st Century Genomics Minimizer Space Computation"

Andy Clark (Jacob Gould Schurman Professor of Population Genetics, Cornell University, and Brown University alumnus): "Allele-Specific Expression as a Pairwise Contest"

Ken Dill (Laufer Family Endowed Chair in Physical Biology and SUNY Distinguished Professor of Chemistry & Physics, Director of the Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University), a John von Neumann Distinguished Lecture: "The Molecular Origins of Life - The Protein Folding Problem all Over Again?"

Misha Gromov (Institut des Hautes Études Scientifiques and New York University, winner of the Abel Prize), a John von Neumann Distinguished Lecture, "Invisible Mathematics of Learning and Understanding" (on Zoom)

Gene Myers (Director of Max Planck Institute of Molecular Cell Biology and Genetics,  emeritus, former VP of Informatics Research, Celera Genomics), a John von Neumann Distinguished Lecture: "Sorting for Speed"

J. Michael Kosterlitz (Harrison E. Farnsworth Professor of Physics, Brown University, and winner of the Nobel Prize in Physics), an Ising-Onsager Distinguished Lecture: "Topological Defects and Phase Transitions"

Professor Kosterlitz’s lecture will also serve as the inaugural lecture in Brown University’s new Ising-Onsager Distinguished Lecture Series. His research areas include condensed matter, phase transitions, and Ising spin glasses. The initial proposal for this lecture series (“Proposal for the Ernst Ising Distinguished Lecture Series”) was made to Brown University’s Dean of the Faculty on May 20, 2011 by Sorin and colleagues from the Departments of Chemistry and Physics. The Ising-Onsager Distinguished Lecture Series builds on and revises that proposal.

This series honors the memory of Lars Onsager, Brown University Professor of Chemistry from 1928-1933 and winner of the Nobel Prize for Chemistry in 1968. In 1944, Onsager obtained the phase transition and exact solution for the 2D planar Ising Model (Ising ferromagnetic 2D plane grid). His seminal exact mathematical proof of the 2D planar Ising model partition function formula is considered one of the most extraordinary mathematical tour de force proofs in statistical physics. Answering the call to “make [the proof] human”, a dream team of mathematicians and physicists, including Kac, Ward, Feynman, Hurst, Kasteleyn, and Temperley attempted until 1975 to generalize Onsager’s proof to three dimensions, but without success. Kac and Ward, with contributions from Feynman, obtained a combinatorial proof of the Onsager theorem. In 2000, Sorin published the paper "Statistical Mechanics, Three-Dimensionality and NP-completeness. I. Universality of Intractability for the Partition Function of the Ising Model Across Non-Planar Lattices" at the Symposium on the Theory of Computing (STOC). His paper showed, for several Ising spin glass models, that for every non-planar (and therefore every 3D) model, computing the partition function is NP-complete. The proofs were axiomatic: Non-planarity plus Translational Invariance implies NP-completeness.

Attendees (confirmation of participation in progress)

Following the Distinguished Lectures, some of our attendees will present short talks and remembrances:


A talk by Sorin will close the event. His remarks will include an In Memoriam section with remembrances of beloved mentors, friends and heroes:

Organizing Committee

Tentative Schedule

We welcome each of our SorinFest presenters. They are Sorin’s mentors, and heroes, and collaborators carrying the brilliant torch forward. 

Friday, October 6, 2023

CIT 368 and 3rd Floor Atrium
Session Chair: Bjarni Halldorsson


Introductory remarks from Roberto Tamassia, Sohini Ramachandran, and Dan Weinreich


Keynote: Craig Venter (Winner of the US National Medal of Science)
John von Neumann Distinguished Lecture, introduced by Michael Waterman: "The past, the present and the future of genomics"


Sweatbox Session with Dr. Venter 
Graduate students: Computer Science, CCMB, Biology, Applied Math


Bonnie Berger
John von Neumann Distinguished Lecture, introduced by Ritambhara Singh: "21st Century Genomics: Minimizer-space Computation"




Remarks from Provost Francis Doyle

Session Chair: Vineet Bafna


Keynote: Michael Kosterlitz (Nobel Laureate)
Ernst Ising-Lars Onsager Distinguished Lecture: "Topological defect driven phase transitions in two dimensions – an exact result from an approximate theory" Icon pptx (3.1 MB)


Sweatbox Session with Dr. Kosterlitz
Graduate students: Chemistry, Physics, Computer Science, Applied Math, CCMB

Refreshment Break


Bill Camp ("Never make a calculation unless you know the answer")


Henri Luchian ("Sorin's Twenties' Jubilee") (on Zoom)  Icon pptx (30.7 MB)


Andrea Califano ("Defeating Cancer One Cell at a Time"(on Zoom)


Caleb “Tuck” Finch ("Socio-economic Gradients of Development in Pathways of Aging")


Andy Clark 
John von Neumann Distinguished Lecture ("Allele-specific expression as a pairwise contest"), introduced by Sohini Ramachandran


Q+A Session


Laxmi Parida ("Discovery: How, if not AI?")


Ernie Brickell and Bill Hart ("The Origin of Sorin's Computational Biology Research")


Franco Preparata ("How it began at Brown") (on Zoom)

Closing Remarks


Conference dinner, Hope Club
Dinner Keynote: Brown University President Christina Paxson
Dinner Lecture: Barry Cipra - "Ising, Istrail, and I"
Brief Remarks: Sohini Ramachandran, Sorin

Saturday October 7, 2023

CIT 368 and 3rd Floor Atrium
Session Chair: Derek Aguiar


Keynote: Misha Gromov (Winner of the Abel Prize) (on Zoom)
John von Neumann Distinguished Lecture, introduced by Stu Geman: "Invisible Mathematics of Learning and Understanding"


Sweatbox Session with Dr. Gromov
Graduate students: Applied Math, Computer Science, CCMB


Refreshment Break


Jon Kleinberg (on Zoom) ("Transmission, Mutation, and Fitness in Networks of Online Content: An Unexpected Role for Mechanisms in Computational Biology")


Ron Shamir (on Zoom) ("Algorithms for multiomic disease data")


Moshe Vardi (on Zoom) ("How to be an ethical computer scientist")


Peter Shor ("The Motzkin and Fredkin quantum spin chains")


Bjarne Stroustrup ("C++: evolving a useful language")


Ken Dill, introduced by Brenda Rubenstein
John von Neumann Distinguished Lecture: "The molecular origins of life: the Protein Folding Problem all over again?"


Q+A Session



Session Chair: Russell Schwartz


Gene Myers, a John von Neumann Distinguished Lecture ("Sorting for Speed in Bioinformatics"), introduced by Vineet Bafna


Q+A Session


Pavel Pevzner (on Zoom) ("From Ulam’s Problem to Sequence Alignment in the Telomere-to-Telomere Era")


Liliana Florea (on Zoom) ("Unravelling the combinatorial design of genes: Splice graph-based transcript reconstruction from RNA sequencing reads")


Giuseppe Lancia ("Beating the quadratic algorithm for finding the best 2-OPT move")


Refreshment Break


Sridhar Hannenhalli ("Prioritizing non-coding mutations in evolution and in cancer")


Jon Yewdell ("Whither the MHC I Immunopeptidome?")


Jason Miller ("Machine Learning and RNA seq Alignment")


Dan Fasulo ("Changes in the Gut Microbiome Associated With Type 2 Diabetes")


Student presentations


Sorin Istrail


Open Mic Reception



Brown Faculty Club Dinner
Brief Remarks: Sorin, Craig Venter, Bjarni Halldorsson, Serafim Batzoglou, Bonnie Berger, Derek Aguiar, Mike Waterman, Russell Schwartz, Sorin Dragici

History of the Sweatbox Concept

Funded by the National Science Foundation as a workshop called “Q&A Boot Camp at Brown University: Asking Tough Scientific Questions,” the “Sweatbox” session as a didactic concept was inspired by the famous 8-week “Summer Course/Boot Camp on Embryology” at the Marine Biological Laboratory, Woods Hall, MA and the director of the course for 15 years, Professor Eric Davidson of the Division of Biology at California Institute of Technology. The story goes that invited speakers at this course would talk in the laboratory’s Warm Room and would be subjected there to tough scientific questions about their scientific findings and claims. Professor Davidson, professor-in-chief of developmental gene regulatory network biology and a beacon of critical discourse, mentored about 300 PhDs, postdocs and faculty in his laboratory. Basing his work on causality-focused and genomics-based systems, and with insights from experimental biology, biochemistry, physics and engineering, he brought together all us biologists, physicists, biochemists, engineers, mathematicians, statisticians, and computer scientists in a renaissance research quest for the functional meaning of DNA. The resulting symbiosis of insights is von Neumannesque in spirit and fits well with von Neumann’s unfinished research towards a new logical and computational model for the biological cell by unifying continuous and discrete mathematics via a concept of thermodynamic error. Our “Sweatbox” is so named to honor Professor Davidson’s academic legacy.