Scientific

Variation in the descent of genome: modeling and inference

Speaker: 
Elizabeth Thompson
Date: 
Wed, Nov 20, 2019
Location: 
PIMS, University of Manitoba
Conference: 
PIMS-UManitoba Distinguished Lecture
Abstract: 

In meiosis, DNA is copied from parents to offspring, so that individuals who share common ancestors may have identical DNA copies from those ancestors through repeated meiosis. This identical-by-descent (IBD) DNA underlies the similarities between relatives, at both the family level and at the population level. However, the process of meiosis is quite variable, and DNA is inherited generation-to-generation in large segments. The patterns of IBD genome among relatives are complex, and in remote relatives segments of IBD DNA are rare but not short. Modern genetic data on millions of markers across the genome allows estimation of shared DNA, but accurate estimation requires modelling the processes that give rise to these complex IBD patterns. IBD must be estimated jointly among individuals and across the genome. Pedigree information, if available, provides prior probabilities of IBD patterns. Where inferred IBD is discordant with pedigree information, there is potential to detect selection or other processes distorting the outcomes of the meiotic process.

 

Speaker Biography: Elizabeth Thompson received her B.A. and Ph.D. in mathematics from Cambridge University, UK. After postdoctoral work in genetics at Stanford University, she joined the mathematics faculty of the University of Cambridge in 1976. She was a Professor of Statistics at the University of Washington from 1985 until her (semi-) retirement in 2018. Her research is in the development of methods for model-based likelihood inference from genetic data on both humans and other species, including inference of relationships among individuals and among populations. Dr. Thompson has received an Sc.D degree from the University of Cambridge, the Jerome Sacks award for cross-disciplinary statistical research, the Weldon Prize for contributions to Biometric Science, and a Guggenheim fellowship. She is an honorary fellow of Newnham College, Cambridge, and an elected member of the International Statistical Institute, the American Academy of Arts and Sciences, and the US National Academy of Sciences.

Surjectivity of random integral matrices on integral vectors

Speaker: 
Melanie Matchett Wood
Date: 
Fri, Nov 8, 2019
Location: 
PIMS, University of British Columbia
Conference: 
PIMS Distinguished Colloquium
Abstract: 
A random nxm matrix gives a random linear transformation from \Z^m to \Z^n (between vectors with integral coordinates). Asking for the probability that such a map is injective is a question of the non-vanishing of determinants. In this talk, we discuss the probability that such a map is surjective, which is a more subtle integral question. We show that when m=n+u, for u at least 1, as n goes to infinity, the surjectivity probability is a non-zero product of inverse values of the Riemann zeta function. This probability is universal, i.e. we prove that it does not depend on the distribution from which you choose independent entries of the matrix, and this probability also arises in the Cohen-Lenstra heuristics predicting the distribution of class groups of real quadratic fields. This talk is on joint work with Hoi Nguyen.

Scalable approximation of integrals using non-reversible methods: from Riemann to Lebesgue, and why you should care

Speaker: 
Alexandre Bouchard Côté
Date: 
Fri, Nov 15, 2019
Location: 
PIMS, University of British Columbia
Conference: 
PIMS - UBC Mathematical Sciences Young Faculty Award
Abstract: 

How to approximate intractable integrals? This is an old problem which is still a pain point in many disciplines (including mine, Bayesian inference, but also statistical mechanics, computational chemistry, combinatorics, etc).

 

The vast majority of current work on this problem (HMC, SGLD, variational) is based on mimicking the field of optimization, in particular gradient based methods, and as a consequence focusses on Riemann integrals. This severely limits the applicability of these methods, making them inadequate to the wide range of problems requiring the full expressivity of Lebesgue integrals, for example integrals over phylogenetic tree spaces or other mixed combinatorial-continuous problems arising in networks models, record linkage and feature allocation.

 

I will describe novel perspectives on the problem of approximating Lebesgue integrals, coming from the nascent field of non-reversible Monte Carlo methods. In particular, I will present an adaptive, non-reversible Parallel Tempering (PT) allowing MCMC exploration of challenging problems such as single cell phylogenetic trees.

 

By analyzing the behaviour of PT algorithms using a novel asymptotic regime, a sharp divide emerges in the behaviour and performance of reversible versus non-reversible PT schemes: the performance of the former eventually collapses as the number of parallel cores used increases whereas non-reversible benefits from arbitrarily many available parallel cores. These theoretical results are exploited to develop an adaptive scheme approximating the optimal annealing schedule.

 

My group is also interested in making these advanced non-reversible Monte Carlo methods easily available to data scientists. To do so, we have designed a Bayesian modelling language to perform inference over arbitrary data types using non-reversible, highly parallel algorithms.

If Space Turned out to be Time: Resonances and Patterns in the Visual Cortex

Speaker: 
Bard Ermentrout
Date: 
Wed, Oct 9, 2019
Location: 
PIMS, University of Manitoba
Conference: 
PIMS-UManitoba Distinguished Lecture
Abstract: 

When subjects are exposed to full field flicker in certain frequencies, they perceive a variety of complex geometric patterns that are often called flicker hallucinations. On the other had, when looking at high contrast geometric patterns like op art, shimmering and flickering is observed. In some people, flicker or such op art can induce seizures. In this talk, I describe a simple network model of excitatory and inhibitory neurons that comprise the visual area of the brain. I show that these phenomena are reproduced and then give an explanation based on symmetry breaking bifurcations and Floquet theory. Symmetric bifurcation theory also shows why one expects a different class of patterns at high frequencies from those at low frequencies.

 

On the other hand, the visual system is also very sensitive to specific spatial frequencies and this sensitivity can be pathological in the case of so-called pattern-senstive epilepsy. It has been shown that certain types of "op art"can cause visual discomfort. We show that the network that we used in flicker is also sensitive to spatially periodic inputs and suggest that a Hopf bifurcation instability is responsible for the discomfort and seizures.

 

Speaker Biography

Bard Ermentrout received his PhD in Theoretical Biology at the University of Chicago and was a postdoctoral fellow at the NIH from 1979-1982. He has been at the University of Pittsburgh since then. He is the author of over 200 papers and two books as well as the simulation package, XPPAUT. He is a Sloan Fellow and a SIAM Fellow and received the Mathematical Neuroscience Prize in 2015.

An Application of Homotopy Theory to Condensed Matter Physics

Speaker: 
Daniel Freed
Date: 
Mon, Sep 16, 2019
Location: 
PIMS, University of Saskatchewan
Conference: 
Peter Scherk Lecture in Geometry
Abstract: 
The classification of phases of matter is a topic of much current interest. While descriptions of quantum mechanical systems often use discrete lattice models, one can typically approximate by continuous field theories. There is a well-developed mathematical framework for studying field theories, and this brings powerful techniques to the table. In this general talk, I will describe joint work with Mike Hopkins (Harvard) in which we carry out this scheme for invertible phases of matter and deduce the classification in terms of bordism groups of manifolds. Much of the talk will focus on general ideas at an elementary level.

DINOSAUR WARS: Extinction by Asteroid or Volcanism? Are we the Dinosaurs of the 6th Mass Extinction?

Speaker: 
Gerta Keller
Date: 
Wed, Jul 24, 2019
Location: 
PIMS, University of Victoria
Conference: 
Hugh C. Morris Lecture
Abstract: 

For the past 40 years the demise of the dinosaurs has been attributed to an asteroid impact on Yucatan, a theory that is imaginative, popular and even sexy. From the very beginning, scientists who doubted this theory were threatened into silence or their careers destroyed by the main theory proponents. Thus began the Dinosaur wars in 1980 – and still continuing. As in any war, there are two sides to the Dinosaur wars. The majority believes an asteroid hit Yucatan and instantaneously wiped out 75% of all life including the dinosaurs in a global firestorm and nuclear type winter. A small minority tested this theory and found contrary evidence that supported Deccan volcanism in India that caused rapid climate warming due to greenhouse gases (CO2), environmental stress, acid rain and ocean acidification culminating in the mass extinctions. This lecture highlights the four decades of the dinosaur wars, the increasing acceptance of volcanism’s catastrophic effects and likely cause of the mass extinction and the resulting ad hoc revisions to accommodate the impact theory. The talk ends with the ongoing 6th mass extinction initiated by rapid fuel burning that is causing the most rapid climate warming in Earth’s history and ocean acidification, which is predicted to reach the 6th mass extinction in as little as 50-75 years and maximum of 250 years. We could be the Dinosaurs of the 6th mass extinction.

 

Speaker Biography

Gerta Keller is Professor of Paleontology and Geology in the Geosciences Department of Princeton University since 1984. She was born on March 7, 1945 in Liechtenstein. She grew up on a small farm in Switzerland as the sixth of a dozen children with no prospect for education. At age 14 she entered apprenticeship as dressmaker, at 17 she worked for the DIOR Fashion House in Zurich. With no prospect for advancement she began her adventure travels through North Africa and the Middle East, supporting herself by waitressing. She immigrated to Australia at 21, was shot by a bank robber and nearly died at 22. After recovery, she resumed her adventure travels through Southeast Asia and arrived in San Francisco in 1968. There she found the first opportunity for education and entered City College, continued her undergraduate studies at San Francisco State College majoring in Anthropology and Geology, concentrating on climate and environmental changes and their effects on mass extinctions. She was awarded a Danforth Fellowship for her graduate studies at Stanford University in 1974 and received her PhD in 1978. She continued her work at Stanford University and the U.S. Geological Survey in Menlo Park and steadily researched climatic and environmental effects on life all the way back to the dinosaur mass extinction 66 million years ago. In 1984 she was hired as tenured faculty at Princeton University.

 

Prof. Gerta Keller’s major research and discoveries ranged from climate change and its effects on ocean circulation, ocean anoxic events, polar warming, Deccan volcanism, comet showers, extraterrestrial impacts, the dinosaur mass extinction, the age of the Chicxulub impact and the 6th mass extinction. Her research frequently challenged accepted scientific dogma and placed her at the center of acrimonious debates fighting for survival of truth-based evidence. All but the cause of the Chicxulub impact were soon accepted by scientists and integrated into new research. After four decades, impact proponents still fiercely defend the impact theory, deny contrary evidence and at best incorporate volcanism as ad hoc revisions, proclaiming the impact triggered volcanism that caused the mass extinction.

 

Gerta Keller has over 260 scientific publications in international journals and is a leading authority on catastrophes and mass extinctions, and the biotic and environmental effects of impacts and volcanism. She has co-authored and edited several books and she has been featured in many films and documentaries by very popular TV channels and Film Corporations, including BBC, The History Channel, and Hollywood.

Geometricity and Galois actions on fundamental groups

Speaker: 
Daniel Litt
Date: 
Fri, Jun 14, 2019
Location: 
PIMS, University of British Columbia
Conference: 
Workshop on Arithmetic Topology
Abstract: 
Which local systems on a Riemann surface X arise from geometry, i.e. as (subquotients of) monodromy representations on the cohomology of a family of varieties over X? For example, what are the possible level structures on Abelian schemes over X? We describe several new results on this topic which arise from an analysis of the outer Galois action on etale fundamental groups of varieties over finitely generated fields.

The stable cohomology of the moduli space of curves with level structures

Speaker: 
Andrew Putman
Date: 
Fri, Jun 14, 2019
Location: 
PIMS, University of British Columbia
Conference: 
Workshop on Arithmetic Topology
Abstract: 
I will prove that in a stable range, the rational cohomology of the moduli space of curve with level structures is the same as the ordinary moduli space of curves: a polynomial ring in the Miller-Morita-Mumford classes.

The Grothendieck ring of varieties, and stabilization in the algebro-geometric setting - 2 of 2

Speaker: 
Aaron Landesman
Date: 
Fri, Jun 14, 2019
Location: 
PIMS, University of British Columbia
Conference: 
Workshop on Arithmetic Topology
Abstract: 
A central theme of this workshop is the fact that arithmetic and topological structures become best behaved “in the limit”. The Grothendieck ring of varieties (or stacks) gives an algebro-geometric means of discovering, proving, or suggesting such phenomena.

 


In the first lecture of this minicourse, Ravi Vakil will introduce the ring, and describe how it can be used to prove or suggest such stabilization in several settings.

 


In the second lecture of the minicourse, Aaron Landesman will use these ideas to describe a stability of the space of low degree covers (up to degree 5) of the projective line (joint work with Vakil and Wood). The results are cognate to Bhargava’s number field counts, the philosophy of Ellenberg-Venkatesh-Westerland, and Anand Patel’s fever dream.

 


This is the second lecture in a two part series: part 1.
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