Mathematics

Stochasticity in an ecological model of the microbiome influences the efficacy of simulated bacteriotherapies

Speaker: 
Eric Jones
Date: 
Wed, Apr 28, 2021
Location: 
Zoom
Online
PIMS, Simon Fraser University
Conference: 
Emergent Research: The PIMS Postdoctoral Fellow Seminar
Abstract: 

We consider a stochastic bistable two-species generalized Lotka-Volterra model of the microbiome and use it as a testbed to analytically and numerically explore the role of direct (e.g., fecal microbiota transplantation) and indirect (e.g., changes in diet) bacteriotherapies. Two types of noise are included in this model, representing the immigration of bacteria into and within the gut (additive noise) and variations in growth rate associated with the spatially inhomogeneous distribution of resources (multiplicative noise). The efficacy of a bacteriotherapy is determined by comparing the mean first-passage times (the average time required for the system to transition from one basin of attraction to the other) with and without the intervention. Concepts from transition path theory are used to investigate how the role of noise affects these bacteriotherapies.

Class: 

Density estimation under total positivity and conditional independence

Speaker: 
Elina Robeva
Date: 
Wed, Apr 21, 2021
Location: 
Zoom
Online
PIMS, University of British Columbia
Conference: 
UBC-PIMS Mathematical Sciences Faculty Award
Abstract: 

Nonparametric density estimation is a challenging problem in theoretical statistics -- in general a maximum likelihood estimate (MLE) does not even exist! Introducing shape constraints allows a path forward.

In this talk I will first discuss non-parametric density estimation under total positivity (i.e. log-supermodularity) and log-concavity. Although they possess very special structure, totally positive random variables are quite common in real world data and have appealing mathematical properties. Given i.i.d. samples from a totally positive and log-concave distribution, we prove that the MLE exists with probability one assuming there are at least 3 samples. We characterize the domain of the MLE and if the observations are 2-dimensional, we show that the logarithm of the MLE is a tent function (i.e. a piecewise linear function) with "poles" at the observations, and we show that a certain convex program can find it.

I will finish by discussing density estimation for log-concave graphical models. As before, we show that the MLE exists and is unique with probability 1. We also characterize the domain of the MLE, and show how to find it if the graphical model corresponds to a chordal graph. I will conclude by discussing some future directions.

Speaker Biography

Dr. Robeva is an Assistant Professor with the Department of Mathematics at the University of British Columbia. From 2016 – 2019, Dr. Robeva was a Statistics Instructor and an NSF Postdoctoral Fellow in the Department of Mathematics and the Institute for Data, Systems, and Society, at the Massachusetts Institute of Technology. Dr. Robeva completed her PhD in 2016 from UC Berkeley, and won the Bernard Friedman Memorial Prize in Applied Mathematics, for her thesis.

About the Prize

The UBC-PIMS Mathematical Sciences Young Faculty Award prize was created by two founding donors, Anton Kuipers and Darrell Duffie, to recognize UBC researchers for their leading edge work in mathematics or its applications in the sciences. Dr Elina Robeva is the 2020 winner and will give her colloquium on Thursday April 21, 2021.

Class: 
Subject: 

Feedback onto cellular polarization from paxillin, implications for migrating cells

Speaker: 
Laurent MacKay
Date: 
Wed, Apr 14, 2021
Location: 
Zoom
Online
PIMS, University of British Columbia
Conference: 
Mathematical Biology Seminar
Abstract: 

Cellular polarization plays a critical during cellular differentiation, development, and cellular migration through the establishment of a long-lived cell-front and cell-rear. Although mechanisms of polarization vary across cells types, some common biochemical players have emerged, namely the RhoGTPases Rac and Rho. The low diffusion coefficient of the active form of these molecules combined with their mutual inhibitory interaction dynamics have led to a prototypical pattern-formation system that can polarizes cell through a non-Turing pattern formation mechanism termed wave-pinning. We investigate the effects of paxillin, a master regulator of adhesion dynamics, on the Rac-Rho system through a positive feedback loop that amplifies Rac activation. We find that paxillin feedback onto the Rac-Rho system produces cells that (i) self-polarize in the absence of any input signal (i.e., paxllin feedback causes a Turing instability) and (ii) become arrested due to the development of multiple protrusive regions. The former effect is a positive finding that can be related to certain cell-types, while the latter outcome is likely an artefact of the model. In order to minimize the effects of this artefact and produce cells that can both self-polarize as well as migrate for extended periods of time, we revisit some of model's parameter values and use lessons from previous models of polarization. This approach allows us to draw conclusions about the biophysical properties and spatiotemporal dynamics of molecular systems required for autonomous decision making during cellular migration.

Class: 

Extrinsic and intrinsic controls of cortical flow regulate C. elegans embryogenesis

Speaker: 
Kenji Sugioka
Date: 
Wed, Apr 21, 2021
Location: 
Zoom
Online
PIMS, University of British Columbia
Conference: 
Mathematical Biology Seminar
Abstract: 

Cell division is a vital mechanism for cell proliferation, but it often breaks its symmetry during animal development. Symmetry-breaking of cell division, such as the orientation of the cell division axis and asymmetry of daughter cell sizes, regulates morphogenesis and cell fate decision during embryogenesis, organogenesis, and stem cell division in a range of organisms. Despite its significance in development and disease, the mechanisms of symmetry-breaking of cell division remain unclear. Previous studies heavily focused on the mechanism of symmetry-breaking at metaphase of mitosis, wherein a localized microtubule-motor protein activity pulls the mitotic spindle. Recent studies found that cortical flow, the collective migration of the cell surface actin-myosin network, plays an independent role in the symmetry-breaking of cell division after anaphase. Using nematode C. elegans embryos, we identified extrinsic and intrinsic cues that pattern cortical flow during early embryogenesis. Each cue specifies distinct cellular arrangements and is involved in a critical developmental event such as the establishment of the left-right body axis, the dorsal-ventral body axis, and the formation of endoderm. Our research started to uncover the regulatory mechanisms underlying the cortical flow patterning during early embryogenesis.

Class: 

Random walks and graphs in materials, biology, and quantum information science

Speaker: 
Maria Emelianenko
Date: 
Wed, Apr 14, 2021
Location: 
Zoom
PIMS, University of Saskachewan
Conference: 
quanTA CRG Seminar
Abstract: 

What does mathematics, materials science, biology, and quantum
information science have in common? It turns out, there are many
connections worth exploring. I this talk, I will focus on graphs and random
walks, starting from the classical mathematical constructs and moving on to
quantum descriptions and applications. We will see how the notions of graph
entropy and KL divergence appear in the context of characterizing
polycrystalline material microstructures and predicting their performance
under mechanical deformation, while also allowing to measure adaptation in
cancer networks and entanglement of quantum states. We will discover
unified conditions under which master equations for classical random walks
exhibit nonlocal and non-diffusive behavior and see how quantum walks allow
to realize the coveted exponential speedup in quantum Hamiltonian
simulations. Recent classical and quantum breakthroughs and open questions
will be discussed.

For other events in this series see the quanTA events website.

Class: 

Geometry of Numbers: Lecture 13 of 13

Speaker: 
Barak Weiss
Date: 
Sun, Jan 3, 2021
Location: 
Zoom
Tel Aviv University
Conference: 
Geometry of Numbers
Abstract: 

This lecture is part of a course on the geometry of numbers.

For more information about these lectures, please see the course website (external).

Class: 
Subject: 

Geometry of Numbers: Lecture 12 of 13

Speaker: 
Barak Weiss
Date: 
Sun, Jan 3, 2021
Location: 
Zoom
Tel Aviv University
Conference: 
Geometry of Numbers
Abstract: 

This lecture is part of a course on the geometry of numbers.

For more information about these lectures, please see the course website (external).

Class: 
Subject: 

Geometry of Numbers: Lecture 11 of 13

Speaker: 
Barak Weiss
Date: 
Sun, Jan 3, 2021
Location: 
Zoom
Tel Aviv University
Conference: 
Geometry of Numbers
Abstract: 

This lecture is part of a course on the geometry of numbers.

For more information about these lectures, please see the course website (external).

Class: 
Subject: 

Geometry of Numbers: Lecture 10 of 13

Speaker: 
Barak Weiss
Date: 
Sat, Jan 2, 2021 to Sun, Jan 3, 2021
Location: 
Zoom
Tel Aviv University
Conference: 
Geometry of Numbers
Abstract: 

This lecture is part of a course on the geometry of numbers.

For more information about these lectures, please see the course website (external).

Class: 
Subject: 

Geometry of Numbers: Lecture 9 of 13

Speaker: 
Barak Weiss
Date: 
Sat, Jan 2, 2021
Location: 
Zoom
Tel Aviv University
Conference: 
Geometry of Numbers
Abstract: 

This lecture is part of a course on the geometry of numbers.

For more information about these lectures, please see the course website (external).

Class: 
Subject: 

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