Scientific

A reproducing kernel Hilbert space framework for functional classification

Speaker: 
Peijun Sang
Date: 
Wed, Sep 22, 2021
Location: 
Online
Abstract: 

The intrinsic infinite-dimensional nature of functional data creates a bottleneck in the application of traditional classifiers to functional settings. These classifiers are generally either unable to generalize to infinite dimensions or have poor performance due to the curse of dimensionality. To address this concern, we propose building a distance-weighted discrimination (DWD) classifier on scores obtained by projecting data onto one specific direction. We choose this direction by minimizing, over a reproducing kernel Hilbert space, an empirical risk function containing the DWD classifier loss function. Our proposed classifier avoids overfitting and enjoys the appealing properties of DWD classifiers. We further extend this framework to accommodate functional data classification problems where scalar covariates are involved. In contrast to previous work, we establish a non-asymptotic estimation error bound on the relative misclassification rate. Through simulation studies and a real-world application, we demonstrate that the proposed classifier performs favourably relative to other commonly used functional classifiers in terms of prediction accuracy in finite-sample settings.

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Optimal Study Design for Reducing Variances of Coefficient Estimators in Change-Point Models

Speaker: 
Li Xing
Date: 
Wed, Oct 6, 2021
Location: 
Online
Abstract: 

In longitudinal studies, we measure the same variables at multiple time-points to track their change over time. The exact data collection schedules (i.e., time of participants' visits) are often pre-determined to accommodate the ease of project management and compliance. Therefore, it is common to schedule those visits at equally spaced time intervals. However, recent publications based on simulated experiments indicate that the power of studies and the precision of model parameter estimators is related to the participants' visiting scheme. So, in this work, we investigate how to schedule participants' visits to better study the accelerated cognitive decline of senior adults, where a broken-stick model is often applied. We formulate this optimal design problem on scheduling participants' visiting into a high- dimensional optimization problem and derive its approximate solution by adding reasonable constraints. Based on this approximation, we propose a novel design of the visiting scheme that aims to maximize the power (i.e. reduce the variance of estimators) in identifying the onset of accelerated decline. Using both simulation studies and evidence from real data, we demonstrate that our design outperforms the standard equally-spaced one when we have strong prior knowledge on the change-points. This novel design helps researchers plan their longitudinal studies with improved power in detecting pattern change without collecting extra data. Also, this individual-level scheduling system helps monitor seniors' cognitive function and, therefore, benefits the development of personal level treatment for cognitive decline, which agrees with the trend of the health care system.

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Variational Autoencoders: an introduction to new applications and a new regularization approach

Speaker: 
Cedric Beaulac
Date: 
Wed, Oct 13, 2021
Location: 
Online
Abstract: 

In this presentation, we discuss the Variational AutoEncodeur (VAE): a latent variable model emerging from the machine learning community. To begin, we introduce the theoretical foundations of the model and its relationship with well-established statistical models. Then, we discuss how we used VAEs to solve two widely different problems. First, we tackled a classic statistical problem, survival analysis, and then a classic machine learning problems, image analysis and image generation. We conclude with a short discussion of our latest research project where we establish a new metric for the evaluation or regularization of latent variable models such a Gaussian Mixture Models and VAEs.​

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Programmable Human Organoids via Genetic Design and Engineering

Speaker: 
Mo Ebrahimkhani
Date: 
Wed, Oct 13, 2021
Location: 
PIMS, University of British Columbia
Zoom
Online
Conference: 
Mathematical Biology Seminar
Abstract: 

Synthetic biology offers bottom-up engineering strategies that intends to understand complex systems via design-build-test cycles. In development, gene regulatory networks emerge into collective cellular behaviors with multicellular forms and functions. Here, I will introduce a synthetic developmental biology approach for tissue engineering. It involves building developmental trajectories in stem cells via programmed gene circuits and network analysis. The outcome of our approach is decoding our own development and to create programmable organoids with both natural or artificial designs and augmented functions.

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High-Order Accuracy Computation of Coupling Functions for Strongly Coupled Oscillators

Speaker: 
Youngmin Park
Date: 
Wed, Oct 13, 2021
Location: 
PIMS, University of Manitoba
Zoom
Online
Conference: 
Emergent Research: The PIMS Postdoctoral Fellow Seminar
Abstract: 

We develop a general framework for identifying phase reduced equations for finite populations of coupled oscillators that is valid far beyond the weak coupling approximation. This strategy represents a general extension of the theory from [Wilson and Ermentrout, Phys. Rev. Lett 123, 164101 (2019)] and yields coupling functions that are valid to higher-order accuracy in the coupling strength for arbitrary types of coupling (e.g., diffusive, gap-junction, chemical synaptic). These coupling functions can be used to understand the behavior of potentially high-dimensional, nonlinear oscillators in terms of their phase differences. The proposed formulation accurately replicates nonlinear bifurcations that emerge as the coupling strength increases and is valid in regimes well beyond those that can be considered using classic weak coupling assumptions. We demonstrate the performance of our approach through two examples. First, we use diffusively coupled complex Ginzburg-Landau (CGL) model and demonstrate that our theory accurately predicts bifurcations far beyond the range of existing coupling theory. Second, we use a realistic conductance-based model of a thalamic neuron and show that our theory correctly predicts asymptotic phase differences for non-weak synaptic coupling. In both examples, our theory accurately captures model behaviors that weak coupling theories can not.

Speaker Biography

Youngmin Park, Ph.D., is currently a PIMS Postdoc at the University of Manitoba under the supervision of Prof. Stéphanie Portet. He received his PhD in Mathematics from the University of Pittsburgh in 2018, where he applied dynamical systems methods to problems in neuroscience. His first postdoc involved auditory neuroscience research at the University of Pennsylvania in the Department of Otorhinolaryngology, before moving on to his next postdoc researching molecular motor dynamics in the Department of Mathematics at Brandeis University. He is now at Manitoba, continuing to apply dynamical systems methods to biological questions related to molecular motor transport and neural oscillators.

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Footnotes to Turing (1952): Some Modern Challenges in Pattern Formation

Speaker: 
Andrew Krause
Date: 
Wed, Oct 6, 2021
Location: 
PIMS, University of British Columbia
Online
Zoom
Conference: 
Mathematical Biology Seminar
Abstract: 

Motivated by recent work with biologists, I will showcase some mathematical results on Turing instabilities in complex domains. This is scientifically related to understanding developmental tuning in a variety of settings such as mouse whiskers, human fingerprints, bat teeth, and more generally pattern formation on multiple scales and evolving domains. Some of these problems are natural extensions of classical reaction-diffusion models, amenable to standard linear stability analysis, whereas others require the development of new tools and approaches. These approaches also help close the vast gap between the simple theory of diffusion-driven pattern formation, and the messy reality of biological development, though there is still much work to be done in validating even complex theories against the rich pattern dynamics observed in nature. I will emphasize throughout the role that Turing's 1952 paper had in these developments, and how much of our modern progress (and difficulties) were predicted in this paper. I will close by discussing a range of open questions, many of which fall well beyond the extensions I will discuss, but at least some of which were known to Turing.

Class: 

Large Systems of Interacting Particles and their Applications in Optimization

Speaker: 
Hui Huang
Date: 
Wed, Sep 15, 2021
Location: 
PIMS, University of Calgary
Zoom
Online
Conference: 
Emergent Research: The PIMS Postdoctoral Fellow Seminar
Abstract: 

Large systems of interacting particles (or agents) are widely used to investigate self-organization and collective behavior. They frequently appear in modeling phenomena such as biological swarms, crowd dynamics, self-assembly of nanoparticles and opinion formation. Similar particle models are also used in metaheuristics, which provide empirically robust solutions to tackle hard optimization problems with fast algorithms. In this talk I will start with introducing some generic particle models and their underlying mean-field equations. Then we will focus on a specific particle model that belongs to the class of Consensus-Based Optimization (CBO) methods, and we show that it is able to perform essentially as good as ad hoc state of the art methods in challenging problems in signal processing and machine learning.

Speaker Biography

Hui Huang, Ph.D., is currently a PIMS Postdoc at the University of Calgary under the supervision of Prof. Jinniao Qiu. Before moving to Calgary, he worked as a postdoctoral researcher in the Chair for Applied Numerical Analysis at the Technical University of Munich, Germany. Prior to being at TUM he was an Alan Mekler Postdoctoral Fellow in the Department of Mathematics at Simon Fraser University. In 2017, he received his PhD in Mathematics from Tsinghua University. His doctoral dissertation was conducted in consultations with Prof. Jian¬-Guo Liu from Duke University, where he studied as a joint PhD student from 2014 to 2016. His research has been focused on complex dynamical systems and their related kinetic equations.

Read more about Hui Huang on the PIMS Medium blog.

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Finite sample rates for optimal transport estimation problems

Speaker: 
Jan-Christian Hütter
Date: 
Thu, Sep 30, 2021
Location: 
PIMS, University of Washington
Zoom
Online
Conference: 
Kantorovich Initiative Seminar
Abstract: 

The theory of optimal transport (OT) gives rise to distance measures between probability distributions that take the geometry of the underlying space into account. OT is often used in the analysis of point cloud data, for example in domain adaptation problems, computer graphics, and trajectory analysis of single-cell RNA-Seq data. However, from a statistical perspective, straight-forward plug-in estimators for OT distances and couplings suffer from the curse of dimensionality in high dimensions. One way of alleviating this problem is to employ regularized statistical procedures, either by changing the transport objective or exploiting additional structure in the underlying probability distributions or ground truth couplings. In this talk, I will outline the problem and give an overview of recent solution approaches, in particular those employing entropically regularized optimal transport or imposing smoothness assumptions on the ground truth transport map.

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Using Observations to Accurately and Efficiently Model Turbulent Flows: Parameter Recovery, Sensitivity Analysis, Nonlinear Data Assimilation Algorithms, and a Real-World Implementation.

Speaker: 
Elizabeth Carlson
Date: 
Wed, Sep 29, 2021
Location: 
PIMS, University of British Columbia
Zoom
Online
Conference: 
Emergent Research: The PIMS Postdoctoral Fellow Seminar
Abstract: 

One of the challenges of the accurate simulation of turbulent flows is that initial data is often incomplete. Data assimilation circumvents this issue by continually incorporating the observed data into the model. A new approach to data assimilation known as the Azouani-Olson-Titi algorithm (AOT) introduced a feedback control term to the 2D incompressible Navier-Stokes equations (NSE) in order to incorporate sparse measurements. The solution to the AOT algorithm applied to the 2D NSE was proven to converge exponentially to the true solution of the 2D NSE with respect to the given initial data. In this talk, we present our tests on the robustness, improvements, and implementation of the AOT algorithm, as well as generate new ideas based off of these investigations. First, we discuss the application of the AOT algorithm to the 2D NSE with an incorrect parameter and prove it still converges to the correct solution up to an error determined by the error in the parameters. This led to the development of a simple parameter recovery algorithm, whose convergence we recently proved in the setting of the Lorenz equations. The implementation of this algorithm led us to provide rigorous proofs that solutions to the corresponding sensitivity equations are in fact the Fréchet derivative of the solutions to the original equations. Next, we present a proof of the convergence of a nonlinear version of the AOT algorithm in the setting of the 2D NSE, where for a portion of time the convergence rate is proven to be double exponential. Finally, we implement the AOT algorithm in the large scale Model for Prediction Across Scales - Ocean model, a real-world climate model, and investigate the effectiveness of the AOT algorithm in recovering subgrid scale properties.

Speaker Biography

Elizabeth Carlson, is a homeschooler turned math PhD! She grew up in Helena, MT, USA, where she also graduated from Carroll College with a Bachelor's in mathematics and minor in physics. She became interested in fluid dynamics as an undergraduate, and followed this interest through her graduate work at the University of Nebraska - Lincoln in Lincoln, NE, USA, where she just earned my PhD in May 2021. Her research focus is in fluid dynamics, focusing on the well-posedness of systems of partial differential equations and numerical computations and analysis in fluid dynamics. In her free time, she enjoys hiking, playing piano, reading, and martial arts.

Read more about Elizabeth Carlson on our PIMS Medium blog here.

Class: 

Topological Data Analysis of Collective Behavior

Speaker: 
Dhananjay Bhaskar
Date: 
Wed, Sep 29, 2021
Location: 
PIMS, University of British Columbia
Online
Zoom
Conference: 
Mathematical Biology Seminar
Abstract: 

Active matter systems, ranging from liquid crystals to populations of cells and animals, exhibit complex collective behavior characterized by pattern formation and dynamic phase transitions. However, quantitative classification is challenging for heterogeneous populations of varying size, and typically requires manual supervision. In this talk, I will demonstrate that a combination of topological data analysis (TDA) and machine learning can uniquely identify the spatial arrangement of agents by keeping track of clusters, loops, and voids at multiple scales. To validate the approach, I will present 3 case studies: (1) data-driven modeling and analysis of epithelial-mesenchymal transition (EMT) in mammary epithelia, (2) unsupervised classification of cell sorting, and self-assembly patterns in co-cultures, and (3) parameter recovery from animal swarming trajectories.

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