Title: The Potential Role of Subclinical Infection in Outbreaks of Emerging Pathogens

Abstract: Many rare or emerging diseases exhibit different epidemioligical behaviors from

outbreak to outbreak, leaving it unclear how to best characterize the relevant facets

that could be exploited for outbreak mitigation/control. Some studies have already

proposed considering the role of active subclinical infections co-emerging and cocirculating

as part of the process of emergence of a novel pathogen. However,

consideration of the role of subclinical infections in emerging disease dynamics

have usually avoided considering the full set of possible influences. Most recently,

the Ebola outbreak 2014 seems to fit all the criteria for possible involvement of

subclinical circulation. We argue that an understanding of the potential mechanism

for diversity in observed epidemiological dynamics may be of considerable

importance in understanding and preparing for outbreaks of novel and/or emerging

diseases.

Title: Ubiquitous Doubling Algorithms, General Theory, and Applications

Abstract: Iterative methods are widely and indispensably used in numerical approximations. Basically, any iterative method is a rule that produces a sequence of approximations and with a reasonable expectation that newer approximations in the sequence are better. The goal of a doubling algorithm is to significantly speed up the approximation process by seeking ways to skip computing most of the approximations in the sequence but sporadically few, in fact, extremely very few: only the $2^i$-th approximations in the sequence, kind of like computing $\alpha^{2^i}$ via repeatedly squaring. However, this idea is only worthwhile if there is a much cheaper way to directly obtain the $2^i$-th approximation from the $2^{i-1}$-st one  than simply following the rule to generate every approximation between the $2^{i-1}$-st and $2^i$-th approximations in order to obtain the $2^i$-th approximation. Anderson (1978) had sought the idea to speed up the simple fixed point iteration for solving the discrete-time algebraic Riccati equation via repeatedly compositions of the fixed point iterative function. As can be imagined, under repeatedly compositions, even a simple function can usually and quickly turn into nonetheless a complicated and unworkable one. In the last 20 years or so in large part due to an extremely elegant way of formulation and analysis, the research in doubling algorithms thrived and continues to be very active, leading to numerical effective and robust algorithms not only for the continuous-time and discrete-time algebraic Riccati equations from optimal control that motivated the research  in the first place but also for $M$-matrix algebraic Riccati equations (MARE), structured eigenvalue problems, and other nonlinear matrix equations. But the resulting theory is somewhat fragmented and sometimes ad hoc. In this talk, we will seek to provide a general and coherent theory, discuss new highly accurate doubling algorithm for MARE, and look at several important applications.

Title:  Orthogonal Recurrent Neural Networks with Scaled Cayley Transform

Abstract: Recurrent Neural Networks (RNNs) are designed to handle sequential data but suffer from vanishing or exploding gradients.  Recent work on Unitary Recurrent Neural Networks (uRNNs) have been used to address this issue and in some cases, exceed the capabilities of Long Short-Term Memory networks (LSTMs).  We propose a simpler and novel update scheme to maintain orthogonal recurrent weight matrices without using complex valued matrices. This is done by parametrizing with a skew-symmetric matrix using the Cayley transform. Such a parametrization is unable to represent matrices with negative one eigenvalues, but this limitation is overcome by scaling the recurrent weight matrix by a diagonal matrix consisting of ones and negative ones.  The proposed training scheme involves a straightforward gradient calculation and update step. In several experiments, the proposed scaled Cayley orthogonal recurrent neural network (scoRNN) achieves superior results with fewer trainable parameters than other unitary RNNs.

Title: Dynamic Programming in Secondary Structure Inference

Abstract: Given an RNA sequence, secondary structure inference is the problem of predicting that sequence's base pairs. A variety of methods for this problem exist; among the most popular are minimum free energy (MFE) methods, which assign each possible secondary structure an energy based on the presence or absence of various substructures, with negative energy structures being more likely to occur naturally. These methods then use dynamic programming to predict the lowest free energy structure(s) efficiently. We will give an introduction to dynamic programming, talk about why it is necessary for approaching this problem efficiently, and discuss some of the shortcomings of the method. If time permits, we will also talk about connections to machine learning methods for secondary structure prediction.

Title: Spatial Dynamics of Vector Borne Diseases

Abstract: Vector-borne diseases affects approximately 1 billion people and accounts for 17% of all infectious diseases. With travel becoming more frequent across the global, it is important to understand the spatial dynamics of vector-borne diseases. Host movement plays a key part on how a disease can be distributed as it enables a pathogen to invade a new environment, and helps the persistence of a disease in locations that would otherwise be isolated. In this talk, we will explore how spatial heterogeneity combines with mobility network structure to influence vector-borne disease dynamics

Title: Model-dependent and model-independent control of biological network models

Abstract: Network models of intracellular signaling and regulation are ubiquitous in systems biology research because of their ability to integrate the current knowledge of a biological process and test new findings and hypotheses. An often asked question is how to control a network model and drive it towards its dynamical attractors (which have been found to be identifiable with phenotypes or stable patterns of activity of the modeled system), and which nodes and interventions are required to do so. In this talk, we will introduce two recently developed network control methods -feedback vertex set control and stable motif control- that use the graph structure of a network model to identify nodes that drive the system towards an attractor of interest (i.e., nodes sufficient for attractor control). Feedback vertex set control makes predictions that apply to all network models with a given graph structure and stable motif control makes predictions for a specific model instance, and this allows us to compare the results of model-independent and model-dependent network control. We illustrate these methods with various examples and discuss the aspects of each method that makes its predictions dependent or independent of the model.

See abstract in this link, http://www.ms.uky.edu/~dmu228/AppliedMathSeminar.html

Title: Radiative transport and optical tomography

Abstract: Optical tomography is the process of reconstructing the optical parameters of the inside of an object from measurements taken on the boundary.  This problem is hard if light inside the object is scattered -- if it bounces around a lot and refuses to travel in straight lines. To solve optical tomography problems, we need a mathematical model for light propagation inside a scattering medium. In this talk I'll give a brief introduction to one such model -- the radiative transport model -- and talk a little bit about its behavior and its implications for optical tomography.

Title: Preconditioning for Accurate Solutions of Linear Systems and Eigenvalue Problems

Abstract: This paper develops the preconditioning technique as a method to address the accuracy issue caused by ill-conditioning. Given a preconditioner M for an ill-conditioned linear system Ax=b, we show that, if the inverse of the preconditioner can be applied to vectors accurately, then the linear system can be solved accurately. A stability concept called inverse-equivalent accuracy is introduced to describe higher accuracy that is achieved and an error analysis will be presented. As an application, we use the preconditioning approach to accurately compute a few smallest eigenvalues of certain ill-conditioned matrices. Numerical examples are presented to illustrate the error analysis and the performance of the methods.

Title: Algebraic Statistics Applications in Epidemiology

Abstract: Interactions between single nucleotide polymorphisms (SNPs) and complex diseases have been an important topic throughout epidemiological studies. Previous studies have mostly focused on gene variables at a single locus. In this talk, I will discuss a focused candidate gene study to test the interaction of multiple SNPs with the risk of different types of cancer.
We will exemplify the fact that traditional asympotic results in statistical analysis do not apply in our setting. This is due mainly to the fact that we have a relatively small fixed data set.  In our work we develop a new statistical approach using techniques from the field of algebraic statistics. Algebraic statistics focuses on mathematical aspects of statistical models, where algebraic, geometric and combinatorial insights can be useful to study behavior of statistical procedures.

Using the R package algstat, developed by Kahle, Garcia Puente, and Yoshida, we implemented an algebraic statistics method that can test for independence between several variables and the desease. We applied our methods to the study of gene-gene interaction on cancer data obtained from the European case-control study Gen-Air extending previous work by Ricceri, Fassino, Matullo, Roggero, Torrente, Vineis, and Terracini.