TBA

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

Fano varieties are algebraic varieties with positive curvature; they are basic building blocks of algebraic varieties. Great progress has been recently made by Xu et al. to construct moduli spaces of Fano varieties by using K-stability (which is related to the existence of Kähler-Einstein metrics). These moduli spaces are called K-moduli. In this talk I will explain how to easily deduce some geometric properties of K-moduli by using toric geometry and deformation theory. In particular, I will show how to construct a 1-dimensional component of K-moduli which parametrises certain K-polystable del Pezzo surfaces. * ZOOM information will not be provided. Please send an email to Jinhyung Park if you are interested in.

TBD

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

A linear $3$-graph is called a (3-)hypertree if there exists exactly one path between each pair of two distinct vertices.  A linear $3$-graph is called a Steiner triple system if each pair of two distinct vertices belong to a unique edge. A simple greedy algorithm shows that every $n$-vertex Steiner triple system $G$ contains all hypertrees $T$ of order at most $\frac{n+3}{2}$. On the other hand, it is not immediately clear whether one can always find larger hypertrees in $G$. In 2011, Goodall and de Mier proved that a Steiner triple system $G$ contains at least one spanning tree. However, one cannot expect the Steiner triple system to contain all possible spanning trees, as there are many Steiner triple systems that avoid numerous spanning trees as subgraphs. Hence it is natural to wonder how much one can improve the bound from the greedy algorithm. Indeed, Elliott and Rödl conjectured that an $n$-vertex Steiner triple system $G$ contains all hypertrees of order at most $(1-o(1))n$. We prove the conjecture by Elliott and Rödl. This is joint work with Jaehoon Kim, Joonkyung Lee, and Abhishek Methuku.

TBA

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

In this talk, we will introduce the absolute coregularity of Fano varieties. The coregularity measures the singularities of the anti-pluricanonical sections. Philosophically, most Fano varieties have coregularity 0. In the talk, we will explain some theorems that support this philosophy. We will show that a Fano variety of coregularity 0 admits a non-trivial section in |-2K_X|, independently of the dimension of X. This is joint work with Fernando Figueroa, Stefano Filipazzo, and Junyao Peng. * ZOOM information will not be provided. Please send an email to Jinhyung Park if you are interested in.

By a seminal result of Valiant, computing the permanent of (0, 1)-matrices is, in general, #P-hard. In 1913 Pólya asked for which (0, 1)-matrices A it is possible to change some signs such that the permanent of A equals the determinant of the resulting matrix. In 1975, Little showed these matrices to be exactly the biadjacency matrices of bipartite graphs excluding $K_{3,3}$ as a matching minor. This was turned into a polynomial time algorithm by McCuaig, Robertson, Seymour, and Thomas in 1999. However, the relation between the exclusion of some matching minor in a bipartite graph and the tractability of the permanent extends beyond K3,3. Recently it was shown that the exclusion of any planar bipartite graph as a matching minor yields a class of bipartite graphs on which the permanent of the corresponding (0, 1)-matrices can be computed efficiently. In this paper we unify the two results above into a single, more general result in the style of the celebrated structure theorem for single-crossing minor-free graphs. We identify a class of bipartite graphs strictly generalising planar bipartite graphs and $K_{3,3}$ which includes infinitely many non-Pfaffian graphs. The exclusion of any member of this class as a matching minor yields a structure that allows for the efficient evaluation of the permanent. Moreover, we show that the evaluation of the permanent remains #P-hard on bipartite graphs which exclude $K_{5,5}$ as a matching minor. This establishes a first computational lower bound for the problem of counting perfect matchings on matching minor closed classes. As another application of our structure theorem, we obtain a strict generalisation of the algorithm for the k-vertex disjoint directed paths problem on digraphs of bounded directed treewidth. This is joint work with Archontia Giannopoulou and Dimitrios Thilikos.

Wearable analytics hold far more potential than sleep tracking or step counting. In recent years, a number of applications have emerged which leverage the massive quantities of data being amassed by wearables around the world, such as real-time mood detection, advanced COVID screening, and heart rate variability analysis. Yet packaging insights from research for success in the consumer market means prioritizing design and understandability, while also seamlessly managing the sometimes-unreliable stream of data from the device. In this presentation, I will discuss my own experiences building apps which interface with wearable data and process the data using mathematical modeling, as well as recent work extending to other wearable streams and environmental controls.

Cells make individual fate decisions through linear and nonlinear regulation of gene network, generating diverse dynamics from a single reaction pathway. In this colloquium, I will present two topics of our recent work on signaling dynamics at cellular and patient levels. The first example is about the initial value of the model, as a mechanism to generate different dynamics from a single pathway in cancer and the use of the dynamics for stratification of the patients [1-3]. Models of ErbB receptor signaling have been widely used in prediction of drug sensitivity for many types of cancers. We trained the ErbB model with the data obtained from cancer cell lines and predicted the common parameters of the model. By simulation of the ErbB model with those parameters and individual patient transcriptome data as initial values, we were able to classify the prognosis of breast cancer patients and drug sensitivity based on their in silico signaling dynamics. This result raises the question whether gene expression levels, rather than genetic mutations, might be better suited to classify the disease. Another example is about the regulation of transcription factors, the recipients of signal dynamics, for target gene expression [4-6]. By focusing on the NFkB transcription factor, we found that the opening and closing of chromatin at the DNA regions of the putative transcription factor binding sites and the cooperativity in their interaction significantly influenced the cell-to cell heterogeneity in gene expression levels. This study indicates that the noise in gene expression is rather strongly regulated by the DNA side, even though the signals are similarly regulated in a cell population. Overall these mechanisms are important in our understanding the cell as a system for encoding and decoding signals for fate decisions and its application to human diseases.

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ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

Shift workers experience profound circadian disruption due to the nature of their work, which often has them working at times when their internal clock is sending a strong signal for sleep. Mathematical models can be used to generate recommendations for shift workers that shift their body’s clock to better align with their work schedules, to help them sleep, feel, and perform better. In this talk, I will discuss our recent mobile app, Shift, which pulls wearable data from user’s devices and generates personalized recommendations to help them manage shift work schedules. I will also discuss how this product was designed, how it can interface with Internet of Things devices, and how its insights can be useful for other groups beyond shift workers.

Let $\mathcal{F}$ be a family of graphs, and let $p$ and $r$ be nonnegative integers. The $(p,r,\mathcal{F})$-Covering problem asks whether for a graph $G$ and an integer $k$, there exists a set $D$ of at most $k$ vertices in $G$ such that $G^p\setminus N_G^r[D]$ has no induced subgraph isomorphic to a graph in $\mathcal{F}$, where $G^p$ is the $p$-th power of $G$ and $N^r_G[D]$ is the set of all vertices in $G$ at distance at most $r$ from $D$ in $G$. The $(p,r,\mathcal{F})$-Packing problem asks whether for a graph $G$ and an integer $k$, $G^p$ has $k$ induced subgraphs $H_1,\ldots,H_k$ such that each $H_i$ is isomorphic to a graph in $\mathcal{F}$, and for distinct $i,j\in \{1, \ldots, k\}$, the distance between $V(H_i)$ and $V(H_j)$ in $G$ is larger than $r$. The $(p,r,\mathcal{F})$-Covering problem generalizes Distance-$r$ Dominating Set and Distance-$r$ Vertex Cover, and the $(p,r,\mathcal{F})$-Packing problem generalizes Distance-$r$ Independent Set and Distance-$r$ Matching. By taking $(p',r',\mathcal{F}')=(pt, rt, \mathcal{F})$, we may formulate the $(p,r,\mathcal{F})$-Covering and $(p, r, \mathcal{F})$-Packing problems on the $t$-th power of a graph. Moreover, $(1,0,\mathcal{F})$-Covering is the $\mathcal{F}$-Free Vertex Deletion problem, and $(1,0,\mathcal{F})$-Packing is the Induced-$\mathcal{F}$-Packing problem. We show that for every fixed nonnegative integers $p,r$ and every fixed nonempty finite family $\mathcal{F}$ of connected graphs, the $(p,r,\mathcal{F})$-Covering problem with $p\leq2r+1$ and the $(p,r,\mathcal{F})$-Packing problem with $p\leq2\lfloor r/2\rfloor+1$ admit almost linear kernels on every nowhere dense class of graphs, and admit linear kernels on every class of graphs with bounded expansion, parameterized by the solution size $k$. We obtain the same kernels for their annotated variants. As corollaries, we prove that Distance-$r$ Vertex Cover, Distance-$r$ Matching, $\mathcal{F}$-Free Vertex Deletion, and Induced-$\mathcal{F}$-Packing for any fixed finite family $\mathcal{F}$ of connected graphs admit almost linear kernels on every nowhere dense class of graphs and linear kernels on every class of graphs with bounded expansion. Our results extend the results for Distance-$r$ Dominating Set by Drange et al. (STACS 2016) and Eickmeyer et al. (ICALP 2017), and the result for Distance-$r$ Independent Set by Pilipczuk and Siebertz (EJC 2021). This is joint work with Jinha Kim and O-joung Kwon.

The classification of terminal Fano 3-folds has been tackled from different directions: for instance, using the Minimal Model Program, via explicit Birational Geometry, and via Graded Rings methods. In this talk I would like to introduce the Graded Ring Database - an upper bound to the numerics of Fano 3-folds - and discuss the role it plays in the classification and construction of codimension 4 Fano 3-folds having Fano index 2.

Castelnuovo-Mumford regularity, simply regularity, is one of the most interesting invariants in projective algebraic geometry, and the regularity conjecture due to Eisenbud and Goto says that the regularity can be controlled by the degree for any projective variety. But counterexamples to the conjecture have been constructed by some methods. In this talk we review the counterexample constructions including the Rees-like algebra method by McCullough and Peeva and the unprojection method.

We’re all familiar with sleep, but how can we mathematically model it? And what determines how long and when we sleep? In this talk I’ll introduce the nonsmooth coupled oscillator systems that form the basis of current models of sleep-wake regulation and discuss their dynamical behaviour. I will describe how we are using models to unravel environmental, societal and physiological factors that determine sleep timing and outline how we are using models to inform the quantitative design of light interventions for mental health disorders and address contentious societal questions such as whether to move school start time for adolescents.

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This talk will be presented online. ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

TBA

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This talk will be presented online. ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

Cellular, chemical, and population processes are all often represented via networks that describe the interactions between the different population types (typically called the “species”). If the counts of the species are low, then these systems are often modeled as continuous-time Markov chains on the d-dimensional integer lattice (with d being the number of species), with transition rates determined by stochastic mass-action kinetics. A natural (broad) mathematical question is: how do the qualitative properties of the dynamical system relate to the graph properties of the network? For example, it is of particular interest to know which graph properties imply that the stochastically modeled reaction network is positive recurrent, and therefore admits a stationary distribution. After a general introduction to the models of interest, I will discuss this problem, giving some of the known results. I will also discuss recent progress on the Chemical Recurrence Conjecture, which has been open for decades, which is the following: if each connected component of the network is strongly connected, then the associated stochastic model is positive recurrent.

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This talk will be presented online. ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

In computer science, random expressions are commonly used to analyze algorithms, either to study their average complexity, or to generate benchmarks to test them experimentally. In general, these approaches only consider the expressions as purely syntactic trees, and completely ignore their semantics — i.e. the mathematical object represented by the expression. However, two different expressions can be equivalent (for example “0*(x+y)” and “0” represent the same expression, the null expression). Can these redundancies question the relevance of the analyses and tests that do not take into account the semantics of the expressions? I will present how the uniform distribution over syntactic expression becomes completely degenerate when we start taking into account their semantics, in a very simple but common case where there is an absorbing element. If time permits it, I will briefly explain why the BST distribution offers more hope. This is a joint work with Cyril Nicaud and Pablo Rotondo.

We determine the maximum number of copies of $K_{s,s}$ in a $C_{2s+2}$-free $n$-vertex graph for all integers $s \ge 2$ and sufficiently large $n$. Moreover, for $s\in\{2,3\}$ and any integer $n$ we obtain the maximum number of cycles of length $2s$ in an $n$-vertex $C_{2s+2}$-free bipartite graph. This is joint work with Ervin Győri (Renyi Institute), Zhen He (Tsinghua University), Zequn Lv (Tsinghua University), Casey Tompkins (Renyi Institute), Kitti Varga (Technical University of Budapest BME), and Xiutao Zhu (Nanjing University).

The driving passion of molecular cell biologists is to understand the molecular mechanisms that control important aspects of cell physiology, but this ambition is – paradoxically – limited by the very wealth of molecular details currently known about these mechanisms. Their complexity overwhelms our intuitive notions of how molecular regulatory networks might respond under normal and stressful conditions. To make progress we need a new paradigm for connecting molecular biology to cell physiology. I will outline an approach that uses precise mathematical methods to associate the qualitative features of dynamical systems, as conveyed by ‘bifurcation diagrams’, with ‘signal–response’ curves measured by cell biologists.

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This talk will be presented online. ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

Cell growth, DNA replication, mitosis and division are the fundamental processes by which life is passed on from one generation of eukaryotic cells to the next. The eukaryotic cell cycle is intrinsically a periodic process but not so much a ‘clock’ as a ‘copy machine’, making new daughter cells as warranted. Cells growing under ideal conditions divide with clock-like regularity; however, if they are challenged with DNA-damaging agents or mitotic spindle disruptors, they will not progress to the next stage of the cycle until the damage is repaired. These ‘decisions’ (to exit and re-enter the cell cycle) are essential to maintain the integrity of the genome from generation to generation. A crucial challenge for molecular cell biologists in the 1990s was to unravel the genetic and biochemical mechanisms of cell cycle control in eukaryotes. Central to this effort were biochemical studies of the clock-like regulation of ‘mitosis promoting factor’ during synchronous mitotic cycles of fertilized frog eggs and genetic studies of the switch-like regulation of ‘cyclin-dependent kinases’ in yeast cells. The complexity of these control systems demands a dynamical approach, as described in the first lecture. Using mathematical models of the control systems, I will uncover some of the secrets of cell cycle ‘clocks’ and ‘switches’.

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This talk will be presented online. ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)

For a graph $F$, the Turán number is the maximum number of edges in an $n$-vertex simple graph not containing $F$. The celebrated Erdős-Stone-Simonovits Theorem gives that \[ \text{ex}(n,F)=\bigg(1-\frac{1}{\chi(F)-1}+o(1)\bigg)\binom{n}{2},\] where $\chi(F)$ is the chromatic number of $H$. This theorem asymptotically solves the problem when $\chi(F)\geqslant 3$. In case of bipartite graphs $F$, not even the order of magnitude is known in general. In this talk, I will introduce some recent progress on Turán numbers of bipartite graphs and related generalizations and discuss several methods developed in recent years. Finally, I will introduce some interesting open problems on this topic.