Department Seminars & Colloquia
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Zoom: https://kaist.zoom.us/j/87516570701
ACM Seminars
Xueyu Zhu (University of Iowa)
Efficient Bayesian physics informed neural networks for inverse problems via ensemble Kalman inversion
Zoom: https://kaist.zoom.us/j/87516570701
ACM Seminars
Bayesian Physics Informed Neural Networks (B-PINNs) have gained significant attention for inferring physical parameters and learning the forward solutions for problems based on partial differential equations. However, the overparameterized nature of neural networks poses a computational challenge for high-dimensional posterior inference. Existing inference approaches, such as particle-based or variance inference methods, are either computationally expensive for highdimensional posterior inference or provide unsatisfactory uncertainty estimates. In this paper, we present a new efficient inference algorithm for B-PINNs that uses Ensemble Kalman Inversion (EKI) for high-dimensional inference tasks. By reframing the setup of B-PINNs as a traditional Bayesian inverse problem, we can take advantage of EKI’s key features: (1) gradient-free, (2) computational complexity scales linearly with the dimension of the parameter spaces, and (3) rapid convergence with typically O(100) iterations. We demonstrate the applicability and performance of the proposed method through various types of numerical examples. We find that our proposed method can achieve inference results with informative uncertainty estimates comparable to Hamiltonian Monte Carlo (HMC)-based B-PINNs with a much reduced computational cost. These findings suggest that our proposed approach has great potential for uncertainty quantification in physics-informed machine learning for practical applications.
We will first introduce Homogeneous dynamics, especially the mixing property of flows on spaces of hyperbolic nature. We will then survey applications of homogeneous dynamics to various problems in Number theory. (Part of the talk is based on joint work with Keivan Mallahi-Karai and Jiyoung Han.)
The date has been postponed from March 16 to March 30.
The date has been postponed from March 16 to March 30.
Room B332, IBS (기초과학연구원)
Discrete Mathematics
Tianchi Yang (National University of Singapore)
On the maximum number of edges in k-critical graphs
Room B332, IBS (기초과학연구원)
Discrete Mathematics
In this talk, we will discuss the problem of determining the maximum number of edges in an n-vertex k-critical graph. A graph is considered k-critical if its chromatic number is k, but any proper subgraph has a chromatic number less than k. The problem remains open for any integer k ≥ 4. Our presentation will showcase an improvement on previous results achieved by employing a combination of extremal graph theory and structural analysis. We will introduce a key lemma, which may be of independent interest, as it sheds light on the partial structure of dense k-critical graphs. This is joint work with Cong Luo and Jie Ma.
B378 Seminar room, IBS
Math Biology
조성웅 (한국과학기술원 / 확률 해석 및 응용 연구센터)
HyperDeepONet: learning operator with complex target function space using the limited resources via hypernetwork
B378 Seminar room, IBS
Math Biology
Fast and accurate predictions for complex physical dynamics are a big challenge across various applications. Real-time prediction on resource-constrained hardware is even more crucial in the real-world problems. The deep operator network (DeepONet) has recently been proposed as a framework for learning nonlinear mappings between function spaces. However, the DeepONet requires many parameters and has a high computational cost when learning operators, particularly those with complex (discontinuous or non-smooth) target functions. In this study, we propose HyperDeepONet, which uses the expressive power of the hypernetwork to enable learning of a complex operator with smaller set of parameters. The DeepONet and its variant models can be thought of as a method of injecting the input function information into the target function. From this perspective, these models can be viewed as a special case of HyperDeepONet. We analyze the complexity of DeepONet and conclude that HyperDeepONet needs relatively lower complexity to obtain the desired accuracy for operator learning. HyperDeepONet was successfully applied to various operator learning problems using low computational resources compared to other benchmarks.
Zoom: https://kaist.zoom.us/j/87516570701
ACM Seminars
Amirhossein Arzani (University of Utah)
Scientific machine learning for modeling near-wall mass transport and boundary layers
Zoom: https://kaist.zoom.us/j/87516570701
ACM Seminars
Modeling mass or heat transfer near a wall is of broad interest in various fluid flows. Specifically, in cardiovascular flows, mass transport near the vessel wall plays an important role in cardiovascular disease. However, due to very thin concentration boundary layers, accurate computational modeling is challenging. Additionally, experimental approaches have limitations in measuring near-wall flow metrics such as wall shear stress (WSS).
In this talk, first, I will briefly review the complex flow physics near the wall in diseased vascular flows and introduce the concept of WSS manifolds in near-wall transport. Specifically, I will talk about stable and unstable manifolds calculated for a surface vector field. Next, I will discuss reduced-order data assimilation modeling as well as physics-informed neural network (PINN) approaches for obtaining WSS from measurement data away from the wall. Finally, I present a boundary-layer PINN (BL-PINN) approach inspired by the classical perturbation theory and asymptotic expansions to solve challenging thin boundary layer mass transport problems. BL-PINN demonstrates how classical theoretical approaches could be replicated in a deep learning framework.
Zoom (ID: 683 181 3833 / PW: saarc)
SAARC Seminar
Shin, Won-Yong (Yonsei University)
Fundamentals of Graph Neural Networks and Their Real-World Applications to Network Alignment
Zoom (ID: 683 181 3833 / PW: saarc)
SAARC Seminar
그래프 신경망 (GNN: graph neural network)은 그래프에서 높은 표현 능력과 함께 특징 정보를 추출하는 방법론으로 학계와 산업체에서 최근 폭발적인 관심을 받고 있다. 본 세미나에서는 그래프 신경망의 개요 및 주요 동작 원리를 다룬다. 구체적으로, message passing의 원리를 이해하고 state-of-the-art 알고리즘에서 사용한 다양한 message passing 함수를 소개한다. 그래프 신경망을 활용한 다양한 downstream 응용 문제들이 존재하지만, 본 세미나에서는 근본적인 그래프 마이닝 문제 중 하나인 네트워크 정렬 (network alignment)으로의 적용을 다룬다. 네트워크 정렬 문제를 정의하고, 기존 연구 결과물들을 요약하고 한계점에 대해 설명한다. 이를 바탕으로 발표자 연구실에서 제안한 그래프 신경망을 활용한 새로운 점진적 네트워크 정렬 방법을 소개한다. 마지막으로, 그래프 신경망을 사용해 해결할 수 있는 다양한 실세계 응용 문제를 공유하고 토의한다.
B378 Seminar room, IBS
Math Biology
Candan Celik (Biomedical Mathematics Group, IBS)
The effect of microRNA on protein variability and gene expression fidelity
B378 Seminar room, IBS
Math Biology
Small regulatory RNA molecules such as microRNA modulate gene expression through inhibiting the translation of messenger RNA (mRNA). Such post-transcriptional regulation has been recently hypothesized to reduce the stochastic variability of gene expression around average levels. Here we quantify noise in stochastic gene expression models with and without such regulation. Our results suggest that silencing mRNA post-transcriptionally will always increase rather than decrease gene expression noise when the silencing of mRNA also increases its degradation as is expected for microRNA interactions with mRNA. In that regime we also find that silencing mRNA generally reduces the fidelity of signal transmission from deterministically varying upstream factors to protein levels. These findings suggest that microRNA binding to mRNA does not generically confer precision to protein expression
B378 Seminar room, IBS / ZOOM
Math Biology
Stefan Bauer (Helmholtz and TU Munich)
Neural Causal Models for Experimental Design
B378 Seminar room, IBS / ZOOM
Math Biology
Many questions in everyday life as well as in research are causal in nature: How would the climate change if we lower train prices or will my headache go away if I take an aspirin? Inherently, such questions need to specify the causal variables relevant to the question and their interactions. However, existing algorithms for learning causal graphs from data are often not scaling well both with the number of variables or the number of observations. This talk will provide a brief introduction to causal structure learning, recent efforts in using continuous optimization to learn causal graphs at scale and systematic approaches for causal experimental design at scale.
ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)
ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)
In this seminar, I will provide an overview of diffusion generative models, inverse problems, and their applications in solving such problems. Furthermore, I will present a novel interpretation of diffusion generative models and their translation to inverse problems.
In collaboration with Hyungjin Chung and Dohoon Ryu, we propose that when data lies in a low-dimensional structure, the set of data with intermediate noise represents the interpolating manifold between the data manifold and the hypersphere of pure noise. Our new method, which respects this geometry, outperforms previous methods, and we provide experimental results as proof of concept.
Discipline of talk: Applied math, deep learning / Advisor: 예종철 (Jong Chul Ye)
Discipline of talk: Applied math, deep learning / Advisor: 예종철 (Jong Chul Ye)
In this lecture we introduce some challenging problems in the mathematical fluid mechanics. Although fluid mechanics is one of the most important physical phenomena we experience in everyday life, and has been studied for long time in history by top class mathematicians, still there are many problems which are open even at the fundamental level. We explain these problems and briefly review some of the recent progress.
We present new (mostly determinantal) expressions for various eigenvalue statistics in random matrix theory. Whenever the eigenvalue $n$-point correlation function is given in terms of $n \times n$ determinants with some kernel, we propose a new kernel that gives the $n$-point correlation function of the eigenvalues conditioned on the event of some eigenvalues already existing at fixed positions. Using such new kernels we obtain determinantal expressions for the joint densities of the $k$ largest eigenvalues, probability density function of the $k$-th largest eigenvalue, density of the first eigenvalue spacing, and many more. Our formulae is highly amenable to numerical computation through the method proposed by Bornemann (2008).
B378 Seminar room, IBS
Math Biology
Marko Ćosić (The University of Belgrade)
Stewart’s Catastrophic Swing
B378 Seminar room, IBS
Math Biology
The standard approach to problem-solving in physics consists of identifying state variables of the system, setting differential equations governing the state evolution, and solving the obtained. The behavior of the system for different values of parameters can be examined only as a fourth step. On the contrary, the modern approach to studying dynamical systems relies on Morphological/Topological analysis which alleviates the necessity for the explicit solution of differential equations.
The stability analysis of the parabolic swing will demonstrate the merit of such an approach. It will be shown how to construct a qualitatively correct model of system dynamics that is surprisingly quantitatively correct as well. The sudden (catastrophic) change in the swing’s stability, caused by a slight change in the critical value of system parameters, will be linked to the drastic topological change of the corresponding phase-space portraits.
It will be shown that for a system’s parameters close to critical ones, the system’s behavior is identical to a specific simple universal prototype given by catastrophe theory. A short survey of the simplest elementary catastrophes will be given that represents the basis for applying catastrophe theory in other fields of science.
Symmetric spaces from Lie theory and differential geometry are often represented by special set of structured matrices. The Cartan decomposition and its generalization of symmetric spaces and classical Lie groups recover many of the known matrix factorizations in numerical linear algebra, such as the singular value decomposition, CS decomposition, generalized SVD and many more. We discuss a blueprint for generating fifty-three matrix factorizations from the generalized Cartan decomposition, most of which appear to be new. The underlying mathematics may be traced back to Cartan (1927), Harish-Chandra (1956), and Flensted-Jensen (1978). This is joint work with Alan Edelman.
Zoom (ID: 683 181 3833 / PW: saarc)
SAARC Seminar
Kang, Nam-Gyu (KIAS)
Analysis of random conformal fields
Zoom (ID: 683 181 3833 / PW: saarc)
SAARC Seminar
Since conformal field theory (CFT) was introduced to relate various critical statistical physics models to Virasoro representation theory, it has been applied to string theory, condensed matter physics, vertex operator algebra, and probability theory. In this talk, I will explain how the boundary CFT of central charges c (less than or equal to 1) relates to the boundary CFT of 26 - c in terms of boundary conditions. (On the algebraic side, Feigin and Fuchs described the duality between the categories of Verma modules with central charges c and 26 - c to explain the appearance of the critical dimension 26 of the bosonic string theory.) I will present the connection between the boundary CFT and the theory of Schramm-Loewner evolution in various conformal types.
산업경영학동(E2) Room 2216
ACM Seminars
Jae Yong Lee (KIAS)
Two Approaches Using Deep Learning to Solve Partial Differential Equations
산업경영학동(E2) Room 2216
ACM Seminars
Many differential equations and partial differential equations (PDEs) are being studied to model physical phenomena in nature with mathematical expressions. Recently, new numerical approaches using machine learning and deep learning have been actively studied. There are two mainstream deep learning approaches to approximate solutions to the PDEs, i.e., using neural networks directly to parametrize the solution to the PDE and learning operators from the parameters of the PDEs to their solutions. As the first direction, Physics-Informed Neural Network was introduced in (Raissi, Perdikaris, and Karniadakis 2019), which learns the neural network parameters to minimize the PDE residuals in the least-squares sense. On the other side, operator learning using neural networks has been studied to approximate a PDE solution operator, which is nonlinear and complex in general. In this talk, I will introduce these two ways to approximate the solution of PDE and my research related to them.
(Online participation) Zoom Link: https://kaist.zoom.us/j/87516570701
(Online participation) Zoom Link: https://kaist.zoom.us/j/87516570701
B378 Seminar room, IBS
Math Biology
(KAIST)
Detecting early‐warning signals of influenza outbreak based on dynamic network marker
B378 Seminar room, IBS
Math Biology
The seasonal outbreaks of influenza infection cause globally respiratory illness, or even death in all age groups. Given early-warning signals preceding the influenza outbreak, timely intervention such as vaccination and isolation management effectively decrease the morbidity. However, it is usually a difficult task to achieve the real-time prediction of influenza outbreak due to its complexity intertwining both biological systems and social systems. By exploring rich dynamical and high-dimensional information, our dynamic network marker/biomarker (DNM/DNB) method opens a new way to identify the tipping point prior to the catastrophic transition into an influenza pandemics. In order to detect the early-warning signals before the influenza outbreak by applying DNM method, the historical information of clinic hospitalization caused by influenza infection between years 2009 and 2016 were extracted and assembled from public records of Tokyo and Hokkaido, Japan. The early-warning signal, with an average of 4-week window lead prior to each seasonal outbreak of influenza, was provided by DNM-based on the hospitalization records, providing an opportunity to apply proactive strategies to prevent or delay the onset of influenza outbreak. Moreover, the study on the dynamical changes of hospitalization in local district networks unveils the influenza transmission dynamics or landscape in network level.
For complex number $\alpha$, let $ A = \begin{bmatrix}
1 & 1 \\ 0 & 1
\end{bmatrix}$ and
$B = \begin{bmatrix}
1 & 0 \\ \alpha & 1
\end{bmatrix} $
be two parabolic matrices and let $G_\alpha$ be the group generated by these two matrices.
Determining whether $G_\alpha$ is the free group rank 2 or not, is one of the important problems.
In this talk, I will introduce a geometric aspect of the group $G_\alpha$ and give previous results of the problem.
Next, I will introduce my work joint with KyeongRo Kim.
Discipline of talk: Geometric Group Theory / Advisor: 백형렬 교수님
Discipline of talk: Geometric Group Theory / Advisor: 백형렬 교수님
B378 Seminar room, IBS / ZOOM
Math Biology
Saez-Rodriguez, Julio (Heidelberg University)
Dynamic logic models complement machine learning for personalized medicine
B378 Seminar room, IBS / ZOOM
Math Biology
Multi-omics technologies, and in particular those with single-cell and spatial resolution, provide unique opportunities to study the deregulation of intra- and inter-cellular signaling processes in disease. I will present recent methods and applications from our group toward this aim, focusing on computational approaches that combine data with biological knowledge within statistical and machine learning methods. This combination allows us to increase both the statistical power of our analyses and the mechanistic interpretability of the results. These approaches allow us to identify key processes, that can be in turn studied in detailed with dynamic mechanistic models. I will then present how cell-specific logic models, trained with measurements upon perturbations, can provides new biomarkers and treatment opportunities. Finally, I will show how, using novel microfluidics-based technologies, this approach can also be applied directly to biopsies, allowing to build mechanistic models for individual cancer patients, and use these models to prose new therapies.
ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)
ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)
Room B332, IBS (기초과학연구원)
Discrete Mathematics
Stijn Cambie (IBS Extremal Combinatorics and Probability Group)
Recent progress on the Union-closed conjecture and related
Room B332, IBS (기초과학연구원)
Discrete Mathematics
We give a summary on the work of the last months related to Frankl's Union-Closed conjecture and its offsprings. The initial conjecture is stated as a theorem in extremal set theory; when a family F is union-closed (the union of sets of F is itself a set of $\mathcal F$), then $\mathcal F$ contains an (abundant) element that belongs to at least half of the sets. Meanwhile, there are many related versions of the conjecture due to Frankl. For example, graph theorists may prefer the equivalent statement that every bipartite graph has a vertex that belongs to no more than half of the maximal independent sets. While even proving the ε-Union-Closed Sets Conjecture was out of reach, Poonen and Cui & Hu conjectured already stronger forms.
At the end of last year, progress was made on many of these conjectures. Gilmer proved the ε-Union-Closed Sets Conjecture using an elegant entropy-based method which was sharpened by many others. Despite a sharp approximate form of the union-closed conjecture as stated by Chase and Lovett, a further improvement was possible. In a different direction, Kabela, Polak and Teska constructed union-closed family sets with large sets and few abundant elements.
This talk will keep the audience up-to-date and give them insight in the main ideas.
People who would like more details, can join the Ecopro-reading session on the 7th of March (10 o'clock, B332) as well. Here we go deeper in the core of the proofs and discuss possible directions for the full resolution.
B378 Seminar room, IBS
Math Biology
Marko Cosic (The University of Belgrade)
The morphological analysis of the collagen straightness in the colon mucosa away from the cancer
B378 Seminar room, IBS
Math Biology
The morphological method – based on the topology and singularity theory and originally developed for the analysis of the scattering experiments – was extended to be applicable for the analysis of biological data. The usefulness of the topological viewpoint was demonstrated by quantification of the changes of collagen fiber straightness in the human colon mucosa (healthy mucosa, colorectal cancer, and uninvolved mucosa far from cancer).
This has been done by modeling the distribution of collagen segment angles by the polymorphic beta-distribution. Its shapes were classified according to the number and type of critical points. We found that biologically relevant shapes could be classified as shapes without any preferable orientation (i.e. shapes without local extrema), transitional forms (i.e. forms with one broad local maximum), and highly oriented forms (i.e. forms with two minima at both ends and one very narrow maximum between them). Thus, changes in the fiber organization were linked to the metamorphoses of the beta-distribution forms.
The obtained classification was used to define a new, shape-aware/based, measure of the collagen straightness, which revealed a slight, and moderate increase of the straightness in mucosa samples taken 20 cm and 10 cm away from the tumor. The largest increase of collagen straightness was found in samples of cancer tissue. Samples of the healthy individuals have a uniform distribution of beta-distribution forms. We found that this distribution has the maximal information entropy. At 20 cm and 10 cm away from cancer, the transition forms redistribute into unoriented and highly oriented forms. Closer to cancer the number of unoriented forms decreases rapidly leaving only highly oriented forms present in the samples of the cancer tissue, whose distribution has minimal information entropy. The polarization of the distribution was followed by a significant increase in the number of quasi-symmetrical forms in samples 20 cm away from cancer which decreases closer to cancer.
This work shows that the evolution of the distribution of the beta-distribution forms – an abstract construction of the mind – follows the familiar laws of statistical mechanics. Additionally, the polarization of the beta-distribution forms together with the described change in the number of quasi-symmetrical forms, clearly visible in the parametric space of the beta-distribution and very difficult to notice in the observable space, can be a useful indicator of the early stages in the development of colorectal cancer.
B378 Seminar room, IBS / ZOOM
Math Biology
Martin Nowak (Harvard University)
Evolution of cooperation
B378 Seminar room, IBS / ZOOM
Math Biology
Cooperation means that one individual pays a cost for another to receive a benefit. Cooperation can be at variance with natural selection. Why should you help competitors? Yet cooperation is abundant in nature and is important component of evolutionary innovation. Cooperation can be seen as the master architect of evolution and as the third fundamental principle of evolution beside mutation and selection. I will present five mechanisms for the evolution of cooperation: direct reciprocity, indirect reciprocity, spatial selection, group selection and kin selection. Global cooperation and the cooperation with future generations is necessary to ensure the survival of our species.
Further reading:
Nowak MA (2006). Evolutionary Dynamics. Harvard University Press
Nowak MA & Highfield R (2011) SuperCooperators. Simon & Schuster.
Hauser OP, Rand DG, Peysakhovich A & Nowak MA (2014). Cooperating with the future. Nature 511: 220-223
Hilbe C, Šimsa Š, Chatterjee K & Nowak MA (2018). Evolution of cooperation in stochastic games. Nature 559: 246-249
Hauser OP, Hilbe C, Chatterjee K & Nowak MA (2019). Social dilemmas among unequals. Nature 572: 524-527
ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)
ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)
B378 Seminar room, IBS
Math Biology
Eui Min Jung (Biomedical Mathematics Group, IBS)
Noise properties of adaptation-conferring biochemical control modules
B378 Seminar room, IBS
Math Biology
A key goal of synthetic biology is to establish functional biochemical modules with network-independent properties. Antithetic integral feedback (AIF) is a recently developed control module in which two control species perfectly annihilate each other’s biological activity. The AIF module confers robust perfect adaptation to the steady-state average level of a controlled intracellular component when subjected to sustained perturbations. Recent work has suggested that such robustness comes at the unavoidable price of increased stochastic fluctuations around average levels. We present theoretical results that support and quantify this trade-off for the commonly analyzed AIF variant in the idealized limit with perfect annihilation. However, we also show that this trade-off is a singular limit of the control module: Even minute deviations from perfect adaptation allow systems to achieve effective noise suppression as long as cells can pay the corresponding energetic cost. We further show that a variant of the AIF control module can achieve significant noise suppression even in the idealized limit with perfect adaptation. This atypical configuration may thus be preferable in synthetic biology applications.
Room B332, IBS (기초과학연구원)
Discrete Mathematics
Eunjin Oh (POSTECH)
Parameterized algorithms for the planar disjoint paths problem
Room B332, IBS (기초과학연구원)
Discrete Mathematics
Given an undirected planar graph $G$ with $n$ vertices and a set $T$ of $k$ pairs $(s_i,t_i)_{i=1}^k$ of vertices, the goal of the planar disjoint paths problem is to find a set $\mathcal P$ of $k$ pairwise vertex-disjoint paths connecting $s_i$ and $t_i$ for all indices $i\in\{1,\ldots,k\}$. This problem has been studied extensively due to its numerous applications such as VLSI layout and circuit routing. However, this problem is NP-complete even for grid graphs. This motivates the study of this problem from the viewpoint of parameterized algorithms.
In this talk, I will present a $2^{O(k^2)}n$-time algorithm for the planar disjoint paths problem. This improves the two previously best-known algorithms: $2^{2^{O(k)}}n$-time algorithm [Discrete Applied Mathematics 1995] and $2^{O(k^2)}n^6$-time algorithm [STOC 2020].
This is joint work with Kyungjin Cho and Seunghyeok Oh.
This talk reviews two notable papers in self-supervised graphical neural networks; they are "Graph contrastive learning with augmentations" presented at NeurIPS 2020 and "Contrastive multi-view representation learning on graphs" presented at ICML 2020. This will be an introduction of self-supervised graphical neural networks that has emerged as one of the hottest research fields in artificial intelligence, which requires mathematical methodology across all fields of mathematics, including graph theory, algebra, topology, analysis, and geometry.
B378 Seminar room, IBS / ZOOM
Math Biology
Shinya Kuroda (Tokyo University)
Systems Biology of Insulin Action
B378 Seminar room, IBS / ZOOM
Math Biology
1. The “temporal information code” of insulin action: a bottom-up approach One of the essential elements of signaling networks is to encode information from a wide variety of inputs into a limited set of molecules. We have proposed a “temporal information code” that regulates a variety of physiological functions by encoding input information in temporal patterns of molecular activity, and based on this concept, we are analyzing biological homeostasis by insulin signaling. Taking blood insulin as an example, we will explain how the temporal information of blood insulin is selectively decoded by downstream networks.
2. Transomics of insulin action: a top-down approach In order to obtain a complete picture of insulin action, we performed transomics measurements integrating metabolomics and transcriptomics, and found that metabolism is regulated by allosteric regulation in the liver of normal mice and by compensatory gene expression in the liver of obese mice. (Top-down approach). I will talk about approach the principle of homeostasis of living organisms by temporal patterns, using the analysis of systems biology of insulin action using two different approaches.
ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)
ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium), (pw: 1234)
B378 Seminar room, IBS
Math Biology
Seho Park (Korea Advanced Institute of Science and Technology)
Dynamical information enables inference of gene regulation at single-cell scale
B378 Seminar room, IBS
Math Biology
Cellular dynamics and emerging biological function are governed by patterns of gene expression arising from networks of interacting genes. Inferring these interactions from data is a notoriously difficult inverse problem that is central to systems biology. The majority of existing network inference methods work at the population level and construct a static representations of gene regulatory networks; they do not naturally allow for inference of differential regulation across a heterogeneous cell population. Building upon recent dynamical inference methods that model single cell dynamics using Markov processes, we propose locaTE, an information-theoretic approach which employs a localised transfer entropy to infer cell-specific, causal gene regulatory networks. LocaTE uses high-resolution estimates of dynamics and geometry of the cellular gene expression manifold to inform inference of regulatory interactions. We find that this approach is generally superior to using static inference methods, often by a significant margin. We demonstrate that factor analysis can give detailed insights into the inferred cell-specific GRNs. In application to two experimental datasets, we recover key transcription factors and regulatory interactions that drive mouse primitive endoderm formation and pancreatic development. For both simulated and experimental data, locaTE provides a powerful, efficient and scalable network inference method that allows us to distil cell-specific networks from single cell data.
In this talk, we study the dissipative structure for the linear symmetric hyperbolic system with general relaxation. If the relaxation matrix of the system has symmetric properties, Shizuta and Kawashima(1985) introduced the suitable stability condition, and Umeda, Kawashima and Shizuta(1984) analyzed the dissipative structure. On the other hand, Ueda, Duan and Kawashima(2012,2018) focused on the system with non-symmetric relaxation and got partial results. Furthermore, they argued the new dissipative structure called the regularity-loss type. In this situation, this talk aims to extend the stability theory introduced by Shizuta and Kawashima(1985) and Umeda, Kawashima and Shizuta(1984) to our general system. Furthermore, we will consider the optimality of the dissipative structure. If we have time, I would like to discuss some physical models for its application and new dissipative structures.
Room B332, IBS (기초과학연구원)
Discrete Mathematics
Maya Sankar (Stanford University)
The Turán Numbers of Homeomorphs
Room B332, IBS (기초과학연구원)
Discrete Mathematics
Let $X$ be a 2-dimensional simplicial complex. Denote by $\text{ex}_{\hom}(n,X)$ the maximum number of 2-simplices in an $n$-vertex simplicial complex that has no sub-simplicial complex homeomorphic to $X$. The asymptotics of $\text{ex}_{\hom}(n,X)$ have recently been determined for all surfaces $X$. I will discuss these results, as well as ongoing work bounding $\text{ex}_{\hom}(n,X)$ for arbitrary 2-dimensional simplicial complexes $X$.
Room B332, IBS (기초과학연구원)
Discrete Mathematics
Meike Hatzel (National Institute of Informatics)
Fixed-Parameter Tractability of Directed Multicut with Three Terminal Pairs Parametrised by the Size of the Cutset: Twin-Width Meets Flow-Augmentation
Room B332, IBS (기초과학연구원)
Discrete Mathematics
We show fixed-parameter tractability of the Directed Multicut problem with three terminal pairs (with a randomized algorithm). This problem, given a directed graph $G$, pairs of vertices (called terminals) $(s_1,t_1)$, $(s_2,t_2)$, and $(s_3,t_3)$, and an integer $k$, asks to find a set of at most $k$ non-terminal vertices in $G$ that intersect all $s_1t_1$-paths, all $s_2t_2$-paths, and all $s_3t_3$-paths. The parameterized complexity of this case has been open since Chitnis, Cygan, Hajiaghayi, and Marx proved fixed-parameter tractability of the 2-terminal-pairs case at SODA 2012, and Pilipczuk and Wahlström proved the W[1]-hardness of the 4-terminal-pairs case at SODA 2016.
On the technical side, we use two recent developments in parameterized algorithms. Using the technique of directed flow-augmentation [Kim, Kratsch, Pilipczuk, Wahlström, STOC 2022] we cast the problem as a CSP problem with few variables and constraints over a large ordered domain. We observe that this problem can be in turn encoded as an FO model-checking task over a structure consisting of a few 0-1 matrices. We look at this problem through the lenses of twin-width, a recently introduced structural parameter [Bonnet, Kim, Thomassé, Watrigant, FOCS 2020]: By a recent characterization [Bonnet, Giocanti, Ossona de Mendez, Simon, Thomassé, Toruńczyk, STOC 2022] the said FO model-checking task can be done in FPT time if the said matrices have bounded grid rank. To complete the proof, we show an irrelevant vertex rule: If any of the matrices in the said encoding has a large grid minor, a vertex corresponding to the "middle" box in the grid minor can be proclaimed irrelevant — not contained in the sought solution — and thus reduced.
자연과학동 (E6-1), Room 3438
Number Theory Seminar
Wansu Kim (KAIST), Chol Park (UNIST)
Introduction to Breuil-Kisin modules and application to Galois deformation theory
자연과학동 (E6-1), Room 3438
Number Theory Seminar
The aim of the lecture series is twofold:
(1) give an overview of the “classical” theory of Breuil-Kisin modules, and
(2) discuss its application to the construction of certain p-adic Galois deformation rings.
In the first talk by Wansu Kim (Moday at 10am), we will give a general introduction to the p-adic Hodge theory (focusing on p-adic Galois representations). In the first half of the lecture series, Wansu Kim will explain the “classical” theory of Breuil-Kisin modules following the seminal paper of Kisin’s (Crystalline representations and F-crystals, from Drinfeld’s 50th birthday conference proceeding). In the second half of the lecture series, Chol Park will explain its application to the explicit computation of p-adic local Galois deformation rings cut out by certain p-adic Hodge-theoretic condition.
Here is the time and venue for each talk:
13 Feb (Mon): 3 talks
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) 16:00 -17:30 at E6-1, Rm 3434
14 Feb (Tue): 1 talk
*) 16:15 -17:45 at E6-1, Rm 3434
15 Feb (Wed) to 16 Feb (Thu):
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) (TBD) 16:00 -17:30 at E6-1, Rm 3434 (in case we need extra lecture)
17 Feb (Fri)
*) 10-11:30 at E6-1, Rm 3438
*) (TBD) 14-15:30 at E6-1, Rm 3438 (in case we need extra lecture)
In the context of science, the well-known adage “a picture is worth a thousand words” might well be “a model is worth a thousand datasets.” In this manuscript we introduce the SciML software ecosystem as a tool for mixing the information of physical laws and scientific models with data-driven machine learning approaches. We describe a mathematical object, which we denote universal differential equations (UDEs), as the unifying framework connecting the ecosystem. We show how a wide variety of applications, from automatically discovering biological mechanisms to solving high-dimensional Hamilton-Jacobi-Bellman equations, can be phrased and efficiently handled through the UDE formalism and its tooling. We demonstrate the generality of the software tooling to handle stochasticity, delays, and implicit constraints. This funnels the wide variety of SciML applications into a core set of training mechanisms which are highly optimized, stabilized for stiff equations, and compatible with distributed parallelism and GPU accelerators.
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
Wansu Kim (KAIST), Chol Park (UNIST)
Introduction to Breuil-Kisin modules and application to Galois deformation theory
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
The aim of the lecture series is twofold:
(1) give an overview of the “classical” theory of Breuil-Kisin modules, and
(2) discuss its application to the construction of certain p-adic Galois deformation rings.
In the first talk by Wansu Kim (Moday at 10am), we will give a general introduction to the p-adic Hodge theory (focusing on p-adic Galois representations). In the first half of the lecture series, Wansu Kim will explain the “classical” theory of Breuil-Kisin modules following the seminal paper of Kisin’s (Crystalline representations and F-crystals, from Drinfeld’s 50th birthday conference proceeding). In the second half of the lecture series, Chol Park will explain its application to the explicit computation of p-adic local Galois deformation rings cut out by certain p-adic Hodge-theoretic condition.
Here is the time and venue for each talk:
13 Feb (Mon): 3 talks
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) 16:00 -17:30 at E6-1, Rm 3434
14 Feb (Tue): 1 talk
*) 16:15 -17:45 at E6-1, Rm 3434
15 Feb (Wed) to 16 Feb (Thu):
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) (TBD) 16:00 -17:30 at E6-1, Rm 3434 (in case we need extra lecture)
17 Feb (Fri)
*) 10-11:30 at E6-1, Rm 3438
*) (TBD) 14-15:30 at E6-1, Rm 3438 (in case we need extra lecture)
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
Wansu Kim (KAIST), Chol Park (UNIST)
Introduction to Breuil-Kisin modules and application to Galois deformation theory
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
The aim of the lecture series is twofold:
(1) give an overview of the “classical” theory of Breuil-Kisin modules, and
(2) discuss its application to the construction of certain p-adic Galois deformation rings.
In the first talk by Wansu Kim (Moday at 10am), we will give a general introduction to the p-adic Hodge theory (focusing on p-adic Galois representations). In the first half of the lecture series, Wansu Kim will explain the “classical” theory of Breuil-Kisin modules following the seminal paper of Kisin’s (Crystalline representations and F-crystals, from Drinfeld’s 50th birthday conference proceeding). In the second half of the lecture series, Chol Park will explain its application to the explicit computation of p-adic local Galois deformation rings cut out by certain p-adic Hodge-theoretic condition.
Here is the time and venue for each talk:
13 Feb (Mon): 3 talks
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) 16:00 -17:30 at E6-1, Rm 3434
14 Feb (Tue): 1 talk
*) 16:15 -17:45 at E6-1, Rm 3434
15 Feb (Wed) to 16 Feb (Thu):
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) (TBD) 16:00 -17:30 at E6-1, Rm 3434 (in case we need extra lecture)
17 Feb (Fri)
*) 10-11:30 at E6-1, Rm 3438
*) (TBD) 14-15:30 at E6-1, Rm 3438 (in case we need extra lecture)
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
Wansu Kim (KAIST), Chol Park (UNIST)
Introduction to Breuil-Kisin modules and application to Galois deformation theory
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
The aim of the lecture series is twofold:
(1) give an overview of the “classical” theory of Breuil-Kisin modules, and
(2) discuss its application to the construction of certain p-adic Galois deformation rings.
In the first talk by Wansu Kim (Moday at 10am), we will give a general introduction to the p-adic Hodge theory (focusing on p-adic Galois representations). In the first half of the lecture series, Wansu Kim will explain the “classical” theory of Breuil-Kisin modules following the seminal paper of Kisin’s (Crystalline representations and F-crystals, from Drinfeld’s 50th birthday conference proceeding). In the second half of the lecture series, Chol Park will explain its application to the explicit computation of p-adic local Galois deformation rings cut out by certain p-adic Hodge-theoretic condition.
Here is the time and venue for each talk:
13 Feb (Mon): 3 talks
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) 16:00 -17:30 at E6-1, Rm 3434
14 Feb (Tue): 1 talk
*) 16:15 -17:45 at E6-1, Rm 3434
15 Feb (Wed) to 16 Feb (Thu):
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) (TBD) 16:00 -17:30 at E6-1, Rm 3434 (in case we need extra lecture)
17 Feb (Fri)
*) 10-11:30 at E6-1, Rm 3438
*) (TBD) 14-15:30 at E6-1, Rm 3438 (in case we need extra lecture)
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
Wansu Kim (KAIST), Chol Park (UNIST)
Introduction to Breuil-Kisin modules and application to Galois deformation theory
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
The aim of the lecture series is twofold:
(1) give an overview of the “classical” theory of Breuil-Kisin modules, and
(2) discuss its application to the construction of certain p-adic Galois deformation rings.
In the first talk by Wansu Kim (Moday at 10am), we will give a general introduction to the p-adic Hodge theory (focusing on p-adic Galois representations). In the first half of the lecture series, Wansu Kim will explain the “classical” theory of Breuil-Kisin modules following the seminal paper of Kisin’s (Crystalline representations and F-crystals, from Drinfeld’s 50th birthday conference proceeding). In the second half of the lecture series, Chol Park will explain its application to the explicit computation of p-adic local Galois deformation rings cut out by certain p-adic Hodge-theoretic condition.
Here is the time and venue for each talk:
13 Feb (Mon): 3 talks
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) 16:00 -17:30 at E6-1, Rm 3434
14 Feb (Tue): 1 talk
*) 16:15 -17:45 at E6-1, Rm 3434
15 Feb (Wed) to 16 Feb (Thu):
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) (TBD) 16:00 -17:30 at E6-1, Rm 3434 (in case we need extra lecture)
17 Feb (Fri)
*) 10-11:30 at E6-1, Rm 3438
*) (TBD) 14-15:30 at E6-1, Rm 3438 (in case we need extra lecture)
In this talk, we derive effective dynamics governed by PDEs (nonlinear Schrodinger equation, Vlasov-Poisson equation) from the N-body Schrödinger equation with interactions in the large N limit. For the derivation, we first visit quantum mechanics. Then, using the knowledge of many-body quantum mechanics given in the talk and with the suitable conditions for each situation, we derive PDEs describing the effective motion of the system.
자연과학동 (E6-1), Room 3434
Number Theory Seminar
Wansu Kim (KAIST), Chol Park (UNIST)
Introduction to Breuil-Kisin modules and application to Galois deformation theory
자연과학동 (E6-1), Room 3434
Number Theory Seminar
The aim of the lecture series is twofold:
(1) give an overview of the “classical” theory of Breuil-Kisin modules, and
(2) discuss its application to the construction of certain p-adic Galois deformation rings.
In the first talk by Wansu Kim (Moday at 10am), we will give a general introduction to the p-adic Hodge theory (focusing on p-adic Galois representations). In the first half of the lecture series, Wansu Kim will explain the “classical” theory of Breuil-Kisin modules following the seminal paper of Kisin’s (Crystalline representations and F-crystals, from Drinfeld’s 50th birthday conference proceeding). In the second half of the lecture series, Chol Park will explain its application to the explicit computation of p-adic local Galois deformation rings cut out by certain p-adic Hodge-theoretic condition.
Here is the time and venue for each talk:
13 Feb (Mon): 3 talks
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) 16:00 -17:30 at E6-1, Rm 3434
14 Feb (Tue): 1 talk
*) 16:15 -17:45 at E6-1, Rm 3434
15 Feb (Wed) to 16 Feb (Thu):
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) (TBD) 16:00 -17:30 at E6-1, Rm 3434 (in case we need extra lecture)
17 Feb (Fri)
*) 10-11:30 at E6-1, Rm 3438
*) (TBD) 14-15:30 at E6-1, Rm 3438 (in case we need extra lecture)
Room B332, IBS (기초과학연구원)
Discrete Mathematics
Raphael Steiner (ETH Zürich)
Strengthening Hadwiger’s conjecture for 4- and 5-chromatic graphs
Room B332, IBS (기초과학연구원)
Discrete Mathematics
Hadwiger's famous coloring conjecture states that every t-chromatic graph contains a $K_t$-minor. Holroyd [Bull. London Math. Soc. 29, (1997), pp. 139-144] conjectured the following strengthening of Hadwiger's conjecture: If G is a t-chromatic graph and S⊆V(G) takes all colors in every t-coloring of G, then G contains a $K_t$-minor rooted at S. We prove this conjecture in the first open case of t=4. Notably, our result also directly implies a stronger version of Hadwiger's conjecture for 5-chromatic graphs as follows: Every 5-chromatic graph contains a $K_5$-minor with a singleton branch-set. In fact, in a 5-vertex-critical graph we may specify the singleton branch-set to be any vertex of the graph. Joint work with Anders Martinsson (ETH).
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
(Wansu Kim (KAIST), Chol Park (UNIST))
Introduction to Breuil-Kisin modules and application to Galois deformation theory
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
The aim of the lecture series is twofold:
(1) give an overview of the “classical” theory of Breuil-Kisin modules, and
(2) discuss its application to the construction of certain p-adic Galois deformation rings.
In the first talk by Wansu Kim (Moday at 10am), we will give a general introduction to the p-adic Hodge theory (focusing on p-adic Galois representations). In the first half of the lecture series, Wansu Kim will explain the “classical” theory of Breuil-Kisin modules following the seminal paper of Kisin’s (Crystalline representations and F-crystals, from Drinfeld’s 50th birthday conference proceeding). In the second half of the lecture series, Chol Park will explain its application to the explicit computation of p-adic local Galois deformation rings cut out by certain p-adic Hodge-theoretic condition.
Here is the time and venue for each talk:
13 Feb (Mon): 3 talks
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) 16:00 -17:30 at E6-1, Rm 3434
14 Feb (Tue): 1 talk
*) 16:15 -17:45 at E6-1, Rm 3434
15 Feb (Wed) to 16 Feb (Thu):
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) (TBD) 16:00 -17:30 at E6-1, Rm 3434 (in case we need extra lecture)
17 Feb (Fri)
*) 10-11:30 at E6-1, Rm 3438
*) (TBD) 14-15:30 at E6-1, Rm 3438 (in case we need extra lecture)
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
Wansu Kim (KAIST), Chol Park (UNIST)
Introduction to Breuil-Kisin modules and application to Galois deformation theory
자연과학동 (E6-1), Room 1401 (최석정강의실)
Number Theory Seminar
The aim of the lecture series is twofold:
(1) give an overview of the “classical” theory of Breuil-Kisin modules, and
(2) discuss its application to the construction of certain p-adic Galois deformation rings.
In the first talk by Wansu Kim (Moday at 10am), we will give a general introduction to the p-adic Hodge theory (focusing on p-adic Galois representations). In the first half of the lecture series, Wansu Kim will explain the “classical” theory of Breuil-Kisin modules following the seminal paper of Kisin’s (Crystalline representations and F-crystals, from Drinfeld’s 50th birthday conference proceeding). In the second half of the lecture series, Chol Park will explain its application to the explicit computation of p-adic local Galois deformation rings cut out by certain p-adic Hodge-theoretic condition.
Here is the time and venue for each talk:
13 Feb (Mon): 3 talks
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) 16:00 -17:30 at E6-1, Rm 3434
14 Feb (Tue): 1 talk
*) 16:15 -17:45 at E6-1, Rm 3434
15 Feb (Wed) to 16 Feb (Thu):
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) (TBD) 16:00 -17:30 at E6-1, Rm 3434 (in case we need extra lecture)
17 Feb (Fri)
*) 10-11:30 at E6-1, Rm 3438
*) (TBD) 14-15:30 at E6-1, Rm 3438 (in case we need extra lecture)
자연과학동 (E6-1), Room 3434
Number Theory Seminar
Wansu Kim (KAIST), Chol Park (UNIST)
Introduction to Breuil-Kisin modules and application to Galois deformation theory
자연과학동 (E6-1), Room 3434
Number Theory Seminar
The aim of the lecture series is twofold:
(1) give an overview of the “classical” theory of Breuil-Kisin modules, and
(2) discuss its application to the construction of certain p-adic Galois deformation rings.
In the first talk by Wansu Kim (Moday at 10am), we will give a general introduction to the p-adic Hodge theory (focusing on p-adic Galois representations). In the first half of the lecture series, Wansu Kim will explain the “classical” theory of Breuil-Kisin modules following the seminal paper of Kisin’s (Crystalline representations and F-crystals, from Drinfeld’s 50th birthday conference proceeding). In the second half of the lecture series, Chol Park will explain its application to the explicit computation of p-adic local Galois deformation rings cut out by certain p-adic Hodge-theoretic condition.
Here is the time and venue for each talk:
13 Feb (Mon): 3 talks
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) 16:00 -17:30 at E6-1, Rm 3434
14 Feb (Tue): 1 talk
*) 16:15 -17:45 at E6-1, Rm 3434
15 Feb (Wed) to 16 Feb (Thu):
*) 10-11:30 & 14-15:30 at E6-1, Rm 1401 (최석정강의실)
*) (TBD) 16:00 -17:30 at E6-1, Rm 3434 (in case we need extra lecture)
17 Feb (Fri)
*) 10-11:30 at E6-1, Rm 3438
*) (TBD) 14-15:30 at E6-1, Rm 3438 (in case we need extra lecture)
B378 Seminar room, IBS
Math Biology
Dongju Lim (KAIST)
Mobile footprinting: linking individual distinctiveness in mobility patterns to mood, sleep, and brain functional connectivity
B378 Seminar room, IBS
Math Biology
Mapping individual differences in behavior is fundamental to personalized neuroscience, but quantifying complex behavior in real world settings remains a challenge. While mobility patterns captured by smartphones have increasingly been linked to a range of psychiatric symptoms, existing research has not specifically examined whether individuals have person-specific mobility patterns. We collected over 3000 days of mobility data from a sample of 41 adolescents and young adults (age 17–30 years, 28 female) with affective instability. We extracted summary mobility metrics from GPS and accelerometer data and used their covariance structures to identify individuals and calculated the individual identification accuracy—i.e., their “footprint distinctiveness”. We found that statistical patterns of smartphone-based mobility features represented unique “footprints” that allow individual identification (p < 0.001). Critically, mobility footprints exhibited varying levels of person-specific distinctiveness (4–99%), which was associated with age and sex. Furthermore, reduced individual footprint distinctiveness was associated with instability in affect (p < 0.05) and circadian patterns (p < 0.05) as measured by environmental momentary assessment. Finally, brain functional connectivity, especially those in the somatomotor network, was linked to individual differences in mobility patterns (p < 0.05). Together, these results suggest that real-world mobility patterns may provide individual-specific signatures relevant for studies of development, sleep, and psychopathology.
The syzygies of a curve are the algebraic relation amongst the equation defining it. They are an algebraic concept but they have surprising applications to geometry. For example, the Green-Lazarsfeld secant conjecture predicts that the syzygies of a curve of sufficiently high degree are controlled by its special secants. We prove this conjecture for all curves of Clifford index at least two and not bielliptic and for all line bundles of a certain degree. Our proof is based on a classic result of Martens and Mumford on Brill-Noether varieties and on a simple vanishing criterion that comes from the interpretation of syzygies through symmetric products of curves.
B378 Seminar room, IBS
Math Biology
Hyukpyo Hong (KAIST)
Estimating and Assessing Differential Equation Models with Time-Course Data
B378 Seminar room, IBS
Math Biology
Ordinary differential equation (ODE) models are widely used to describe chemical or biological processes. This article considers the estimation and assessment of such models on the basis of time-course data. Due to experimental limitations, time-course data are often noisy and some components of the system may not be observed. Furthermore, the computational demands of numerical integration have hindered the widespread adoption of time-course analysis using ODEs. To address these challenges, we explore the efficacy of the recently developed MAGI (MAnifold-constrained Gaussian process Inference) method for ODE inference. First, via a range of examples we show that MAGI is capable of inferring the parameters and system trajectories, including unobserved components, with appropriate uncertainty quantification. Second, we illustrate how MAGI can be used to assess and select different ODE models with time-course data based on MAGI’s efficient computation of model predictions. Overall, we believe MAGI is a useful method for the analysis of time-course data in the context of ODE models, which bypasses the need for any numerical integration.