BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//Biomedical Mathematics Group - ECPv6.16.2//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
X-ORIGINAL-URL:https://www.ibs.re.kr/bimag
X-WR-CALDESC:Events for Biomedical Mathematics Group
REFRESH-INTERVAL;VALUE=DURATION:PT1H
X-Robots-Tag:noindex
X-PUBLISHED-TTL:PT1H
BEGIN:VTIMEZONE
TZID:Asia/Seoul
BEGIN:STANDARD
TZOFFSETFROM:+0900
TZOFFSETTO:+0900
TZNAME:KST
DTSTART:20200101T000000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220421T160000
DTEND;TZID=Asia/Seoul:20220421T170000
DTSTAMP:20260522T090839
CREATED:20220420T220000Z
LAST-MODIFIED:20220416T063046Z
UID:5864-1650556800-1650560400@www.ibs.re.kr
SUMMARY:Dynamical and topological hallmarks of regulatory networks driving phenotypic plasticity and heterogeneity in cancers
DESCRIPTION:This talk will be presented online. Zoom link: 997 8258 4700 (pw: 1234) \nAbstract: \nMetastasis and therapy resistance cause over 90% of cancer-related deaths. Despite extensive ongoing efforts\, no unique genetic or mutational signature has emerged for metastasis. Instead\, the ability of genetically identical cells to adapt reversibly by exhibiting multiple phenotypes (phenotypic/non-genetic heterogeneity) and switch among them (phenotypic plasticity) is proposed as a hallmark of metastasis. Also\, drug resistance can emerge from such non-genetic adaptive cellular changes. However\, the origins of such non-genetic heterogeneity in most cancers are poorly understood. I will present our findings on a) how non-genetic heterogeneity emerges in a population of cancer\, and b) what design principles underlie regulatory networks enabling non-genetic heterogeneity across multiple cancers. Our results unravel how systems-levels approaches integrating mechanistic mathematical modeling with in vitro and in vivo data can identify causes and consequences of such non-genetic heterogeneity.
URL:https://www.ibs.re.kr/bimag/event/2022-04-21/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220208T113000
DTEND;TZID=Asia/Seoul:20220208T120000
DTSTAMP:20260522T090839
CREATED:20220208T173000Z
LAST-MODIFIED:20220207T064404Z
UID:5673-1644319800-1644321600@www.ibs.re.kr
SUMMARY:수리모델을 통한 전염병 통제 분석
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2022-02-09-2/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220208T110000
DTEND;TZID=Asia/Seoul:20220208T113000
DTSTAMP:20260522T090839
CREATED:20220208T170000Z
LAST-MODIFIED:20220207T064429Z
UID:5670-1644318000-1644319800@www.ibs.re.kr
SUMMARY:Stochastic Modeling of Foot and Mouth Diseases with Vehicle Network & Assessment of Social Distancing for Controlling COVID-19 in Korea
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2022-02-09/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220127T110000
DTEND;TZID=Asia/Seoul:20220127T130000
DTSTAMP:20260522T090839
CREATED:20220126T170000Z
LAST-MODIFIED:20220125T115708Z
UID:5507-1643281200-1643288400@www.ibs.re.kr
SUMMARY:Introduction to Bayesian Variable Selection.  
DESCRIPTION:Abstract:\nVariable selection is an approach to identifying a set of covariates that are truly important to explain the feature of a response variable. It is closely connected or belongs to model selection approaches. This talk provides a gentle introduction to Bayesian variable selection methods. The basic notion of variable selection is introduced\, followed by several Bayesian approaches with a simple application example.
URL:https://www.ibs.re.kr/bimag/event/2022-01-27-2/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220118T160000
DTEND;TZID=Asia/Seoul:20220118T170000
DTSTAMP:20260522T090839
CREATED:20220117T220000Z
LAST-MODIFIED:20220115T115221Z
UID:5466-1642521600-1642525200@www.ibs.re.kr
SUMMARY:다중 오믹스 분야의 현황 및 유전자-환경 상호 모델링의 필요성 (Current status of multi-omics research field and necessity of gene-by-environment (GxE) interaction modeling)
DESCRIPTION:본 발표에서는 다양한 기초 생명-의학 분야에서 생성되고 있는 오믹스 자료의 연구 개발 현황에 대해서 다룰 예정이다. 보다 큰 규모로\, 보다 빠르게\, 보다 정확하게\, 보다 정밀하게 라는 궁극적인 목표하에 이뤄지고 있는 오믹스 자료의 진화에 발맞춰\, 이를 분석하는 수리통계적 모형 역시 진화하고 있다. 그 중\, 이번 발표에서는 미국의 초 대형 정밀의료 프로젝트인 TopMed에서 진행하고 있는 COPD에 관한 다중 오믹스 자료의 통합 분석 방법 및 결과에 대해서 자세히 다룰 예정이다. 아울러 정밀의료라는 목표를 달성하기 위해 반드시 모형에서 고려해야 하는 “환경 특이적 효과”에 대해 강연할 예정이다. \n 
URL:https://www.ibs.re.kr/bimag/event/2022-01-18/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220106T160000
DTEND;TZID=Asia/Seoul:20220106T173000
DTSTAMP:20260522T090839
CREATED:20220105T220000Z
LAST-MODIFIED:20211224T001917Z
UID:5369-1641484800-1641490200@www.ibs.re.kr
SUMMARY:Structure-based analysis of chemical reaction networks 2/2
DESCRIPTION:Inside living cells\, chemical reactions form a large web of networks. Understanding the behavior of those complex reaction networks is an important and challenging problem. In many situations\, it is hard to identify the details of the reactions\, such as the reaction kinetics and parameter values. It would be good if we can clarify what we can say about the behavior of reaction systems\, when we know the structure of reaction networks but reaction kinetics is unknown. In these talks\, I plan to introduce two approaches in this spirit. Firstly\, we will discuss the sensitivity analysis of reaction systems based on the structural information of reaction networks [1]. I will give an introduction to the method of identifying subnetworks inside which the effects of the perturbation of reaction parameters are confined. Secondly\, I will introduce the reduction method that we developed recently [2]. In those two methods\, an integer determined by the topology of a subnetwork\, which we call an influence index\, plays a crucial role. \n[1] T. Okada\, A. Mochizuki\, “Law of Localization in Chemical Reaction Networks\,” Phys. Rev. Lett. 117\, 048101 (2016); T. Okada\, A. Mochizuki\, “Sensitivity and network topology in chemical reaction systems\,” Phys. Rev. E 96\, 022322 (2017). \n[2] Y. Hirono\, T. Okada\, H. Miyazaki\, Y. Hidaka\, “Structural reduction of chemical reaction networks based on topology”\, Phys. Rev. Research 3\, 043123 (2021).
URL:https://www.ibs.re.kr/bimag/event/2022-01-06/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220105T160000
DTEND;TZID=Asia/Seoul:20220105T173000
DTSTAMP:20260522T090839
CREATED:20220104T220000Z
LAST-MODIFIED:20211224T001927Z
UID:5366-1641398400-1641403800@www.ibs.re.kr
SUMMARY:Structure-based analysis of chemical reaction networks 1/2
DESCRIPTION:Abstract: Inside living cells\, chemical reactions form a large web of networks. Understanding the behavior of those complex reaction networks is an important and challenging problem. In many situations\, it is hard to identify the details of the reactions\, such as the reaction kinetics and parameter values. It would be good if we can clarify what we can say about the behavior of reaction systems\, when we know the structure of reaction networks but reaction kinetics is unknown. In these talks\, I plan to introduce two approaches in this spirit. Firstly\, we will discuss the sensitivity analysis of reaction systems based on the structural information of reaction networks [1]. I will give an introduction to the method of identifying subnetworks inside which the effects of the perturbation of reaction parameters are confined. Secondly\, I will introduce the reduction method that we developed recently [2]. In those two methods\, an integer determined by the topology of a subnetwork\, which we call an influence index\, plays a crucial role. \nReferences \n[1] T. Okada\, A. Mochizuki\, “Law of Localization in Chemical Reaction Networks\,” Phys. Rev. Lett. 117\, 048101 (2016); T. Okada\, A. Mochizuki\, “Sensitivity and network topology in chemical reaction systems\,” Phys. Rev. E 96\, 022322 (2017). \n[2] Y. Hirono\, T. Okada\, H. Miyazaki\, Y. Hidaka\, “Structural reduction of chemical reaction networks based on topology”\, Phys. Rev. Research 3\, 043123 (2021).
URL:https://www.ibs.re.kr/bimag/event/2022-01-05/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20220104T111000
DTEND;TZID=Asia/Seoul:20220104T120000
DTSTAMP:20260522T090839
CREATED:20220103T002320Z
LAST-MODIFIED:20220103T002320Z
UID:5432-1641294600-1641297600@www.ibs.re.kr
SUMMARY:Stem cell dynamics in the intestine and stomach
DESCRIPTION:In adult tissues\, stem cells undergo clonal competition because they proliferate while the stem cell niche provides limited space. This clonal competition allows the selection of healthy stem cells over time as unfit stem cells tend to lose from the competition. It could also be a mechanism to select a supercompetitor with tumorigenic mutations\, which may lead to tumorigenesis. I am going to explain general concepts of clonal competition and how a simple model can explain the behaviour of adult stem cells. I will also show how geometric constraints affect the overall dynamics of stem cell competition.
URL:https://www.ibs.re.kr/bimag/event/2022-01-03/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211229T150000
DTEND;TZID=Asia/Seoul:20211229T160000
DTSTAMP:20260522T090839
CREATED:20211228T210000Z
LAST-MODIFIED:20211227T001218Z
UID:5385-1640790000-1640793600@www.ibs.re.kr
SUMMARY:디지털 표현형의 진단 및 치료적 적용
DESCRIPTION:디지털 표현형의 진단 및 치료적 적용 조철현(세종충남대학교병원) 디지털 표현형(digital phenotype)은 각 개개인이 일상생활에서 사용하는 다양한 디지털 기기를 통해서 실시간으로 얻어지는 다양한 형태의 데이터를 뜻하는 것으로\, 디지털 기기의 사용이 보편화되면서 의료적 적용에 대한 가능성이 한층 높아지고 있다. 디지털 표현형은 이전에는 측정(measure)하기 힘들었던 영역에 대한 측정을 가능케 함으로써\, 의학적 평가나 진단적인 측면에서 임상적 함의를 갖는다고 볼 수 있겠다. 실제 의료현장에서 충분히 접근하고 파악하지 못했던 임상적인 의미를 도출해 내거나 새로운 발견을 할 수 있는 근거로 활용할 수도 있겠다. 임상적 상태의 변화나 치료 효과\, 예후 평가를 위한 기준으로 활용할 수도 있겠다. 또한\, 디지털치료제의 개발과 적용에 있어서 디지털 표현형을 고려하고 반영하는 것은 매우 중요한 부분이 될 것이다. 디지털치료제(Digital Therapeutics)는 사람을 대상으로 치료\, 예방\, 예후 개선 등을 목적으로 인지\, 행동\, 생활습관 등의 변화를 이끌어내기 위한 소프트웨어 형태로서 디지털 시대의 새로운 치료적 옵션으로 주목받고 있다. 특히\, 개인별\, 맞춤형 치료적 접근을 위해서는 디지털 표현형에 대한 이해를 높이고 잘 활용하는 것이 필수적이다. 본 발표에서는 디지털 표현형의 정의와 특성\, 임상적으로 어떤 함의를 가지고 있는 지에 대해 논의하고자 한다. 아울러\, 디지털 표현형의 활용 가능성\, 실제적 적용\, 디지털치료제에의 적용을 위한 방향성에 대해 발표하고자 한다.
URL:https://www.ibs.re.kr/bimag/event/2021-12-29/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211223T163000
DTEND;TZID=Asia/Seoul:20211223T173000
DTSTAMP:20260522T090839
CREATED:20211222T220000Z
LAST-MODIFIED:20211220T121513Z
UID:5357-1640277000-1640280600@www.ibs.re.kr
SUMMARY:Methods for characterizing circadian physiology from wearables
DESCRIPTION:Abstract \nNon-invasive data collection in real-world settings with wearables provides a new opportunity for characterizing daily physiology. However\, accurate and efficient characterization remains an open problem because the complex autoregressive noise of the data makes it challenging to use a simple and efficient method for inference of clock proxies\, least squares method. In this talk\, we will introduce a simple approximation that alters the noise structure and thus enables one to use the least squares method. We will show its usefulness for real-time personalized fever detection in cancer patients.
URL:https://www.ibs.re.kr/bimag/event/2021-12-23-2/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211210T150000
DTEND;TZID=Asia/Seoul:20211210T170000
DTSTAMP:20260522T090839
CREATED:20211209T210000Z
LAST-MODIFIED:20211209T112916Z
UID:5122-1639148400-1639155600@www.ibs.re.kr
SUMMARY:The Graph convolutional Networks (GCN) with Persistent Homology and its applications 3/4
DESCRIPTION:Neural Networks with the Persistent Diagrams and Graph Classification. We introduce the first paper connecting persistent diagrams to the Neural Networks by Carrier et al\,” A neural Network Layer for Persistent Diagrams and New Graph Topological Signatures\, 2019\, arXiv. We are going to analyse the End-to-End algorithm and learning processes and applications.\nCode; tensorflow at https:// github.com/MathieuCarriere/perslay
URL:https://www.ibs.re.kr/bimag/event/2021-12-10/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211112T133000
DTEND;TZID=Asia/Seoul:20211112T153000
DTSTAMP:20260522T090839
CREATED:20211111T210000Z
LAST-MODIFIED:20211109T062309Z
UID:5120-1636723800-1636731000@www.ibs.re.kr
SUMMARY:The Graph convolutional Networks (GCN) with Persistent Homology and its application 2/4
DESCRIPTION:Simplicial Complexes\, Persistent Homology and Persistent Diagrams. After a brief review on the persistent homology( Cohen-Steiner\, Edelsbrunner\, Harer\,2010)\, we discuss constructive procedures persistent diagrams from the persistent homology. Code; 9 software packages generating persistent homology are introduced at ” A roadmap for the computation of persistent homology”\, EPJ Data Science\, a Springer Open Journal.
URL:https://www.ibs.re.kr/bimag/event/2021-11-12/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211029T150000
DTEND;TZID=Asia/Seoul:20211029T170000
DTSTAMP:20260522T090839
CREATED:20211028T210000Z
LAST-MODIFIED:20211029T113540Z
UID:5117-1635519600-1635526800@www.ibs.re.kr
SUMMARY:The Graph convolutional Networks (GCN) with Persistent Homology and its application 1/4
DESCRIPTION:(1) GCN and its Application.\nWe introduce the GCN by reviewing the monumental paper ” Semi-Supervised Classification with the Graph Convolutional Networks”\, ICLR 2018 by Kipf and Welling. We are going to much detail the algorithm of message aggregation and passings and learning processes.\nCode ; https://github.com/tkipf/gcn \n(2) Graph Attention networks(GAT) and its Applications. Bengio et al improved greatly the capability of GCN by employing the Attention mechanism to GCN on the paper\,” Graph Attention Networks\, ICLR\,2018. We review closely the derivation of algirithms\, learning processes and discuss its super performance.\nCode; https://github.com/PetarV-/GAT
URL:https://www.ibs.re.kr/bimag/event/2021-10-29/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20211027T110000
DTEND;TZID=Asia/Seoul:20211027T120000
DTSTAMP:20260522T090839
CREATED:20211028T190000Z
LAST-MODIFIED:20211024T160104Z
UID:5058-1635332400-1635336000@www.ibs.re.kr
SUMMARY:Inferring causality in biological oscillators
DESCRIPTION:Abstract \nTBA
URL:https://www.ibs.re.kr/bimag/event/2021-10-29-2/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210909T110000
DTEND;TZID=Asia/Seoul:20210909T120000
DTSTAMP:20260522T090839
CREATED:20210902T140000Z
LAST-MODIFIED:20210903T055016Z
UID:4981-1631185200-1631188800@www.ibs.re.kr
SUMMARY:COVID19 – Mathematical Modeling and Machine Learning
DESCRIPTION:Abstract \nThis presentation include the following two topics. First of all\, we consider a spread model of COVID-19 with time-dependent parameters via deep learning. We developed a SIR model with time-dependent parameters via deep learning methods. Furthermore\, we validated the model with the conventional model to confirm its convergent nature. Next\, We also developed a machine learning model that predicts the mortality of infected patients by using basic patients information such as age\, residence\, comorbidity\, and past medical history. Furthermore\, we aim to establish a medical system that allows patients to check their own severity\, and informs them to visit the appropriate clinic center by referring to the past treatment details of other patients with similar severity.
URL:https://www.ibs.re.kr/bimag/event/covid19-mathematical-modeling-and-machine-learning/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210813T110000
DTEND;TZID=Asia/Seoul:20210813T120000
DTSTAMP:20260522T090839
CREATED:20210727T190000Z
LAST-MODIFIED:20210731T015814Z
UID:4750-1628852400-1628856000@www.ibs.re.kr
SUMMARY:Bayesian model calibration and sensitivity analysis for oscillating biochemical experiments
DESCRIPTION:Abstract: Most organisms exhibit various endogenous oscillating behaviors\, which provides crucial information about how the internal biochemical processes are connected and regulated. Along with physical experiments\, studying such periodicity of organisms often utilizes computer experiments relying on ordinary differential equations (ODE) because configuring the internal processes is difficult. Simultaneously utilizing both experiments\, however\, poses a significant statistical challenge due to its ill behavior in high dimension\, identifiability\, and numerical instability. This article devises a new Bayesian calibration strategy for oscillating biochemical models. The proposed methodology can efficiently estimate the computer experiments’ (ODE) parameters that match the physical experiments. The proposed framework is illustrated with circadian oscillations observed in a model filamentous fungus\, Neurospora crassa.
URL:https://www.ibs.re.kr/bimag/event/2021-08-13/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/07/HJK_profile-e1626653369732.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210723T150000
DTEND;TZID=Asia/Seoul:20210723T160000
DTSTAMP:20260522T090839
CREATED:20210629T013222Z
LAST-MODIFIED:20210629T013222Z
UID:4686-1627052400-1627056000@www.ibs.re.kr
SUMMARY:Scalable Modeling Approaches in Systems Immunology
DESCRIPTION:Abstract: \nSystems biology seeks to build quantitative predictive models of biological system behavior. Biological systems\, such as the mammalian immune system\, operate across multiple spatiotemporal scales with a myriad of molecular and cellular players. Thus\, mechanistic\, predictive models describing such systems need to address this multiscale nature. A general outstanding problem is to cope with the high-dimensional parameter space arising when building reasonably detailed models. Another challenge is to devise integrated frameworks incorporating behavioral characteristics manifested at various organizational levels seamlessly. First\, we aimed to understand how cell-to-cell heterogeneities are regulated through gene expression variations and their propagation at the single-cell level. To better understand detailed gene regulatory circuit models with many parameters without analytical solutions\, we developed a framework called MAchine learning of Parameter-Phenotype Analysis (MAPPA). MAPPA combines machine learning approaches and stochastic simulation methods to dissect the mapping between high-dimensional parameters and phenotypes. MAPPA elucidated regulatory features of stochastic gene-gene correlation phenotypes. Next\, we sought to quantitatively dissect immune homeostasis conferring tolerance to self-antigens and responsiveness to foreign antigens. Towards this goal\, we built a series of models spanning from intracellular to organismal levels to describe the recurrent reciprocal relationships between self-reactive T cells and regulatory T cells in collaboration with an experimentalist. This effort elucidated critical immune parameters regulating the circuitry enabling the robust suppression of self-reactive T cells\, followed by experimental validation. Moreover\, by bridging these models across organizational scales\, we derived a framework describing immune homeostasis as a dynamical equilibrium between self-activated T cells and regulatory T cells\, typically operating well below thresholds that could result in clonal expansion and subsequent autoimmune diseases. We propose that our framework and predictions may help guide therapeutic manipulation of immune homeostasis to treat cancer and autoimmune diseases. \n  \nReferences: \nPark\, K.\, Prüstel\, T.\, Lu\, Y.\, and Tsang\, J.S. (2019). Machine learning of stochastic gene network phenotypes. BioRxiv 825943. \nWong\, H.S.\, Park\, K.\, Gola\, A.\, Baptista\, A.P.\, Miller\, C.H.\, Deep\, D.\, Lou\, M.\, Boyd\, L.F.\, Rudensky\, A.Y.\, Savage\, P.A.\, et al. (2021). A local regulatory T cell feedback circuit maintains immune homeostasis by pruning self-activated T cells. Cell S0092867421006589.
URL:https://www.ibs.re.kr/bimag/event/2021-07-23/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210723T110000
DTEND;TZID=Asia/Seoul:20210723T120000
DTSTAMP:20260522T090839
CREATED:20210707T160416Z
LAST-MODIFIED:20210707T160416Z
UID:4715-1627038000-1627041600@www.ibs.re.kr
SUMMARY:Inference method for a stochastic target-mediated drug disposition model via ABC-MCMC
DESCRIPTION:Abstract: Inference method for a stochastic target-mediated drug disposition model via ABC-MCMC In this study\, we discuss model robustness. Model robustness is consistent performance over variations of parameters. We formulate a stochastic target-mediated drug (TMDD) model\, one of the pharmacokinetic models\, to capture bi-exponential drug decay in plasma. A stochastic process is used to account for system randomness\, and this process is transformed into system of stochastic differential equations. Parameter inference is performed by Approximation Bayesian Computation using the likelihood-free method. Using these collected samples\, global sensitivity of parameters is compared to Uniform and Normal distributions. This approach in the TMDD model may improve model robustness without changing the global sensitivity of parameters and the model.
URL:https://www.ibs.re.kr/bimag/event/inference-method-for-a-stochastic-target-mediated-drug-disposition-model-via-abc-mcmc/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210712T100000
DTEND;TZID=Asia/Seoul:20210712T120000
DTSTAMP:20260522T090839
CREATED:20210617T030615Z
LAST-MODIFIED:20210617T030615Z
UID:4658-1626084000-1626091200@www.ibs.re.kr
SUMMARY:Analysis of sleep-wake cycles via machine learning and mathematical modeling
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2021-07-21/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210701T110000
DTEND;TZID=Asia/Seoul:20210701T120000
DTSTAMP:20260522T090839
CREATED:20210603T003009Z
LAST-MODIFIED:20210604T082929Z
UID:4605-1625137200-1625140800@www.ibs.re.kr
SUMMARY:Statistical Inference with Neural Network Imputation for Item Nonresponse
DESCRIPTION:Abstract: We consider the problem of nonparametric imputation using neural network models. Neural network models can capture complex nonlinear trends and interaction effects\, making it a powerful tool for predicting missing values under minimum assumptions on the missingness mechanism. Statistical inference with neural network imputation\, including variance estimation\, is challenging because the basis for function estimation is estimated rather than known. In this paper\, we tackle the problem of statistical inference with neural network imputation by treating the hidden nodes in a neural network as data-driven basis functions. We prove that the uncertainty in estimating the basis functions can be safely ignored and hence the linearization method for neural network imputation can be greatly simplified. A simulation study confirms that the proposed approach results in efficient and well-calibrated confidence intervals even when classic approaches fail due to severe nonlinearity and complicated interactions.
URL:https://www.ibs.re.kr/bimag/event/2021-07-01/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/06/JKK_profile2.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210629T130000
DTEND;TZID=Asia/Seoul:20210629T140000
DTSTAMP:20260522T090839
CREATED:20210607T235505Z
LAST-MODIFIED:20210607T235505Z
UID:4627-1624971600-1624975200@www.ibs.re.kr
SUMMARY:Deciphering circadian clock cell network morphology within the biological master clock\, the suprachiasmatic nucleus
DESCRIPTION:Abstract: The biological master clock\, the suprachiasmatic nucleus (SCN) of a mouse\, contains many (~20\,000) clock cells heterogeneous\, particularly with respect to their circadian period. Despite the inhomogeneity\, within an intact SCN\, they maintain a very high degree of circadian phase coherence\, which is generally rendered visible as system-wide propagating phase waves. The phase coherence is vital for mammals sustaining various circadian rhythmic activities. It is supposedly achieved not by one but a few different cell-to-cell coupling mechanisms: Among others\, action potential (AP)-mediated connectivity is known to be essential. However\, due to technical difficulties and limitations in experiments\, so far\, very little information is available about the (connectome) morphology of the AP-mediated SCN neural connectivity. With that limited amount of information\, here we exhaustively and systematically explore a large (~25\,000) pool of various model network morphologies to come up with the most realistic case for the SCN. All model networks within this pool reflect an actual indegree distribution as well as a physical range distribution of afferent clock cells\, which were acquired in earlier optogenetic connectome experiments. Subsequently\, our network selection scheme is based on a collection of multitude criteria\, testing the properties of SCN circadian phase waves in perturbed (or driven) as well as in their natural states: Key properties include\, 1) degree of phase synchrony (or dispersal) and direction of wave propagation\, 2) entrainability of the model oscillator networks to an external circadian forcing (mimicking the light modulation subject to the geophysical circadian rhythm)\, and 3) emergence of “phase-singularities” following a global perturbation and their decay. The selected network morphologies require several common features that 1) the indegree – outdegree relation must have a positive correlation; 2) the cells in the SCN core region have a larger total (in+out) degree than that of the shell region; 3) core to shell (or shell to core) connections should be much less than core to core (and shell to shell) connections. Taken all together\, our comprehensive test results strongly suggest that degree distribution over the whole SCN is not uniform but position-dependent and raise a question of whether this inhomogeneous degree distribution is related to the distribution of known subpopulations of SCN cells.
URL:https://www.ibs.re.kr/bimag/event/deciphering-circadian-clock-cell-network-morphology-within-the-biological-master-clock-the-suprachiasmatic-nucleus/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210618T130000
DTEND;TZID=Asia/Seoul:20210618T140000
DTSTAMP:20260522T090839
CREATED:20210608T152356Z
LAST-MODIFIED:20210612T121922Z
UID:4635-1624021200-1624024800@www.ibs.re.kr
SUMMARY:Introduction to immersed boundary method for biofluids
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2021-06-18-2/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/02/SookkyungLim-e1706058905732.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210430T160000
DTEND;TZID=Asia/Seoul:20210430T170000
DTSTAMP:20260522T090839
CREATED:20210319T021820Z
LAST-MODIFIED:20210412T013739Z
UID:4282-1619798400-1619802000@www.ibs.re.kr
SUMMARY:What is the role of oscillatory signals in intracellular systems?
DESCRIPTION:Oscillatory signals are ubiquitously observed in many different intracellular systems such as immune systems and DNA repair processes. While we know how oscillatory signals are created\, we do not fully understand what a critical role they play to regulate signal pathway systems in cells. Recently by using a stochastic nucleosome system\, we found that a special signal (NFkB signal) in an immune cell can enhance the variability of the immune response to inflammatory stimulations when the signal is oscillatory. Hence in this talk\, we discuss the roles of oscillatory and non-oscillatory NFkB signals in an inflammatory system of immune cells as the main example for revealing the role of oscillatory signals. And then we will talk about how this finding can be generalized for other intra- or extra-cellular systems to study why cells use oscillations.
URL:https://www.ibs.re.kr/bimag/event/2021-04-30/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/03/Jinsu-Kim-9-e1617756454410.jpeg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210415T170000
DTEND;TZID=Asia/Seoul:20210415T173000
DTSTAMP:20260522T090839
CREATED:20210411T124935Z
LAST-MODIFIED:20210412T012752Z
UID:4429-1618506000-1618507800@www.ibs.re.kr
SUMMARY:Practical considerations for measuring the effective reproductive number
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2021-04-15_2/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/04/SHC_profile2.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210415T163000
DTEND;TZID=Asia/Seoul:20210415T170000
DTSTAMP:20260522T090839
CREATED:20210411T124649Z
LAST-MODIFIED:20210412T013301Z
UID:4426-1618504200-1618506000@www.ibs.re.kr
SUMMARY:Mathematical modeling for infectious disease using epidemiological data
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/2021-04-15_1/
LOCATION:B305 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/04/HJL_profile5.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210322T100000
DTEND;TZID=Asia/Seoul:20210322T110000
DTSTAMP:20260522T090839
CREATED:20210315T062250Z
LAST-MODIFIED:20210406T075215Z
UID:4261-1616407200-1616410800@www.ibs.re.kr
SUMMARY:Dae Wook Kim\, Revealing causes of disrupted wake-sleep cycles using mathematical model (BRIC Webinar)
DESCRIPTION:Registration is required to attend this talk (link: https://www.ibric.org/seminar/#)\, and it will be presented in Korean. \nAbstract: 생체 시계 (Circadian clock)를 구성하는 핵심 단백질인 PERIOD (PER)의 양은 12시간 동안 증가했다가 12시간 동안 감소하며 24시간 주기로 변화한다. 이 24시간 주기의 PER 리듬이 우리 몸의 시계 역할을 하여 수면 시간 등 다양한 행동 및 생리 작용의 시간을 결정한다. PER의 24시간 주기 리듬 생성 원리는 2017년 노벨생리의학상을 수상한 마이클 영\, 제프리 홀 그리고 마이클 로스배시 교수에 의해서 밝혀졌다. 12시간 동안 세포질에서 축적된 PER 단백질은 세포 핵 안으로 들어가 스스로 PER 유전자의 전사 (Transcription)를 방해함으로써 12시간 동안 PER 단백질의 양을 감소 시킨다. 하지만 12시간 동안 다른 시간에 생산된 수 천개의 PER 분자들이 어떻게 매일 같은 시간에 핵 안으로 들어가는지는 생체시계 분야의 큰 난제였다. \n본 연구에서는 PER 단백질의 세포 내 움직임을 묘사하는 시공간적 확률론적 모형을 개발하여 분석함으로써 이 난제를 해결하였다. 구체적으로\, PER 단백질이 핵에 들어가는데 필요한 인산화가 핵 주변에서 PER 단백질의 농도가 충분히 높을 때에만 발생함을 밝혔다. 이러한 PER 인산화의 동기화 덕분에 수천 개의 PER 단백질이 매일 일정한 시간에 함께 핵 안으로 들어갈 수 있었고 안정적인 24시간 주기의 일주기 리듬 (Circadian rhythms)과 수면 사이클을 유지할 수 있었던 것이다. \n이러한 핵 주변에서 PER인산화 동기화가 발생하기 위해서는 핵 주변으로 PER이 충분히 응축되어야 한다. 하지만\, 세포 내 환경이 과도하게 혼잡해져 PER 분자의 움직임이 크게 방해를 받으면 PER이 충분히 응축되지 않고 PER 인산화 동기화가 발생하지 않게 된다. 그 결과\, PER이 핵 안으로 들어가는 시간이 불규칙해져 일주기 리듬과 수면 사이클이 불안정해진다. \n이러한 수리 모델 예측은 미국 플로리다 주립대학 이주곤 교수 팀과의 협업을 통해 실험으로 검증하였다. 이는 세포질 혼잡 (Cytoplasmic trafficking)을 유발하는 것으로 알려진 비만\, 치매\, 노화가 어떻게 수면 질환을 유발하는지에 대한 메커니즘과 더불어 새로운 수면 장애 치료법을 제시한다. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-03-22/
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/03/DaeWookKim_profile.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210205T100000
DTEND;TZID=Asia/Seoul:20210205T110000
DTSTAMP:20260522T090839
CREATED:20210228T071217Z
LAST-MODIFIED:20210406T075239Z
UID:4140-1612519200-1612522800@www.ibs.re.kr
SUMMARY:Jaewoo Park\, Introduction to RcppArmadillo for Statistical Programming
DESCRIPTION:The speaker presents how to use Rcpp (Seamless R and C++ Integration) and RcppArmadillo packages (‘Rcpp’ Integration for the ‘Armadillo’ Templated Linear Algebra Library) for statistical programming. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-02-05/
LOCATION:ZOOM ID: 709 120 4849 (ibsbimag)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ATTACH;FMTTYPE=image/png:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2021/02/JaewooPark_20210205_Rcpp.png
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210125T160000
DTEND;TZID=Asia/Seoul:20210125T170000
DTSTAMP:20260522T090839
CREATED:20210223T120915Z
LAST-MODIFIED:20210406T075255Z
UID:4005-1611590400-1611594000@www.ibs.re.kr
SUMMARY:Eui Min Jeong\, Mathematical modeling of circadian clocks of mammal and Drosophila to reveal molecular mechanism for rhythm generation
DESCRIPTION:
URL:https://www.ibs.re.kr/bimag/event/2021-01-25_1/
LOCATION:KAIST E2-1 room 3221\, E2-1 building\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210125T150000
DTEND;TZID=Asia/Seoul:20210125T160000
DTSTAMP:20260522T090839
CREATED:20210223T121036Z
LAST-MODIFIED:20210406T075132Z
UID:4010-1611586800-1611590400@www.ibs.re.kr
SUMMARY:Dae Wook Kim\, Development of mathematical models and theoretical frameworks to unravel mysteries of complex dynamics in biology
DESCRIPTION:
URL:https://www.ibs.re.kr/bimag/event/2021-01-25_2/
LOCATION:KAIST E2-1 room 3221\, E2-1 building\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20210108T143000
DTEND;TZID=Asia/Seoul:20210108T160000
DTSTAMP:20260522T090839
CREATED:20210228T061102Z
LAST-MODIFIED:20210406T075128Z
UID:4114-1610116200-1610121600@www.ibs.re.kr
SUMMARY:Hyukpyo Hong\, Introduction to Git and GitHub
DESCRIPTION:In this talk\, the speaker introduces what Git and GitHub are and explains how to use them. \n 
URL:https://www.ibs.re.kr/bimag/event/2021-01-08/
CATEGORIES:Biomedical Mathematics Seminar,Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
END:VCALENDAR