BEGIN:VCALENDAR
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PRODID:-//Biomedical Mathematics Group - ECPv6.15.20//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
X-WR-CALNAME:Biomedical Mathematics Group
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:20220101T000000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230501T160000
DTEND;TZID=Asia/Seoul:20230501T170000
DTSTAMP:20260425T220333
CREATED:20230409T052337Z
LAST-MODIFIED:20230414T024627Z
UID:7582-1682956800-1682960400@www.ibs.re.kr
SUMMARY:Understanding Trade-offs in Biological Information Processing
DESCRIPTION:High accuracy of major biological processes relies on the ability of the participating enzymatic molecules to preferentially select the correct substrate from a pool of chemically similar substrates by activating the so-called proofreading mechanisms. While the importance of such mechanisms is widely accepted\, it is still unclear how evolution has optimized biological systems with respect to their characteristic properties. We developed a comprehensive first-passage theoretical framework that allowed us to quantitatively investigate the trade-offs between the three properties of enzymatic systems: error\, speed\, noise\, and energy dissipation. Within this framework\, we simultaneously analyzed the speed and accuracy of several fundamental biological processes\, including DNA replication\, transcription\, tRNA charging\, and tRNA selection during the translation. The results indicate that the speed-accuracy trade-off is not always observed contrary to typical assumptions. However\, when the trade-off is present\, the biological systems tend to optimize the speed rather than the accuracy of the processes\, as long as the error level is tolerable. When systems function in a regime where no speed-accuracy trade-off is observed\, constraints due to energy dissipation in the proofreading play a key role. Our theory demonstrates a universal Pareto front in error-dissipation trade-off and shows how naturally selected kinetic parameters position their system close to this boundary. Our findings\, therefore\, provide a new system-level picture of how complex biological processes are able to function so fast with high accuracy and low dissipation.
URL:https://www.ibs.re.kr/bimag/event/uncovering-the-mechanisms-of-pattern-formation-and-emergent-collective-behaviors-in-myxobacteria/
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:20230504T161500
DTEND;TZID=Asia/Seoul:20230504T171500
DTSTAMP:20260425T220333
CREATED:20230409T053139Z
LAST-MODIFIED:20230414T024516Z
UID:7585-1683216900-1683220500@www.ibs.re.kr
SUMMARY:Uncovering the mechanisms of pattern formation and emergent collective behaviors in myxobacteria
DESCRIPTION:Collective cell movement is critical to the emergent properties of many multicellular systems including microbial self-organization in biofilms\, wound healing\, and cancer metastasis. However\, even the best-studied systems lack a complete picture of how diverse physical and chemical cues act upon individual cells to ensure coordinated multicellular behavior. Myxococcus xanthus is a model bacteria famous for its coordinated multicellular behavior resulting in dynamic patterns formation. For example\, when starving millions of cells coordinate their movement to organize into fruiting bodies – aggregates containing tens of thousands of bacteria. Relating these complex self-organization patterns to the behavior of individual cells is a complex-reverse engineering problem that cannot be solved solely by experimental research. In collaboration with experimental colleagues\, we use a combination of quantitative microscopy\, image processing\, agent-based modeling\, and kinetic theory PDEs to uncover the mechanisms of emergent collective behaviors.
URL:https://www.ibs.re.kr/bimag/event/understanding-trade-offs-in-biological-information-processing/
LOCATION:KAIST E6-1 1501 Auditorium\, 291 Daehak-ro\, Yuseong-gu\, Daejeon\, 34141\, 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:20230508T160000
DTEND;TZID=Asia/Seoul:20230508T170000
DTSTAMP:20260425T220333
CREATED:20230425T045600Z
LAST-MODIFIED:20230425T045600Z
UID:7637-1683561600-1683565200@www.ibs.re.kr
SUMMARY:Kyongwon Kim\, On sufficient graphical models
DESCRIPTION:We introduce a sufficient graphical model by applying the recently developed nonlinear sufficient dimension reduction techniques to the evaluation of conditional independence. The graphical model is nonparametric in nature\, as it does not make distributional assumptions such as the Gaussian or copula Gaussian assumptions. However\, unlike a fully nonparametric graphical model\, which relies on the high-dimensional kernel to characterize conditional independence\,  our graphical model is based on conditional independence given a set of sufficient predictors with a substantially reduced dimension. In this way we avoid the curse of dimensionality that comes with a high-dimensional kernel. We develop the population-level properties\,  convergence rate\, and variable selection consistency of our estimate. \nBy simulation comparisons and an analysis of the DREAM 4 Challenge data set\, we demonstrate that our method outperforms the existing methods when the Gaussian or copula Gaussian assumptions are violated\, and its performance remains excellent in the high-dimensional setting.
URL:https://www.ibs.re.kr/bimag/event/kyongwon-kim-on-sufficient-graphical-models/
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:20230510T160000
DTEND;TZID=Asia/Seoul:20230510T170000
DTSTAMP:20260425T220333
CREATED:20230213T110735Z
LAST-MODIFIED:20230308T101512Z
UID:7339-1683734400-1683738000@www.ibs.re.kr
SUMMARY:Mogens Jensen\, Droplet formation\, DNA repair and chaos in CellsBD
DESCRIPTION:Abstract: TBD
URL:https://www.ibs.re.kr/bimag/event/tbd/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/02/Mogens_Hogh_Jensen.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230512T110000
DTEND;TZID=Asia/Seoul:20230512T130000
DTSTAMP:20260425T220333
CREATED:20230430T155858Z
LAST-MODIFIED:20230508T134254Z
UID:7653-1683889200-1683896400@www.ibs.re.kr
SUMMARY:Hyukpyo Hong\, Inference and uncertainty quantification of stochastic gene expression via synthetic models
DESCRIPTION:We will discuss about “Inference and uncertainty quantification of stochastic gene expression via synthetic models”\, Öcal et al.\, J. R. Soc. Interface. \nAbstract \n\n\n\n\nEstimating uncertainty in model predictions is a central task in quantitativebiology. Biological models at the single-cell level are intrinsically stochastic and nonlinear\, creating formidable challenges for their statistical estimation which inevitably has to rely on approximations that trade accuracy for tractability. Despite intensive interest\, a sweet spot in this trade-off has not been found yet. We propose a flexible procedure for uncertainty quantification in a wide class of reaction networks describing stochastic gene expression including those with feedback. The method is based on creating a tractable coarse-graining of the model that is learned from simulations\, a synthetic model\, to approximate the likelihood function. We demonstrate that synthetic models can substantially outperform state-of-the-art approaches on a number of non-trivial systems and datasets\, yielding an accurate and computationally viable solution to uncertainty quantification in stochastic models of gene expression.
URL:https://www.ibs.re.kr/bimag/event/2023-05-12-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230519T140000
DTEND;TZID=Asia/Seoul:20230519T160000
DTSTAMP:20260425T220333
CREATED:20230430T033701Z
LAST-MODIFIED:20230515T040214Z
UID:7648-1684504800-1684512000@www.ibs.re.kr
SUMMARY:Dongju Lim\, A multi-scale model explains oscillatory slowing and neuronal hyperactivity in Alzheimer’s disease
DESCRIPTION:We will discuss about “A multi-scale model explains oscillatory slowing and neuronal hyperactivity in Alzheimer’s disease”\, Alexandersen\, Christoffer G.\, et al.\, Journal of the Royal Society Interface 20.198 (2023): 20220607. \nAbstract \n\n\n\n\n\n\nAlzheimer’s disease is the most common cause of dementia and is linked to the spreading of pathological amyloid-β and tau proteins throughout the brain. Recent studies have highlighted stark differences in how amyloid-β and tau affect neurons at the cellular scale. On a larger scale\, Alzheimer’s patients are observed to undergo a period of early-stage neuronal hyperactivation followed by neurodegeneration and frequency slowing of neuronal oscillations. Herein\, we model the spreading of both amyloid-β and tau across a human connectome and investigate how the neuronal dynamics are affected by disease progression. By including the effects of both amyloid-β and tau pathology\, we find that our model explains AD-related frequency slowing\, early-stage hyperactivation and late-stage hypoactivation. By testing different hypotheses\, we show that hyperactivation and frequency slowing are not due to the topological interactions between different regions but are mostly the result of local neurotoxicity induced by amyloid-β and tau protein.
URL:https://www.ibs.re.kr/bimag/event/2023-05-19-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230522T120000
DTEND;TZID=Asia/Seoul:20230522T130000
DTSTAMP:20260425T220333
CREATED:20230509T062709Z
LAST-MODIFIED:20230509T062709Z
UID:7730-1684756800-1684760400@www.ibs.re.kr
SUMMARY:Pan Li\, Modeling the circadian control of cardiac function
DESCRIPTION:Abstract: TBA
URL:https://www.ibs.re.kr/bimag/event/pan-li-modeling-the-circadian-control-of-cardiac-function/
LOCATION:IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 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:20230524T160000
DTEND;TZID=Asia/Seoul:20230524T170000
DTSTAMP:20260425T220333
CREATED:20230213T110844Z
LAST-MODIFIED:20230308T101313Z
UID:7342-1684944000-1684947600@www.ibs.re.kr
SUMMARY:Thomas Philipp\, Stochastic gene expression in lineage trees
DESCRIPTION:Abstract: Stochasticity in gene expression is an important source of cell-to-cell variability (or noise) in clonal cell populations. So far\, this phenomenon has been studied using the Gillespie Algorithm\, or the Chemical Master Equation\, which implicitly assumes that cells are independent and do neither grow nor divide. This talk will discuss recent developments in modelling populations of growing and dividing cells through agent-based approaches. I will show how the lineage structure affects gene expression noise over time\, which leads to a straightforward interpretation of cell-to-cell variability in population snapshots. I will also illustrate how cell cycle variability shapes extrinsic noise across lineage trees. Finally\, I outline how to construct effective chemical master equation models based on dilution reactions and extrinsic variability that provide surprisingly accurate approximations of the noise statistics across growing populations. The results highlight that it is crucial to consider cell growth and division when quantifying cellular noise.
URL:https://www.ibs.re.kr/bimag/event/stochastic-gene-expression-in-lineage-trees/
LOCATION:ZOOM ID: 997 8258 4700 (Biomedical Mathematics Online Colloquium)\, (pw: 1234)
CATEGORIES:Biomedical Mathematics Online Colloquium
ATTACH;FMTTYPE=image/jpeg:https://www.ibs.re.kr/bimag/cms/wp-content/uploads/2023/02/PThomastojpeg_1587640386131_x2.jpg
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230525T110000
DTEND;TZID=Asia/Seoul:20230525T120000
DTSTAMP:20260425T220333
CREATED:20230522T134427Z
LAST-MODIFIED:20230522T134449Z
UID:7767-1685012400-1685016000@www.ibs.re.kr
SUMMARY:Nonparametric predictive model for sparse and irregular longitudinal data
DESCRIPTION:We propose a kernel-based estimator to predict the mean response trajectory for sparse and irregularly measured longitudinal data. The kernel estimator is constructed by imposing weights based on the subject-wise similarity on L2 metric space between predictor trajectories\, where we assume that an analogous fashion in predictor trajectories over time would result in a similar trend in the response trajectory among subjects. In order to deal with the curse of dimensionality caused by the multiple predictors\, we propose an appealing multiplicative model with multivariate Gaussian kernels. This model is capable of achieving dimension reduction as well as selecting functional covariates with predictive significance. The asymptotic properties of the proposed nonparametric estimator are investigated under mild regularity conditions. We illustrate the robustness and flexibility of our proposed method via the simulation study and an application to Framingham Heart Study
URL:https://www.ibs.re.kr/bimag/event/2023-05-25-seminar/
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:20230526T140000
DTEND;TZID=Asia/Seoul:20230526T160000
DTSTAMP:20260425T220333
CREATED:20230430T034034Z
LAST-MODIFIED:20230524T094243Z
UID:7650-1685109600-1685116800@www.ibs.re.kr
SUMMARY:Hyeontae Jo\,Parameter Estimation of Power Electronic Converters With Physics-Informed Machine Learning
DESCRIPTION:We will discuss about “Parameter Estimation of Power Electronic Converters With Physics-Informed Machine Learning”\, Zhao\, Shuai\, et al.\, IEEE Transactions on Power Electronics 37.10 (2022): 11567-11578. \nAbstract \nPhysics-informed machine learning (PIML) has been emerging as a promising tool for applications with domain knowledge and physical models. To uncover its potentials in power electronics\, this article proposes a PIML-based parameter estimation method demonstrated by a case study of dc–dc Buck converter. A deep neural network and the dynamic models of the converter are seamlessly coupled. It overcomes the challenges related to training data\, accuracy\, and robustness which a typical data-driven approach has. This exemplary application envisions to provide a new perspective for tailoring existing machine learning tools for power electronics.
URL:https://www.ibs.re.kr/bimag/event/2023-05-26-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20230530T160000
DTEND;TZID=Asia/Seoul:20230530T170000
DTSTAMP:20260425T220333
CREATED:20230524T125426Z
LAST-MODIFIED:20230524T125651Z
UID:7788-1685462400-1685466000@www.ibs.re.kr
SUMMARY:Trivial but not trivial things in data science: From a statistical perspective
DESCRIPTION:TBA
URL:https://www.ibs.re.kr/bimag/event/t/
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:20230531T120000
DTEND;TZID=Asia/Seoul:20230531T130000
DTSTAMP:20260425T220333
CREATED:20230529T035221Z
LAST-MODIFIED:20230529T102040Z
UID:7809-1685534400-1685538000@www.ibs.re.kr
SUMMARY:Dongju Lim\, Eui Min Jeong\, Hyeontae Jo
DESCRIPTION:Dongju Lim: Mood Prediction for Bipolar Disorder Patient with Sleep Pattern Information \n  \nEui Min Jeong:Noise attenuation through the multiple repression mechanism in transcription \n  \nHyeontae Jo: Parameter estimation with discontinuously switching system
URL:https://www.ibs.re.kr/bimag/event/2023-05-31-lls/
LOCATION:Tea Room\, IBS\, Daejeon\, Daejeon\, 34141\, Korea\, Republic of
CATEGORIES:Lunch Lab Meeting Seminar
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
END:VCALENDAR