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[Big data analysis for complex biological systems, 1/3] A Bayesian Convolutional Neural Network-based Generalized Linear Model

B378 Seminar room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Korea, Republic of

Abstract: Convolutional neural networks (CNNs) provide flexible function approximations for a wide variety of applications when the input variables are in the form of images or spatial data. Although CNNs often outperform traditional statistical models in prediction accuracy, statistical inference such as estimating the effects of covariates and quantifying the prediction uncertainty is not trivial …

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[Big data analysis for complex biological systems, 2/3] DCLEAR: Reconstructing Single Cell Lineage Trees from CRISPR recorders by Distance-based Methods

B378 Seminar room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Korea, Republic of

Abstract: A fundamental challenge in biology is the reconstruction of developmental trajectories as they divide and progress through different stages. The recent advance of CRISPR-based molecular tools, such as intMEMOIR and scGESTALT, have produced a new generation of techniques that enable the reconstruction of cell lineages of complex organisms at single-cell resolution. However, there are …

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[Big data analysis for complex biological systems, 3/3] Short presentation session

B378 Seminar room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Korea, Republic of

In this short presentation session, six researchers from IBS BIMAG present 10-minute talks. 4:00 -- 4:10, Hyeontae Jo 4:15 -- 4:25, Hyun Kim 4:30 -- 4:40, Aurelio de los Reyes V 4:45 -- 4:55, Yun Min Song 5:00 -- 5:10, Seokmin Ha 5:15 -- 5:25, Hyukpyo Hong

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

B378 Seminar room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Korea, Republic of

We will discuss about "Inferring Regulatory Networks from Expression Data Using Tree-Based Methods," Huynh-Thu et al., PLoS ONE (2010). Abstract: One of the pressing open problems of computational systems biology is the elucidation of the topology of genetic regulatory networks (GRNs) using high throughput genomic data, in particular microarray gene expression data. The Dialogue for …

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Cell signaling in 2D vs. 3D

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

Abstract: The activation of Ras depends upon the translocation of its guanine nucleotide exchange factor, Sos, to the plasma membrane. Moreover, artificially inducing Sos to translocate to the plasma membrane is sufficient to bring about Ras activation and activation of Ras’s targets. There are many other examples of signaling proteins that must translocate to the …

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Hidden Markov models for monitoring circadian rhythmicity in telemetric activity data

B378 Seminar room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Korea, Republic of

We will discuss about "Hidden Markov models for monitoring circadian rhythmicity in telemetric activity data", Huang, Qi, Journal of The Royal Society Interface 15.139 (2018): 20170885. Abstract: Wearable computing devices allow collection of densely sampled real-time information on movement enabling researchers and medical experts to obtain objective and non-obtrusive records of actual activity of a …

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Physics-informed neural networks for PDE-constrained optimization and control

B378 Seminar room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Korea, Republic of

We will discuss about "Physics-informed neural networks for PDE-constrained optimization and control", Barry-Straume, Jostein, et al., arXiv preprint arXiv:2205.03377 (2022). Abstract: A fundamental problem of science is designing optimal control policies that manipulate a given environment into producing a desired outcome. Control PhysicsInformed Neural Networks simultaneously solve a given system state, and its respective optimal …

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STEM Initiatives for Agricultural 4.0 and Beyond

This talk will be given online. Abstract: The establishment of UN Sustainable Development Goals (SDG) has led to widespread initiative in STEM learning and research in realising these goals. Here, we will look at some of the works that use control engineering approaches for smart farming (also known as Agriculture 4.0) applications that addresses UN …

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Design frameworks for engineering efficient cell factory performance within host and industrial constraints

This talk will be given online. Abstract: Synthetic biology and microbial biotechnology offer sustainable routes to the manufacture of commodity and high value chemicals from agricultural by-products instead of petrochemical feedstocks. However, engineered gene circuits and metabolic pathways both co-opt the cell’s gene expression machinery for protein/enzyme production and divert metabolic flux away from key …

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Cell clustering for spatial transcriptomics data with graph neural networks

B378 Seminar room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Korea, Republic of

We will discuss about "Cell clustering for spatial transcriptomics data with graph neural networks", Li, J., Chen, S., Pan, X. et al., Nat Comput Sci 2, 399–408 (2022) Abstract: Spatial transcriptomics data can provide high-throughput gene expression profiling and the spatial structure of tissues simultaneously. Most studies have relied on only the gene expression information but …

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Causal Inference – basics and examples

B378 Seminar room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Korea, Republic of

Abstract: In real world, people are interested in causality rather than association. For example, pharmaceutical companies want to know effectiveness of their new drugs against diseases. South Korea Government officials are concerned about the effects of recent regulation with respect to an electric car subsidy from United States. Due to this reason, causal inference has …

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Absolute concentration robustness in networks with low-dimensional stoichiometric subspace

B378 Seminar room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Korea, Republic of

We will discuss about "Absolute concentration robustness in networks with low-dimensional stoichiometric subspace", Meshkat, Nicolette, Anne Shiu, and Angelica Torres., Vietnam Journal of Mathematics 50.3 (2022): 623-651. Abstract: A reaction system exhibits “absolute concentration robustness” (ACR) in some species if the positive steady-state value of that species does not depend on initial conditions. Mathematically, this …

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IBS 의생명수학그룹 Biomedical Mathematics Group
기초과학연구원 수리및계산과학연구단 의생명수학그룹
대전 유성구 엑스포로 55 (우) 34126
IBS Biomedical Mathematics Group (BIMAG)
Institute for Basic Science (IBS)
55 Expo-ro Yuseong-gu Daejeon 34126 South Korea
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