• Network inference from short, noisy, low time-resolution, partial measurements: Application to C. elegans neuronal calcium dynamics – Olive Cawiding

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Network inference from short, noisy, low time-resolution, partial measurements: Application to C. elegans neuronal calcium dynamics" by Amitava Banerjee, Sarthak Chandra, and Edward Ott, PNAS, 2023. Abstract Network link inference from measured time series data of the behavior of dynamically interacting network nodes is an important problem with wide-ranging applications, e.g., estimating synaptic

  • Direct Estimation of Parameters in ODE Models Using WENDy – Kangmin Lee

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Direct Estimation of Parameters in ODE Models Using WENDy: Weak-Form Estimation of Nonlinear Dynamics" by David M. Bortz, Daniel A. Messenger, and Vanja Dukic, Bulletin of Mathematical Biology, 2023. Abstract We introduce the Weak-form Estimation of Nonlinear Dynamics (WENDy) method for estimating model parameters for non-linear systems of

  • Deep learning for universal linear embeddings of nonlinear dynamics – Hyukpyo Hong

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Deep learning for universal linear embeddings of nonlinear dynamics" by B. Lusch, J. N. Kutz, and S. Brunton, Nat. Comm. 2018. Abstract  Identifying coordinate transformations that make strongly nonlinear dynamics approximately linear has the potential to enable nonlinear prediction, estimation, and control using linear theory. The Koopman operator

  • Large language models for scientific discovery in molecular property prediction – Aqsa Awan

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Large language models for scientific discovery in molecular property prediction" by Yizhen Zheng et.al., nature machine intelligence, 2025. Abstract Large language models (LLMs) are a form of artificial intelligence system encapsulating vast knowledge in the form of natural language. These systems are adept at numerous complex tasks including

  • Data splitting to avoid information leakage with DataSAIL – Myna Lim

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper, "Data splitting to avoid information leakage with DataSAIL" by Roman Joeres, et al., Nature Communications, 2025. Abstract Information leakage is an increasingly important topic in machine learning research for biomedical applications. When information leakage happens during a model’s training, it risks memorizing the training data instead of learning

  • Machine learning methods trained on simple models can predict critical transitions in complex natural systems – Shingo Gibo

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Machine learning methods trained on simple models can predict critical transitions in complex natural systems" by  Smita Deb, Sahil Sidheekh, Christopher F. Clements, Narayanan C. Krishnan, and Partha S. Dutta, in Royal Society Open Science, (2022). Abstract:  Forecasting sudden changes in complex systems is a critical but challenging task, with previously developed methods varying widely in their reliability. Here we develop a novel detection method, using simple theoretical models to train a deep neural network to detect critical transitions—the Early Warning Signal Network (EWSNet). We then demonstrate that this network, trained on simulated data, can reliably predict observed real-world transitions in systems ranging from rapid climatic change to the collapse of ecological populations. Importantly, our model appears to capture latent properties in time series missed by previous warning signals approaches, allowing us to not only detect if a transition is approaching, but critically whether the collapse will be catastrophic or non-catastrophic. These novel properties mean EWSNet has the potential to serve as an indicator of transitions across a broad spectrum of complex systems, without requiring information on the structure of the system being monitored. Our work highlights the practicality of deep learning for addressing further questions pertaining to ecosystem collapse and has much broader management implications.

  • Optimal transport for generating transition states in chemical reactions – Gyuyoung Hwang

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Optimal transport for generating transition states in chemical reactions" by C. Duan et.al., Nat. Machine. Intelligence, 2025. Abstract Transition states (TSs) are transient structures that are key to understanding reaction mechanisms and designing catalysts but challenging to capture in experiments. Many optimization algorithms have been developed to search

  • scGPT: toward building a foundation model for single-cell multi-omics using generative AI – Hyun Kim

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "scGPT: toward building a foundation model for single-cell multi-omics using generative AI" by Haotian Cui, et.al. Nature Methods, 2024. Abstract Generative pretrained models have achieved remarkable success in various domains such as language and computer vision. Specifically, the combination of large-scale diverse datasets and pretrained transformers has emerged

  • Effective Markovian dynamics method of solving non-Markovian dynamics of stochastic gene expression – Dongju Lim

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Effective Markovian dynamics method of solving non-Markovian dynamics of stochastic gene expression" by Youming Li and Chen Jia, Physical Review Letters, to appear. Abstract Experiments have shown that over 10% of proteins are degraded non-exponentially. Gene expression models for non-exponentially degraded proteins are notoriously difficult to solve since the underlying

  • Quantifying the energy landscape of high-dimensional oscillatory systems by diffusion decomposition – Eui Min Jeong

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Quantifying the energy landscape of high-dimensional oscillatory systems by diffusion decomposition" by S. Bian et.al., Cell Reports Physical Science, 2025. Abstract High-dimensional networks producing oscillatory dynamics are ubiquitous in biological systems. Unraveling the mechanism of oscillatory dynamics in biological networks with stochastic perturbations becomes of paramount significance. Although

  • Circadian rhythm analysis using wearable-based accelerometry as a digital biomarker of aging and healthspan – Yun Min Song

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Circadian rhythm analysis using wearable-based accelerometry as a digital biomarker of aging and healthspan" by J. Shim et.al., npj digital medicine, 2024. Abstract Recognizing the pivotal role of circadian rhythm in the human aging process and its scalability through wearables, we introduce CosinorAge, a digital biomarker of aging

  • Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters – Kevin Spinicci

    B232 Seminar Room, IBS 55 Expo-ro Yuseong-gu, Daejeon, Daejeon, Korea, Republic of

    In this talk, we discuss the paper "Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters" by L. Xia et.al. Nature Communications, 2024. Abstract Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection