KERMIT group structure 2025

Transcript

1. Bioinformatics (IMCEGB) 9 December 2025 michiel.stock@ugent.be Computing for Bioscience Engineering Michiel Stock 1
3. Knowledge Extraction, Representation & Management by means of Intelligent Techniques KERMIT’s mission is to harness mathematics and computation to unravel life's complexities, optimize biological functions, and drive innovation in biodesign and decision-making under uncertainty. 3
6. 1. Simulation intelligence 6
7. Simulation intelligence AI + simulation 7 Lavin, A., Zenil, H., Paige, B., Krakauer, D., Gottschlich, J., Mattson, T., Anandkumar, A., Choudry, S., Rocki, K., Baydin, A.G., Prunkl, C., Paige, B., Isayev, O., Peterson, E., McMahon, P.L., Macke, J., Cranmer, K., Zhang, J., Wainwright, H., Hanuka, A., Veloso, M., Assefa, S., Zheng, S., Pfeffer, A., 2021. Simulation intelligence: towards a new generation of scienti fi c methods. https://doi.org/10.48550/arXiv.2112.03235
8. Simulation intelligence for bioengineering 8 Computer-aided design of genetic circuits 𝐼𝑏 ↓ ; 𝐼↓ ; 𝐼↑ input drivers prognostic variables LE H G Rn 𝐿↓ ; 𝐿↑ 𝐼𝑠𝑘𝑦,𝑏 ↓ ; 𝐼𝑠𝑘𝑦 ↓ ; 𝐿𝑠𝑘𝑦 ↓ ; 𝑇𝑚 𝑇𝑠𝑜𝑖𝑙 𝑇𝑓 ; 𝑇𝑎𝑖𝑟 ; 𝑇𝑠 towards forest core towards forest edge ForeEdgeClim model for forest microclimate Emma Van de Walle PlantModules.jl Bram Spanoghe Metabolic model of egg hatching (industrial PhD with Petersime) Mathias Creyf
9. 2. Evolution for AI & biodesign 9
10. Biology = metaengineering 10
11. Evolution for synbio and AI novelty before f itness 11 AI Phenotype realization Entity itself Selection Adaptable GP map Genetic variation Other entities Bioengineer System Interaction with phenotype (e.g., via stress response) Predation, Competition, Symbiosis Growth control Kill switch Artificial selection Changing environment Synthetic genetic circuits Developmental reprogramming Engineered mutagenesis and recombination Dynamic genetic operators Horizontal gene transfer Induced mutagenesis wires.wiley.com/compstats COMPUTATIONAL STATISTICS Volume 17, Number 4, December 2025 Stock, M., Van Hauwermeiren, D., De Baets, B., Taelman, S., Marzougui, D., Van Haeverbeke, M., 2025. Quality- Diversity Methods for the Modern Data Scientist. WIREs Computational Statistics 17, e70047. https://doi.org/10.1002/ wics.70047
12. Modularity of synthetic biology 12 Dimi Boeckaerts Victor Németh Ste f f Taelman Miguel De Block
13. 3. Non-conventional computing 13 Pieters, O., De Swaef, T., Stock, M., Wyffels, F., 2022. Leveraging plant physiological dynamics using physical reservoir computing. Sci Rep 12, 12594. https://doi.org/ 10.1038/s41598-022-16874-0
14. Representation building blocks (in the hyperdimensional space) 14 Check out our tutorial
15. Trees of life beyond sequences 15 Carlos Vigil Vásquez
16. Bottom-up vs top-down biology 16 The Embodied Mind of a New Robot Scientist" by Michael Levin Bottom-up Top-down
17. Talk to me about! • Hyperdimensional computing (chemistry, proteins!) • Algorithmic information theory / program synthesis • Fractional di ff erential equations, fractals, ergodicity… • Everything evolution! 17 Recommended reading!
18. Bioinformatics (IMCEGB) 9 December 2025 michiel.stock@ugent.be Computing for Bioscience Engineering Michiel Stock 18