Description
Leader of the group Life Sciences and Health: Leen Stougie.
The CWI Life Sciences and Health (LSH) group is a group of computer scientists and mathematicians whose research focus is on the analysis and design of models and algorithms as well as their direct application to important challenges in the LSH domain.
On the application side, our present team of researchers has expertise in, e.g., computational genomics, medical informatics, computational phylogenetics, and biological network analysis. On the methodological side, we come from different backgrounds, e.g., computational intelligence, computational data science, and operations research. Methodologically, we develop new theories, models, algorithms and decision support tools, for problems that arise mostly in collaboration with experimental biologists and medical experts. We actively collaborate in projects with academic hospitals, biological and biochemical research institutes, and industry. Click here for more information about our group structure.
The LSH group participates in the INRIA International team ERABLE.
Seminars: The LSH group organizes a monthly seminar.
Watch our group video to get a glimpse of our activities.
Vacancies
Scientific programmer on artificial intelligence prototype software for medicine
Centrum Wiskunde & Informatica (CWI) has a vacancy for a talented Scientific programmer, for the development of prototype software to bring evolutionary machine learning into clinical practice.
News
CWI develops unique method for genome-reconstruction of mutated viruses
Jasmijn Baaijens, PhD student in CWI’s Life Sciences and Health group, has developed a new computational tool that can reconstruct genomes of mutated versions of viruses like HIV, Zika and Ebola
Humies Silver award for Peter Bosman and colleagues
CWI researchers Peter Bosman and Hoang Luong, along with colleagues from Amsterdam UMC, have been awarded the Humies Silver award at the GECCO 2019 conference, for their efforts in the automated generation of treatment plans for prostate cancer using brachytherapy.
Three Veni grants for CWI researchers
The Dutch Research Council (NWO) has awarded a Veni grant to Georgios Amanatidis, Marleen Balvert and Christian Majenz. The grant provides them with the opportunity to further elaborate their research ideas during a period of three years.
KWF grant for Peter Bosman together with Amsterdam UMC
Peter Bosman of CWI's Life Sciences & Health group has been awarded a project by the Dutch Cancer Society (KWF) together with the Oncology department of Amsterdam UMC.
Members
- Matthias Bakker
- Peter Bosman
- Anton Bouter
- Aleksandr Chebykin
- Nick Cleintuar
- Joost Commandeur
- Arkadiy Dushatskiy
- Luc Everse
- Esteban Gabory
- Monika Grewal
- Arthur Guijt
- Damy Ha
- Joe Harrison
- Iwan Hoogenboom
- Nando Kartoredjo
- Jan Karel Lenstra
- Dazhuang Liu
- Anne Luesink
- Vincent Luo
- Joas Mulder
- Solon Pissis
- Renzo Scholman
- Evi Sijben
- Leen Stougie
- Michelle Sweering
- Marco Virgolin
- Wiktor Zuba
Associated Members
- Sanne Abeln
- Tanja Alderliesten
- Georgios Andreadis
- Giulia Bernardini
- Timo Deist
- Leah Dickhoff
- Ernst Harderwijk
- Xiongbin Kang
- Gerard Kindervater
- Geert Klop
- Evangelos Kostoulas
- Hoang Luong
- Adriënne Mendrik
- Sumanta Ray
- Alejandro Lopez Rincon
- Cedric Rodriguez
- Jelmen Roorda
- Alexander Schönhuth
- Dustin van Weersel
Publications
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Sijben, E.M.C, Alderliesten, T, & Bosman, P.A.N. (2022). Multi-modal multi-objective model-based genetic programming to find multiple diverse high-quality models. In GECCO 2022 - Proceedings of the 2022 Genetic and Evolutionary Computation Conference (pp. 440–448). doi:https://dl.acm.org/doi/abs/10.1145/3512290.3528850
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Dickhoff, L.R.M, Kerkhof, E.M, Deuzeman, H.H, Creutzberg, C.L, Alderliesten, T, & Bosman, P.A.N. (2022). Adaptive objective configuration in bi-objective evolutionary optimization for cervical cancer brachytherapy treatment planning. In GECCO 2022 - Proceedings of the 2022 Genetic and Evolutionary Computation Conference (pp. 1173–1181). doi:10.1145/3512290.3528822
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Bernardini, G, Chen, H, Loukides, G, Pissis, S, Stougie, L, & Sweering, M.J.M. (2022). Making de Bruijn graphs Eulerian. In Leibniz International Proceedings in Informatics, LIPIcs. doi:10.4230/LIPIcs.CPM.2022.12
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Loukides, G, & Pissis, S. (2022). All-pairs suffix/prefix in optimal time using Aho-Corasick space. Information Processing Letters. doi:10.1016/j.ipl.2022.106275
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Andreadis, G. (Georgios), Bosman, P.A.N, & Alderliesten, T. (2022). Multi-objective dual simplex-mesh based deformable image registration for 3D medical images – proof of concept. In Medical Imaging 2022: Image Processing. doi:10.1117/12.2605498
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Dushatskiy, A, Lowe, G, Bosman, P.A.N, & Alderliesten, T. (2022). Data variation-aware medical image segmentation. In Medical Imaging 2022: Image Processing. doi:10.1117/12.2608611
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Bernardini, G, Conte, A., Gourdel, G., Grossi, R, Loukides, G, Pisanti, N, … Sweering, M.J.M. (2022). Hide and mine in strings: Hardness, algorithms, and experiments. IEEE Transactions on Knowledge and Data Engineering. doi:10.1109/TKDE.2022.3158063
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Zhong, H, Loukides, G, & Pissis, S. (2022). Clustering sequence graphs. Data & Knowledge Engineering, 138, 101981.1–101981.21. doi:10.1016/j.datak.2022.101981
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Chen, H, Dong, C, Fan, L, Loukides, G, Pissis, S, & Stougie, L. (2021). Differentially Private string sanitization for frequency-based mining tasks. In Proceedings of the 21st IEEE International Conference on Data Mining, ICDM 2021 (pp. 41–50). doi:10.1109/ICDM51629.2021.00014
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Luo, X, Kang, X, & Schönhuth, A. (2021). phasebook: haplotype-aware de novo assembly of diploid genomes from long reads. Genome Biology, 22(1). doi:10.1186/s13059-021-02512-x
Software
VirtualLeaf: a modeling framework for plant tissue morphogenesis
VirtualLeaf is a computer modeling framework for the simulation of plant tissue morphogenesis, i.e., the biological development of an organism's shape
Current projects with external funding
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Statistical Models for Structural Genetic Variants in the Genome of the Netherlands
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Algorithms for PAngenome Computational Analysis (ALPACA)
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Fast, accurate, and insightful brachytherapy treatment planning for cervical cancer through artificial intelligence (Brachytherapy treatment)
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Distributed and Automated Evolutionary Deep Architecture Learning with Unprecedented Scalability (DAEDALUS)
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Evolutionary eXplainable Artificial Medical INtelligence Engine (EXAMINE)
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Fusible Evolutionary Deep Neural Network Mixture Learning from Distributed Data for Robust Medical Image Analysis (FEDMix)
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Multi-Objective Deformable Image Registration (MODIR) – An Innovative Synergy of Multi-Objective Optimization, Machine Learning, and Biomechanical Modeling for the Registration of Medical Images with (MODIR)
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Networks
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Networks COFUND postdocs
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Uitlegbare kunstmatige intelligentie (None)
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Optimization for and with Machine Learning (OPTIMAL)
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Pan-genome Graph Algorithms and Data Integration (PANGAIA)
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Transparent, Reliable and Unbiased Smart Tool for AI (TRUST-AI)
Related partners
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AMC Medical Research
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CNRS
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Elekta Limited
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European Molecular Biology Laboratory
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INRIA
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Universita di Pisa
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Xomnia
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Academisch Medisch Centrum
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Biomedical Imaging Group Rotterdam
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Erasmus Universiteit Rotterdam
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Geneton S.R.O.
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Heinrich-Heine-Universitaet Dusseldorf
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Illumina Cambridge
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Institut Pasteur
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Leids Universitair Mediach Centrum
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Univerzita Komenskeho V Bratislave
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Universiteit Leiden
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Universitaet Bielefeld
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Universita' Degli Studi di Milano-Bicocca
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Universiteit van Tilburg