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 biweekly seminar.
Watch our group video to get a glimpse of our activities.
Vacancies
No vacancies currently.
News
Marie Curie ITN grant awarded to ALPACA network
Recently, CWI and others were awarded an EU Marie Skłodowska-Curie Innovative Training Networks (ITN) consortium grant for ALPACA –'Algorithms for PAngenome Computational Analysis'. The research project involves a total funding of 3.67 million euros.
CWI designs algorithms for the improvement of Genetic Programming
Marco Virgolin of CWI’s Life Sciences & Health group has researched ways to improve the efficiency and effectiveness of Genetic Programming (GP). He defends his thesis ‘Design and Application of Gene-Pool Optimal Mixing Evolutionary Algorithms for Genetic Programming’ on Monday 6 June.
Peter Bosman awarded grant of 1M euros from NWO’s Open Technology Programme
Peter Bosman’s project proposal DAEDALUS (Distributed and Automated Evolutionary Deep Architecture Learning with Unprecedented Scalability) has been granted by NWO TTW in its Open Technology Programme.
€1.5 million European grant for mathematics consortium NETWORKS
The NETWORKS consortium can now continue growing thanks to a €1.5 million grant from the European Union’s Horizon2020 programme.
Current events
PhD Defense Stef Maree
- 2021-03-17T14:00:00+01:00
- 2021-03-17T15:00:00+01:00
PhD Defense Stef Maree
Start: 2021-03-17 14:00:00+01:00 End: 2021-03-17 15:00:00+01:00
Everyone is invited to attend the public defense of Stef of his PhD thesis:
Model-based evolutionary algorithms for finding diverse high-quality solutions - with an application in brachytherapy for prostate cancer
Promotor 1: Prof.dr. Peter A.N. Bosman, CWI, Amsterdam / TU Delft
Promotor 2: Prof.dr. C.R.N. Rasch, AMC / UvA
Copromotor 1: Dr. Tanja Alderliesten, LUMC, Leiden / UvA
Copromotor 2: Dr. A. Bel, AMC / UvA
- Email: Stef Maree
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iCal
Members
Associated Members
Publications
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Bjelde, A, Hackfeld, J, Disser, Y, Hansknecht, C, Lipmann, M, Meißner, J, … Stougie, L. (2021). Tight bounds for online TSP on the line. ACM Transactions on Algorithms, 17(1). doi:10.1145/3422362
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Jones, M.E.L, Kelk, S.M, & Stougie, L. (2021). Maximum parsimony distance on phylogenetic trees: A linear kernel and constant factor approximation algorithm. Journal of Computer and System Sciences, 117, 165–181. doi:10.1016/j.jcss.2020.10.003
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Alamro, H, Alzamel, M, Iliopoulos, C.S, Pissis, S, & Watts, S. (2021). IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences. BMC Bioinformatics, 22. doi:10.1186/s12859-021-03983-2
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Charalampopoulos, P, Kociumaka, T, Pissis, S, Radoszewski, J, Rytter, W, Straszyński, J, … Zuba, W. (2021). Circular pattern matching with k mismatches. Journal of Computer and System Sciences, 115, 73–85. doi:10.1016/j.jcss.2020.07.003
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Amir, A, Charalampopoulos, P, Pissis, S, & Radoszewski, J. (2020). Dynamic and Internal Longest Common Substring. Algorithmica, 82(12), 3707–3743. doi:10.1007/s00453-020-00744-0
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Maree, S.C, Alderliesten, T, & Bosman, P.A.N. (2020). Ensuring smoothly navigable approximation sets by Bézier curve parameterizations in evolutionary bi-objective optimization. In Lecture Notes in Computer Science/Lecture Notes in Artificial Intelligence. doi:10.1007/978-3-030-58115-2_15
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Deist, T.M, Maree, S.C, Alderliesten, T, & Bosman, P.A.N. (2020). Multi-objective optimization by uncrowded hypervolume gradient ascent. In Lecture Notes in Computer Science/Lecture Notes in Artificial Intelligence. doi:10.1007/978-3-030-58115-2_13
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Ayad, L.A.K, Dourou, A.-M, Arhondakis, S, & Pissis, S. (2020). IsoXpressor: A Tool to Assess Transcriptional Activity within Isochores. Genome biology and evolution, 12(9), 1573–1578. doi:10.1093/gbe/evaa171
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Alamro, H, Alzamel, M, Iliopoulos, C.S, Pissis, S, Sung, W.-K, & Watts, S. (2020). Efficient Identification of k -Closed Strings. International Journal of Foundations of Computer Science, 31(5), 595–610. doi:10.1142/S0129054120500288
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Thierens, D, & Bosman, P.A.N. (2020). Model-based evolutionary algorithms: GECCO 2020 tutorial. In GECCO 2020 Companion - Proceedings of the 2020 Genetic and Evolutionary Computation Conference Companion (pp. 590–619). doi:10.1145/3377929.3389868
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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Improving Childhood Cancer Care when Parents Cannot be There - Reducing Medical Traumatic Stress in Childhood Cancer Patients by Bonding with a Robot Companion ()
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Enhancing protein-drug binding prediction
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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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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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Technische Universiteit Delft
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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