Wouter Boomsma
@WouterBoomsmaDK
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Professor at the Department of Computer Science, University of Copenhagen
Copenhagen, Denmark
Joined August 2018
Great work by my former PhD student and PD, @ArtsMarloes! Good things come to those who wait :).
🐛➡️🦋 The first project I worked on during my PhD got published in @TmlrPub! It started off as a protein folding method and ended up as a neat way to incorporate 3D constraints into internal-coordinate modeling of protein ensembles. [1/6].
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Do you like machine learning, proteins and Copenhagen? Check out our open PhD position: Deadline Jan 22. Please RT.
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Code and jupyter notebooks are available: Thanks to @novonordiskfond, @VILLUMFONDEN, @ERC_Research and @nvidia for supporting this work. 5/5.
github.com
Contribute to MachineLearningLifeScience/meaningful-protein-representations development by creating an account on GitHub.
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This effect is quite striking when doing latent space interpolation, where we get much richer interpolants when following geodesics. 4/5
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We also consider how to define meaningful distances in the latent space of variational autoencoders. In short: Euclidean distances are problematic. More interpretable/robust distances can be obtained by calculating geodesics that take the geometry of the space into account. 3/5
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In the paper we investigate how modelling architecture choices affect learned representations of protein sequences. 2/5
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I'm very happy to share our work on representation learning of protein sequences, just out in @NatureComms. This was a joint project with Nicki Skafte Detlefsen and Søren Hauberg through the #MLLS center (. 1/5.
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Open PhD position on machine learning for protein engineering. Collaboration between @pengfei10, @deboramarks and myself - hosted @Novozymes. Great opportunity to work on non-trivial problems with non-trivial methods.
📢 Open PhD scholarship (ML for Protein Design) at Novozymes Enzyme Research. We build AI-Centric protein engineering framework to guide directed protein evolution. I am looking for people who have passions in machine learning to join us. Apply👉
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5 fully funded PhD positions available in the Center for Basic Machine Learning Research in Life Science (MLLS) in Copenhagen. Check out this great opportunity to do fundamental ML research on problems that matter. Deadline Aug 31. Please RT.
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Interested in fundamental research in machine learning - motivated by problems in biology? Our newly established MLLS center in Copenhagen has 6 open PhD positions. Deadline Feb 25. Please RT.
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Interested in doing a PhD with me @uni_copenhagen on #machinelearning for improving our understanding of #proteins? Open PhD call Get in touch if you would like to apply (and meet the eligibility requirements). Deadline Feb 13.
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PhD position available on developing Machine Learning methods for protein modelling. University of Copenhagen, Denmark. Deadline March 31.
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RT @MoAlQuraishi: Some thoughts on @DeepMindAI’s entry in #CASP13, after being there and chatting with the AlphaFold team and many others:….
moalquraishi.wordpress.com
Update: An updated version of this blogpost was published as a (peer-reviewed) Letter to the Editor at Bioinformatics, sans the “sociology” commentary. I just came back from CASP13, the…
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