Wouter Boomsma

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 17

Top Topics

Biologically Meaningful

Top Venues

PLoS Comput. Biol.

Publications

Miguel González Duque, Richard Michael, Simon Bartels, Yevgen Zainchkovskyy, Søren Hauberg, Wouter Boomsma
A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences. CoRR (2024)
Frederikke Isa Marin, Felix Teufel, Marc Horlacher, Dennis Madsen, Dennis Pultz, Ole Winther, Wouter Boomsma
BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks. ICLR (2024)
Marloes Arts, Jes Frellsen, Wouter Boomsma
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters. Trans. Mach. Learn. Res. 2024 (2024)
Richard Michael, Simon Bartels, Miguel González Duque, Yevgen Zainchkovskyy, Jes Frellsen, Søren Hauberg, Wouter Boomsma
A Continuous Relaxation for Discrete Bayesian Optimization. CoRR (2024)
Peter Mørch Groth, Mads Herbert Kerrn, Lars Olsen, Jesper Salomon, Wouter Boomsma
Kermut: Composite kernel regression for protein variant effects. CoRR (2024)
Simon Bartels, Wouter Boomsma, Jes Frellsen, Damien Garreau
Kernel-Matrix Determinant Estimates from stopped Cholesky Decomposition. J. Mach. Learn. Res. 24 (2023)
Anshuk Uppal, Kristoffer Stensbo-Smidt, Wouter Boomsma, Jes Frellsen
Implicit Variational Inference for High-Dimensional Posteriors. NeurIPS (2023)
Frederikke Isa Marin, Felix Teufel, Marc Horlacher, Dennis Madsen, Dennis Pultz, Ole Winther, Wouter Boomsma
BEND: Benchmarking DNA Language Models on biologically meaningful tasks. CoRR (2023)
Simon Bartels, Kristoffer Stensbo-Smidt, Pablo Moreno-Muñoz, Wouter Boomsma, Jes Frellsen, Søren Hauberg
Adaptive Cholesky Gaussian Processes. AISTATS (2023)
Marloes Arts, Jes Frellsen, Wouter Boomsma
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters. CoRR (2023)
Simon Bartels, Kristoffer Stensbo-Smidt, Pablo Moreno-Muñoz, Wouter Boomsma, Jes Frellsen, Søren Hauberg
Adaptive Cholesky Gaussian Processes. CoRR (2022)
Nicki Skafte Detlefsen, Søren Hauberg, Wouter Boomsma
What is a meaningful representation of protein sequences? CoRR (2020)
Anton Mallasto, Jes Frellsen, Wouter Boomsma, Aasa Feragen
(q, p)-Wasserstein GANs: Comparing Ground Metrics for Wasserstein GANs. CoRR (2019)
Maurice Weiler, Mario Geiger, Max Welling, Wouter Boomsma, Taco Cohen
3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data. CoRR (2018)
Maurice Weiler, Mario Geiger, Max Welling, Wouter Boomsma, Taco Cohen
3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data. NeurIPS (2018)
Wouter Boomsma, Jes Frellsen
Spherical convolutions and their application in molecular modelling. NIPS (2017)
Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff-Larsen
ENCORE: Software for Quantitative Ensemble Comparison. PLoS Comput. Biol. 11 (10) (2015)
Wouter Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen
Combining Experiments and Simulations Using the Maximum Entropy Principle. PLoS Comput. Biol. 10 (2) (2014)
Wouter Boomsma, Jes Frellsen, Tim Harder, Sandro Bottaro, Kristoffer E. Johansson, Pengfei Tian, Kasper Stovgaard, Christian Andreetta, Simon Olsson, Jan B. Valentin, Lubomir D. Antonov, Anders S. Christensen, Mikael Borg, Jan H. Jensen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Thomas Hamelryck
PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure. J. Comput. Chem. 34 (19) (2013)
Tim Harder, Mikael Borg, Wouter Boomsma, Peter Røgen, Thomas Hamelryck
Fast large-scale clustering of protein structures using Gauss integrals. Bioinform. 28 (4) (2012)
Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E. Johansson, Thomas Hamelryck
Beyond rotamers: a generative, probabilistic model of side chains in proteins. BMC Bioinform. 11 (2010)
Wouter Boomsma, Thomas Hamelryck
space. BMC Bioinform. 6 (2005)
René Thomsen, Wouter Boomsma
Multiple Sequence Alignment Using SAGA: Investigating the Effects of Operator Scheduling, Population Seeding, and Crossover Operators. EvoWorkshops (2004)
Wouter Boomsma
A Comparison of Adaptive Operator Scheduling Methods on the Traveling Salesman Problem. EvoCOP (2004)
Wouter Boomsma
Using adaptive operator scheduling on problem domains with an operator manifold: applications to the travelling salesman problem. IEEE Congress on Evolutionary Computation (2003)