Wouter Boomsma

29 papers A* 5A 1B 2Journal 19Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
Zero-shot protein stability prediction by inverse folding models: a free energy interpretation.
CoRR
Jes Frellsen, Maher M. Kassem, Tone Bengtsen, Lars Olsen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Wouter Boomsma
2024 J jnl
A Continuous Relaxation for Discrete Bayesian Optimization.
CoRR
Richard Michael, Simon Bartels, Miguel González Duque, Yevgen Zainchkovskyy, Jes Frellsen, Søren Hauberg, Wouter Boomsma
2024 A* conf
A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences.
NeurIPS
Miguel González Duque, Richard Michael, Simon Bartels, Yevgen Zainchkovskyy, Søren Hauberg, Wouter Boomsma
2024 J jnl
A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences.
CoRR
Miguel González Duque, Richard Michael, Simon Bartels, Yevgen Zainchkovskyy, Søren Hauberg, Wouter Boomsma
2024 J jnl
A systematic analysis of regression models for protein engineering.
PLoS Comput. Biol.
Richard Michael, Jacob Kæstel-Hansen, Peter Mørch Groth, Simon Bartels, Jesper Salomon, Pengfei Tian, Nikos S. Hatzakis, Wouter Boomsma
2024 A* conf
BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks.
ICLR
Frederikke Isa Marin, Felix Teufel, Marc Horlacher, Dennis Madsen, Dennis Pultz, Ole Winther, Wouter Boomsma
2024 J jnl
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters.
Trans. Mach. Learn. Res.
Marloes Arts, Jes Frellsen, Wouter Boomsma
2024 A* conf
Kermut: Composite kernel regression for protein variant effects.
NeurIPS
Peter Mørch Groth, Mads Herbert Kerrn, Lars Olsen, Jesper Salomon, Wouter Boomsma
2024 J jnl
Kermut: Composite kernel regression for protein variant effects.
CoRR
Peter Mørch Groth, Mads Herbert Kerrn, Lars Olsen, Jesper Salomon, Wouter Boomsma
2023 A conf
Adaptive Cholesky Gaussian Processes.
AISTATS
Simon Bartels, Kristoffer Stensbo-Smidt, Pablo Moreno-Muñoz, Wouter Boomsma, Jes Frellsen, Søren Hauberg
2023 J jnl
BEND: Benchmarking DNA Language Models on biologically meaningful tasks.
CoRR
Frederikke Isa Marin, Felix Teufel, Marc Horlacher, Dennis Madsen, Dennis Pultz, Ole Winther, Wouter Boomsma
2023 A* conf
Implicit Variational Inference for High-Dimensional Posteriors.
NeurIPS
Anshuk Uppal, Kristoffer Stensbo-Smidt, Wouter Boomsma, Jes Frellsen
2023 J jnl
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters.
CoRR
Marloes Arts, Jes Frellsen, Wouter Boomsma
2023 J jnl
Kernel-Matrix Determinant Estimates from stopped Cholesky Decomposition.
J. Mach. Learn. Res.
Simon Bartels, Wouter Boomsma, Jes Frellsen, Damien Garreau
2022 J jnl
Adaptive Cholesky Gaussian Processes.
CoRR
Simon Bartels, Kristoffer Stensbo-Smidt, Pablo Moreno-Muñoz, Wouter Boomsma, Jes Frellsen, Søren Hauberg
2020 J jnl
What is a meaningful representation of protein sequences?
CoRR
Nicki Skafte Detlefsen, Søren Hauberg, Wouter Boomsma
2019 J jnl
(q, p)-Wasserstein GANs: Comparing Ground Metrics for Wasserstein GANs.
CoRR
Anton Mallasto, Jes Frellsen, Wouter Boomsma, Aasa Feragen
2018 A* conf
3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data.
NeurIPS
Maurice Weiler, Mario Geiger, Max Welling, Wouter Boomsma, Taco Cohen
2018 J jnl
3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data.
CoRR
Maurice Weiler, Mario Geiger, Max Welling, Wouter Boomsma, Taco Cohen
2017 — conf
Spherical convolutions and their application in molecular modelling.
NIPS
Wouter Boomsma, Jes Frellsen
2015 J jnl
ENCORE: Software for Quantitative Ensemble Comparison.
PLoS Comput. Biol.
Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff-Larsen
2014 J jnl
Combining Experiments and Simulations Using the Maximum Entropy Principle.
PLoS Comput. Biol.
Wouter Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen
2013 J jnl
PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure.
J. Comput. Chem.
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
2012 J jnl
Fast large-scale clustering of protein structures using Gauss integrals.
Bioinform.
Tim Harder, Mikael Borg, Wouter Boomsma, Peter Røgen, Thomas Hamelryck
2010 J jnl
Beyond rotamers: a generative, probabilistic model of side chains in proteins.
BMC Bioinform.
Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E. Johansson, Thomas Hamelryck
2005 J jnl
Full cyclic coordinate descent: solving the protein loop closure problem in C
BMC Bioinform.
Wouter Boomsma, Thomas Hamelryck
2004 B conf
A Comparison of Adaptive Operator Scheduling Methods on the Traveling Salesman Problem.
EvoCOP
Wouter Boomsma
2004 — conf
Multiple Sequence Alignment Using SAGA: Investigating the Effects of Operator Scheduling, Population Seeding, and Crossover Operators.
EvoWorkshops
René Thomsen, Wouter Boomsma
2003 B conf
Using adaptive operator scheduling on problem domains with an operator manifold: applications to the travelling salesman problem.
IEEE Congress on Evolutionary Computation
Wouter Boomsma