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2020 – today
- 2024
[j8]Marloes Arts, Jes Frellsen, Wouter Boomsma:
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters. Trans. Mach. Learn. Res. 2024 (2024)- [c8]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 - [i10]Richard Michael, Simon Bartels, Miguel González Duque, Yevgen Zainchkovskyy, Jes Frellsen, Søren Hauberg, Wouter Boomsma:
A Continuous Relaxation for Discrete Bayesian Optimization. CoRR abs/2404.17452 (2024) - [i9]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 abs/2406.04739 (2024) - [i8]Peter Mørch Groth, Mads Herbert Kerrn, Lars Olsen, Jesper Salomon, Wouter Boomsma:
Kermut: Composite kernel regression for protein variant effects. CoRR abs/2407.00002 (2024) - 2023
- [j7]Simon Bartels, Wouter Boomsma, Jes Frellsen, Damien Garreau:
Kernel-Matrix Determinant Estimates from stopped Cholesky Decomposition. J. Mach. Learn. Res. 24: 71:1-71:57 (2023) - [c7]Simon Bartels, Kristoffer Stensbo-Smidt
, Pablo Moreno-Muñoz, Wouter Boomsma, Jes Frellsen, Søren Hauberg:
Adaptive Cholesky Gaussian Processes. AISTATS 2023: 408-452 - [c6]Anshuk Uppal, Kristoffer Stensbo-Smidt, Wouter Boomsma, Jes Frellsen:
Implicit Variational Inference for High-Dimensional Posteriors. NeurIPS 2023 - [i7]Marloes Arts, Jes Frellsen, Wouter Boomsma:
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters. CoRR abs/2302.13711 (2023) - [i6]Anshuk Uppal, Kristoffer Stensbo-Smidt, Wouter K. Boomsma, Jes Frellsen:
Implicit Variational Inference for High-Dimensional Posteriors. CoRR abs/2310.06643 (2023) - [i5]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 abs/2311.12570 (2023) - 2022
- [i4]Simon Bartels, Kristoffer Stensbo-Smidt, Pablo Moreno-Muñoz, Wouter Boomsma, Jes Frellsen, Søren Hauberg:
Adaptive Cholesky Gaussian Processes. CoRR abs/2202.10769 (2022) - 2020
- [i3]Nicki Skafte Detlefsen, Søren Hauberg, Wouter Boomsma:
What is a meaningful representation of protein sequences? CoRR abs/2012.02679 (2020)
2010 – 2019
- 2019
- [i2]Anton Mallasto, Jes Frellsen, Wouter Boomsma, Aasa Feragen:
(q, p)-Wasserstein GANs: Comparing Ground Metrics for Wasserstein GANs. CoRR abs/1902.03642 (2019) - 2018
- [c5]Maurice Weiler, Mario Geiger, Max Welling, Wouter Boomsma, Taco Cohen:
3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data. NeurIPS 2018: 10402-10413 - [i1]Maurice Weiler, Mario Geiger, Max Welling, Wouter Boomsma, Taco Cohen:
3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data. CoRR abs/1807.02547 (2018) - 2017
- [c4]Wouter Boomsma, Jes Frellsen:
Spherical convolutions and their application in molecular modelling. NIPS 2017: 3433-3443 - 2015
- [j6]Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff-Larsen:
ENCORE: Software for Quantitative Ensemble Comparison. PLoS Comput. Biol. 11(10) (2015) - 2014
- [j5]Wouter Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen:
Combining Experiments and Simulations Using the Maximum Entropy Principle. PLoS Comput. Biol. 10(2) (2014) - 2013
- [j4]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): 1697-1705 (2013) - 2012
- [j3]Tim Harder, Mikael Borg, Wouter Boomsma, Peter Røgen, Thomas Hamelryck:
Fast large-scale clustering of protein structures using Gauss integrals. Bioinform. 28(4): 510-515 (2012) - 2010
- [j2]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: 306 (2010)
2000 – 2009
- 2005
- [j1]Wouter Boomsma, Thomas Hamelryck:
Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. BMC Bioinform. 6: 159 (2005) - 2004
- [c3]Wouter Boomsma:
A Comparison of Adaptive Operator Scheduling Methods on the Traveling Salesman Problem. EvoCOP 2004: 31-40 - [c2]René Thomsen, Wouter Boomsma:
Multiple Sequence Alignment Using SAGA: Investigating the Effects of Operator Scheduling, Population Seeding, and Crossover Operators. EvoWorkshops 2004: 113-122 - 2003
- [c1]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: 1274-1279
Coauthor Index
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