Thomas Hamelryck

28 papers A* 3B 1C 2Journal 17Unranked 5
YearRankTypeTitle / Venue / Authors
2026 J jnl
Compact Circulant Layers with Spectral Priors.
CoRR
Joseph Margaryan, Thomas Hamelryck
2025 A* conf
ELBOing Stein: Variational Bayes with Stein Mixture Inference.
ICLR
Ola Rønning, Eric T. Nalisnick, Christophe Ley, Padhraic Smyth, Thomas Hamelryck
2025 J jnl
Unfolding AlphaFold's Bayesian Roots in Probability Kinematics.
CoRR
Thomas Hamelryck, Kanti V. Mardia
2024 — conf
AI Implementation and Capability Development in Manufacturing: An Action Research Case.
HICSS
Jon Eklof, Ulrika Snis, Thomas Hamelryck, Alexander Grima, Ola Rønning
2024 J jnl
Abstraction, mimesis and the evolution of deep learning.
AI Soc.
Jon Eklof, Thomas Hamelryck, Cadell Last, Alexander Grima, Ulrika Lundh Snis
2024 J jnl
ELBOing Stein: Variational Bayes with Stein Mixture Inference.
CoRR
Ola Rønning, Eric T. Nalisnick, Christophe Ley, Padhraic Smyth, Thomas Hamelryck
2022 A* conf
Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder.
ICLR
Lys Sanz Moreta, Ola Rønning, Ahmad Salim Al-Sibahi, Jotun Hein, Douglas L. Theobald, Thomas Hamelryck
2021 A* conf
Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model.
ICML
Christian B. Thygesen, Christian Skjødt Steenmans, Ahmad Salim Al-Sibahi, Lys Sanz Moreta, Anders Bundgård Sørensen, Thomas Hamelryck
2021 — conf
Time-efficient Bayesian Inference for a (Skewed) Von Mises Distribution on the Torus in a Deep Probabilistic Programming Language.
MFI
Ola Rønning, Christophe Ley, Kanti V. Mardia, Thomas Hamelryck
2020 C conf
Bayesian protein superposition using Hamiltonian Monte Carlo.
BIBE
Lys Sanz Moreta, Ahmad Salim Al-Sibahi, Thomas Hamelryck
2019 C conf
A Probabilistic Programming Approach to Protein Structure Superposition.
CIBCB
Lys Sanz Moreta, Ahmad Salim Al-Sibahi, Douglas L. Theobald, William Bullock, Basile Nicolas Rommes, Andreas Manoukian, Thomas Hamelryck
2019 J jnl
Langevin diffusions on the torus: estimation and applications.
Stat. Comput.
Eduardo García-Portugués, Michael Sørensen, Kanti V. Mardia, Thomas Hamelryck
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 — conf
An Efficient Parallel GPU Evaluation of Small Angle X-ray Scattering Profiles.
BIOINFORMATICS
Lubomir D. Antonov, Christian Andreetta, 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
2012 — conf
Parallel GPGPU Evaluation of Small Angle X-Ray Scattering Profiles in a Markov Chain Monte Carlo Framework.
BIOSTEC (Selected Papers)
Lubomir D. Antonov, Christian Andreetta, 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
2010 J jnl
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models.
BMC Bioinform.
Kasper Stovgaard, Christian Andreetta, Jesper Ferkinghoff-Borg, Thomas Hamelryck
2010 J jnl
Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networks.
BMC Bioinform.
Martin Paluszewski, Thomas Hamelryck
2009 J jnl
A Probabilistic Model of RNA Conformational Space.
PLoS Comput. Biol.
Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck
2009 J jnl
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Bioinform.
Peter J. A. Cock, Tiago Rodrigues Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon
2009 — conf
The Voronoi Diagram of Half-Balls and its Application to the Prediction of the 3D Structure of Proteins.
ISVD
Francois Anton, Thomas Hamelryck
2007 J jnl
An evolutionary method for learning HMM structure: prediction of protein secondary structure.
BMC Bioinform.
Kyoung-Jae Won, Thomas Hamelryck, Adam Prügel-Bennett, Anders Krogh
2006 J jnl
Reconstructing protein structure from solvent exposure using tabu search.
Algorithms Mol. Biol.
Martin Paluszewski, Thomas Hamelryck, Pawel Winter
2006 J jnl
Sampling Realistic Protein Conformations Using Local Structural Bias.
PLoS Comput. Biol.
Thomas Hamelryck, John T. Kent, Anders Krogh
2005 B conf
Evolving hidden Markov models for protein secondary structure prediction.
Congress on Evolutionary Computation
Kyoung-Jae Won, Thomas Hamelryck, Adam Prügel-Bennett, Anders Krogh
2005 J jnl
Full cyclic coordinate descent: solving the protein loop closure problem in C
BMC Bioinform.
Wouter Boomsma, Thomas Hamelryck
2003 J jnl
PDB file parser and structure class implemented in Python.
Bioinform.
Thomas Hamelryck, Bernard Manderick