OW
Ole Winther
cs.LGstat.MLcs.CVbioinformaticscs.CLcs.AIGene Expression ProfilingDeep LearningAlgorithmscs.IT
On Valency
published · living versionsW_yaar2ca2·v1 · currentpublished
BEND 2.0: Benchmarking the Capabilities Needed to Design DNA
with Andreas Bjerregaard, Rachael DeVries, Dionysia Danai Brilli, Panagiotis Antoniadis +4
1 version
Preprints & journals
183 papers in the corpus · 1965–2026RAGenome: Scaling Retrieval-Based Genomic Language Models to Long Contexts2610.11761v1 · Frederikke Isa Marin, Panagiotis Antoniadis, Dionysia Danai Brilli et al.2026 · 0 citationsarXiv
Learning Functional Subspaces for Neural Network Compression2609.40127v1 · Massimo Bini, Anders Christensen, Stephan Alaniz et al.2026 · 0 citationsarXiv
SpatialFormer: universal spatial representation learning from subcellular molecular to multicellular landscapes.42533054 · Wang, Jun, Huang, Yuanhua, Winther, Ole2026 · 2 citationsNature computational science. 2026;6(9):971-987
Introduction to Stochastic Differential Equations for Generative Machine Learning: A Variational Perspective2606.31576v1 · Ole Winther, Paul Jeha, Sander Dieleman et al.2026 · 0 citationsarXiv
DeepCDS: Ab initio coding sequence prediction in prokaryotic short nucleotide sequences10.64898/2026.06.17.732633v2 · Nielsen, L. S., Nielsen, H., Winther, O.2026 · 0 citationsbioRxiv
Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators2602.11216v2 · Panagiotis Antoniadis, Beatrice Pavesi, Simon Olsson et al.2026 · 1 citationarXiv
Few-shot Protein Fitness Prediction via In-context Learning and Test-time Training2512.02315v1 · Felix Teufel, Aaron W. Kollasch, Yining Huang et al.2025 · 0 citationsarXiv
Towards Self-Supervised Foundation Models for Critical Care Time Series2509.19885v1 · Katja Naasunnguaq Jagd, Rachael DeVries, Ole Winther2025 · 0 citationsarXiv
NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model.40830753 · Nielsen, Line Sandvad, Pedersen, Anders Gorm, Winther, Ole et al.2025 · 10 citationsBMC bioinformatics. 2025;26(1):216
Bi-Axial Transformers: Addressing the Increasing Complexity of EHR Classification2508.12418v1 · Rachael DeVries, Casper Christensen, Marie Lisandra Zepeda Mendoza et al.2025 · 0 citationsarXiv
Temporal Variational Implicit Neural Representations2506.01544v2 · Batuhan Koyuncu, Rachael DeVries, Ole Winther et al.2025 · 0 citationsarXiv
Predicting the subcellular location of prokaryotic proteins with DeepLocPro.39540738 · Moreno, Jaime, Nielsen, Henrik, Winther, Ole et al.2024 · 76 citationsBioinformatics (Oxford, England). 2024;40(12)
Generative Diffusion Models for Sequential Recommendations2410.19429v1 · Sharare Zolghadr, Ole Winther, Paul Jeha2024 · 0 citationsarXiv
Physician Level Assessment of Hirsute Women and of Their Eligibility for Laser Treatment With Deep Learning.39308029 · Thomsen, Kenneth, Jalaboi, Raluca, Winther, Ole et al.2025 · 2 citationsLasers in surgery and medicine. 2025;57(1):80-87
Geometry Fidelity for Spherical Images2407.18207v1 · Anders Christensen, Nooshin Mojab, Khushman Patel et al.2024 · 3 citationsarXiv
DeepLoc 2.1: multi-label membrane protein type prediction using protein language models.38587188 · Ødum, Marius Thrane, Teufel, Felix, Thumuluri, Vineet et al.2024 · 227 citationsNucleic acids research. 2024;52(W1):W215-W220
Can large language models reason about medical questions?38487804 · Liévin, Valentin, Hother, Christoffer Egeberg, Motzfeldt, Andreas Geert et al.2026 · 342 citationsPatterns (New York, N.Y.). 2024;5(3):100943
CURATOR: Building Robust Machine Learning Potentials for Atomistic Simulations Autonomously with Batch Active Learning10.26434/chemrxiv-2024-p5t3l · Xin Yang, Martin Hoffmann Petersen, Renata Sechi et al.2024 · 5 citationsChemRxiv
DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations.38390326 · Høie, Magnus Haraldson, Gade, Frederik Steensgaard, Johansen, Julie Maria et al.2024 · 149 citationsFrontiers in immunology. 2024;15:1322712
DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning.38317052 · Wang, Jun, Horlacher, Marc, Cheng, Lixin et al.2024 · 19 citationsBioinformatics (Oxford, England). 2024;40(2)
Coherent energy and force uncertainty in deep learning force fields2312.04174v1 · Peter Bj\orn J\orgensen, Jonas Busk, Ole Winther et al.2023 · 6 citationsarXiv
BEND: Benchmarking DNA Language Models on biologically meaningful tasks2311.12570v4 · Frederikke Isa Marin, Felix Teufel, Marc Horlacher et al.2023 · 31 citationsarXiv
DiffEnc: Variational Diffusion with a Learned Encoder2310.19789v2 · Beatrix M. G. Nielsen, Anders Christensen, Andrea Dittadi et al.2023 · 2 citationsInternational Conference on Representation Learning 2024 (ICLR 2024)
GraphPart: homology partitioning for biological sequence analysis.37850036 · Teufel, Felix, Gíslason, Magnús Halldór, Almagro Armenteros, José Juan et al.2023 · 41 citationsNAR genomics and bioinformatics. 2023;5(4):lqad088
DeepPeptide predicts cleaved peptides in proteins using conditional random fields.37812217 · Teufel, Felix, Refsgaard, Jan Christian, Madsen, Christian Toft et al.2023 · 14 citationsBioinformatics (Oxford, England). 2023;39(10)
Graph neural network interatomic potential ensembles with calibrated aleatoric and epistemic uncertainty on energy and forces.37724552 · Busk, Jonas, Schmidt, Mikkel N, Winther, Ole et al.2023 · 18 citationsPhysical chemistry chemical physics : PCCP. 2023;25(37):25828-25837
RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies.37466130 · Wang, Jun, Horlacher, Marc, Cheng, Lixin et al.2023 · 41 citationsBriefings in bioinformatics. 2023;24(5)
Image-free Classifier Injection for Zero-Shot Classification2308.10599v1 · Anders Christensen, Massimiliano Mancini, A. Sophia Koepke et al.2023 · 21 citationsarXiv
ThoughtSource: A central hub for large language model reasoning data.37553439 · Ott, Simon, Hebenstreit, Konstantin, Liévin, Valentin et al.2023 · 51 citationsScientific data. 2023;10(1):528
Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning.37542318 · Horlacher, Marc, Wagner, Nils, Moyon, Lambert et al.2023 · 33 citationsGenome biology. 2023;24(1):180
Addressing caveats of neural persistence with deep graph persistence2307.10865v3 · Leander Girrbach, Anders Christensen, Ole Winther et al.2023 · 0 citationsarXiv
Deep integrative models for large-scale human genomics.37224538 · Sigurdsson, Arnór I, Louloudis, Ioannis, Banasik, Karina et al.2023 · 36 citationsNucleic acids research. 2023;51(12):e67
FindZebra online search delving into rare disease case reports using natural language processing.37384616 · Liévin, Valentin, Hansen, Jonas Meinertz, Lund, Allan et al.2023 · 10 citationsPLOS digital health. 2023;2(6):e0000269
Molecular Representations in Machine-Learning-Based Prediction of PK Parameters for Insulin Analogs.37426277 · Einarson, Kasper A, Bendtsen, Kristian M, Li, Kang et al.2023 · 8 citationsACS omega. 2023;8(26):23566-23578
Implicit Transfer Operator Learning: Multiple Time-Resolution Surrogates for Molecular Dynamics2305.18046v2 · Mathias Schreiner, Ole Winther, Simon Olsson2023 · 7 citationsarXiv
Aligning Optimization Trajectories with Diffusion Models for Constrained Design Generation2305.18470v1 · Giorgio Giannone, Akash Srivastava, Ole Winther et al.2023 · 23 citationsarXiv
Deorphanizing Peptides Using Structure Prediction.37092865 · Teufel, Felix, Refsgaard, Jan C, Kasimova, Marina A et al.2023 · 26 citationsJournal of chemical information and modeling. 2023;63(9):2651-2655
Transfer learning identifies sequence determinants of cell-type specific regulatory element accessibility.37007588 · Salvatore, Marco, Horlacher, Marc, Marsico, Annalisa et al.2024 · 13 citationsNAR genomics and bioinformatics. 2023;5(2):lqad026
Dermatological Diagnosis Explainability Benchmark for Convolutional Neural Networks2302.12084v1 · Raluca Jalaboi, Ole Winther, Alfiia Galimzianova2023 · 1 citationarXiv
Explainable Image Quality Assessments in Teledermatological Photography.36735575 · Jalaboi, Raluca, Winther, Ole, Galimzianova, Alfiia2023 · 21 citationsTelemedicine journal and e-health : the official journal of the American Telemedicine Association. 2023;29(9):1342-1348
Unifying Molecular and Textual Representations via Multi-task Language Modelling2301.12586v2 · Dimitrios Christofidellis, Giorgio Giannone, Jannis Born et al.2023 · 26 citationsarXiv
Transition1x - a dataset for building generalizable reactive machine learning potentials.36566281 · Schreiner, Mathias, Bhowmik, Arghya, Vegge, Tejs et al.2022 · 124 citationsScientific data. 2022;9(1):779
MembraneFold: Visualising transmembrane protein structure and topology10.1101/2022.12.06.518085v1 · Gutierrez, S., Tyczynski, W. G., Boomsma, W. et al.2022 · 21 citationsbioRxiv
Reconstructing the exit wave of 2D materials in high-resolution transmission electron microscopy using machine learning.36401890 · Leth Larsen, Matthew Helmi, Dahl, Frederik, Hansen, Lars P et al.2022 · 14 citationsUltramicroscopy. 2023;243:113641
Improved prediction of blood biomarkers using deep learning10.1101/2022.10.27.22281549v1 · Sigurdsson, A. I., Ravn, K., Winther, O. et al.2022 · 6 citationsmedRxiv
Identifying endogenous peptide receptors bycombining structure and transmembrane topologyprediction10.1101/2022.10.28.514036v1 · Teufel, F., Refsgaard, J. C., Kasimova, M. A. et al.2022 · 3 citationsbioRxiv
DermX: An end-to-end framework for explainable automated dermatological diagnosis.36272237 · Jalaboi, Raluca, Faye, Frederik, Orbes-Arteaga, Mauricio et al.2022 · 25 citationsMedical image analysis. 2023;83:102647
Variational Open-Domain Question Answering2210.06345v2 · Valentin Li'evin, Andreas Geert Motzfeldt, Ida Riis Jensen et al.2022 · 3 citationsarXiv
NeuralNEB -- Neural Networks can find Reaction Paths Fast2207.09971v3 · Mathias Schreiner, Arghya Bhowmik, Tejs Vegge et al.2022 · 39 citationsarXiv
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models.35489069 · Thumuluri, Vineet, Almagro Armenteros, José Juan, Johansen, Alexander Rosenberg et al.2023 · 729 citationsNucleic acids research. 2022;50(W1):W228-W234
Career total: 348 works. 183 are in this corpus.Showing the 50 most recent.
Profile built from the corpus for this byline.
Author records are still filling in while the Hub is in alpha. If this is your page, you'll be able to claim it soon. Spot a mistake? Tell us.