Knowledge communication in rate.ee, a web picture-rating community. - Anni Oja; Jaak Simm (Int. J. Web Based Communities, 2008)

Direct Importance Estimation with a Mixture of Probabilistic Principal Component Analyzers. - Makoto Yamada; Masashi Sugiyama; Gordon Wichern; Jaak Simm (IEICE Trans. Inf. Syst., 2010)

Improving the Accuracy of Least-Squares Probabilistic Classifiers. - Makoto Yamada; Masashi Sugiyama; Gordon Wichern; Jaak Simm (IEICE Trans. Inf. Syst., 2011)

Computationally Efficient Multi-task Learning with Least-squares Probabilistic Classifiers. - Jaak Simm; Masashi Sugiyama; Tsuyoshi Kato (IPSJ Trans. Comput. Vis. Appl., 2011)

Multi-Task Approach to Reinforcement Learning for Factored-State Markov Decision Problems. - Jaak Simm; Masashi Sugiyama; Hirotaka Hachiya (IEICE Trans. Inf. Syst., 2012)

Easy Hyperparameter Search Using Optunity. - Marc Claesen; Jaak Simm; Dusan Popovic; Yves Moreau; Bart De Moor (CoRR, 2014)

Tree-Based Ensemble Multi-Task Learning Method for Classification and Regression. - Jaak Simm; Ildefons Magrans de Abril; Masashi Sugiyama (IEICE Trans. Inf. Syst., 2014)

Topic modeling of biomedical text. - Sarah ElShal; Mithila Mathad; Jaak Simm; Jesse Davis; Yves Moreau (BIBM, 2016)

A Comprehensive Comparison of Two MEDLINE Annotators for Disease and Gene Linkage: Sometimes Less is More. - Sarah ElShal; Jaak Simm; Adam Arany; Pooya Zakeri; Jesse Davis; Yves Moreau (IWBBIO, 2016)

Macau: Scalable Bayesian factorization with high-dimensional side information using MCMC. - Jaak Simm; Adam Arany; Pooya Zakeri; Tom Haber; Jörg K. Wegner; Vladimir I. Chupakhin; Hugo Ceulemans; Yves Moreau (MLSP, 2017)

Privacy-Preserving Genome-Wide Association Study is Practical. - Charlotte Bonte; Eleftheria Makri; Amin Ardeshirdavani; Jaak Simm; Yves Moreau; Frederik Vercauteren (IACR Cryptol. ePrint Arch., 2017)

Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information. - Pooya Zakeri; Jaak Simm; Adam Arany; Sarah ElShal; Yves Moreau (Bioinform., 2018)

Towards practical privacy-preserving genome-wide association study. - Charlotte Bonte; Eleftheria Makri; Amin Ardeshirdavani; Jaak Simm; Yves Moreau; Frederik Vercauteren (BMC Bioinform., 2018)

Multilevel preconditioning for Ridge Regression. - Joris Tavernier; Jaak Simm; Karl Meerbergen; Yves Moreau (CoRR, 2018)

Deep Ensemble Tensor Factorization for Longitudinal Patient Trajectories Classification. - Edward De Brouwer; Jaak Simm; Adam Arany; Yves Moreau (CoRR, 2018)

SMURFF: A High-Performance Framework for Matrix Factorization Methods. - Tom Vander Aa; Imen Chakroun; Tom Ashby; Jaak Simm; Adam Arany; Yves Moreau; Thanh Le Van; José Felipe Golib Dzib; Jörg K. Wegner; Vladimir I. Chupakhin; Hugo Ceulemans; Roel Wuyts; et al. (BNAIC/BENELEARN, 2019)

GRU-ODE-Bayes: Continuous Modeling of Sporadically-Observed Time Series. - Edward De Brouwer; Jaak Simm; Adam Arany; Yves Moreau (NeurIPS, 2019)

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks. - Thomas Moerman; Sara Aibar Santos; Carmen Bravo González-Blas; Jaak Simm; Yves Moreau; Jan Aerts; Stein Aerts (Bioinform., 2019)

Graph Informer Networks for Molecules. - Jaak Simm; Adam Arany; Edward De Brouwer; Yves Moreau (CoRR, 2019)

Fast semi-supervised discriminant analysis for binary classification of large data sets. - Joris Tavernier; Jaak Simm; Karl Meerbergen; Jörg Kurt Wegner; Hugo Ceulemans; Yves Moreau (Pattern Recognit., 2019)

Multilevel Gibbs Sampling for Bayesian Regression. - Joris Tavernier; Jaak Simm; Adam Arany; Karl Meerbergen; Yves Moreau (CoRR, 2020)

ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning. - Martijn Oldenhof; Adam Arany; Yves Moreau; Jaak Simm (J. Chem. Inf. Model., 2020)

Self-labeling of Fully Mediating Representations by Graph Alignment. - Martijn Oldenhof; Adam Arany; Yves Moreau; Jaak Simm (BNAIC/BENELEARN, 2021)

Latent Convergent Cross Mapping. - Edward De Brouwer; Adam Arany; Jaak Simm; Yves Moreau (ICLR, 2021)

Expressive Graph Informer Networks. - Jaak Simm; Adam Arany; Edward De Brouwer; Yves Moreau (LOD, 2021)

A novel method for data fusion over entity-relation graphs and its application to protein-protein interaction prediction. - Daniele Raimondi; Jaak Simm; Adam Arany; Yves Moreau (Bioinform., 2021)

Splitting chemical structure data sets for federated privacy-preserving machine learning. - Jaak Simm; Lina Humbeck; Adam Zalewski; Noé Sturm; Wouter Heyndrickx; Yves Moreau; Bernd Beck; Ansgar Schuffenhauer (J. Cheminformatics, 2021)

Two-level preconditioning for Ridge Regression. - Joris Tavernier; Jaak Simm; Karl Meerbergen; Yves Moreau (Numer. Linear Algebra Appl., 2021)

SparseChem: Fast and accurate machine learning model for small molecules. - Adam Arany; Jaak Simm; Martijn Oldenhof; Yves Moreau (CoRR, 2022)

Industry-Scale Orchestrated Federated Learning for Drug Discovery. - Martijn Oldenhof; Gergely Ács; Balázs Pejó; Ansgar Schuffenhauer; Nicholas Holway; Noé Sturm; Arne Dieckmann; Oliver Fortmeier; Eric Boniface; Clément Mayer; Arnaud Gohier; Peter Schmidtke; et al. (CoRR, 2022)

Industry-Scale Orchestrated Federated Learning for Drug Discovery. - Martijn Oldenhof; Gergely Ács; Balázs Pejó; Ansgar Schuffenhauer; Nicholas Holway; Noé Sturm; Arne Dieckmann; Oliver Fortmeier; Eric Boniface; Clément Mayer; Arnaud Gohier; Peter Schmidtke; et al. (AAAI, 2023)

MELLODDY: Cross-pharma Federated Learning at Unprecedented Scale Unlocks Benefits in QSAR without Compromising Proprietary Information. - Wouter Heyndrickx; Lewis H. Mervin; Tobias Morawietz; Noé Sturm; Lukas Friedrich; Adam Zalewski; Anastasia Pentina; Lina Humbeck; Martijn Oldenhof; Ritsuya Niwayama; Peter Schmidtke; Nikolas Fechner; et al. (J. Chem. Inf. Model., 2024)

Continuous time and dynamic suicide attempt risk prediction with neural ordinary differential equations. - Yi-han Sheu; Jaak Simm; Bo Wang 034; Hyunjoon Lee; Jordan W. Smoller (npj Digit. Medicine, 2025)