Jaak Simm

According to our database, Jaak Simm authored at least 32 papers between 2008 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

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, Jaak Simm, Adam Arany, Nicolas Drizard, Rama Jabal, Arina Afanasyeva, Regis Loeb, Shlok Verma, Simon Harnqvist, Matthew Holmes, Balazs Pejo, Maria Telenczuk, Nicholas Holway, Arne Dieckmann, Nicola Rieke, Friederike Zumsande, Djork-Arné Clevert, Michael Krug, Christopher N. Luscombe, Darren V. S. Green, Peter Ertl, Peter Antal, David Marcus, Nicolas Do Huu, Hideyoshi Fuji, Stephen D. Pickett, Gergely Ács, Eric Boniface, Bernd Beck, Yax Sun, Arnaud Gohier, Friedrich Rippmann, Ola Engkvist, Andreas H. Göller, Yves Moreau, Mathieu N. Galtier, Ansgar Schuffenhauer, Hugo Ceulemans

J. Chem. Inf. Model., 2024

2023

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, Ritsuya Niwayama, Dieter Kopecky, Lewis H. Mervin, Prakash Chandra Rathi, Lukas Friedrich, András Formanek, Peter Antal, Jordon Rahaman, Adam Zalewski, Wouter Heyndrickx, Ezron Oluoch, Manuel Stößel, Michal Vanco, David Endico, Fabien Gelus, Thaïs de Boisfossé, Adrien Darbier, Ashley Nicollet, Matthieu Blottière, Maria Telenczuk, Van Tien Nguyen, Thibaud Martinez, Camille Boillet, Kelvin Moutet, Alexandre Picosson, Aurélien Gasser, Inal Djafar, Antoine Simon, Adam Arany, Jaak Simm, Yves Moreau, Ola Engkvist, Hugo Ceulemans, Camille Marini, Mathieu Galtier

Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023

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, Ritsuya Niwayama, Dieter Kopecky, Lewis H. Mervin, Prakash Chandra Rathi, Lukas Friedrich, András Formanek, Peter Antal, Jordon Rahaman, Adam Zalewski, Ezron Oluoch, Manuel Stößel, Michal Vanco, David Endico, Fabien Gelus, Thaïs de Boisfossé, Adrien Darbier, Ashley Nicollet, Matthieu Blottière, Maria Telenczuk, Van Tien Nguyen, Thibaud Martinez, Camille Boillet, Kelvin Moutet, Alexandre Picosson, Aurélien Gasser, Inal Djafar, Adam Arany, Jaak Simm, Yves Moreau, Ola Engkvist, Hugo Ceulemans, Camille Marini, Mathieu Galtier

CoRR, 2022

SparseChem: Fast and accurate machine learning model for small molecules.

Adam Arany, Jaak Simm, Martijn Oldenhof, Yves Moreau

CoRR, 2022

2021

Two-level preconditioning for Ridge Regression.

Joris Tavernier, Jaak Simm, Karl Meerbergen, Yves Moreau

Numer. Linear Algebra Appl., 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

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

Expressive Graph Informer Networks.

Jaak Simm, Adam Arany, Edward De Brouwer, Yves Moreau

Proceedings of the Machine Learning, Optimization, and Data Science, 2021

Latent Convergent Cross Mapping.

Edward De Brouwer, Adam Arany, Jaak Simm, Yves Moreau

Proceedings of the 9th International Conference on Learning Representations, 2021

Self-labeling of Fully Mediating Representations by Graph Alignment.

Martijn Oldenhof, Adam Arany, Yves Moreau, Jaak Simm

Proceedings of the Artificial Intelligence and Machine Learning, 2021

2020

ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning.

Martijn Oldenhof, Adam Arany, Yves Moreau, Jaak Simm

J. Chem. Inf. Model., 2020

Multilevel Gibbs Sampling for Bayesian Regression.

Joris Tavernier, Jaak Simm, Adam Arany, Karl Meerbergen, Yves Moreau

CoRR, 2020

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

Graph Informer Networks for Molecules.

Jaak Simm, Adam Arany, Edward De Brouwer, Yves Moreau

CoRR, 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

GRU-ODE-Bayes: Continuous Modeling of Sporadically-Observed Time Series.

Edward De Brouwer, Jaak Simm, Adam Arany, Yves Moreau

Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019

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, Wilfried Verachtert

Proceedings of the 31st Benelux Conference on Artificial Intelligence (BNAIC 2019) and the 28th Belgian Dutch Conference on Machine Learning (Benelearn 2019), 2019

2018

Deep Ensemble Tensor Factorization for Longitudinal Patient Trajectories Classification.

Edward De Brouwer, Jaak Simm, Adam Arany, Yves Moreau

CoRR, 2018

Multilevel preconditioning for Ridge Regression.

Joris Tavernier, Jaak Simm, Karl Meerbergen, Yves Moreau

CoRR, 2018

Towards practical privacy-preserving genome-wide association study.

Charlotte Bonte, Eleftheria Makri, Amin Ardeshirdavani, Jaak Simm, Yves Moreau, Frederik Vercauteren

BMC Bioinform., 2018

Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information.

Pooya Zakeri, Jaak Simm, Adam Arany, Sarah ElShal, Yves Moreau

Bioinform., 2018

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

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

Proceedings of the 27th IEEE International Workshop on Machine Learning for Signal Processing, 2017

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

Proceedings of the Bioinformatics and Biomedical Engineering, 2016

Topic modeling of biomedical text.

Sarah ElShal, Mithila Mathad, Jaak Simm, Jesse Davis, Yves Moreau

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

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

Easy Hyperparameter Search Using Optunity.

Marc Claesen, Jaak Simm, Dusan Popovic, Yves Moreau, Bart De Moor

CoRR, 2014

2012

Multi-Task Approach to Reinforcement Learning for Factored-State Markov Decision Problems.

Jaak Simm, Masashi Sugiyama, Hirotaka Hachiya

IEICE Trans. Inf. Syst., 2012

2011

Computationally Efficient Multi-task Learning with Least-squares Probabilistic Classifiers.

Jaak Simm, Masashi Sugiyama, Tsuyoshi Kato

IPSJ Trans. Comput. Vis. Appl., 2011

Improving the Accuracy of Least-Squares Probabilistic Classifiers.

Makoto Yamada, Masashi Sugiyama, Gordon Wichern, Jaak Simm

IEICE Trans. Inf. Syst., 2011

2010

Direct Importance Estimation with a Mixture of Probabilistic Principal Component Analyzers.

Makoto Yamada, Masashi Sugiyama, Gordon Wichern, Jaak Simm

IEICE Trans. Inf. Syst., 2010

2008

Knowledge communication in rate.ee, a web picture-rating community.

Anni Oja, Jaak Simm

Int. J. Web Based Communities, 2008