Juho Rousu

According to our database, Juho Rousu authored at least 86 papers between 1996 and 2024.

Collaborative distances:

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

2024

Learning symmetry-aware atom mapping in chemical reactions through deep graph matching.

Maryam Astero, Juho Rousu

J. Cheminformatics, December, 2024

Protein function prediction through multi-view multi-label latent tensor reconstruction.

Robert Ebo Armah-Sekum, Sándor Szedmák, Juho Rousu

BMC Bioinform., December, 2024

Scalable variable selection for two-view learning tasks with projection operators.

Sándor Szedmák, Riikka Huusari, Tat Hong Duong Le, Juho Rousu

Mach. Learn., June, 2024

MassSpecGym: A benchmark for the discovery and identification of molecules.

Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Li-Ping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal

CoRR, 2024

New methods for drug synergy prediction: a mini-review.

Fatemeh Abbasi, Juho Rousu

CoRR, 2024

2022

Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data.

Eric Bach, Emma Schymanski, Juho Rousu

Nat. Mac. Intell., December, 2022

Strain design optimization using reinforcement learning.

Maryam Sabzevari, Sándor Szedmák, Merja Penttilä, Paula Jouhten, Juho Rousu

PLoS Comput. Biol., 2022

Vector-Valued Least-Squares Regression under Output Regularity Assumptions.

Luc Brogat-Motte, Alessandro Rudi, Céline Brouard, Juho Rousu, Florence d'Alché-Buc

J. Mach. Learn. Res., 2022

Learning to Predict Graphs with Fused Gromov-Wasserstein Barycenters.

Luc Brogat-Motte, Rémi Flamary, Céline Brouard, Juho Rousu, Florence d'Alché-Buc

Proceedings of the International Conference on Machine Learning, 2022

2021

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.

Grímur Hjörleifsson Eldjárn, Andrew Ramsay, Justin J. J. van der Hooft, Katherine R. Duncan, Sylvia Soldatou, Juho Rousu, Rónán Daly, Joe Wandy, Simon Rogers

PLoS Comput. Biol., 2021

Learning primal-dual sparse kernel machines.

Riikka Huusari, Sahely Bhadra, Cécile Capponi, Hachem Kadri, Juho Rousu

CoRR, 2021

Modeling drug combination effects via latent tensor reconstruction.

Tianduanyi Wang, Sándor Szedmák, Haishan Wang, Tero Aittokallio, Tapio Pahikkala, Anna Cichonska, Juho Rousu

Bioinform., 2021

Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification.

Eric Bach, Simon Rogers, John Williamson, Juho Rousu

Bioinform., 2021

2020

Learning Output Embeddings in Structured Prediction.

Luc Brogat-Motte, Alessandro Rudi, Céline Brouard, Juho Rousu, Florence d'Alché-Buc

CoRR, 2020

A Solution for Large Scale Nonlinear Regression with High Rank and Degree at Constant Memory Complexity via Latent Tensor Reconstruction.

Sándor Szedmák, Anna Cichonska, Heli Julkunen, Tapio Pahikkala, Juho Rousu

CoRR, 2020

2019

Bayesian metabolic flux analysis reveals intracellular flux couplings.

Markus Heinonen, Maria Osmala, Henrik Mannerström, Janne Wallenius, Samuel Kaski, Juho Rousu, Harri Lähdesmäki

Bioinform., 2019

Large-Scale Sparse Kernel Canonical Correlation Analysis.

Viivi Uurtio, Sahely Bhadra, Juho Rousu

Proceedings of the 36th International Conference on Machine Learning, 2019

2018

A Tutorial on Canonical Correlation Methods.

Viivi Uurtio, João M. Monteiro, Jaz S. Kandola, John Shawe-Taylor, Delmiro Fernandez-Reyes, Juho Rousu

ACM Comput. Surv., 2018

Learning with multiple pairwise kernels for drug bioactivity prediction.

Anna Cichonska, Tapio Pahikkala, Sándor Szedmák, Heli Julkunen, Antti Airola, Markus Heinonen, Tero Aittokallio, Juho Rousu

Bioinform., 2018

Principal metabolic flux mode analysis.

Sahely Bhadra, Peter Blomberg, Sandra Castillo, Juho Rousu

Bioinform., 2018

Liquid-chromatography retention order prediction for metabolite identification.

Eric Bach, Sándor Szedmák, Céline Brouard, Sebastian Böcker, Juho Rousu

Bioinform., 2018

Sparse Non-linear CCA through Hilbert-Schmidt Independence Criterion.

Viivi Uurtio, Sahely Bhadra, Juho Rousu

Proceedings of the IEEE International Conference on Data Mining, 2018

2017

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors.

Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio

PLoS Comput. Biol., 2017

Multi-view kernel completion.

Sahely Bhadra, Samuel Kaski, Juho Rousu

Mach. Learn., 2017

Critical Assessment of Small Molecule Identification 2016: automated methods.

Emma Schymanski, Christoph Ruttkies, Martin Krauss, Céline Brouard, Tobias Kind, Kai Dührkop, Felicity Allen, Arpana Vaniya, Dries Verdegem, Sebastian Böcker, Juho Rousu, Huibin Shen, Hiroshi Tsugawa, Tanvir Sajed, Oliver Fiehn, Bart Ghesquière, Steffen Neumann

J. Cheminformatics, 2017

Magnitude-Preserving Ranking for Structured Outputs.

Céline Brouard, Eric Bach, Sebastian Böcker, Juho Rousu

Proceedings of The 9th Asian Conference on Machine Learning, 2017

2016

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016.

Aalt D. J. van Dijk, Harri Lähdesmäki, Dick de Ridder, Juho Rousu

BMC Bioinform., 2016

metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis.

Anna Cichonska, Juho Rousu, Pekka Marttinen, Antti J. Kangas, Pasi Soininen, Terho Lehtimäki, Olli T. Raitakari, Marjo-Riitta Järvelin, Veikko Salomaa, Mika Ala-Korpela, Samuli Ripatti, Matti Pirinen

Bioinform., 2016

Fast metabolite identification with Input Output Kernel Regression.

Céline Brouard, Huibin Shen, Kai Dührkop, Florence d'Alché-Buc, Sebastian Böcker, Juho Rousu

Bioinform., 2016

Soft Kernel Target Alignment for Two-Stage Multiple Kernel Learning.

Huibin Shen, Sándor Szedmák, Céline Brouard, Juho Rousu

Proceedings of the Discovery Science - 19th International Conference, 2016

Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo.

Markus Heinonen, Henrik Mannerström, Juho Rousu, Samuel Kaski, Harri Lähdesmäki

Proceedings of the 19th International Conference on Artificial Intelligence and Statistics, 2016

2015

Multilabel classification through random graph ensembles.

Hongyu Su, Juho Rousu

Mach. Learn., 2015

Computational Metabolomics (Dagstuhl Seminar 15492).

Sebastian Böcker, Juho Rousu, Emma Schymanski

Dagstuhl Reports, 2015

Canonical Correlation Methods for Exploring Microbe-Environment Interactions in Deep Subsurface.

Viivi Uurtio, Malin Bomberg, Kristian Nybo, Merja Itävaara, Juho Rousu

Proceedings of the Discovery Science - 18th International Conference, 2015

2014

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species.

Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas

PLoS Comput. Biol., 2014

Metabolite identification through multiple kernel learning on fragmentation trees.

Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu

Bioinform., 2014

Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.

Mario Marchand, Hongyu Su, Emilie Morvant, Juho Rousu, John Shawe-Taylor

Proceedings of the Advances in Neural Information Processing Systems 27: Annual Conference on Neural Information Processing Systems 2014, 2014

Structured Prediction of Network Response.

Hongyu Su, Aristides Gionis, Juho Rousu

Proceedings of the 31th International Conference on Machine Learning, 2014

2013

Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria.

Juho Rousu, Daniel D. Agranoff, Olugbemiro Sodeinde, John Shawe-Taylor, Delmiro Fernandez-Reyes

PLoS Comput. Biol., 2013

Multilabel Classification throughout Random Graph Ensembles.

Hongyu Su, Juho Rousu

CoRR, 2013

2012

Metabolite identification and molecular fingerprint prediction through machine learning.

Markus Heinonen, Huibin Shen, Nicola Zamboni, Juho Rousu

Bioinform., 2012

Efficient Path Kernels for Reaction Function Prediction.

Markus Heinonen, Niko Välimäki, Veli Mäkinen, Juho Rousu

Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012

2011

Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism.

Markus Heinonen, Sampsa Lappalainen, Taneli Mielikäinen, Juho Rousu

J. Comput. Biol., 2011

Multi-task Drug Bioactivity Classification with Graph Labeling Ensembles.

Hongyu Su, Juho Rousu

Proceedings of the Pattern Recognition in Bioinformatics, 2011

Minimum Mutation Algorithm for Gapless Metabolic Network Evolution.

Esa Pitkänen, Juho Rousu, Mikko Arvas

Proceedings of the BIOINFORMATICS 2011, 2011

Reconstructing Gapless Ancestral Metabolic Networks.

Esa Pitkänen, Mikko Arvas, Juho Rousu

Proceedings of the Biomedical Engineering Systems and Technologies, 2011

2010

Preface.

Saso Dzeroski, Pierre Geurts, Juho Rousu

Proceedings of the third International Workshop on Machine Learning in Systems Biology, 2010

Structured Output Prediction of Anti-cancer Drug Activity.

Hongyu Su, Markus Heinonen, Juho Rousu

Proceedings of the Pattern Recognition in Bioinformatics, 2010

Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function.

Katja Astikainen, Esa Pitkänen, Juho Rousu, Liisa Holm, Sándor Szedmák

Proceedings of the BIOINFORMATICS 2010, 2010

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels.

Katja Astikainen, Liisa Holm, Esa Pitkänen, Sándor Szedmák, Juho Rousu

Proceedings of the Biomedical Engineering Systems and Technologies, 2010

2009

Inferring branching pathways in genome-scale metabolic networks.

Esa Pitkänen, Paula Jouhten, Juho Rousu

BMC Syst. Biol., 2009

2008

An analytic and systematic framework for estimating metabolic flux ratios from ¹³<i>C </i>tracer experiments.

Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen

BMC Bioinform., 2008

A Computational Method for Reconstructing Gapless Metabolic Networks.

Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen

Proceedings of the Bioinformatics Research and Development, 2008

2007

Information Theoretic Methods for Bioinformatics.

Jorma Rissanen, Peter D. Grünwald, Jukka Heikkonen, Petri Myllymäki, Teemu Roos, Juho Rousu

EURASIP J. Bioinform. Syst. Biol., 2007

Probabilistic modeling and machine learning in structural and systems biology.

Samuel Kaski, Juho Rousu, Esko Ukkonen

BMC Bioinform., 2007

2006

Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation.

Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Juho Rousu, Esko Ukkonen

Trans. Comp. Sys. Biology, 2006

Kernel-Based Learning of Hierarchical Multilabel Classification Models.

Juho Rousu, Craig Saunders, Sándor Szedmák, John Shawe-Taylor

J. Mach. Learn. Res., 2006

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes.

Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Esko Ukkonen

Bioinform., 2006

Practical Approximation of Optimal Multivariate Discretization.

Tapio Elomaa, Jussi Kujala, Juho Rousu

Proceedings of the Foundations of Intelligent Systems, 16th International Symposium, 2006

Ab Initio Prediction of Molecular Fragments from Tandem Mass Spectrometry Data.

Markus Heinonen, Ari Rantanen, Taneli Mielikäinen, Esa Pitkänen, Juha Kokkonen, Juho Rousu

Proceedings of the German Conference on Bioinformatics GCB 2006, 19.09. 2006, 2006

2005

Efficient Computation of Gapped Substring Kernels on Large Alphabets.

Juho Rousu, John Shawe-Taylor

J. Mach. Learn. Res., 2005

Finding Feasible Pathways in Metabolic Networks.

Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen

Proceedings of the Advances in Informatics, 2005

Learning hierarchical multi-category text classification models.

Juho Rousu, Craig Saunders, Sándor Szedmák, John Shawe-Taylor

Proceedings of the Machine Learning, 2005

Planning isotopomer measurements for estimation of metabolic fluxes.

Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Esko Ukkonen

Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, 2005

Approximation Algorithms for Minimizing Empirical Error by Axis-Parallel Hyperplanes.

Tapio Elomaa, Jussi Kujala, Juho Rousu

Proceedings of the Machine Learning: ECML 2005, 2005

2004

Efficient Multisplitting Revisited: Optima-Preserving Elimination of Partition Candidates.

Tapio Elomaa, Juho Rousu

Data Min. Knowl. Discov., 2004

2003

Necessary and Sufficient Pre-processing in Numerical Range Discretization.

Tapio Elomaa, Juho Rousu

Knowl. Inf. Syst., 2003

On Decision Boundaries of Naïve Bayes in Continuous Domains.

Tapio Elomaa, Juho Rousu

Proceedings of the Knowledge Discovery in Databases: PKDD 2003, 2003

A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information.

Juho Rousu, Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Katja Saarela, Esko Ukkonen

Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003

2002

Linear-Time Preprocessing in Optimal Numerical Range Partitioning.

Tapio Elomaa, Juho Rousu

J. Intell. Inf. Syst., 2002

Fast Minimum Training Error Discretization.

Tapio Elomaa, Juho Rousu

Proceedings of the Machine Learning, 2002

2001

An integrated approach to bioprocess recipe design.

Juho Rousu, Robert J. Aarts

Integr. Comput. Aided Eng., 2001

On the Computational Complexity of Optimal Multisplitting.

Tapio Elomaa, Juho Rousu

Fundam. Informaticae, 2001

Preprocessing Opportunities in Optimal Numerical Range Partitioning.

Tapio Elomaa, Juho Rousu

Proceedings of the 2001 IEEE International Conference on Data Mining, 29 November, 2001

2000

On the Complexity of Optimal Multisplitting.

Tapio Elomaa, Juho Rousu

Proceedings of the Foundations of Intelligent Systems, 12th International Symposium, 2000

Generalizing Boundary Points.

Tapio Elomaa, Juho Rousu

Proceedings of the Seventeenth National Conference on Artificial Intelligence and Twelfth Conference on on Innovative Applications of Artificial Intelligence, July 30, 2000

1999

General and Efficient Multisplitting of Numerical Attributes.

Tapio Elomaa, Juho Rousu

Mach. Learn., 1999

Speeding Up the Search for Optimal Partitions.

Tapio Elomaa, Juho Rousu

Proceedings of the Principles of Data Mining and Knowledge Discovery, 1999

Predicting the Speed of Beer Fermentation in Laboratory and Industrial Scale.

Juho Rousu, Tapio Elomaa, Robert J. Aarts

Proceedings of the Engineering Applications of Bio-Inspired Artificial Neural Networks, 1999

1998

Postponing the Evaluation of Attributes with a High Number of Boundary Points.

Tapio Elomaa, Juho Rousu

Proceedings of the Principles of Data Mining and Knowledge Discovery, 1998

1997

On the Well-Behavedness of Important Attribute Evaluation Functions.

Tapio Elomaa, Juho Rousu

Proceedings of the Sixth Scandinavian Conference on Artificial Intelligence, 1997

Efficient Multisplitting on Numerical Data.

Tapio Elomaa, Juho Rousu

Proceedings of the Principles of Data Mining and Knowledge Discovery, 1997

Well-Behaved Evaluation Functions for Numerical Attributes.

Tapio Elomaa, Juho Rousu

Proceedings of the Foundations of Intelligent Systems, 10th International Symposium, 1997

Qualitative Knowledge to Support Reasoning About Cases.

Robert J. Aarts, Juho Rousu

Proceedings of the Case-Based Reasoning Research and Development, 1997

1996

Adaptation Cost as a Criterion for Solution Evaluation.

Juho Rousu, Robert J. Aarts

Proceedings of the Advances in Case-Based Reasoning, Third European Workshop, 1996

Towards CBR for Bioprocess Planning.

Robert J. Aarts, Juho Rousu

Proceedings of the Advances in Case-Based Reasoning, Third European Workshop, 1996