Juho Rousu

103 papers A* 8A 1B 2C 6Journal 60Unranked 25
YearRankTypeTitle / Venue / Authors
2025 J jnl
CSGL: chemical synthesis graph learning for molecule representation.
Bioinform.
Anchen Li, Elena Casiraghi, Juho Rousu
2025 J jnl
Efficient 3D kernels for molecular property prediction.
Bioinform.
Ankit, Sahely Bhadra, Juho Rousu
2025 J jnl
Enhancing atom mapping with multitask learning and symmetry-aware deep graph matching.
J. Cheminformatics
Maryam Astero, Juho Rousu
2025 J jnl
Extracting a COVID-19 signature from a multi-omic dataset.
Frontiers Bioinform.
Baptiste Bauvin, Thibaud Godon, Guillaume Bachelot, Claudia Carpentier, Riikka Huusaari, Maxime Déraspe, Juho Rousu, Caroline Quach, Jacques Corbeil
2025 J jnl
Scaling up drug combination surface prediction.
Briefings Bioinform.
Riikka Huusari, Tianduanyi Wang, Sándor Szedmák, Diogo Dias, Tero Aittokallio, Juho Rousu
2024 J jnl
Attention-based approach to predict drug-target interactions across seven target superfamilies.
Bioinform.
Aron Schulman, Juho Rousu, Tero Aittokallio, ZiaurRehman Tanoli
2024 J jnl
Chemical reaction enhanced graph learning for molecule representation.
Bioinform.
Anchen Li, Elena Casiraghi, Juho Rousu
2024 J jnl
Learning symmetry-aware atom mapping in chemical reactions through deep graph matching.
J. Cheminformatics
Maryam Astero, Juho Rousu
2024 A* conf
MassSpecGym: A benchmark for the discovery and identification of molecules.
NeurIPS
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, Liping 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
2024 J jnl
MassSpecGym: A benchmark for the discovery and identification of molecules.
CoRR
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
2024 J jnl
New methods for drug synergy prediction: a mini-review.
CoRR
Fatemeh Abbasi, Juho Rousu
2024 J jnl
Protein function prediction through multi-view multi-label latent tensor reconstruction.
BMC Bioinform.
Robert Ebo Armah-Sekum, Sándor Szedmák, Juho Rousu
2024 J jnl
Scalable variable selection for two-view learning tasks with projection operators.
Mach. Learn.
Sándor Szedmák, Riikka Huusari, Tat Hong Duong Le, Juho Rousu
2023 J jnl
Scalable variable selection for two-view learning tasks with projection operators.
CoRR
Sándor Szedmák, Riikka Huusari, Tat Hong Duong Le, Juho Rousu
2022 J jnl
Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data.
Nat. Mac. Intell.
Eric Bach, Emma Schymanski, Juho Rousu
2022 A* conf
Learning to Predict Graphs with Fused Gromov-Wasserstein Barycenters.
ICML
Luc Brogat-Motte, Rémi Flamary, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
2022 J jnl
Learning to Predict Graphs with Fused Gromov-Wasserstein Barycenters.
CoRR
Luc Brogat-Motte, Rémi Flamary, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
2022 J jnl
Strain design optimization using reinforcement learning.
PLoS Comput. Biol.
Maryam Sabzevari, Sándor Szedmák, Merja Penttilä, Paula Jouhten, Juho Rousu
2022 J jnl
Vector-Valued Least-Squares Regression under Output Regularity Assumptions.
CoRR
Luc Brogat-Motte, Alessandro Rudi, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
2022 J jnl
Vector-Valued Least-Squares Regression under Output Regularity Assumptions.
J. Mach. Learn. Res.
Luc Brogat-Motte, Alessandro Rudi, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
2021 J jnl
Learning primal-dual sparse kernel machines.
CoRR
Riikka Huusari, Sahely Bhadra, Cécile Capponi, Hachem Kadri, Juho Rousu
2021 J jnl
Modeling drug combination effects via latent tensor reconstruction.
Bioinform.
Tianduanyi Wang, Sándor Szedmák, Haishan Wang, Tero Aittokallio, Tapio Pahikkala, Anna Cichonska, Juho Rousu
2021 J jnl
Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification.
Bioinform.
Eric Bach, Simon Rogers, John Williamson, Juho Rousu
2021 J jnl
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.
PLoS Comput. Biol.
Grímur Hjörleifsson Eldjárn, Andrew Ramsay, Justin J. J. van der Hooft, Katherine R. Duncan, Sylvia Soldatou, Juho Rousu, Rónán Daly, Joe Wandy, Simon Rogers
2020 J jnl
A Solution for Large Scale Nonlinear Regression with High Rank and Degree at Constant Memory Complexity via Latent Tensor Reconstruction.
CoRR
Sándor Szedmák, Anna Cichonska, Heli Julkunen, Tapio Pahikkala, Juho Rousu
2020 J jnl
Learning Output Embeddings in Structured Prediction.
CoRR
Luc Brogat-Motte, Alessandro Rudi, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
2019 J jnl
Bayesian metabolic flux analysis reveals intracellular flux couplings.
Bioinform.
Markus Heinonen, Maria Osmala, Henrik Mannerström, Janne Wallenius, Samuel Kaski, Juho Rousu, Harri Lähdesmäki
2019 A* conf
Large-Scale Sparse Kernel Canonical Correlation Analysis.
ICML
Viivi Uurtio, Sahely Bhadra, Juho Rousu
2018 J jnl
A Tutorial on Canonical Correlation Methods.
ACM Comput. Surv.
Viivi Uurtio, João M. Monteiro, Jaz S. Kandola, John Shawe-Taylor, Delmiro Fernandez-Reyes, Juho Rousu
2018 J jnl
Bayesian Metabolic Flux Analysis reveals intracellular flux couplings.
CoRR
Markus Heinonen, Maria Osmala, Henrik Mannerström, Janne Wallenius, Samuel Kaski, Juho Rousu, Harri Lähdesmäki
2018 J jnl
Learning with multiple pairwise kernels for drug bioactivity prediction.
Bioinform.
Anna Cichonska, Tapio Pahikkala, Sándor Szedmák, Heli Julkunen, Antti Airola, Markus Heinonen, Tero Aittokallio, Juho Rousu
2018 J jnl
Liquid-chromatography retention order prediction for metabolite identification.
Bioinform.
Eric Bach, Sándor Szedmák, Céline Brouard, Sebastian Böcker, Juho Rousu
2018 J jnl
Principal metabolic flux mode analysis.
Bioinform.
Sahely Bhadra, Peter Blomberg, Sandra Castillo, Juho Rousu
2018 A* conf
Sparse Non-linear CCA through Hilbert-Schmidt Independence Criterion.
ICDM
Viivi Uurtio, Sahely Bhadra, Juho Rousu
2017 J jnl
A Tutorial on Canonical Correlation Methods.
CoRR
Viivi Uurtio, João M. Monteiro, Jaz S. Kandola, John Shawe-Taylor, Delmiro Fernandez-Reyes, Juho Rousu
2017 J jnl
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors.
PLoS Comput. Biol.
Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio
2017 J jnl
Critical Assessment of Small Molecule Identification 2016: automated methods.
J. Cheminformatics
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
2017 C conf
Magnitude-Preserving Ranking for Structured Outputs.
ACML
Céline Brouard, Eric Bach, Sebastian Böcker, Juho Rousu
2017 J jnl
Multi-view kernel completion.
Mach. Learn.
Sahely Bhadra, Samuel Kaski, Juho Rousu
2016 J jnl
Fast metabolite identification with Input Output Kernel Regression.
Bioinform.
Céline Brouard, Huibin Shen, Kai Dührkop, Florence d'Alché-Buc, Sebastian Böcker, Juho Rousu
2016 J jnl
Multi-view Kernel Completion.
CoRR
Sahely Bhadra, Samuel Kaski, Juho Rousu
2016 A conf
Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo.
AISTATS
Markus Heinonen, Henrik Mannerström, Juho Rousu, Samuel Kaski, Harri Lähdesmäki
2016 J jnl
Selected proceedings of Machine Learning in Systems Biology: MLSB 2016.
BMC Bioinform.
Aalt D. J. van Dijk, Harri Lähdesmäki, Dick de Ridder, Juho Rousu
2016 B conf
Soft Kernel Target Alignment for Two-Stage Multiple Kernel Learning.
DS
Huibin Shen, Sándor Szedmák, Céline Brouard, Juho Rousu
2016 J jnl
metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis.
Bioinform.
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
2015 B conf
Canonical Correlation Methods for Exploring Microbe-Environment Interactions in Deep Subsurface.
Discovery Science
Viivi Uurtio, Malin Bomberg, Kristian Nybo, Merja Itävaara, Juho Rousu
2015 J jnl
Computational Metabolomics (Dagstuhl Seminar 15492).
Dagstuhl Reports
Sebastian Böcker, Juho Rousu, Emma Schymanski
2015 J jnl
Multilabel classification through random graph ensembles.
Mach. Learn.
Hongyu Su, Juho Rousu
2014 J jnl
Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species.
PLoS Comput. Biol.
Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas
2014 J jnl
Metabolite identification through multiple kernel learning on fragmentation trees.
Bioinform.
Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu
2014 — conf
Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.
NIPS
Mario Marchand, Hongyu Su, Emilie Morvant, Juho Rousu, John Shawe-Taylor
2014 A* conf
Structured Prediction of Network Response.
ICML
Hongyu Su, Aristides Gionis, Juho Rousu
2013 J jnl
Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria.
PLoS Comput. Biol.
Juho Rousu, Daniel D. Agranoff, Olugbemiro Sodeinde, John Shawe-Taylor, Delmiro Fernandez-Reyes
2013 C conf
Multilabel Classification through Random Graph Ensembles.
ACML
Hongyu Su, Juho Rousu
2013 J jnl
Multilabel Classification throughout Random Graph Ensembles.
CoRR
Hongyu Su, Juho Rousu
2012 — conf
Efficient Path Kernels for Reaction Function Prediction.
BIOINFORMATICS
Markus Heinonen, Niko Välimäki, Veli Mäkinen, Juho Rousu
2012 J jnl
Metabolite identification and molecular fingerprint prediction through machine learning.
Bioinform.
Markus Heinonen, Huibin Shen, Nicola Zamboni, Juho Rousu
2011 J jnl
Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism.
J. Comput. Biol.
Markus Heinonen, Sampsa Lappalainen, Taneli Mielikäinen, Juho Rousu
2011 — conf
Minimum Mutation Algorithm for Gapless Metabolic Network Evolution.
BIOINFORMATICS
Esa Pitkänen, Juho Rousu, Mikko Arvas
2011 — conf
Multi-task Drug Bioactivity Classification with Graph Labeling Ensembles.
PRIB
Hongyu Su, Juho Rousu
2011 — conf
Reconstructing Gapless Ancestral Metabolic Networks.
BIOSTEC (Selected Papers)
Esa Pitkänen, Mikko Arvas, Juho Rousu
2010 — conf
Preface.
MLSB
Saso Dzeroski, Pierre Geurts, Juho Rousu
2010 — ed.
Proceedings of the third International Workshop on Machine Learning in Systems Biology, MLSB 2009, Ljubljana, Slovenia, September 5-6, 2009
MLSB
Saso Dzeroski, Pierre Geurts, Juho Rousu
2010 — conf
Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function.
BIOINFORMATICS
Katja Astikainen, Esa Pitkänen, Juho Rousu, Liisa Holm, Sándor Szedmák
2010 — conf
Structured Output Prediction of Anti-cancer Drug Activity.
PRIB
Hongyu Su, Markus Heinonen, Juho Rousu
2010 — conf
Structured Output Prediction of Novel Enzyme Function with Reaction Kernels.
BIOSTEC (Selected Papers)
Katja Astikainen, Liisa Holm, Esa Pitkänen, Sándor Szedmák, Juho Rousu
2009 J jnl
Inferring branching pathways in genome-scale metabolic networks.
BMC Syst. Biol.
Esa Pitkänen, Paula Jouhten, Juho Rousu
2008 — conf
A Computational Method for Reconstructing Gapless Metabolic Networks.
BIRD
Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen
2008 J jnl
An analytic and systematic framework for estimating metabolic flux ratios from
BMC Bioinform.
Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen
2008 — conf
Efficient Discriminative Training Method for Structured Predictions.
MLG@ICML
Huizhen Yu, Dimitri P. Bertsekas, Juho Rousu
2007 J jnl
Information Theoretic Methods for Bioinformatics.
EURASIP J. Bioinform. Syst. Biol.
Jorma Rissanen, Peter D. Grünwald, Jukka Heikkonen, Petri Myllymäki, Teemu Roos, Juho Rousu
2007 J jnl
Probabilistic modeling and machine learning in structural and systems biology.
BMC Bioinform.
Samuel Kaski, Juho Rousu, Esko Ukkonen
2006 — conf
Ab Initio Prediction of Molecular Fragments from Tandem Mass Spectrometry Data.
German Conference on Bioinformatics
Markus Heinonen, Ari Rantanen, Taneli Mielikäinen, Esa Pitkänen, Juha Kokkonen, Juho Rousu
2006 J jnl
Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation.
Trans. Comp. Sys. Biology
Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Juho Rousu, Esko Ukkonen
2006 J jnl
Kernel-Based Learning of Hierarchical Multilabel Classification Models.
J. Mach. Learn. Res.
Juho Rousu, Craig Saunders, Sándor Szedmák, John Shawe-Taylor
2006 J jnl
Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes.
Bioinform.
Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Esko Ukkonen
2006 C conf
Practical Approximation of Optimal Multivariate Discretization.
ISMIS
Tapio Elomaa, Jussi Kujala, Juho Rousu
2005 — conf
Approximation Algorithms for Minimizing Empirical Error by Axis-Parallel Hyperplanes.
ECML
Tapio Elomaa, Jussi Kujala, Juho Rousu
2005 J jnl
Efficient Computation of Gapped Substring Kernels on Large Alphabets.
J. Mach. Learn. Res.
Juho Rousu, John Shawe-Taylor
2005 — conf
Finding Feasible Pathways in Metabolic Networks.
Panhellenic Conference on Informatics
Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen
2005 A* conf
Learning hierarchical multi-category text classification models.
ICML
Juho Rousu, Craig Saunders, Sándor Szedmák, John Shawe-Taylor
2005 — conf
Planning isotopomer measurements for estimation of metabolic fluxes.
German Conference on Bioinformatics
Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Esko Ukkonen
2004 J jnl
Efficient Multisplitting Revisited: Optima-Preserving Elimination of Partition Candidates.
Data Min. Knowl. Discov.
Tapio Elomaa, Juho Rousu
2003 — conf
A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information.
CMSB
Juho Rousu, Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Katja Saarela, Esko Ukkonen
2003 J jnl
Necessary and Sufficient Pre-processing in Numerical Range Discretization.
Knowl. Inf. Syst.
Tapio Elomaa, Juho Rousu
2003 — conf
On Decision Boundaries of Naïve Bayes in Continuous Domains.
PKDD
Tapio Elomaa, Juho Rousu
2002 A* conf
Fast Minimum Training Error Discretization.
ICML
Tapio Elomaa, Juho Rousu
2002 J jnl
Linear-Time Preprocessing in Optimal Numerical Range Partitioning.
J. Intell. Inf. Syst.
Tapio Elomaa, Juho Rousu
2001 J jnl
An integrated approach to bioprocess recipe design.
Integr. Comput. Aided Eng.
Juho Rousu, Robert J. Aarts
2001 J jnl
On the Computational Complexity of Optimal Multisplitting.
Fundam. Informaticae
Tapio Elomaa, Juho Rousu
2001 A* conf
Preprocessing Opportunities in Optimal Numerical Range Partitioning.
ICDM
Tapio Elomaa, Juho Rousu
2000 — conf
Generalizing Boundary Points.
AAAI/IAAI
Tapio Elomaa, Juho Rousu
2000 C conf
On the Complexity of Optimal Multisplitting.
ISMIS
Tapio Elomaa, Juho Rousu
1999 J jnl
General and Efficient Multisplitting of Numerical Attributes.
Mach. Learn.
Tapio Elomaa, Juho Rousu
1999 — conf
Predicting the Speed of Beer Fermentation in Laboratory and Industrial Scale.
IWANN (2)
Juho Rousu, Tapio Elomaa, Robert J. Aarts
1999 — conf
Speeding Up the Search for Optimal Partitions.
PKDD
Tapio Elomaa, Juho Rousu
1998 — conf
Postponing the Evaluation of Attributes with a High Number of Boundary Points.
PKDD
Tapio Elomaa, Juho Rousu
1997 — conf
Efficient Multisplitting on Numerical Data.
PKDD
Tapio Elomaa, Juho Rousu
1997 — conf
On the Well-Behavedness of Important Attribute Evaluation Functions.
SCAI
Tapio Elomaa, Juho Rousu
1997 C conf
Qualitative Knowledge to Support Reasoning About Cases.
ICCBR
Robert J. Aarts, Juho Rousu
1997 C conf
Well-Behaved Evaluation Functions for Numerical Attributes.
ISMIS
Tapio Elomaa, Juho Rousu
1996 — conf
Adaptation Cost as a Criterion for Solution Evaluation.
EWCBR
Juho Rousu, Robert J. Aarts
1996 — conf
Towards CBR for Bioprocess Planning.
EWCBR
Robert J. Aarts, Juho Rousu