Juho Rousu

Publication Activity (10 Years)

Years Active: 1996-2024
Publications (10 Years): 36

Top Topics

Mass Spectrometry

Canonical Correlation Analysis

Kernel Learning

Top Venues

PLoS Comput. Biol.

Publications

Sándor Szedmák, Riikka Huusari, Tat Hong Duong Le, Juho Rousu
Scalable variable selection for two-view learning tasks with projection operators. Mach. Learn. 113 (6) (2024)
Robert Ebo Armah-Sekum, Sándor Szedmák, Juho Rousu
Protein function prediction through multi-view multi-label latent tensor reconstruction. BMC Bioinform. 25 (1) (2024)
Maryam Astero, Juho Rousu
Learning symmetry-aware atom mapping in chemical reactions through deep graph matching. J. Cheminformatics 16 (1) (2024)
Fatemeh Abbasi, Juho Rousu
New methods for drug synergy prediction: a mini-review. CoRR (2024)
Sándor Szedmák, Riikka Huusari, Tat Hong Duong Le, Juho Rousu
Scalable variable selection for two-view learning tasks with projection operators. CoRR (2023)
Luc Brogat-Motte, Rémi Flamary, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
Learning to Predict Graphs with Fused Gromov-Wasserstein Barycenters. CoRR (2022)
Luc Brogat-Motte, Alessandro Rudi, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
Vector-Valued Least-Squares Regression under Output Regularity Assumptions. CoRR (2022)
Maryam Sabzevari, Sándor Szedmák, Merja Penttilä, Paula Jouhten, Juho Rousu
Strain design optimization using reinforcement learning. PLoS Comput. Biol. 18 (6) (2022)
Luc Brogat-Motte, Rémi Flamary, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
Learning to Predict Graphs with Fused Gromov-Wasserstein Barycenters. ICML (2022)
Luc Brogat-Motte, Alessandro Rudi, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
Vector-Valued Least-Squares Regression under Output Regularity Assumptions. J. Mach. Learn. Res. 23 (2022)
Eric Bach, Emma Schymanski, Juho Rousu
Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data. Nat. Mac. Intell. 4 (12) (2022)
Grímur Hjörleifsson Eldjárn, Andrew Ramsay, Justin J. J. van der Hooft, Katherine R. Duncan, Sylvia Soldatou, Juho Rousu, Rónán Daly, Joe Wandy, Simon Rogers
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions. PLoS Comput. Biol. 17 (5) (2021)
Eric Bach, Simon Rogers, John Williamson, Juho Rousu
Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification. Bioinform. 37 (12) (2021)
Riikka Huusari, Sahely Bhadra, Cécile Capponi, Hachem Kadri, Juho Rousu
Learning primal-dual sparse kernel machines. CoRR (2021)
Tianduanyi Wang, Sándor Szedmák, Haishan Wang, Tero Aittokallio, Tapio Pahikkala, Anna Cichonska, Juho Rousu
Modeling drug combination effects via latent tensor reconstruction. Bioinform. 37 (Supplement) (2021)
Sándor Szedmák, Anna Cichonska, Heli Julkunen, Tapio Pahikkala, Juho Rousu
A Solution for Large Scale Nonlinear Regression with High Rank and Degree at Constant Memory Complexity via Latent Tensor Reconstruction. CoRR (2020)
Luc Brogat-Motte, Alessandro Rudi, Céline Brouard, Juho Rousu, Florence d'Alché-Buc
Learning Output Embeddings in Structured Prediction. CoRR (2020)
Viivi Uurtio, Sahely Bhadra, Juho Rousu
Large-Scale Sparse Kernel Canonical Correlation Analysis. ICML (2019)
Markus Heinonen, Maria Osmala, Henrik Mannerström, Janne Wallenius, Samuel Kaski, Juho Rousu, Harri Lähdesmäki
Bayesian metabolic flux analysis reveals intracellular flux couplings. Bioinform. 35 (14) (2019)
Anna Cichonska, Tapio Pahikkala, Sándor Szedmák, Heli Julkunen, Antti Airola, Markus Heinonen, Tero Aittokallio, Juho Rousu
Learning with multiple pairwise kernels for drug bioactivity prediction. Bioinform. 34 (13) (2018)
Viivi Uurtio, Sahely Bhadra, Juho Rousu
Sparse Non-linear CCA through Hilbert-Schmidt Independence Criterion. ICDM (2018)
Markus Heinonen, Maria Osmala, Henrik Mannerström, Janne Wallenius, Samuel Kaski, Juho Rousu, Harri Lähdesmäki
Bayesian Metabolic Flux Analysis reveals intracellular flux couplings. CoRR (2018)
Viivi Uurtio, João M. Monteiro, Jaz S. Kandola, John Shawe-Taylor, Delmiro Fernandez-Reyes, Juho Rousu
A Tutorial on Canonical Correlation Methods. ACM Comput. Surv. 50 (6) (2018)
Sahely Bhadra, Peter Blomberg, Sandra Castillo, Juho Rousu
Principal metabolic flux mode analysis. Bioinform. 34 (14) (2018)
Eric Bach, Sándor Szedmák, Céline Brouard, Sebastian Böcker, Juho Rousu
Liquid-chromatography retention order prediction for metabolite identification. Bioinform. 34 (17) (2018)
Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PLoS Comput. Biol. 13 (8) (2017)
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
Critical Assessment of Small Molecule Identification 2016: automated methods. J. Cheminformatics 9 (1) (2017)
Viivi Uurtio, João M. Monteiro, Jaz S. Kandola, John Shawe-Taylor, Delmiro Fernandez-Reyes, Juho Rousu
A Tutorial on Canonical Correlation Methods. CoRR (2017)
Céline Brouard, Eric Bach, Sebastian Böcker, Juho Rousu
Magnitude-Preserving Ranking for Structured Outputs. ACML (2017)
Sahely Bhadra, Samuel Kaski, Juho Rousu
Multi-view kernel completion. Mach. Learn. 106 (5) (2017)
Markus Heinonen, Henrik Mannerström, Juho Rousu, Samuel Kaski, Harri Lähdesmäki
Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo. AISTATS (2016)
Céline Brouard, Huibin Shen, Kai Dührkop, Florence d'Alché-Buc, Sebastian Böcker, Juho Rousu
Fast metabolite identification with Input Output Kernel Regression. Bioinform. 32 (12) (2016)
Sahely Bhadra, Samuel Kaski, Juho Rousu
Multi-view Kernel Completion. CoRR (2016)
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
metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis. Bioinform. 32 (13) (2016)
Aalt D. J. van Dijk, Harri Lähdesmäki, Dick de Ridder, Juho Rousu
Selected proceedings of Machine Learning in Systems Biology: MLSB 2016. BMC Bioinform. 17 (S-16) (2016)
Huibin Shen, Sándor Szedmák, Céline Brouard, Juho Rousu
Soft Kernel Target Alignment for Two-Stage Multiple Kernel Learning. DS (2016)
Hongyu Su, Juho Rousu
Multilabel classification through random graph ensembles. Mach. Learn. 99 (2) (2015)
Sebastian Böcker, Juho Rousu, Emma Schymanski
Computational Metabolomics (Dagstuhl Seminar 15492). Dagstuhl Reports 5 (11) (2015)
Viivi Uurtio, Malin Bomberg, Kristian Nybo, Merja Itävaara, Juho Rousu
Canonical Correlation Methods for Exploring Microbe-Environment Interactions in Deep Subsurface. Discovery Science (2015)
Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas
Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. PLoS Comput. Biol. 10 (2) (2014)
Hongyu Su, Aristides Gionis, Juho Rousu
Structured Prediction of Network Response. ICML (2014)
Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu
Metabolite identification through multiple kernel learning on fragmentation trees. Bioinform. 30 (12) (2014)
Mario Marchand, Hongyu Su, Emilie Morvant, Juho Rousu, John Shawe-Taylor
Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks. NIPS (2014)
Hongyu Su, Juho Rousu
Multilabel Classification throughout Random Graph Ensembles. CoRR (2013)
Juho Rousu, Daniel D. Agranoff, Olugbemiro Sodeinde, John Shawe-Taylor, Delmiro Fernandez-Reyes
Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria. PLoS Comput. Biol. 9 (4) (2013)
Hongyu Su, Juho Rousu
Multilabel Classification through Random Graph Ensembles. ACML (2013)
Markus Heinonen, Niko Välimäki, Veli Mäkinen, Juho Rousu
Efficient Path Kernels for Reaction Function Prediction. BIOINFORMATICS (2012)
Markus Heinonen, Huibin Shen, Nicola Zamboni, Juho Rousu
Metabolite identification and molecular fingerprint prediction through machine learning. Bioinform. 28 (18) (2012)
Hongyu Su, Juho Rousu
Multi-task Drug Bioactivity Classification with Graph Labeling Ensembles. PRIB (2011)
Esa Pitkänen, Mikko Arvas, Juho Rousu
Reconstructing Gapless Ancestral Metabolic Networks. BIOSTEC (Selected Papers) (2011)
Markus Heinonen, Sampsa Lappalainen, Taneli Mielikäinen, Juho Rousu
Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism. J. Comput. Biol. 18 (1) (2011)
Esa Pitkänen, Juho Rousu, Mikko Arvas
Minimum Mutation Algorithm for Gapless Metabolic Network Evolution. BIOINFORMATICS (2011)
Saso Dzeroski, Pierre Geurts, Juho Rousu
Preface. MLSB (2010)
Katja Astikainen, Esa Pitkänen, Juho Rousu, Liisa Holm, Sándor Szedmák
Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function. BIOINFORMATICS (2010)
Hongyu Su, Markus Heinonen, Juho Rousu
Structured Output Prediction of Anti-cancer Drug Activity. PRIB (2010)
Katja Astikainen, Liisa Holm, Esa Pitkänen, Sándor Szedmák, Juho Rousu
Structured Output Prediction of Novel Enzyme Function with Reaction Kernels. BIOSTEC (Selected Papers) (2010)
Esa Pitkänen, Paula Jouhten, Juho Rousu
Inferring branching pathways in genome-scale metabolic networks. BMC Syst. Biol. 3 (2009)
Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen
tracer experiments. BMC Bioinform. 9 (2008)
Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen
A Computational Method for Reconstructing Gapless Metabolic Networks. BIRD (2008)
Samuel Kaski, Juho Rousu, Esko Ukkonen
Probabilistic modeling and machine learning in structural and systems biology. BMC Bioinform. 8 (S-2) (2007)
Jorma Rissanen, Peter D. Grünwald, Jukka Heikkonen, Petri Myllymäki, Teemu Roos, Juho Rousu
Information Theoretic Methods for Bioinformatics. EURASIP J. Bioinform. Syst. Biol. 2007 (2007)
Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Esko Ukkonen
Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes. Bioinform. 22 (10) (2006)
Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Juho Rousu, Esko Ukkonen
Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation. Trans. Comp. Sys. Biology 6 (2006)
Tapio Elomaa, Jussi Kujala, Juho Rousu
Practical Approximation of Optimal Multivariate Discretization. ISMIS (2006)
Juho Rousu, Craig Saunders, Sándor Szedmák, John Shawe-Taylor
Kernel-Based Learning of Hierarchical Multilabel Classification Models. J. Mach. Learn. Res. 7 (2006)
Markus Heinonen, Ari Rantanen, Taneli Mielikäinen, Esa Pitkänen, Juha Kokkonen, Juho Rousu
Ab Initio Prediction of Molecular Fragments from Tandem Mass Spectrometry Data. German Conference on Bioinformatics (2006)
Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen
Finding Feasible Pathways in Metabolic Networks. Panhellenic Conference on Informatics (2005)
Tapio Elomaa, Jussi Kujala, Juho Rousu
Approximation Algorithms for Minimizing Empirical Error by Axis-Parallel Hyperplanes. ECML (2005)
Juho Rousu, John Shawe-Taylor
Efficient Computation of Gapped Substring Kernels on Large Alphabets. J. Mach. Learn. Res. 6 (2005)
Juho Rousu, Craig Saunders, Sándor Szedmák, John Shawe-Taylor
Learning hierarchical multi-category text classification models. ICML (2005)
Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Esko Ukkonen
Planning isotopomer measurements for estimation of metabolic fluxes. German Conference on Bioinformatics (2005)
Tapio Elomaa, Juho Rousu
Efficient Multisplitting Revisited: Optima-Preserving Elimination of Partition Candidates. Data Min. Knowl. Discov. 8 (2) (2004)
Juho Rousu, Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Katja Saarela, Esko Ukkonen
A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information. CMSB (2003)
Tapio Elomaa, Juho Rousu
On Decision Boundaries of Naïve Bayes in Continuous Domains. PKDD (2003)
Tapio Elomaa, Juho Rousu
Necessary and Sufficient Pre-processing in Numerical Range Discretization. Knowl. Inf. Syst. 5 (2) (2003)
Tapio Elomaa, Juho Rousu
Linear-Time Preprocessing in Optimal Numerical Range Partitioning. J. Intell. Inf. Syst. 18 (1) (2002)
Tapio Elomaa, Juho Rousu
Fast Minimum Training Error Discretization. ICML (2002)
Tapio Elomaa, Juho Rousu
On the Computational Complexity of Optimal Multisplitting. Fundam. Informaticae 47 (1-2) (2001)
Tapio Elomaa, Juho Rousu
Preprocessing Opportunities in Optimal Numerical Range Partitioning. ICDM (2001)
Juho Rousu, Robert J. Aarts
An integrated approach to bioprocess recipe design. Integr. Comput. Aided Eng. 8 (4) (2001)
Tapio Elomaa, Juho Rousu
Generalizing Boundary Points. AAAI/IAAI (2000)
Tapio Elomaa, Juho Rousu
On the Complexity of Optimal Multisplitting. ISMIS (2000)
Juho Rousu, Tapio Elomaa, Robert J. Aarts
Predicting the Speed of Beer Fermentation in Laboratory and Industrial Scale. IWANN (2) (1999)
Tapio Elomaa, Juho Rousu
General and Efficient Multisplitting of Numerical Attributes. Mach. Learn. 36 (3) (1999)
Tapio Elomaa, Juho Rousu
Speeding Up the Search for Optimal Partitions. PKDD (1999)
Tapio Elomaa, Juho Rousu
Postponing the Evaluation of Attributes with a High Number of Boundary Points. PKDD (1998)
Tapio Elomaa, Juho Rousu
On the Well-Behavedness of Important Attribute Evaluation Functions. SCAI (1997)
Tapio Elomaa, Juho Rousu
Well-Behaved Evaluation Functions for Numerical Attributes. ISMIS (1997)
Tapio Elomaa, Juho Rousu
Efficient Multisplitting on Numerical Data. PKDD (1997)
Robert J. Aarts, Juho Rousu
Qualitative Knowledge to Support Reasoning About Cases. ICCBR (1997)
Juho Rousu, Robert J. Aarts
Adaptation Cost as a Criterion for Solution Evaluation. EWCBR (1996)
Robert J. Aarts, Juho Rousu
Towards CBR for Bioprocess Planning. EWCBR (1996)