Juho Rousu

发表

On the Well-Behavedness of Important Attribute Evaluation Functions

Tapio Elomaa, Juho Rousu, Juho Rousu, 1998, SCAI.

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

Juho Rousu, Anna Cichonska, Balaguru Ravikumar, 2017, PLoS Comput. Biol..

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

Juho Rousu, John Shawe-Taylor, Mario Marchand, 2014, NIPS.

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

Juho Rousu, Anna Cichonska, Tapio Pahikkala, 2020, ArXiv.

Mass Spectrometry Informatics in Systems Biology

Juho Rousu, Masanori Arita, Markus Heinonen, 2010 .

Information Theoretic Methods for Bioinformatics

Jukka Heikkonen, Juho Rousu, Jorma Rissanen, 2007, EURASIP J. Bioinform. Syst. Biol..

A Computational Method for Reconstructing Gapless Metabolic Networks

Juho Rousu, Esko Ukkonen, Esa Pitkänen, 2008, BIRD.

Probabilistic modeling and machine learning in structural and systems biology

Juho Rousu, Samuel Kaski, Esko Ukkonen, 2007, BMC Bioinformatics.

Applications of evaluation function convexity in data mining algorithms

Tapio Elomaa, Juho Rousu, Juho Rousu, 2000 .

Identification of drug candidates and repurposing opportunities through compound–target interaction networks

Juho Rousu, Anna Cichonska, Tero Aittokallio, 2015, Expert opinion on drug discovery.

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

Juho Rousu, John Shawe-Taylor, Delmiro Fernandez-Reyes, 2013, PLoS Comput. Biol..

An integrated approach to bioprocess recipe design

Juho Rousu, Robert J. Aarts, 2001, Integr. Comput. Aided Eng..

BMC Systems Biology BioMed Central Methodology article

Juho Rousu, Esa Pitkänen, Paula Jouhten, 2009 .

Efficient Multisplitting on Numerical Data

Tapio Elomaa, Juho Rousu, 1997, PKDD.

Efficient Path Kernels for Reaction Function Prediction

Juho Rousu, Veli Mäkinen, Niko Välimäki, 2012, BIOINFORMATICS.

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

Juho Rousu, Aalt D. J. van Dijk, Dick de Ridder, 2016, BMC Bioinformatics.

Towards structured output prediction of enzyme function

Juho Rousu, Liisa Holm, Sandor Szedmak, 2008, BMC proceedings.

Analysis of Fluxomic Experiments with Principal Metabolic Flux Mode Analysis.

Juho Rousu, Sahely Bhadra, 2018, Methods in molecular biology.

Computational Metabolomics (Dagstuhl Seminar 15492)

Juho Rousu, Emma Schymanski, Sebastian Böcker, 2015, Dagstuhl Reports.

Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism

Juho Rousu, Taneli Mielikäinen, Markus Heinonen, 2011, J. Comput. Biol..

Magnitude-Preserving Ranking for Structured Outputs

Juho Rousu, Eric Bach, Sebastian Böcker, 2017, ACML.

Well-Behaved Evaluation Functions for Numerical Attributes

Tapio Elomaa, Juho Rousu, 1997, ISMIS.

Metabolite identification and molecular fingerprint prediction through machine learning

Juho Rousu, Markus Heinonen, Nicola Zamboni, 2012, Bioinform..

Finding Feasible Pathways in Metabolic Networks

Juho Rousu, Esko Ukkonen, Esa Pitkänen, 2005, Panhellenic Conference on Informatics.

Novel computational tools in bakery process data analysis: a comparative study

Juho Rousu, Marjaana Suutarinen, Petri Kontkanen, 2003 .

5th Asian Conference on Machine Learning, Canberra, Australia, November 11 - November 15, 2013

Juho Rousu, Hongyu Su, 2013 .

Multi-view kernel completion

Juho Rousu, Samuel Kaski, Sahely Bhadra, 2016, Machine Learning.

Learning Hierarchy via Embedding at Two-class Complexity

Juho Rousu, John Shawe-Taylor, Craig Saunders, 2005 .

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

Juho Rousu, Justin J. J. van der Hooft, Simon Rogers, 2020, bioRxiv.

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

Juho Rousu, Sebastian Böcker, Markus Fleischauer, 2020, Nature Biotechnology.

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

Juho Rousu, Liisa Holm, Jian Hou, 2014, PLoS Comput. Biol..

Improved Small Molecule Identification through Learning Combinations of Kernel Regression Models

Juho Rousu, Céline Brouard, Antoine Bassé, 2019, Metabolites.

Approximation Algorithms for Minimizing Empirical Error by Axis-Parallel Hyperplanes

Tapio Elomaa, Juho Rousu, Jussi Kujala, 2005, ECML.

Liquid‐chromatography retention order prediction for metabolite identification

Juho Rousu, Eric Bach, Sándor Szedmák, 2018, Bioinform..

Flow analysis of metabolite fragments for ux estimation

Juho Rousu, Esko Ukkonen, Esa Pitkänen, 2005 .

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

Matti Pirinen, Juho Rousu, Anna Cichonska, 2015 .

A Neural Network Tool for Brewery Fermentations

Juho Rousu, Jermu Pollanen, Jukka Kronlof, 2001 .

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

Matti Pirinen, Juho Rousu, Anna Cichonska, 2015, bioRxiv.

Efficient Range Partitioning in Classification Learning

Juho Rousu, Juho Rousu, 2001 .

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

Juho Rousu, Esko Ukkonen, Esa Pitkänen, 2006, Trans. Comp. Sys. Biology.

Minimum Mutation Algorithm for Gapless Metabolic Network Evolution

Juho Rousu, Mikko Arvas, Esa Pitkänen, 2011, BIOINFORMATICS.

Reconstructing Gapless Ancestral Metabolic Networks

Juho Rousu, Mikko Arvas, Esa Pitkänen, 2011, BIOSTEC.

MSiB Mass Spectrometry Informatics in Systems Biology, Abstracts of the Workshop, October 28-29, 2010, Helsinki, Finland

Juho Rousu, Masanori Arita, Markus Heinonen, 2010 .

A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information

Juho Rousu, Esko Ukkonen, Esa Pitkänen, 2003, CMSB.

Machine learning in systems biology: proceedings of The Third International Workshop, September 5-6, 2009, Ljubljana, Slovenia

Juho Rousu, Pierre Geurts, Saso Dzeroskig, 2009 .

On Decision Boundaries of Naïve Bayes in Continuous Domains

Tapio Elomaa, Juho Rousu, Juho Rousu, 2003, PKDD.

Finding Optimal Multi-Splits for Numerical Attributes in Decision Tree Learning

Tapio Elomaa, Juho Rousu, Juho Rousu, 1996 .

Structured Prediction of Network Response

Juho Rousu, Aristides Gionis, Hongyu Su, 2014, ICML.

Proceedings of the Third International Workshop on Machine Learning in Systems Biology: Revised Selected Papers

Juho Rousu, Pierre Geurts, Sašo Džeroski, 2009 .

Necessary and Sufficient Pre-processing in Numerical Range Discretization

Tapio Elomaa, Juho Rousu, Juho Rousu, 2003, Knowledge and Information Systems.

Principal metabolic flux mode analysis

Juho Rousu, Sahely Bhadra, Sandra Castillo, 2017, bioRxiv.

Computational Methods for Metabolic Networks: Invited Presentation at the Fourth International Workshop on Computational Models for Cell Processes

Juho Rousu, 2013 .

Efficient Multisplitting Revisited: Optima-Preserving Elimination of Partition Candidates

Tapio Elomaa, Juho Rousu, Juho Rousu, 2004, Data Mining and Knowledge Discovery.

Computational Methods in Systems Biology

Juho Rousu, Falk Schreiber, Leena Salmela, 2018, Lecture Notes in Computer Science.

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

Juho Rousu, Simon Rogers, John Williamson, 2020, bioRxiv.

Probabilistic Framework for Integration of Mass Spectrum and Retention Time Information in Small Molecule Identification.

Juho Rousu, Simon Rogers, John Williamson, 2020, Bioinformatics.

Practical Approximation of Optimal Multivariate Discretization

Tapio Elomaa, Juho Rousu, Jussi Kujala, 2006, ISMIS.

A Tutorial on Canonical Correlation Methods

Juho Rousu, John Shawe-Taylor, Delmiro Fernandez-Reyes, 2017, ACM Comput. Surv..

Reaction Kernels - Structured Output Prediction Approaches for Novel Enzyme Function

Juho Rousu, Liisa Holm, Sándor Szedmák, 2018, BIOINFORMATICS.

Structured Output Prediction of Novel Enzyme Function with Reaction Kernels

Juho Rousu, Liisa Holm, Sándor Szedmák, 2010, BIOSTEC.

Computational methods for metabolic reconstruction.

Juho Rousu, Esko Ukkonen, Esa Pitkänen, 2010, Current opinion in biotechnology.

Fast Minimum Training Error Discretization

Tapio Elomaa, Juho Rousu, 2002, ICML.

comboFM: leveraging multi-way interactions for systematic prediction of drug combination effects

Juho Rousu, Anna Cichonska, Tapio Pahikkala, 2020, bioRxiv.

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes

Juho Rousu, Taneli Mielikäinen, Esko Ukkonen, 2006, Bioinform..

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

Juho Rousu, Kristian Nybo, Viivi Uurtio, 2015, Discovery Science.

Large-Scale Sparse Kernel Canonical Correlation Analysis

Juho Rousu, Sahely Bhadra, Viivi Uurtio, 2019, ICML.

Principal Metabolic Flux Mode Analysis

Juho Rousu, Sahely Bhadra, Peter Blomberg, 2017 .

Multilabel classification through random graph ensembles

Juho Rousu, Hongyu Su, 2014, Machine Learning.

Structured Output Prediction of Anti-cancer Drug Activity

Juho Rousu, Hongyu Su, Markus Heinonen, 2010, PRIB.

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

Juho Rousu, Esko Ukkonen, Nicola Zamboni, 2008, BMC Bioinformatics.

Towards CBR for Bioprocess Planning

Juho Rousu, Robert J. Aarts, Juho Rousu, 1996, EWCBR.

Non-Stationary Gaussian Process Regression with Hamiltonian Monte Carlo

Juho Rousu, Samuel Kaski, Markus Heinonen, 2015, AISTATS.

General and Efficient Multisplitting of Numerical Attributes

Tapio Elomaa, Juho Rousu, Juho Rousu, 1999, Machine Learning.

Metabolite identification through multiple kernel learning on fragmentation trees

Juho Rousu, Sebastian Böcker, Huibin Shen, 2014, Bioinform..

Learning with multiple pairwise kernels for drug bioactivity prediction

Juho Rousu, Anna Cichonska, Tapio Pahikkala, 2018, Bioinform..

Linear-Time Preprocessing in Optimal Numerical Range Partitioning

Tapio Elomaa, Juho Rousu, 2004, Journal of Intelligent Information Systems.

Research data supporting "A Tool for Exploiting Complex Adaptive Evolution to Optimise Protocols for Biological Experiments"

Juho Rousu, Duygu Dikicioglu, Stephen G. Oliver, 2017 .

Speeding Up the Search for Optimal Partitions

Tapio Elomaa, Juho Rousu, 1999, PKDD.

Planning isotopomer measurements for estimation of metabolic fluxes

Juho Rousu, Taneli Mielikäinen, Esko Ukkonen, 2005, German Conference on Bioinformatics.

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

Tapio Elomaa, Juho Rousu, Juho Rousu, 1998, PKDD.

On the Computational Complexity of Optimal Multisplitting

Tapio Elomaa, Juho Rousu, 2001, Fundam. Informaticae.

Metabolite Identification through Machine Learning — Tackling CASMI Challenge Using FingerID

Juho Rousu, Markus Heinonen, Nicola Zamboni, 2013, Metabolites.

Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects

Juho Rousu, Anna Cichonska, Tapio Pahikkala, 2020, Nature Communications.

Generalizing Boundary Points

Tapio Elomaa, Juho Rousu, 2000, AAAI/IAAI.

Efficient Computation of Gapped Substring Kernels on Large Alphabets

Juho Rousu, John Shawe-Taylor, J. Shawe-Taylor, 2005, J. Mach. Learn. Res..

Learning hierarchical multi-category text classification models

Juho Rousu, John Shawe-Taylor, Sándor Szedmák, 2005, ICML.

Qualitative Knowledge to Support Reasoning About Cases

Juho Rousu, Robert J. Aarts, Juho Rousu, 1997, ICCBR.

Fast metabolite identification with Input Output Kernel Regression

Juho Rousu, Florence d'Alché-Buc, Sebastian Böcker, 2016, Bioinform..

Structured Prediction Models

Juho Rousu, 2008 .

Critical Assessment of Small Molecule Identification 2016: automated methods

Juho Rousu, Martin Krauss, Emma L. Schymanski, 2017, Journal of Cheminformatics.

Kernel-Based Learning of Hierarchical Multilabel Classification Models

Juho Rousu, John Shawe-Taylor, Sándor Szedmák, 2006, J. Mach. Learn. Res..

Bayesian metabolic flux analysis reveals intracellular flux couplings

Juho Rousu, Samuel Kaski, Janne Wallenius, 2018, Bioinform..

On the Complexity of Optimal Multisplitting

Tapio Elomaa, Juho Rousu, 2000, ISMIS.

Sparse Non-linear CCA through Hilbert-Schmidt Independence Criterion

Juho Rousu, Sahely Bhadra, Viivi Uurtio, 2018, 2018 IEEE International Conference on Data Mining (ICDM).

Learning Output Embeddings in Structured Prediction pdf

Juho Rousu, Alessandro Rudi, Florence d'Alch'e-Buc, 2020, ArXiv.

Multi-task Drug Bioactivity Classification with Graph Labeling Ensembles

Juho Rousu, Hongyu Su, Juho Rousu, 2011, PRIB.

Adaptation Cost as a Criterion for Solution Evaluation

Juho Rousu, Robert J. Aarts, Juho Rousu, 1996, EWCBR.

Soft Kernel Target Alignment for Two-Stage Multiple Kernel Learning

Juho Rousu, Sándor Szedmák, Huibin Shen, 2016, DS.

Preprocessing opportunities in optimal numerical range partitioning

Tapio Elomaa, Juho Rousu, Juho Rousu, 2001, Proceedings 2001 IEEE International Conference on Data Mining.

An Efficient Method for Large Margin Parameter

Juho Rousu, Huizhen Yu, Tietojenkäsittelytieteen laitos, 2008 .

CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology

Juho Rousu, Duygu Dikicioglu, Stephen G. Oliver, 2017, Microbiology.

Ab Initio Prediction of Molecular Fragments from Tandem Mass Spectrometry Data

Juho Rousu, Taneli Mielikäinen, Markus Heinonen, 2006, German Conference on Bioinformatics.

Machine Learning of Protein Interactions in Fungal Secretory Pathways

Juho Rousu, Mikko Arvas, Merja Penttilä, 2016, PloS one.

Classes for the masses: Systematic classification of unknowns using fragmentation spectra

Juho Rousu, Pieter C. Dorrestein, Sebastian Böcker, 2020, bioRxiv.

Predicting the Speed of Beer Fermentation in Laboratory and Industrial Scale

Tapio Elomaa, Juho Rousu, Robert J. Aarts, 1999, IWANN.

Learning primal-dual sparse kernel machines pdf

Juho Rousu, Sahely Bhadra, Hachem Kadri, 2021, ArXiv.

Uses of Convexity in Numerical Domain Partitioning

Tapio Elomaa, Juho Rousu, 2000 .

Computing positional isotopomer distributions from tandem mass spectrometric data.

Juho Rousu, Ari Rantanen, Ari Rantanen, 2002, Metabolic engineering.

Meat Processing Plant Microbiome and Contamination Patterns of Cold-Tolerant Bacteria Causing Food Safety and Spoilage Risks in the Manufacture of Vacuum-Packaged Cooked Sausages

Juho Rousu, K. Johanna Björkroth, Jenni Hultman, 2015, Applied and Environmental Microbiology.

An analytic and systematic framework for estimating metabolic flux ratios from ¹³C tracer experiments: methodology article

Juho Rousu, Esko Ukkonen, Nicola Zamboni, 2008 .

On Maximum Margin Hierarchical Multilabel Classification

Juho Rousu, John Shawe-Taylor, 2005 .

Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae

Juho Rousu, Merja Penttilä, Harri Lähdesmäki, 2016, PloS one.

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

Juho Rousu, Sebastian Böcker, Markus Fleischauer, 2019, Nature Methods.

On Maximum Margin Hierarchical Classification

Juho Rousu, John Shawe-Taylor, Craig Saunders, 2004 .

Isotopomer distribution computation from tandem mass spectrometric data with overlapping fragment spectra

Juho Rousu, Ari Rantanen, Juha Kokkonen, 2005 .

Efficient Algorithms for Max-Margin Structured Classification

Juho Rousu, John Shawe-Taylor, Craig Saunders, 2007 .