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Tournament leave-pair-out cross-validation for receiver operating characteristic analysis.
Published in:
2019
By:
- Montoya Perez, Ileana;
- Airola, Antti;
- Boström, Peter J;
- Jambor, Ivan;
- Pahikkala, Tapio
Publication type:
journal article
Effect of processing of bovine milk on gastrointestinal symptoms and intestinal pressure in sensitive individuals.
Published in:
2020
By:
- Nuora, Anu;
- Tupasela, Tuomo;
- Jokioja, Johanna;
- Tahvonen, Raija;
- Kallio, Heikki;
- Yang, Baoru;
- Rokka, Susanna;
- Marnila, Pertti;
- Mäkelä, Petri;
- Pohjankukka, Jonne;
- Pahikkala, Tapio;
- Viitanen, Matti;
- Linderborg, Kaisa
Publication type:
Abstract
Effect of processing of bovine milk on gastrointestinal symptoms and intestinal pressure in sensitive individuals.
Published in:
2020
By:
- Nuora, Anu;
- Tupasela, Tuomo;
- Jokioja, Johanna;
- Tahvonen, Raija;
- Kallio, Heikki;
- Yang, Baoru;
- Rokka, Susanna;
- Marnila, Pertti;
- Mäkelä, Petri;
- Pohjankukka, Jonne;
- Pahikkala, Tapio;
- Viitanen, Matti;
- Linderborg, Kaisa
Publication type:
Abstract
Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments.
Published in:
Electrophoresis, 2007, v. 28, n. 6, p. 879, doi. 10.1002/elps.200600424
By:
- Vähämaa, Heidi;
- Ojala, Pekka;
- Pahikkala, Tapio;
- Nevalainen, Olli S.;
- Lahesmaa, Riitta;
- Aittokallio, Tero
Publication type:
Article
Comparison of chlorophyll fluorescence curves and texture analysis for automatic plant identification.
Published in:
Precision Agriculture, 2013, v. 14, n. 6, p. 621, doi. 10.1007/s11119-013-9320-y
By:
- Mattila, Heta;
- Valli, Pertti;
- Pahikkala, Tapio;
- Teuhola, Jukka;
- Nevalainen, Olli;
- Tyystjärvi, Esa
Publication type:
Article
The spatial leave-pair-out cross-validation method for reliable AUC estimation of spatial classifiers.
Published in:
Data Mining & Knowledge Discovery, 2019, v. 33, n. 3, p. 730, doi. 10.1007/s10618-018-00607-x
By:
- Airola, Antti;
- Pohjankukka, Jonne;
- Torppa, Johanna;
- Middleton, Maarit;
- Nykänen, Vesa;
- Heikkonen, Jukka;
- Pahikkala, Tapio
Publication type:
Article
Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives.
Published in:
BioData Mining, 2013, v. 6, n. 1, p. 1, doi. 10.1186/1756-0381-6-5
By:
- Okser, Sebastian;
- Pahikkala, Tapio;
- Aittokallio, Tero
Publication type:
Article
Circulating Cytokines Predict the Development of Insulin Resistance in a Prospective Finnish Population Cohort.
Published in:
2016
By:
- Santalahti, Kristiina;
- Maksimow, Mikael;
- Airola, Antti;
- Pahikkala, Tapio;
- Hutri-Kähönen, Nina;
- Jalkanen, Sirpa;
- Raitakari, Olli T;
- Salmi, Marko
Publication type:
journal article
Fitting methods for intravoxel incoherent motion imaging of prostate cancer on region of interest level: Repeatability and gleason score prediction.
Published in:
Magnetic Resonance in Medicine, 2017, v. 77, n. 3, p. 1249, doi. 10.1002/mrm.26169
By:
- Merisaari, Harri;
- Movahedi, Parisa;
- Perez, Ileana M.;
- Toivonen, Jussi;
- Pesola, Marko;
- Taimen, Pekka;
- Boström, Peter J.;
- Pahikkala, Tapio;
- Kiviniemi, Aida;
- Aronen, Hannu J.;
- Jambor, Ivan
Publication type:
Article
Mathematical models for diffusion-weighted imaging of prostate cancer using b values up to 2000 s/mm<sup>2</sup>: Correlation with Gleason score and repeatability of region of interest analysis.
Published in:
Magnetic Resonance in Medicine, 2015, v. 74, n. 4, p. 1116, doi. 10.1002/mrm.25482
By:
- Toivonen, Jussi;
- Merisaari, Harri;
- Pesola, Marko;
- Taimen, Pekka;
- Boström, Peter J.;
- Pahikkala, Tapio;
- Aronen, Hannu J.;
- Jambor, Ivan
Publication type:
Article
Modeling drug combination effects via latent tensor reconstruction.
Published in:
Bioinformatics, 2021, v. 37, p. i93, doi. 10.1093/bioinformatics/btab308
By:
- Wang, Tianduanyi;
- Szedmak, Sandor;
- Wang, Haishan;
- Aittokallio, Tero;
- Pahikkala, Tapio;
- Cichonska, Anna;
- Rousu, Juho
Publication type:
Article
Qualitative and Quantitative Reporting of a Unique Biparametric MRI: Towards Biparametric MRI-Based Nomograms for Prediction of Prostate Biopsy Outcome in Men With a Clinical Suspicion of Prostate Cancer (IMPROD and MULTI-IMPROD Trials).
Published in:
2020
By:
- Perez, Ileana Montoya;
- Jambor, Ivan;
- Kauko, Tommi;
- Verho, Janne;
- Ettala, Otto;
- Falagario, Ugo;
- Merisaari, Harri;
- Kiviniemi, Aida;
- Taimen, Pekka;
- Syvänen, Kari T.;
- Knaapila, Juha;
- Seppänen, Marjo;
- Rannikko, Antti;
- Riikonen, Jarno;
- Kallajoki, Markku;
- Mirtti, Tuomas;
- Lamminen, Tarja;
- Saunavaara, Jani;
- Pahikkala, Tapio;
- Boström, Peter J.
Publication type:
journal article
Prostate Cancer Risk Stratification in Men With a Clinical Suspicion of Prostate Cancer Using a Unique Biparametric MRI and Expression of 11 Genes in Apparently Benign Tissue: Evaluation Using Machine-Learning Techniques.
Published in:
2020
By:
- Montoya Perez, Ileana;
- Jambor, Ivan;
- Pahikkala, Tapio;
- Airola, Antti;
- Merisaari, Harri;
- Saunavaara, Jani;
- Alinezhad, Saeid;
- Väänänen, Riina‐Minna;
- Tallgrén, Terhi;
- Verho, Janne;
- Kiviniemi, Aida;
- Ettala, Otto;
- Knaapila, Juha;
- Syvänen, Kari T.;
- Kallajoki, Markku;
- Vainio, Paula;
- Aronen, Hannu J.;
- Pettersson, Kim;
- Boström, Peter J.;
- Taimen, Pekka
Publication type:
journal article
Prediction of biochemical recurrence in prostate cancer patients who underwent prostatectomy using routine clinical prostate multiparametric MRI and decipher genomic score.
Published in:
2020
By:
- Jambor, Ivan;
- Falagario, Ugo;
- Ratnani, Parita;
- Perez, Ileana Montoya;
- Demir, Kadir;
- Merisaari, Harri;
- Sobotka, Stanislaw;
- Haines, George K.;
- Martini, Alberto;
- Beksac, Alp Tuna;
- Lewis, Sara;
- Pahikkala, Tapio;
- Wiklund, Peter;
- Nair, Sujit;
- Tewari, Ash
Publication type:
journal article
IMPROD biparametric MRI in men with a clinical suspicion of prostate cancer (IMPROD Trial): Sensitivity for prostate cancer detection in correlation with whole-mount prostatectomy sections and implications for focal therapy.
Published in:
2019
By:
- Merisaari, Harri;
- Jambor, Ivan;
- Ettala, Otto;
- Boström, Peter J.;
- Montoya Perez, Ileana;
- Verho, Janne;
- Kiviniemi, Aida;
- Syvänen, Kari;
- Kähkönen, Esa;
- Eklund, Lauri;
- Pahikkala, Tapio;
- Vainio, Paula;
- Saunavaara, Jani;
- Aronen, Hannu J.;
- Taimen, Pekka
Publication type:
journal article
All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning.
Published in:
BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-S11-S2
By:
- Airola, Antti;
- Pyysalo, Sampo;
- Björne, Jari;
- Pahikkala, Tapio;
- Ginter, Filip;
- Salakoski, Tapio
Publication type:
Article
Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation.
Published in:
BMC Bioinformatics, 2005, v. 6, p. 157, doi. 10.1186/1471-2105-6-157
By:
- Pahikkala, Tapio;
- Ginter, Filip;
- Boberg, Jorma;
- Järvinen, Jouni;
- Salakoski, Tapio
Publication type:
Article
Quicksort leave-pair-out cross-validation for ROC curve analysis.
Published in:
Computational Statistics, 2023, v. 38, n. 3, p. 1579, doi. 10.1007/s00180-022-01288-3
By:
- Numminen, Riikka;
- Montoya Perez, Ileana;
- Jambor, Ivan;
- Pahikkala, Tapio;
- Airola, Antti
Publication type:
Article
Synthetic minority oversampling of vital statistics data with generative adversarial networks.
Published in:
2020
By:
- Koivu, Aki;
- Sairanen, Mikko;
- Airola, Antti;
- Pahikkala, Tapio
Publication type:
journal article
Prediction of prostate cancer aggressiveness using 18F-Fluciclovine (FACBC) PET and multisequence multiparametric MRI.
Published in:
Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-66255-8
By:
- Movahedi, Parisa;
- Merisaari, Harri;
- Perez, Ileana Montoya;
- Taimen, Pekka;
- Kemppainen, Jukka;
- Kuisma, Anna;
- Eskola, Olli;
- Teuho, Jarmo;
- Saunavaara, Jani;
- Pesola, Marko;
- Kähkönen, Esa;
- Ettala, Otto;
- Liimatainen, Timo;
- Pahikkala, Tapio;
- Boström, Peter;
- Aronen, Hannu;
- Minn, Heikki;
- Jambor, Ivan
Publication type:
Article
Estimating the Rut Depth by UAV Photogrammetry.
Published in:
Remote Sensing, 2017, v. 9, n. 12, p. 1279, doi. 10.3390/rs9121279
By:
- Nevalainen, Paavo;
- Salmivaara, Aura;
- Ala-Ilomäki, Jari;
- Launiainen, Samuli;
- Hiedanpää, Juuso;
- Finér, Leena;
- Pahikkala, Tapio;
- Heikkonen, Jukka
Publication type:
Article
Detecting Terrain Stoniness From Airborne Laser Scanning Data.
Published in:
Remote Sensing, 2016, v. 8, n. 9, p. 720, doi. 10.3390/rs8090720
By:
- Nevalainen, Paavo;
- Middleton, Maarit;
- Sutinen, Raimo;
- Heikkonen, Jukka;
- Pahikkala, Tapio
Publication type:
Article
Developing a pain intensity prediction model using facial expression: A feasibility study with electromyography.
Published in:
PLoS ONE, 2020, v. 15, n. 7, p. 1, doi. 10.1371/journal.pone.0235545
By:
- Mieronkoski, Riitta;
- Syrjälä, Elise;
- Jiang, Mingzhe;
- Rahmani, Amir;
- Pahikkala, Tapio;
- Liljeberg, Pasi;
- Salanterä, Sanna
Publication type:
Article
Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations.
Published in:
Algorithms for Molecular Biology, 2012, v. 7, n. 1, p. 1, doi. 10.1186/1748-7188-7-11
By:
- Pahikkala, Tapio;
- Okser, Sebastian;
- Airola, Antti;
- Salakoski, Tapio;
- Aittokallio, Tero
Publication type:
Article
Algebraic shortcuts for leave-one-out cross-validation in supervised network inference.
Published in:
Briefings in Bioinformatics, 2020, v. 21, n. 1, p. 262, doi. 10.1093/bib/bby095
By:
- Stock, Michiel;
- Pahikkala, Tapio;
- Airola, Antti;
- Waegeman, Willem;
- Baets, Bernard De
Publication type:
Article
Toward more realistic drug-target interaction predictions.
Published in:
Briefings in Bioinformatics, 2015, v. 16, n. 2, p. 325, doi. 10.1093/bib/bbu010
By:
- Pahikkala, Tapio;
- Airola, Antti;
- Pietila, Sami;
- Shakyawar, Sushil;
- Szwajda, Agnieszka;
- Jing Tang;
- Aittokallio, Tero
Publication type:
Article
Parallelized Online Regularized Least-Squares for Adaptive Embedded Systems.
Published in:
International Journal of Embedded & Real-Time Communication Systems, 2012, v. 3, n. 2, p. 73, doi. 10.4018/jertcs.2012040104
By:
- Pahikkala, Tapio;
- Airola, Antti;
- Canhao Xu, Thomas;
- Liljeberg, Pasi;
- Tenhunen, Hannu;
- Salakoski, Tapio
Publication type:
Article
Molecular Atlas of Postnatal Mouse Heart Development.
Published in:
2018
By:
- Talman, Virpi;
- Teppo, Jaakko;
- Pöhö, Päivi;
- Movahedi, Parisa;
- Vaikkinen, Anu;
- Karhu, S. Tuuli;
- Trošt, Kajetan;
- Suvitaival, Tommi;
- Heikkonen, Jukka;
- Pahikkala, Tapio;
- Kotiaho, Tapio;
- Kostiainen, Risto;
- Varjosalo, Markku;
- Ruskoaho, Heikki
Publication type:
journal article
EXTRACTING CONTEXTUALIZED COMPLEX BIOLOGICAL EVENTS WITH RICH GRAPH-BASED FEATURE SETS.
Published in:
Computational Intelligence, 2011, v. 27, n. 4, p. 541, doi. 10.1111/j.1467-8640.2011.00399.x
By:
- Björne, Jari;
- Heimonen, Juho;
- Ginter, Filip;
- Airola, Antti;
- Pahikkala, Tapio;
- Salakoski, Tapio
Publication type:
Article
Regularized Machine Learning in the Genetic Prediction of Complex Traits.
Published in:
PLoS Genetics, 2014, v. 10, n. 11, p. 1, doi. 10.1371/journal.pgen.1004754
By:
- Okser, Sebastian;
- Pahikkala, Tapio;
- Airola, Antti;
- Salakoski, Tapio;
- Ripatti, Samuli;
- Aittokallio, Tero
Publication type:
Article
Radiomics and machine learning of multisequence multiparametric prostate MRI: Towards improved non-invasive prostate cancer characterization.
Published in:
PLoS ONE, 2019, v. 14, n. 7, p. 1, doi. 10.1371/journal.pone.0217702
By:
- Toivonen, Jussi;
- Montoya Perez, Ileana;
- Movahedi, Parisa;
- Merisaari, Harri;
- Pesola, Marko;
- Taimen, Pekka;
- Boström, Peter J.;
- Pohjankukka, Jonne;
- Kiviniemi, Aida;
- Pahikkala, Tapio;
- Aronen, Hannu J.;
- Jambor, Ivan
Publication type:
Article
Generalized vec trick for fast learning of pairwise kernel models.
Published in:
Machine Learning, 2022, v. 111, n. 2, p. 543, doi. 10.1007/s10994-021-06127-y
By:
- Viljanen, Markus;
- Airola, Antti;
- Pahikkala, Tapio
Publication type:
Article
Efficient regularized least-squares algorithms for conditional ranking on relational data.
Published in:
Machine Learning, 2013, v. 93, n. 2-3, p. 321, doi. 10.1007/s10994-013-5354-7
By:
- Pahikkala, Tapio;
- Airola, Antti;
- Stock, Michiel;
- De Baets, Bernard;
- Waegeman, Willem
Publication type:
Article
Efficient cross-validation for kernelized least-squares regression with sparse basis expansions.
Published in:
Machine Learning, 2012, v. 87, n. 3, p. 381, doi. 10.1007/s10994-012-5287-6
By:
- Pahikkala, Tapio;
- Suominen, Hanna;
- Boberg, Jorma
Publication type:
Article
An efficient algorithm for learning to rank from preference graphs.
Published in:
Machine Learning, 2009, v. 75, n. 1, p. 129, doi. 10.1007/s10994-008-5097-z
By:
- Pahikkala, Tapio;
- Tsivtsivadze, Evgeni;
- Airola, Antti;
- Järvinen, Jouni;
- Boberg, Jorma
Publication type:
Article
Matrix representations, linear transformations, and kernels for disambiguation in natural language.
Published in:
Machine Learning, 2009, v. 74, n. 2, p. 133, doi. 10.1007/s10994-008-5082-6
By:
- Pahikkala, Tapio;
- Pyysalo, Sampo;
- Boberg, Jorma;
- Järvinen, Jouni;
- Salakoski, Tapio
Publication type:
Article
Learning with multiple pairwise kernels for drug bioactivity prediction.
Published in:
Bioinformatics, 2018, v. 34, n. 13, p. i509, doi. 10.1093/bioinformatics/bty277
By:
- Cichonska, Anna;
- Pahikkala, Tapio;
- Szedmak, Sandor;
- Julkunen, Heli;
- Airola, Antti;
- Heinonen, Markus;
- Aittokallio, Tero;
- Rousu, Juho
Publication type:
Article
Towards dynamic forest trafficability prediction using open spatial data, hydrological modelling and sensor technology.
Published in:
Forestry: An International Journal of Forest Research, 2020, v. 93, n. 5, p. 662, doi. 10.1093/forestry/cpaa010
By:
- Salmivaara, Aura;
- Launiainen, Samuli;
- Perttunen, Jari;
- Nevalainen, Paavo;
- Pohjankukka, Jonne;
- Ala-Ilomäki, Jari;
- Sirén, Matti;
- Laurén, Ari;
- Tuominen, Sakari;
- Uusitalo, Jori;
- Pahikkala, Tapio;
- Heikkonen, Jukka;
- Finér, Leena
Publication type:
Article
Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-19950-z
By:
- Julkunen, Heli;
- Cichonska, Anna;
- Gautam, Prson;
- Szedmak, Sandor;
- Douat, Jane;
- Pahikkala, Tapio;
- Aittokallio, Tero;
- Rousu, Juho
Publication type:
Article
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors.
Published in:
PLoS Computational Biology, 2017, v. 13, n. 8, p. 1, doi. 10.1371/journal.pcbi.1005678
By:
- Cichonska, Anna;
- Ravikumar, Balaguru;
- Parri, Elina;
- Timonen, Sanna;
- Pahikkala, Tapio;
- Airola, Antti;
- Wennerberg, Krister;
- Rousu, Juho;
- Aittokallio, Tero
Publication type:
Article

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