publications.bib

@article{Gonen2017dream,
  author = {G{\"o}nen, Mehmet and Weir, Barbara A. and Cowley, Glenn S. and Vazquez, Francisca and Guan, Yuanfang and Jaiswal, Alok and Karasuyama, Masayuki and Uzunangelov, Vladislav and Wang, Tao and Tsherniak, Aviad and Howell, Sara and Marbach, Daniel and Hoff, Bruce and Norman, Thea C. and Airola, Antti and Bivol, Adrian and Bunte, Kerstin and Carlin, Daniel and Chopra, Sahil and Deran, Alden and Ellrott, Kyle and Gopalacharyulu, Peddinti and Graim, Kiley and Kaski, Samuel and Khan, Suleiman A. and Newton, Yulia and Ng, Sam and Pahikkala, Tapio and Paull, Evan and Sokolov, Artem and Tang, Hao and Tang, Jing and Wennerberg, Krister and Xie, Yang and Zhan, Xiaowei and Zhu, Fan and Aittokallio, Tero and Mamitsuka, Hiroshi and Stuart, Joshua M. and Boehm, Jesse S. and Root, Dave A. and Xiao, Guanghua and Stolovitzky, Gustavo and Hahn, William C. and Margolin, Adam A.},
  title = {A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines},
  year = {2017},
  doi = {10.1016/j.cels.2017.09.004},
  url = {https://doi.org/10.1016/j.cels.2017.09.004},
  journal = {Cell Systems},
  note = {In Press}
}
@article{Airola2017arXiv160101507A,
  author = {Airola, Antti and Pahikkala, Tapio},
  title = {Fast Kronecker product kernel methods via generalized vec trick},
  journal = {IEEE Transactions on Neural Networks and Learning Systems},
  year = {2017},
  eprint = {arXiv:1601.01507},
  note = {In press},
  doi = {10.1109/TNNLS.2017.2727545}
}
@article{Eberl2017switching,
  author = {Eberl, Anja and Huoponen, Saara and Pahikkala, Tapio and Blom, Marja and Arkkila, Perttu and Sipponen, Taina},
  title = {Switching maintenance infliximab therapy to biosimilar infliximab in inflammatory bowel disease patients},
  journal = {Scandinavian Journal of Gastroenterology},
  volume = {52},
  number = {12},
  pages = {1348--1353},
  year = {2017},
  doi = {10.1080/00365521.2017.1369561},
  url = {http://dx.doi.org/10.1080/00365521.2017.1369561}
}
@article{Cichonska2017compexp,
  author = {Cichonska, Anna and Ravikumar, Balaguru and Parri, Elina and Timonen, Sanna and Pahikkala, Tapio and Airola, Antti and Wennerberg, Krister and Rousu, Juho and Aittokallio, Tero},
  journal = {PLOS Computational Biology},
  title = {Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors},
  year = {2017},
  month = {08},
  volume = {13},
  url = {https://doi.org/10.1371/journal.pcbi.1005678},
  pages = {1-28},
  number = {8},
  doi = {10.1371/journal.pcbi.1005678}
}
@article{Naula2017Assessment,
  author = {Naula, Pekka and Airola, Antti and Pihlasalo, Sari and Montoya Perez, Ileana and Salakoski, Tapio and Pahikkala, Tapio},
  title = {Assessment of metal ion concentration in water with structured feature selection},
  journal = {Chemosphere},
  year = {2017},
  volume = {185},
  pages = {1063--1071},
  month = {October},
  url = {https://doi.org/10.1016/j.chemosphere.2017.07.079},
  doi = {10.1016/j.chemosphere.2017.07.079}
}
@article{viljanen2017playtime,
  author = {Viljanen, Markus and Airola, Antti and Heikkonen, Jukka and Pahikkala, Tapio},
  journal = {IEEE Transactions on Computational Intelligence and AI in Games},
  title = {Playtime Measurement with Survival Analysis},
  year = {2017},
  doi = {10.1109/TCIAIG.2017.2727642},
  note = {In press}
}
@article{Guinney2017dream,
  author = {Guinney, Justin and Wang, Tao and Laajala, Teemu D and Winner, Kimberly Kanigel and Bare, J Christopher and Neto, Elias Chaibub and Khan, Suleiman A and Peddinti, Gopal and Airola, Antti and Pahikkala, Tapio and Mirtti, Tuomas and Yu, Thomas and Bot, Brian M and Shen, Liji and Abdallah, Kald and Norman, Thea and Friend, Stephen and Stolovitzky, Gustavo and Soule, Howard and Sweeney, Christopher J. and Ryan, Charles J and Scher, Howard I. and Sartor, Oliver and Xie, Yang and Aittokallio, Tero and Zhou, Fang Liz and Costello, James C},
  title = {Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data},
  year = {2017},
  journal = {The Lancet Oncology},
  volume = {18},
  number = {1},
  pages = {132--142},
  url = {http://dx.doi.org/10.1016/S1470-2045(16)30560-5},
  doi = {10.1016/S1470-2045(16)30560-5}
}
@article{pohjankukka2017spatialcv,
  author = {Pohjankukka, Jonne and Pahikkala, Tapio and Nevalainen, Paavo and Heikkonen, Jukka},
  title = {Estimating the Prediction Performance of Spatial Models via Spatial k-Fold Cross Validation},
  journal = {International Journal of Geographical Information Science},
  volume = {31},
  number = {10},
  pages = {2001--2019},
  year = {2017},
  doi = {10.1080/13658816.2017.1346255},
  url = {http://dx.doi.org/10.1080/13658816.2017.1346255}
}
@article{hogmander2017luminometric,
  author = {H{\"o}gmander, Milla and Paul, Catherine J. and Chan, Sandy and Hokkanen, Elina and Eskonen, Ville and Pahikkala, Tapio and Pihlasalo, Sari},
  title = {Luminometric Label Array for Counting and Differentiation of Bacteria},
  journal = {Analytical Chemistry},
  year = {2017},
  volume = {89},
  number = {5},
  pages = {3208--3216},
  doi = {10.1021/acs.analchem.6b05142},
  url = {http://dx.doi.org/10.1021/acs.analchem.6b05142}
}
@article{merisaari2017fitting,
  author = {Merisaari, Harri and Movahedi, Parisa and Montoya Perez, Ileana and Toivonen, Jussi and Pesola, Marko and Taimen, Pekka and Bostr{\"o}m, Peter and Kiviniemi, Aida and Pahikkala, Tapio and Aronen, Hannu J. and Jambor, Ivan},
  title = {Fitting methods for intravoxel incoherent motion imaging of prostate cancer on region of interest level: repeatability and {G}leason score prediction},
  journal = {Magnetic Resonance in Medicine},
  year = {2017},
  volume = {77},
  number = {3},
  pages = {1249--1264},
  url = {http://dx.doi.org/10.1002/mrm.26169},
  doi = {10.1002/mrm.26169}
}
@article{Azimi2017hich,
  author = {Azimi, Iman and Anzanpour, Arman and Rahmani, Amir M. and Pahikkala, Tapio and Levorato, Marco and Liljeberg, Pasi and Dutt, Nikil},
  title = {{HiCH}: Hierarchical Fog-assisted Computing Architecture for Healthcare {IoT}},
  journal = {ACM Transactions on Embedded Computing Systems},
  year = {2017},
  volume = {16},
  number = {5s},
  month = {September},
  pages = {174:1--174:20},
  url = {http://doi.acm.org/10.1145/3126501},
  doi = {10.1145/3126501}
}
@article{Taajamaa2017ethics,
  author = {Taajamaa, Ville and Majanoja, Anne-Maarit and Bairaktarova, Diana and Airola, Antti and Pahikkala, Tapio and Sutinen, Erkki},
  title = {How engineers perceive the importance of ethics in Finland},
  journal = {European Journal of Engineering Education},
  year = {2017},
  note = {Accepted for publication},
  doi = {10.1080/03043797.2017.1313198},
  url = {http://dx.doi.org/10.1080/03043797.2017.1313198}
}
@article{pahikkala2016rlscore,
  author = {Pahikkala, Tapio and Airola, Antti},
  title = {RLScore: Regularized Least-Squares Learners},
  journal = {Journal of Machine Learning Research},
  year = {2016},
  volume = {17},
  number = {221},
  pages = {1-5},
  url = {http://jmlr.org/papers/v17/16-470.html}
}
@article{Santalahti2016Circulating,
  author = {Santalahti, Kristiina and Maksimow, Mikael and Airola, Antti and Pahikkala, Tapio and Hutri-Kähönen, Nina and Jalkanen, Sirpa and Raitakari, Olli T. and Salmi, Marko},
  title = {Circulating Cytokines Predict the Development of Insulin Resistance in a Prospective Finnish Population Cohort},
  journal = {The Journal of Clinical Endocrinology \& Metabolism},
  volume = {101},
  number = {9},
  pages = {3361-3369},
  year = {2016},
  doi = {10.1210/jc.2016-2081},
  url = {http://dx.doi.org/10.1210/jc.2016-2081}
}
@article{pihlasalo2016luminometric,
  author = {Pihlasalo, Sari and Montoya Perez, Ileana and Hollo, Niklas and Hokkanen, Elina and Pahikkala, Tapio and H{\"a}rm{\"a}, Harri},
  title = {Luminometric Label Array for Quantification and Identification of Metal Ions},
  journal = {Analytical Chemistry},
  year = {2016},
  volume = {88},
  number = {10},
  pages = {5271--5280},
  doi = {10.1021/acs.analchem.6b00453},
  url = {http://dx.doi.org/10.1021/acs.analchem.6b00453}
}
@article{pohjankukka2016boreal,
  author = {Pohjankukka, Jonne and Riihim{\"a}ki, Henri and Nevalainen, Paavo and Pahikkala, Tapio and Ala-Ilom{\"a}ki, Jari and Hyv{\"o}nen, Eija and Varjo, Jari and Heikkonen, Jukka},
  title = {Predictability of Boreal Forest Soil Bearing Capacity by Machine Learning},
  journal = {Journal of Terramechanics},
  year = {2016},
  volume = {68},
  pages = {1--8},
  doi = {10.1016/j.jterra.2016.09.001},
  url = {http://dx.doi.org/10.1016/j.jterra.2016.09.001}
}
@article{Nevalainen2016airbornelaser,
  author = {Nevalainen, Paavo and Middleton, Maarit and Sutinen, Raimo and Heikkonen, Jukka and Pahikkala, Tapio},
  title = {Detecting Terrain Stoniness From Airborne Laser Scanning Data},
  journal = {Remote Sensing},
  volume = {8},
  year = {2016},
  number = {9},
  pages = {720},
  url = {http://www.mdpi.com/2072-4292/8/9/720},
  doi = {10.3390/rs8090720}
}
@article{farahnakian2016eavm,
  author = {Farahnakian, Fahimeh and Pahikkala, Tapio and Liljeberg, Pasi and Plosila, Juha and Nguyen, Trung Hieu and Tenhunen, Hannu},
  title = {Energy-aware {VM} Consolidation in Cloud Data Centers Using Utilization Prediction Model},
  journal = {IEEE Transactions on Cloud Computing},
  year = {2016},
  doi = {10.1109/TCC.2016.2617374},
  note = {Accepted for publication}
}
@article{moen2016comparison,
  author = {Moen, Hans and Murtola, Laura-Maria and Heimonen, Juho and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio and Salanter{\"a}, Sanna},
  title = {Comparison of automatic summarisation methods for clinical free text notes},
  journal = {Artificial Intelligence in Medicine},
  volume = {67},
  pages = {25--37},
  year = {2016},
  month = {February},
  url = {http://dx.doi.org/10.1016/j.artmed.2016.01.003},
  doi = {10.1016/j.artmed.2016.01.003}
}
@article{Taajamaa2016ocdio,
  author = {Taajamaa, Ville and Eskandari, Mona and Karanian, Barbara A. and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  title = {{O-CDIO}: Emphasizing Design Thinking in {CDIO} Engineering Cycle},
  journal = {International Journal of Engineering Education},
  volume = {32},
  number = {3},
  pages = {1530--1539},
  year = {2016}
}
@article{pahikkala2015overlapping,
  author = {Pahikkala, Tapio and Kari, Kim and Mattila, Heta and Lepist{\"o}, Anna and Teuhola, Jukka and Nevalainen, Olli S. and Tyystj{\"a}rvi, Esa},
  title = {Classification of plant species from images of overlapping leaves},
  journal = {Computers and Electronics in Agriculture},
  year = {2015},
  volume = {118},
  pages = {186--192},
  url = {http://dx.doi.org/10.1016/j.compag.2015.09.003},
  doi = {10.1016/j.compag.2015.09.003}
}
@article{merisaari2015mathematical,
  author = {Merisaari, Harri and Toivonen, Jussi and Pesola, Marko and Taimen, Pekka and Bostr{\"o}m, Peter and Pahikkala, Tapio and Aronen, Hannu J. and Jambor, Ivan},
  title = {Diffusion weighted imaging of prostate cancer: Effect of b-value distribution on repeatability and cancer characterization},
  journal = {Magnetic Resonance Imaging},
  year = {2015},
  url = {http://dx.doi.org/10.1016/j.mri.2015.07.004},
  doi = {10.1016/j.mri.2015.07.004},
  volume = {33},
  number = {10},
  pages = {1212--1218}
}
@article{toivonen2015mathematical,
  author = {Toivonen, Jussi and Merisaari, Harri and Pesola, Marko and Taimen, Pekka and Bostr{\"o}m, Peter and Pahikkala, Tapio and Aronen, Hannu J. and Jambor, Ivan},
  title = {Mathematical models for diffusion weighted imaging of prostate cancer using b-values up to 2000 s/mm2: correlation with Gleason score and repeatability of region of interest analysis},
  journal = {Magnetic Resonance in Medicine},
  year = {2015},
  url = {http://dx.doi.org/10.1002/mrm.25482},
  doi = {10.1002/mrm.25482},
  volume = {74},
  number = {4},
  pages = {1116--1124},
  month = {October}
}
@article{farahnakian2015antcolony,
  author = {Farahnakian, Fahimeh and Ashraf, Adnan and Pahikkala, Tapio and Liljeberg, Pasi and Plosila, Juha and Porres, Ivan and Tenhunen, Hannu},
  title = {Using Ant Colony System to Consolidate {VM}s for Green Cloud Computing},
  journal = {IEEE Transactions on Services Computing},
  year = {2015},
  month = {March},
  volume = {8},
  number = {2},
  pages = {187--198}
}
@article{pahikkala2015realistic,
  author = {Pahikkala, Tapio and Airola, Antti and Pietil{\"a}, Sami and Shakyawar, Sushil and Szwajda, Agnieszka and Tang, Jing and Aittokallio, Tero},
  title = {Toward more realistic drug-target interaction predictions},
  journal = {Briefings in Bioinformatics},
  year = {2015},
  volume = {16},
  number = {2},
  pages = {325--337},
  doi = {10.1093/bib/bbu010},
  url = {http://dx.doi.org/10.1093/bib/bbu010},
  data = {http://staff.cs.utu.fi/~aatapa/data/DrugTarget/}
}
@article{vainio2015pcb,
  author = {Vainio, Frans and Pahikkala, Tapio and Johnsson, Mika and Nevalainen, Olli S. and Knuutila, Timo},
  title = {Estimating the production time of a {PCB} assembly job without solving the optimised machine control},
  journal = {International Journal of Computer Integrated Manufacturing},
  doi = {10.1080/0951192X.2014.902104},
  url = {http://dx.doi.org/10.1080/0951192X.2014.902104},
  volume = {28},
  number = {8},
  pages = {823--835},
  year = {2015}
}
@article{okser2014regularized,
  author = {Okser, Sebastian and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and Ripatti, Samuli and Aittokallio, Tero},
  journal = {PLOS Genetics},
  title = {Regularized Machine Learning in the Genetic Prediction of Complex Traits},
  year = {2014},
  month = {November},
  volume = {10},
  url = {http://dx.doi.org/10.1371/journal.pgen.1004754},
  pages = {e1004754},
  number = {11},
  doi = {10.1371/journal.pgen.1004754}
}
@article{stock2014enzymes,
  author = {Stock, Michiel and Fober, Thomas and H{\"u}llermeier, Eyke and Glinca, Serghei and Klebe, Gerhard and Pahikkala, Tapio and Airola, Antti and De Baets, Bernard and Waegeman, Willem},
  title = {Identification of functionally related enzymes by learning-to-rank methods},
  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  volume = {11},
  number = {6},
  pages = {1157--1169},
  doi = {10.1109/TCBB.2014.2338308},
  url = {http://dx.doi.org/10.1109/TCBB.2014.2338308},
  eprint = {arXiv:1405.4394},
  year = {2014}
}
@article{kontio2014acuity,
  author = {Kontio, Elina and Airola, Antti and Pahikkala, Tapio and Lundgr{\'e}n-Laine, Helj{\"a} and Junttila, Kristiina and Korvenranta, Heikki and Salakoski, Tapio and Salanter{\"{a}}, Sanna},
  title = {Predicting patient acuity from electronic patient records},
  journal = {Journal of Biomedical Informatics},
  year = {2014},
  month = {October},
  volume = {51},
  number = {0},
  pages = {35--40},
  doi = {10.1016/j.jbi.2014.04.001},
  url = {http://dx.doi.org/10.1016/j.jbi.2014.04.001}
}
@article{naula2014mlbudget,
  author = {Naula, Pekka and Airola, Antti and Salakoski, Tapio and Pahikkala, Tapio},
  title = {Multi-Label Learning under Feature Extraction Budgets},
  journal = {Pattern Recognition Letters},
  volume = {40},
  pages = {56--65},
  year = {2014},
  month = {April},
  doi = {10.1016/j.patrec.2013.12.009},
  url = {http://dx.doi.org/10.1016/j.patrec.2013.12.009}
}
@article{gieseke2014simples3vm,
  author = {Gieseke, Fabian and Airola, Antti and Pahikkala, Tapio and Kramer, Oliver},
  title = {Fast and Simple Gradient-Based Optimization for Semi-Supervised Support Vector Machines},
  journal = {Neurocomputing},
  volume = {123},
  pages = {23--32},
  year = {2014},
  month = {January},
  doi = {10.1016/j.neucom.2012.12.056},
  url = {http://dx.doi.org/10.1016/j.neucom.2012.12.056}
}
@article{pahikkala2014onunsupervisedtraining,
  author = {Pahikkala, Tapio and Airola, Antti and Gieseke, Fabian and Kramer, Oliver},
  title = {On Unsupervised Training of Multi-Class Regularized Least-Squares Classifiers},
  journal = {Journal of Computer Science and Technology},
  year = {2014},
  month = {January},
  volume = {29},
  number = {1},
  pages = {90--104},
  doi = {10.1007/s11390-014-1414-0},
  url = {http://dx.doi.org/10.1007/s11390-014-1414-0}
}
@article{pahikkala2013conditional,
  author = {Pahikkala, Tapio and Airola, Antti and Stock, Michiel and De Baets, Bernard and Waegeman, Willem},
  title = {Efficient Regularized Least-Squares Algorithms for Conditional Ranking on Relational Data},
  journal = {Machine Learning},
  year = {2013},
  doi = {10.1007/s10994-013-5354-7},
  url = {http://dx.doi.org/10.1007/s10994-013-5354-7},
  pages = {321--356},
  volume = {93},
  number = {2-3},
  pdf = {pdf/conditional_postprint.pdf}
}
@article{mattila2012fluorescence,
  author = {Mattila, Heta and Valli, Pertti and Pahikkala, Tapio and Teuhola, Jukka and Nevalainen, Olli S. and Tyystj{\"a}rvi, Esa},
  title = {Comparison of Chlorophyll Fluorescence Curves and Texture Analysis for Automatic Plant Identification},
  journal = {Precision Agriculture},
  year = {2013},
  month = {December},
  volume = {14},
  number = {6},
  pages = {621-636},
  url = {http://dx.doi.org/10.1007/s11119-013-9320-y},
  doi = {10.1007/s11119-013-9320-y}
}
@article{okser2013variants,
  author = {Okser, Sebastian and Pahikkala, Tapio and Aittokallio, Tero},
  title = {Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives},
  journal = {BioData Mining},
  volume = {6},
  year = {2013},
  number = {1},
  pages = {5},
  url = {http://www.biodatamining.org/content/6/1/5},
  doi = {10.1186/1756-0381-6-5}
}
@article{waegeman2012learninggraded,
  author = {Waegeman, Willem and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and Stock, Michiel and De Baets, Bernard},
  title = {A Kernel-based Framework for Learning Graded Relations from Data},
  journal = {IEEE Transactions on Fuzzy Systems},
  volume = {20},
  number = {6},
  pages = {1090--1101},
  doi = {10.1109/TFUZZ.2012.2194151},
  url = {http://dx.doi.org/10.1109/TFUZZ.2012.2194151},
  issn = {1063-6706},
  pdf = {graded_postprint.pdf},
  year = {2012},
  month = {December}
}
@article{pahikkala2012efficientcv,
  author = {Pahikkala, Tapio and Suominen, Hanna and Boberg, Jorma},
  affiliation = {Department of Information Technology and Turku Centre for Computer Science, University of Turku, 20014 Turku, Finland},
  title = {Efficient cross-validation for kernelized least-squares regression with sparse basis expansions},
  journal = {Machine Learning},
  publisher = {Springer Netherlands},
  issn = {0885-6125},
  pages = {381-407},
  volume = {87},
  number = {3},
  url = {http://dx.doi.org/10.1007/s10994-012-5287-6},
  doi = {10.1007/s10994-012-5287-6},
  year = {2012},
  month = {June},
  pdf = {CV_postprint.pdf}
}
@article{pahikkala2012wrappergwas,
  author = {Pahikkala, Tapio and Okser, Sebastian and Airola, Antti and Salakoski, Tapio and Aittokallio, Tero},
  title = {Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations},
  journal = {Algorithms for Molecular Biology},
  volume = {7},
  year = {2012},
  number = {1},
  pages = {11},
  url = {http://www.almob.org/content/7/1/11},
  doi = {10.1186/1748-7188-7-11},
  issn = {1748-7188}
}
@article{gieseke2012recurrent,
  author = {Gieseke, Fabian and Kramer, Oliver and Airola, Antti and Pahikkala, Tapio},
  title = {Efficient recurrent local search strategies for semi- and unsupervised regularized least-squares classification},
  journal = {Evolutionary Intelligence},
  publisher = {Springer},
  issn = {1864-5909},
  year = {2012},
  pages = {189--205},
  url = {http://dx.doi.org/10.1007/s12065-012-0068-5},
  doi = {10.1007/s12065-012-0068-5},
  pdf = {pdf/author_version_evolutionary_intelligence_2012.pdf},
  volume = {5},
  number = {3},
  month = {September}
}
@article{pahikkala2012parallelizedonline,
  author = {Pahikkala, Tapio and Airola, Antti and Xu, Thomas Canhao and Liljeberg, Pasi and Tenhunen, Hannu and Salakoski, Tapio},
  title = {Parallelized Online Regularized Least-Squares for Adaptive Embedded Systems},
  journal = {International Journal of Embedded and Real-Time Communication Systems},
  month = {April},
  volume = {3},
  number = {2},
  year = {2012},
  pages = {73--91},
  issn = {1947-3176},
  publisher = {IGI Global},
  doi = {10.4018/jertcs.2012040104}
}
@article{bjorne2011sharedtaskext,
  author = {Bj\"{o}rne, Jari and Heimonen, Juho and Ginter, Filip and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  title = {Extracting Contextualized Complex Biological Events with Rich Graph-Based Feature Sets},
  journal = {Computational Intelligence},
  year = {2011},
  volume = {27},
  number = {4},
  pages = {541--557},
  month = {November}
}
@article{airola2011ranksvm,
  author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  title = {Training linear ranking {SVM}s in linearithmic time using red-black trees},
  journal = {Pattern Recognition Letters},
  year = {2011},
  volume = {32},
  number = {9},
  day = {1},
  month = {July},
  pages = {1328--1336},
  doi = {10.1016/j.patrec.2011.03.014},
  url = {http://dx.doi.org/10.1016/j.patrec.2011.03.014}
}
@article{airola2011experimental,
  author = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
  title = {An experimental comparison of cross-validation techniques for estimating the area under the {ROC} curve},
  journal = {Computational Statistics \& Data Analysis},
  year = {2011},
  volume = {55},
  number = {4},
  pages = {1828--1844},
  month = {April},
  doi = {10.1016/j.csda.2010.11.018},
  url = {http://dx.doi.org/10.1016/j.csda.2010.11.018}
}
@article{airola2011nystromcv,
  author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  title = {On learning and cross-validation with decomposed {N}ystr{\"o}m approximation of kernel matrix},
  journal = {Neural Processing Letters},
  volume = {33},
  number = {1},
  month = {February},
  year = {2011},
  pages = {17--30},
  doi = {10.1007/s11063-010-9159-4},
  url = {http://dx.doi.org/doi:10.1007/s11063-010-9159-4}
}
@article{pahikkala2010reciprocalkm,
  author = {Pahikkala, Tapio and Waegeman, Willem and Tsivtsivadze, Evgeni and Salakoski, Tapio and De Baets, Bernard},
  title = {Learning Intransitive Reciprocal Relations with Kernel Methods},
  journal = {European Journal of Operational Research},
  month = {November},
  year = {2010},
  volume = {206},
  pages = {676--685},
  number = {3},
  doi = {10.1016/j.ejor.2010.03.018},
  url = {http://dx.doi.org/10.1016/j.ejor.2010.03.018}
}
@article{pahikkala2009preferences,
  author = {Pahikkala, Tapio and Tsivtsivadze, Evgeni and Airola, Antti and J{\"a}rvinen, Jouni and Boberg, Jorma},
  title = {An Efficient Algorithm for Learning to Rank from Preference Graphs},
  journal = {Machine Learning},
  year = {2009},
  month = {April},
  volume = {75},
  pages = {129--165},
  number = {1},
  doi = {http://dx.doi.org/10.1007/s10994-008-5097-z},
  pdf = {http://staff.cs.utu.fi/~aatapa/publications/jPaTsAiJaBo09a.full.pdf},
  url = {http://dx.doi.org/10.1007/s10994-008-5097-z}
}
@article{pahikkala2009matrix,
  author = {Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and J\"{a}rvinen, Jouni and Salakoski, Tapio},
  title = {Matrix representations, linear transformations, and kernels for disambiguation in natural language},
  journal = {Machine Learning},
  year = {2009},
  month = {February},
  volume = {74},
  pages = {133--158},
  number = {2},
  address = {Hingham, MA, USA},
  doi = {http://dx.doi.org/10.1007/s10994-008-5082-6},
  pdf = {http://staff.cs.utu.fi/~aatapa/publications/jPaPyBoJaSa08a.pdf},
  issn = {0885-6125},
  publisher = {Kluwer Academic Publishers},
  url = {http://dx.doi.org/10.1007/s10994-008-5082-6}
}
@article{tsivtsivadze2009localityjournal,
  author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
  title = {Locality Kernels for Sequential Data and Their Applications to Parse Ranking},
  journal = {Applied Intelligence},
  year = {2009},
  volume = {31},
  pages = {81--88},
  number = {1}
}
@article{airola08allpathsbmc,
  author = {Airola, Antti and Pyysalo, Sampo and Bj\"{o}rne, Jari and Pahikkala, Tapio and Ginter, Filip and Salakoski, Tapio},
  title = {All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning.},
  journal = {BMC Bioinformatics},
  year = {2008},
  volume = {9 Suppl 11}
}
@article{aittokallio2007inspiratory,
  author = {Aittokallio, Tero and Malminen, Jani S. and Pahikkala, Tapio and Polo, Olli and Nevalainen, Olli},
  title = {Inspiratory Flow Shape Clustering: An Automated Method to Monitor Upper Airway Performance During Sleep},
  journal = {Computer Methods and Programs in Biomedicine},
  year = {2007},
  volume = {85},
  pages = {8--18},
  number = {1},
  month = {Jan},
  doi = {10.1016/j.cmpb.2006.09.012},
  url = {http://dx.doi.org/10.1016/j.cmpb.2006.09.012}
}
@article{hiissa07,
  author = {Hiissa, Marketta and Pahikkala, Tapio and Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salanter{\"a}, Sanna and Salakoski, Tapio},
  title = {Towards automated classification of intensive care nursing narratives},
  journal = {International Journal of Medical Informatics},
  year = {2007},
  month = {December},
  volume = {76},
  number = {Supplement 3},
  pages = {S362--S368},
  doi = {http://dx.doi.org/10.1016/j.ijmedinf.2007.03.003}
}
@article{vahamaa2007dd,
  author = {V{\"a}h{\"a}maa, Heidi and Ojala, Pekka and Pahikkala, Tapio and Nevalainen, Olli S. and Lahesmaa, Riitta and Aittokallio, Tero},
  title = {Computer-assisted identification of multi-trace electrophoretic patterns in differential display experiments},
  journal = {Electrophoresis},
  year = {2007},
  volume = {28},
  pages = {879--893},
  number = {6},
  doi = {doi:10.1002/elps.200600424},
  url = {http://dx.doi.org/doi:10.1002/elps.200600424}
}
@article{pyysalo06evaluation,
  author = {Pyysalo, Sampo and Ginter, Filip and Pahikkala, Tapio and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  title = {Evaluation of Two Dependency Parsers on Biomedical Corpus Targeted at Protein-Protein Interactions},
  journal = {International Journal of Medical Informatics},
  year = {2006},
  month = {June},
  volume = {75},
  pages = {430--442},
  number = {6}
}
@article{pahikkala05contextual,
  author = {Pahikkala, Tapio and Ginter, Filip and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  title = {Contextual Weighting for Support Vector Machines in Literature Mining: {An} Application to Gene Versus Protein Name Disambiguation},
  journal = {BMC Bioinformatics},
  year = {2005},
  volume = {6},
  pages = {157},
  number = {1},
  doi = {http://dx.doi.org/doi:10.1186/1471-2105-6-157}
}
@article{aittokallio2003electrophoretic,
  author = {Aittokallio, Tero and Pahikkala, Tapio and Ojala, Pekka and Nevalainen, Timo J. and Nevalainen, Olli},
  title = {Electrophoretic Signal Comparison Applied to {mRNA} Differential Display Analysis},
  journal = {BioTechniques},
  year = {2003},
  volume = {34},
  pages = {116--122},
  number = {1},
  month = {Jan},
  url = {http://www.biotechniques.com/multimedia/archive/00010/03341rr02_10316a.pdf}
}
@proceedings{tarkoma2012ytp,
  editor = {Tarkoma, Sasu and K{\"a}m{\"a}r{\"a}inen, Joni-Kristian and Pahikkala, Tapio},
  title = {The Federated Computer Science Event},
  publisher = {Unigrafia Oy},
  address = {Helsinki, Finland},
  year = {2012},
  url = {http://www.cs.helsinki.fi/u/starkoma/ytp/YTP-Proceedings-2012.pdf}
}
@proceedings{pahikkala2010step,
  editor = {Pahikkala, Tapio and V{\"a}yrynen, Jaakko and Kortela, Jukka and Airola, Antti},
  title = {Proceedings of the 14th Finnish Artificial Intelligence Conference, STeP 2010},
  year = {2010},
  series = {Publications of the Finnish Artificial Intelligence Society},
  publisher = {Aalto-Print},
  address = {Espoo, Finland},
  number = {25},
  pages = {86}
}
@proceedings{salakoski06fintal,
  editor = {Salakoski, Tapio and Ginter, Filip and Pyysalo, Sampo and Pahikkala, Tapio},
  title = {Proceedings of the Fifth International Conference on Natural Language Processing (FinTAL)},
  year = {2006},
  month = {August},
  volume = {4139},
  series = {Lecture Notes in Artificial Intelligence},
  publisher = {Springer},
  isbn = {3-540-37334-9, 978-3-540-37334-6},
  issn = {0302-9743},
  address = {Berlin, Heidelberg},
  location = {Turku, Finland},
  doi = {10.1007/11816508}
}
@inproceedings{viljanen2016useractivity,
  author = {Viljanen, Markus and Airola, Antti and Pahikkala, Tapio and Heikkonen, Jukka},
  editor = {Karpouzis, Kostas and Smith, Gillian and Yannakakis, Georgios N. and Thompson, Tommy},
  title = {User Activity Decay in Mobile Games Determined by Simple Differential Equations?},
  booktitle = {The annual IEEE Conference on Computational Intelligence and Games (IEEE CIG)},
  year = {2016},
  pages = {126--133},
  publisher = {IEEE},
  doi = {10.1109/CIG.2016.7860403}
}
@inproceedings{viljanen2016modeling,
  author = {Viljanen, Markus and Airola, Antti and Pahikkala, Tapio and Heikkonen, Jukka},
  editor = {Karpouzis, Kostas and Smith, Gillian and Yannakakis, Georgios N. and Thompson, Tommy},
  title = {Modelling User Retention in Mobile Games},
  booktitle = {The annual IEEE Conference on Computational Intelligence and Games (IEEE CIG)},
  year = {2016},
  pages = {62--69},
  publisher = {IEEE},
  doi = {10.1109/CIG.2016.7860393}
}
@inproceedings{montoya2015detecting,
  author = {Montoya Perez, Ileana and Toivonen, Jussi and Movahedi, Parisa and Merisaari, Harri and Pesola, Marko and Taimen, Pekka and Bostr{\"o}m, Peter J. and Kiviniemi, Aida and Aronen, Hannu J. and Pahikkala, Tapio and Jambor, Ivan},
  editor = {Bordallo L{\'{o}}pez, Miguel and Hadid, Abdenour and Pietik{\"{a}}inen, Matti},
  title = {Diffusion Weighted Imaging of Prostate Cancer: Prediction of Cancer using Texture Features from Parametric Maps of the Monoexponential and Kurtosis functions},
  booktitle = {The 6th International Conference on Image Processing Theory, Tools and Applications (IPTA 2016)},
  year = {2016},
  doi = {10.1109/IPTA.2016.7820993},
  month = {December}
}
@inproceedings{farahnakian2016selfadaptive,
  author = {Farahnakian, Fahimeh and Bahsoon, Rami and Liljeberg, Pasi and Pahikkala, Tapio},
  editor = {Foster, Ian and Radia, Nimish},
  title = {Self-adaptive Resource Management System in IaaS Clouds},
  booktitle = {IEEE International Conference on Cloud Computing (CLOUD 2016)},
  year = {2016},
  publisher = {IEEE},
  pages = {553--560},
  doi = {10.1109/CLOUD.2016.0079},
  month = {June}
}
@incollection{gieseke2015batchinteractive,
  author = {Gieseke, Fabian and Pahikkala, Tapio and Heskes, Tom},
  editor = {Fromont, Elisa and De Bie, Tijl and van Leeuwen, Matthijs},
  title = {Batch Steepest-Descent-Mildest-Ascent for Interactive Maximum Margin Clustering},
  booktitle = {The Fourteenth International Symposium on Intelligent Data Analysis (IDA 2015)},
  year = {2015},
  volume = {9385},
  series = {Lecture Notes in Computer Science},
  doi = {10.1007/978-3-319-24465-5_9},
  url = {http://dx.doi.org/10.1007/978-3-319-24465-5_9},
  publisher = {Springer International Publishing},
  pages = {95--107}
}
@inproceedings{Nevalainen2015detecting,
  author = {Nevalainen, Paavo and Middleton, Maarit and Kaate, Ilkka and Pahikkala, Tapio and Sutinen, Raimo and Heikkonen, Jukka},
  editor = {Jennane, Rachid},
  title = {Detecting stony areas based on ground surface curvature distribution},
  booktitle = {The 5th International Conference on Image Processing Theory, Tools and Applications (IPTA 2015)},
  year = {2015},
  pages = {581--587},
  doi = {10.1109/IPTA.2015.7367215},
  month = {November}
}
@inproceedings{Fattah2015LowOverhead,
  author = {Fattah, Mohammad and Airola, Antti and Ausavarungnirun, Rachata and Mirzaei, Nima and Liljeberg, Pasi and Plosila, Juha and Mohammadi, Siamak and Pahikkala, Tapio and Mutlu, Onur and Tenhunen, Hannu},
  editor = {Ivanov, Andr{\'{e}} and Marculescu, Diana and Pande, Partha Pratim and Flich, Jos{\'{e}} and Pattabiraman, Karthik},
  title = {A Low-Overhead, Fully-Distributed, Guaranteed-Delivery Routing Algorithm for Faulty Network-on-Chips},
  booktitle = {Proceedings of the 9th International Symposium on Networks-on-Chip (NOCS'15)},
  location = {Vancouver, BC, Canada},
  month = {September},
  year = {2015},
  pages = {18:1--18:8},
  publisher = {{ACM}},
  doi = {10.1145/2786572.2786591},
  url = {http://doi.acm.org/10.1145/2786572.2786591}
}
@inproceedings{naula2015lowcost,
  author = {Naula, Pekka and Airola, Antti and Salakoski, Tapio and Pahikkala, Tapio},
  editor = {Ali, Moonis and Kwon, Young Sig and Lee, Chang{-}Hwan and Kim, Juntae and Kim, Yongdai},
  title = {Learning Low Cost Multi-Target Models by Enforcing Sparsity},
  booktitle = {The 28th International Conference on Industrial, Engineering \& Other Applications of Applied Intelligent Systems (IEA/AIE 2015)},
  publisher = {Springer},
  series = {Lecture Notes in Computer Science},
  url = {http://dx.doi.org/10.1007/978-3-319-19066-2_25},
  doi = {10.1007/978-3-319-19066-2_25},
  year = {2015},
  pages = {252--261}
}
@inproceedings{Xu2015traffic,
  author = {Xu, Thomas Canhao and Pohjankukka, Jonne and Nevalainen, Paavo and Lepp{\"{a}}nen, Ville and Pahikkala, Tapio},
  editor = {Lorenz, Pascal and Maciaszek, Leszek A.},
  title = {Parallel Applications and On-chip Traffic Distributions: Observation, Implication and Modelling},
  booktitle = {Proceedings of the 10th International Conference on Software Engineering and Applications (ICSOFT-EA)},
  location = {Colmar, Alsace, France},
  month = {July},
  pages = {443--449},
  year = {2015},
  url = {http://dx.doi.org/10.5220/0005553604430449},
  doi = {10.5220/0005553604430449}
}
@inproceedings{Farahnakian2015Utilization,
  author = {Farahnakian, Fahimeh and Pahikkala, Tapio and Liljeberg, Pasi and Plosila, Juha and Tenhunen, Hannu},
  editor = {Pu, Calton and Mohindra, Ajay},
  title = {Utilization Prediction Aware {VM} Consolidation Approach for Green Cloud Computing},
  booktitle = {8th {IEEE} International Conference on Cloud Computing (CLOUD 2015)},
  location = {New York City, NY, USA},
  month = {June},
  pages = {381--388},
  year = {2015},
  publisher = {{IEEE}}
}
@inproceedings{movahedi2015rlskmeansid,
  author = {Movahedi, Parisa and Nevalainen, Paavo and Viljanen, Markus and Pahikkala, Tapio},
  editor = {De Marsico, Maria and Figueiredo, M{\'{a}}rio A. T. and Fred, Ana L. N.},
  title = {Fast Regularized Least Squares and k-means Clustering Method For Intrusion Detection Systems},
  booktitle = {Proceedings of the 4th International Conference on Pattern Recognition Applications and Methods (ICPRAM 2015)},
  year = {2015},
  publisher = {SciTePress},
  pages = {264--269},
  doi = {10.5220/0005246802640269}
}
@inproceedings{pahikkala2014twostep,
  author = {Pahikkala, Tapio and Stock, Michiel and Airola, Antti and Aittokallio, Tero and De Baets, Bernard and Waegeman, Willem},
  editor = {Calders, Toon and Esposito, Floriana and H{\"u}llermeier, Eyke and Meo, Rosa},
  title = {A two-step learning approach for solving full and almost full cold start problems in dyadic prediction},
  booktitle = {Machine Learning and Knowledge Discovery in Databases (ECML PKDD 2014)},
  volume = {8725},
  pages = {517--532},
  series = {Lecture Notes in Computer Science},
  year = {2014},
  publisher = {Springer},
  doi = {10.1007/978-3-662-44851-9_33}
}
@inproceedings{pahikkala2014fastgradient,
  author = {Pahikkala, Tapio},
  editor = {Fr{\"a}nti, Pasi and Brown, Gavin and Loog, Marco and Escolano, Francisco and Pelillo, Marcello},
  title = {Fast Gradient Computation for Learning with Tensor Product Kernels and Sparse Training Labels},
  booktitle = {Structural, Syntactic, and Statistical Pattern Recognition (S+SSPR 2014)},
  year = {2014},
  publisher = {Springer},
  series = {Lecture Notes in Computer Science},
  volume = {8621},
  pages = {123--132},
  doi = {10.1007/978-3-662-44415-3_13},
  preprint = {http://staff.cs.utu.fi/~aatapa/publications/Pahikkala2014SSSPR.pdf}
}
@inproceedings{heimonen2014properties,
  author = {Heimonen, Juho and Salakoski, Tapio and Pahikkala, Tapio},
  editor = {Fr{\"a}nti, Pasi and Brown, Gavin and Loog, Marco and Escolano, Francisco and Pelillo, Marcello},
  title = {Properties of Object-Level Cross-Validation Schemes for Symmetric Pair-Input Data},
  booktitle = {Structural, Syntactic, and Statistical Pattern Recognition (S+SSPR 2014)},
  year = {2014},
  publisher = {Springer},
  series = {Lecture Notes in Computer Science},
  volume = {8621},
  pages = {384--393},
  doi = {10.1007/978-3-662-44415-3_39}
}
@inproceedings{pohjankukka2014arcticsoil,
  author = {Pohjankukka, Jonne and Nevalainen, Paavo and Pahikkala, Tapio and Hyv{\"o}nen, Eija and Sutinen, Raimo and H{\"a}nninen, Pekka and Heikkonen, Jukka},
  editor = {Borga, Magnus and Heyden, Anders and Laurendeau, Denis and Felsberg, Michael and Boyer, Kim},
  title = {Arctic soil hydraulic conductivity and soil type recognition based on aerial gamma-ray spectroscopy and topographical data},
  booktitle = {Proceedings of the 22nd International Conference on Pattern Recognition (ICPR 2014)},
  year = {2014},
  month = {Aug},
  pages = {1822--1827},
  doi = {10.1109/ICPR.2014.319},
  publisher = {IEEE}
}
@inproceedings{pohjankukka2014permeability,
  author = {Pohjankukka, Jonne and Nevalainen, Paavo and Pahikkala, Tapio and Hyv\"onen, Eija and H\"anninen, Pekka and Sutinen, Raimo and Ala-Ilom\"aki, Jari and Heikkonen, Jukka},
  editor = {Iliadis, Lazaros and Maglogiannis, Ilias and Papadopoulos, Harris},
  title = {Predicting water permeability of the soil based on open data},
  year = {2014},
  booktitle = {Proceedings of the 10th International Conference on Artificial Intelligence Applications and Innovations (AIAI 2014)},
  series = {IFIP Advances in Information and Communication Technology},
  volume = {436},
  pages = {436--446},
  publisher = {Springer},
  doi = {10.1007/978-3-662-44654-6_43}
}
@inproceedings{moen2014towards,
  author = {Moen, Hans and Heimonen, Juho and Murtola, Laura-Maria and Airola, Antti and Pahikkala, Tapio and Ter{\"a}v{\"a}, Virpi and Danielsson-Ojala, Riitta and Salakoski, Tapio and Salanter{\"a}, Sanna},
  editor = {Jaatun, Ellen A.A. and Brooks, Elizabeth and Berntsen, Kirsti and Gilstad, Heidi and Jaatun, Martin Gilje},
  title = {On Evaluation of Automatically Generated Clinical Discharge Summaries},
  booktitle = {Proceedings of the 2nd European Workshop on Practical Aspects of Health Informatics (PAHI 2014)},
  pages = {101--114},
  year = {2014},
  series = {CEUR Workshop Proceedings},
  volume = {1251},
  publisher = {CEUR-WS.org}
}
@inproceedings{xu2014bdmap,
  author = {Xu, Thomas Canhao and Toivonen, Jussi and Pahikkala, Tapio and Lepp{\"a}nen, Ville},
  title = {BDMap: A Heuristic Application Mapping Algorithm for the Big Data Era},
  booktitle = {Proceedings of the 14th IEEE International Conference on Scalable Computing and Communications (ScalCom-2014)},
  year = {2014},
  publisher = {IEEE},
  pages = {821--828}
}
@inproceedings{farahnakian2014Hierarchical,
  author = {Farahnakian, Fahimeh and Liljeberg, Pasi and Pahikkala, Tapio and Plosila, Juha and Tenhunen, Hannu},
  title = {Hierarchical VM Management Architecture for Cloud Data Centers},
  booktitle = {The 6th International Conference on Cloud Computing (CloudCom 2014)},
  year = {2014},
  month = {December},
  pages = {306--311}
}
@inproceedings{farahnakian2014multiagent,
  author = {Farahnakian, Fahimeh and Pahikkala, Tapio and Liljeberg, Pasi and Plosila, Juha and Tenhunen, Hannu},
  title = {Multi-Agent based Architecture for Dynamic VM Consolidation in Cloud Data Centers},
  booktitle = {40th Euromicro Conference on Software Engineering and Advanced Applications (SEAA 2014)},
  year = {2014},
  month = {August},
  pages = {111--118}
}
@inproceedings{farahnakian2014antcloud,
  author = {Farahnakian, Fahimeh and Ashraf, Adnan and Liljeberg, Pasi and Pahikkala, Tapio and Plosila, Juha and Porres, Ivan and Tenhunen, Hannu},
  editor = {Sussman, Alan and Fong, Liana L. and Yau, Stephen S. and Feig, Ephraim and Kesselman, Carl},
  title = {Energy-Aware Dynamic {VM} Consolidation in Cloud Data Centers Using Ant Colony System},
  booktitle = {IEEE International Conference on Cloud Computing (CLOUD 2014)},
  year = {2014},
  month = {June},
  pages = {104--111},
  publisher = {IEEE}
}
@inproceedings{gieseke2013polynomialbounds,
  author = {Gieseke, Fabian and Pahikkala, Tapio and Igel, Christian},
  editor = {Ong, Cheng Soon and Ho, Tu Bao},
  title = {Polynomial Runtime Bounds for Fixed-Rank Unsupervised Least-Squares Classification},
  journal = {Journal of Machine Learning Research -- Proceedings Track},
  booktitle = {Proceedings of the 5th Asian Conference on Machine Learning (ACML 2013)},
  year = {2013},
  volume = {29},
  series = {JMLR Workshop and Conference Proceedings},
  pages = {62--71},
  month = {November},
  publisher = {JMLR},
  url = {http://jmlr.org/proceedings/papers/v29/Gieseke13.pdf}
}
@inproceedings{xu2013nocfft,
  author = {Xu, Thomas Canhao and Pahikkala, Tapio and Liljeberg, Pasi and Plosila, Juha and Tenhunen, Hannu},
  title = {Optimized Multicore Architectures for Data Parallel Fast Fourier Transform},
  booktitle = {Proceedings of the 14th International Conference on Computer Systems and Technologies},
  year = {2013},
  publisher = {The Association for Computing Machinery (ACM)},
  series = {CompSysTech '13},
  location = {Ruse, Bulgaria},
  pages = {75--82},
  url = {http://doi.acm.org/10.1145/2516775.2516808},
  doi = {10.1145/2516775.2516808},
  address = {New York, NY, USA}
}
@inproceedings{bjorne2013japanese,
  author = {Bj\"{o}rne, Jari and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  title = {Analyzing the Japanese Toxicogenomics Project Dataset with SVM and RLS Classifiers},
  booktitle = {13th Annual International Conference on Critical Assessment of Massive Data Analysis (CAMDA 2013)},
  year = {2013}
}
@inproceedings{okser2013parallelfs,
  author = {Okser, Sebastian and Airola, Antti and Salakoski, Tapio and Aittokallio, Tero and Pahikkala, Tapio},
  editor = {Manninen, Pekka and {\"O}ster, Per},
  title = {Parallel Feature Selection for Regularized Least-Squares},
  booktitle = {Proceedings of the 11th international conference on Applied Parallel and Scientific Computing (PARA 2012), Revised Selected Papers},
  volume = {7782},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer},
  pages = {280--294},
  year = {2013},
  doi = {10.1007/978-3-642-36803-5_20}
}
@inproceedings{airola2013healthcare,
  author = {Airola, Antti and Pahikkala, Tapio and Lundgr{\'e}n-Laine, Helj{\"a} and Santalahti, Anne and Salanter{\"a}, Sanna and Salakoski, Tapio},
  editor = {Suominen, Hanna},
  title = {A Machine Learning Approach Towards Early Detection of Frequent Health Care Users},
  booktitle = {The 4th International Louhi Workshop on Health Document Text Mining and Information Analysis (Louhi 2013)},
  year = {2013}
}
@inproceedings{farahnakian2013cloudstuff,
  author = {Farahnakian, Fahimeh and Pahikkala, Tapio and Liljeberg, Pasi and Plosila, Juha},
  title = {Energy Aware Consolidation Algorithm Based on K-Nearest Neighbor Regression for Cloud Data Centers},
  booktitle = {IEEE/ACM Utility and Cloud Computing conference (UCC)},
  year = {2013},
  pages = {256--259},
  publisher = {IEEE},
  month = {December}
}
@inproceedings{pahikkala2012shakingrls,
  author = {Pahikkala, Tapio and Airola, Antti and Gieseke, Fabian and Kramer, Oliver},
  editor = {Zaki, Mohammed J. and Siebes, Arno and Yu, Jeffrey Xu and Goethals, Bart and Webb, Geoff and Wu, Xindong},
  title = {Unsupervised Multi-Class Regularized Least-Squares Classification},
  booktitle = {The 12th IEEE International Conference on Data Mining (ICDM 2012)},
  publisher = {IEEE Computer Society},
  pages = {585--594},
  year = {2012},
  month = {December},
  pdf = {pdf/icdm2012preprint.pdf},
  doi = {10.1109/ICDM.2012.71}
}
@inproceedings{stock2012monadic,
  author = {Stock, Michiel and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and De Baets, Bernard and Waegeman, Willem},
  editor = {Ray, Oliver and Inoue, Katsumi},
  title = {Learning Monadic and Dyadic Relations: Three Case Studies in Systems Biology},
  booktitle = {Proceedings of the ECML/PKDD 2012 Workshop on Learning and Discovery in Symbolic Systems Biology},
  year = {2012},
  pages = {74--84},
  month = {September}
}
@inproceedings{gieseke2012sqn,
  author = {Gieseke, Fabian and Airola, Antti and Pahikkala, Tapio and Kramer, Oliver},
  editor = {Latorre Carmona, Pedro and S{\'a}nchez, J. Salvador and Fred, Ana L. N.},
  title = {Sparse Quasi-Newton Optimization for Semi-Supervised Support Vector Machines},
  booktitle = {Proceedings of the 1st International Conference on Pattern Recognition Applications and Methods (ICPRAM)},
  year = {2012},
  publisher = {SciTePress},
  pages = {45--54}
}
@inproceedings{xu2012blunoc,
  author = {Xu, Thomas Canhao and Pahikkala, Tapio and Airola, Antti and Liljeberg, Pasi and Plosila, Juha and Salakoski, Tapio and Tenhunen, Hannu},
  editor = {Min, Geyong and Hu, Jia and Liu, Lei (Chris) and Yang, Laurence T. and Seelam, Seetharami and Lefevre, Laurent},
  title = {Implementation and Analysis of Block Dense Matrix Decomposition on Network-on-Chips},
  booktitle = {The 14th IEEE International Conference on High Performance Computing and Communications (HPCC-2012)},
  year = {2012},
  publisher = {IEEE Computer Society},
  month = {June},
  pages = {516--523},
  doi = {10.1109/HPCC.2012.76}
}
@inproceedings{waegeman2011learningvalued,
  author = {Waegeman, Willem and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and De Baets, Bernard},
  editor = {Melo-Pinto, Pedro and Couto, Pedro and Ser\^{o}dio, Carlos and Fodor, J\'{a}nos and De Baets, Bernard},
  title = {Learning Valued Relations from Data},
  booktitle = {Eurofuse 2011},
  year = {2012},
  publisher = {Springer},
  series = {Advances in Intelligent and Soft Computing},
  volume = {107},
  pages = {257--268},
  doi = {10.1007/978-3-642-24001-0_24},
  url = {http://dx.doi.org/10.1007/978-3-642-24001-0_24}
}
@inproceedings{naula2011grlsmultitask,
  author = {Naula, Pekka and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  editor = {Spiliopoulou, Myra and Wang, Haixun and Cook, Diane and Pei, Jian and Wang, Wei and Za{\"i}ane, Osmar and Wu, Xindong},
  title = {Greedy Regularized Least-Squares for Multi-Task Learning},
  booktitle = {11th IEEE International Conference on Data Mining Workshops (ICDMW'11)},
  publisher = {IEEE Computer Society},
  pages = {527--533},
  year = {2011},
  month = {December},
  doi = {10.1109/ICDMW.2011.91}
}
@inproceedings{okser2011fastgwas,
  author = {Okser, Sebastian and Pahikkala, Tapio and Airola, Antti and Aittokallio, Tero and Salakoski, Tapio},
  editor = {Chen, Yidong and Huang, Yufei and Dougherty, Edward},
  title = {Fast and Parallelized Greedy Forward Selection of Genetic Variants in Genome-Wide Association Studies},
  booktitle = {IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'11)},
  publisher = {IEEE Signal Processing Society},
  pages = {214--217},
  year = {2011},
  month = {December},
  doi = {10.1109/GENSiPS.2011.6169483}
}
@inproceedings{gieseke2011speedy,
  author = {Gieseke, Fabian and Kramer, Oliver and Airola, Antti and Pahikkala, Tapio},
  editor = {Bach, Joscha and Edelkamp, Stefan},
  title = {Speedy Local Search for Semi-Supervised Regularized Least-Squares},
  booktitle = {KI 2011: Advances in Artificial Intelligence},
  location = {Berlin, Germany},
  year = {2011},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer},
  pages = {87--98},
  volume = {7006},
  url = {http://dx.doi.org/10.1007/978-3-642-24455-1_8},
  doi = {10.1007/978-3-642-24455-1_8}
}
@inproceedings{bjorne2011drugchallenge,
  author = {Bj\"{o}rne, Jari and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  editor = {Segura-Bedmar, Isabel and Martinez, Paloma and Sanchez-Cisneros, Daniel},
  title = {Drug-Drug Interaction Extraction with {SVM} and {RLS} Classifiers},
  booktitle = {Proceedings of the 1st Challenge Task on Drug-Drug Interaction Extraction 2011},
  volume = {761},
  series = {CEUR Workshop Proceedings},
  publisher = {CEUR-WS.org},
  year = {2011},
  month = {September}
}
@inproceedings{airola2011improvedranksvm,
  author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  editor = {Honkela, Timo and Duch, W{\l}odzis{\l}aw and Girolami, Mark and Kaski, Samuel},
  booktitle = {Artificial Neural Networks and Machine Learning -- ICANN 2011},
  publisher = {Springer},
  location = {Heidelberg},
  series = {Lecture Notes in Computer Science},
  volume = {6791},
  year = {2011},
  isbn = {978-3-642-21734-0},
  title = {An Improved Training Algorithm for the Linear Ranking Support Vector Machine},
  pages = {134--141},
  month = {June}
}
@inproceedings{naula2011budgeted,
  author = {Naula, Pekka and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  editor = {Kofod-Petersen, Anders and Heintz, Fredrik and Langseth, Helge},
  title = {Learning Multi-Label Predictors under Sparsity Budget},
  booktitle = {Eleventh Scandinavian Conference on Artificial Intelligence, SCAI 2011},
  publisher = {IOS Press},
  volume = {227},
  series = {Frontiers in Artificial Intelligence and Applications},
  pages = {30--39},
  year = {2011},
  month = {May},
  isbn = {978-1-60750-753-6}
}
@inproceedings{pahikkala2011parallelonline,
  author = {Pahikkala, Tapio and Airola, Antti and Xu, Thomas Canhao and Liljeberg, Pasi and Tenhunen, Hannu and Salakoski, Tapio},
  editor = {Benavente-Peces, C{\'e}sar and Filipe, Joaquim},
  title = {A parallel online regularized least-squares machine learning algorithm for future multi-core processors},
  booktitle = {Proceedings of the 1st International Conference on Pervasive and Embedded Computing and Communication Systems (PECCS 2011)},
  month = {March},
  year = {2011},
  publisher = {SciTePress},
  pages = {590--599},
  location = {Algarve, Portugal},
  isbn = {978-989-8425-48-5}
}
@inproceedings{airola2010comparison,
  author = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
  editor = {D\v{z}eroski, Sa\v{s}o and Geurts, Pierre and Rousu, Juho},
  title = {A comparison of {AUC} estimators in small-sample studies},
  booktitle = {Proceedings of the third International Workshop on Machine Learning in Systems Biology},
  series = {JMLR Workshop and Conference Proceedings},
  year = {2010},
  volume = {8},
  pages = {3--13},
  publisher = {Journal of Machine Learning Research},
  url = {http://jmlr.csail.mit.edu/proceedings/papers/v8/airola10a/airola10a.pdf}
}
@inproceedings{pahikkala2010conditional,
  author = {Pahikkala, Tapio and Waegeman, Willem and Airola, Antti and Salakoski, Tapio and De Baets, Bernard},
  editor = {Balc{\'a}zar, Jos{\'e} L. and Bonchi, Francesco and Gionis, Aristides and Sebag, Mich{\`e}le},
  title = {Conditional Ranking on Relational Data},
  booktitle = {Machine Learning and Knowledge Discovery in Databases (ECML PKDD 2010)},
  location = {Barcelona, Spain},
  publisher = {Springer},
  series = {Lecture Notes in Computer Science},
  pages = {499--514},
  volume = {6322},
  year = {2010},
  url = {http://dx.doi.org/10.1007/978-3-642-15883-4_32},
  doi = {10.1007/978-3-642-15883-4_32}
}
@inproceedings{pahikkala2010greedyrls,
  author = {Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  editor = {Draghici, Sorin and Khoshgoftaar, Taghi M. and Palade, Vasile and Pedrycz, Witold and Wani, M. Arif and Zhu, Xingquan},
  title = {Speeding up Greedy Forward Selection for Regularized Least-Squares},
  booktitle = {Proceedings of The Ninth International Conference on Machine Learning and Applications (ICMLA'10)},
  publisher = {IEEE Computer Society},
  year = {2010},
  month = {December},
  pages = {325--330},
  url = {http://staff.cs.utu.fi/~aatapa/publications/inpPaAiSa10b.full.pdf},
  doi = {10.1109/ICMLA.2010.55}
}
@inproceedings{airola2010permutation,
  author = {Airola, Antti and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
  editor = {Draghici, Sorin and Khoshgoftaar, Taghi M. and Palade, Vasile and Pedrycz, Witold and Wani, M. Arif and Zhu, Xingquan},
  title = {Applying permutation tests for assessing the statistical significance of wrapper based feature selection},
  booktitle = {Proceedings of The Ninth International Conference on Machine Learning and Applications (ICMLA'10)},
  publisher = {IEEE},
  year = {2010},
  month = {December},
  pages = {989--994}
}
@inproceedings{airola2010largescale,
  author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  editor = {H{\"u}llermeier, Eyke and F{\"u}rnkranz, Johannes},
  title = {Large scale training methods for linear {RankRLS}},
  booktitle = {Proceedings of the {ECML/PKDD}-Workshop on Preference Learning {(PL-10)}},
  year = {2010}
}
@inproceedings{pahikkala2010fsrls,
  author = {Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  editor = {Kaski, Samuel and Miller, David J. and Oja, Erkki and Honkela, Antti},
  title = {Feature Selection for Regularized Least-Squares: New Computational Short-Cuts and Fast Algorithmic Implementations},
  booktitle = {Proceedings of the Twentieth IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010)},
  publisher = {IEEE},
  pages = {295--300},
  year = {2010},
  isbn = {978-1-4244-7876-7},
  url = {http://dx.doi.org/10.1109/MLSP.2010.5589210},
  doi = {10.1109/MLSP.2010.5589210},
  location = {Kittil{\"a}, Finland}
}
@inproceedings{pahikkala2010grankrls,
  author = {Pahikkala, Tapio and Airola, Antti and Naula, Pekka and Salakoski, Tapio},
  editor = {Gabrilovich, Evgeniy and Smola, Alexander J. and Tishby, Naftali},
  title = {Greedy {RankRLS}: a Linear Time Algorithm for Learning Sparse Ranking Models},
  booktitle = {SIGIR 2010 Workshop on Feature Generation and Selection for Information Retrieval},
  pages = {11--18},
  year = {2010},
  publisher = {ACM},
  url = {http://alex.smola.org/workshops/sigir10/contrib/Pahikkala.pdf}
}
@inproceedings{airola2009comparison,
  author = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
  editor = {D\v{z}eroski, Sa\v{s}o and Geurts, Pierre and Rousu, Juho},
  title = {A comparison of {AUC} estimators in small-sample studies},
  booktitle = {Proceedings of the Third International Workshop on Machine Learning in Systems Biology (MLSB'09)},
  publisher = {Helsinki University Printing House},
  year = {2009},
  pages = {15--23},
  address = {Helsinki, Finland}
}
@inproceedings{pahikkala2009beyond,
  author = {Pahikkala, Tapio and Waegeman, Willem and Tsivtsivadze, Evgeni and Salakoski, Tapio and De Baets, Bernard},
  editor = {H{\"u}llermeier, Eyke and F{\"u}rnkranz, Johannes},
  title = {From Ranking to Intransitive Preference Learning: Rock-Paper-Scissors and beyond},
  booktitle = {Proceedings of the {ECML/PKDD}-Workshop on Preference Learning {(PL-09)}},
  year = {2009},
  pages = {84--100}
}
@inproceedings{bjorne09sharedtask,
  author = {Bj\"{o}rne, Jari and Heimonen, Juho and Ginter, Filip and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  editor = {Tsujii, Jun'ichi},
  title = {Extracting Complex Biological Events with Rich Graph-Based Feature Sets},
  booktitle = {Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task},
  isbn = {978-1-932432-44-2},
  url = {http://www.aclweb.org/anthology/W09-1402},
  month = {June},
  location = {Boulder, Colorado},
  publisher = {Association for Computational Linguistics},
  year = {2009},
  pages = {10--18}
}
@inproceedings{gieseke2009evolutionary,
  author = {Gieseke, Fabian and Pahikkala, Tapio and Kramer, Oliver},
  editor = {Bottou, L\'{e}on and Littman, Michael},
  title = {Fast evolutionary maximum margin clustering},
  booktitle = {ICML '09: Proceedings of the 26th Annual International Conference on Machine Learning},
  year = {2009},
  volume = {382},
  series = {ACM International Conference Proceeding Series},
  pages = {361--368},
  address = {New York, NY, USA},
  month = {June},
  publisher = {ACM},
  doi = {http://doi.acm.org/10.1145/1553374.1553421},
  pdf = {http://www.cs.mcgill.ca/~icml2009/papers/245.pdf},
  url = {http://doi.acm.org/10.1145/1553374.1553421},
  isbn = {978-1-60558-516-1},
  location = {Montreal, Quebec, Canada}
}
@inproceedings{pahikkala2009holdout,
  author = {Pahikkala, Tapio and Suominen, Hanna and Boberg, Jorma and Salakoski, Tapio},
  editor = {Kolehmainen, Mikko and Toivanen, Pekka and Beliczynski, Bartlomiej},
  title = {Efficient Hold-Out for Subset of Regressors},
  booktitle = {{Proceedings of the 9th International Conference on Adaptive and Natural Computing Algorithms (ICANNGA'09)}},
  year = {2009},
  volume = {5495},
  series = {Lecture Notes in Computer Science},
  pages = {350--359},
  address = {Berlin, Germany},
  publisher = {Springer},
  doi = {10.1007/978-3-642-04921-7_36},
  url = {http://dx.doi.org/10.1007/978-3-642-04921-7_36}
}
@inproceedings{pahikkala2009benelearn,
  author = {Pahikkala, Tapio and Waegeman, Willem and Tsivtsivadze, Evgeni and De Baets, Bernard and Salakoski, Tapio},
  editor = {van Zaanen, Menno and Stehouwer, Herman and van Erp, Marieke},
  title = {Learning Intransitive Reciprocal Relations with Regularized Least-Squares},
  booktitle = {{Proceedings of the 18th Annual Belgian-Dutch Conference on Machine Learning (Benelearn 09)}},
  year = {2009},
  pages = {13--20},
  publisher = {Tilburg centre for Creative Computing},
  address = {Tilburg, The Netherlands}
}
@incollection{pahikkala2008aucmax,
  author = {Pahikkala, Tapio and Airola, Antti and Suominen, Hanna and Boberg, Jorma and Salakoski, Tapio},
  editor = {Holst, Anders and Kreuger, Per and Funk, Peter},
  title = {Efficient {AUC} Maximization with Regularized Least-Squares},
  booktitle = {Tenth Scandinavian Conference on Artificial Intelligence, SCAI 2008},
  publisher = {IOS Press},
  year = {2008},
  volume = {173},
  series = {Frontiers in Artificial Intelligence and Applications},
  pages = {12--19},
  address = {Amsterdam, Netherlands},
  pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaAiSuBoSa08a.pdf},
  location = {Stockholm, Sweden}
}
@inproceedings{pahikkala2008lpocv,
  author = {Pahikkala, Tapio and Airola, Antti and Boberg, Jorma and Salakoski, Tapio},
  editor = {Honkela, Timo and P{\"o}ll{\"a}, Matti and Paukkeri, Mari-Sanna and Simula, Olli},
  title = {Exact and Efficient Leave-Pair-Out Cross-Validation for Ranking {RLS}},
  booktitle = {Proceedings of the 2nd International and Interdisciplinary Conference on Adaptive Knowledge Representation and Reasoning (AKRR'08)},
  year = {2008},
  pages = {1--8},
  address = {Espoo, Finland},
  publisher = {Helsinki University of Technology},
  isbn = {978-951-22-9525-8},
  pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaAiBoSa08a.pdf}
}
@inproceedings{tsivtsivadze2008coreg,
  author = {Tsivtsivadze, Evgeni and Gieseke, Fabian and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
  editor = {H{\"u}llermeier, Eyke and F{\"u}rnkranz, Johannes},
  title = {Learning Preferences with Co-Regularized Least Squares},
  booktitle = {{ECML/PKDD-Workshop on Preference Learning (PL-08)}},
  year = {2008},
  pages = {55--62}
}
@inproceedings{tsivtsivadze08sparse,
  author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Airola, Antti and Boberg, Jorma and Salakoski, Tapio},
  editor = {Holst, Anders and Kreuger, Per and Funk, Peter},
  title = {A Sparse Regularized Least-Squares Preference Learning Algorithm},
  booktitle = {Tenth Scandinavian Conference on Artificial Intelligence, SCAI 2008},
  year = {2008},
  volume = {173},
  pages = {76--83},
  publisher = {IOS Press},
  series = {Frontiers in Artificial Intelligence and Applications}
}
@inproceedings{SuominenetalAKRR,
  author = {Suominen, Hanna and Pahikkala, Tapio and Salakoski, Tapio},
  editor = {Honkela, Timo and P{\"o}ll{\"a}, Matti and Paukkeri, Mari-Sanna and Simula, Olli},
  title = {Critical points in assessing learning performance via cross-validation},
  booktitle = {Proceedings of the 2nd International and Interdiciplinary Conference on Adaptive Knowledge Representation and Reasoning (AKRR 2008)},
  year = {2008},
  pages = {9--22},
  address = {Espoo, Finland},
  publisher = {Helsinki University of Technology},
  isbn = {978-951-22-9525-8}
}
@inproceedings{airola08bionlp,
  author = {Airola, Antti and Pyysalo, Sampo and Bj{\"{o}}rne, Jari and Pahikkala, Tapio and Ginter, Filip and Salakoski, Tapio},
  editor = {Demner-Fushman, Dina and Ananiadou, Sophia and Cohen, Kevin Bretonnel and Pestian, John and Tsujii, Jun'ichi and Webber, Bonnie},
  title = {A Graph Kernel for Protein-Protein Interaction Extraction},
  booktitle = {Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP'08)},
  year = {2008},
  pages = {1--9},
  publisher = {Association for Computational Linguistics},
  address = {Stroudsburg, PA, USA},
  url = {http://aclweb.org/anthology-new/W/W08/W08-0601.pdf},
  isbn = {978-1-932432-11-4}
}
@inproceedings{pahikkala07mlg,
  author = {Pahikkala, Tapio and Suominen, Hanna and Boberg, Jorma and Salakoski, Tapio},
  editor = {Frasconi, P and Kersting, K and Tsuda, K},
  title = {Transductive Ranking via Pairwise Regularized Least-Squares},
  booktitle = {The 5th International Workshop on Mining and Learning with Graphs (MLG'07)},
  year = {2007},
  pages = {175--178},
  location = {Florence, Italy}
}
@inproceedings{pahikkala2007rankrls,
  author = {Pahikkala, Tapio and Tsivtsivadze, Evgeni and Airola, Antti and Boberg, Jorma and Salakoski, Tapio},
  editor = {Joachims, Thorsten and Li, Hang and Liu, Tie-Yan and Zhai, ChengXiang},
  title = {Learning to Rank with Pairwise Regularized Least-Squares},
  booktitle = {SIGIR 2007 Workshop on Learning to Rank for Information Retrieval},
  year = {2007},
  pages = {27--33},
  pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaTsAiBoSa07a.pdf}
}
@inproceedings{hiissa2006towards,
  author = {Hiissa, Marketta and Pahikkala, Tapio and Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Eija Helena and Salanter{\"a}, Sanna and Salakoski, Tapio},
  editor = {Hasman, A and Haux, R and Van Der Lei, J and De Clercq, E and Roger France, FH},
  title = {Towards automated classification of intensive care nursing narratives},
  booktitle = {Ubiquity: Technologies for Better Health in Aging Societies. Proceedings of MIE 2006, the 20th International Congress of the European Federation of Medical Informatics},
  year = {2006},
  volume = {124},
  series = {Studies in Health Technology and Informatics},
  pages = {789--794},
  address = {Amsterdam, the Netherlands},
  publisher = {IOS Press}
}
@inproceedings{pahikkala06ltbayes,
  author = {Pahikkala, Tapio and Boberg, Jorma and Myll\"{a}ri, Aleksandr and Salakoski, Tapio},
  editor = {Salakoski, Tapio and Ginter, Filip and Pyysalo, Sampo and Pahikkala, Tapio},
  title = {Incorporating External Information in Bayesian Classifiers via Linear Feature Transformations},
  booktitle = {Proceedings of the 5th International Conference on Natural Language Processing FinTAL 06, Turku, Finland},
  year = {2006},
  volume = {4139},
  series = {Lecture Notes in Artificial Intelligence},
  pages = {399--410},
  publisher = {Springer},
  address = {Heidelberg},
  pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaBoMySa06a.pdf}
}
@inproceedings{tsivtsivadze2006locality,
  author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
  editor = {Ali, Moonis and Dapoigny, Richard},
  title = {Locality-Convolution Kernel and Its Application to Dependency Parse Ranking},
  booktitle = {Proceedings of the The 19th International Conference on Industrial, Engineering {\&} Other Applications of Applied Intelligent Systems},
  year = {2006},
  volume = {4031},
  series = {Lecture Notes in Artificial Intelligence},
  pages = {610--618},
  address = {Berlin},
  publisher = {Springer}
}
@inproceedings{pahikkala06rls,
  author = {Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
  editor = {Honkela, Timo and Raiko, Tapani and Kortela, Jukka and Valpola, Harri},
  title = {Fast n-Fold Cross-Validation for Regularized Least-Squares},
  booktitle = {Proceedings of the Ninth Scandinavian Conference on Artificial Intelligence (SCAI 2006)},
  year = {2006},
  series = {Publications of the Finnish Artificial Intelligence Society},
  volume = {22},
  pages = {83--90},
  address = {Espoo, Finland},
  publisher = {Helsinki University of Technology},
  isbn = {978-952-5677-00-3},
  pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaBoSa06a.pdf},
  location = {Espoo, Finland}
}
@inproceedings{pahikkala2006graph,
  author = {Pahikkala, Tapio and Tsivtsivadze, Evgeni and Boberg, Jorma and Salakoski, Tapio},
  editor = {G{\"a}rtner, Thomas and Garriga, Gemma C. and Meinl, Thorsten},
  title = {Graph Kernels versus Graph Representations: a Case Study in Parse Ranking},
  booktitle = {Proceedings of the ECML/PKDD'06 workshop on Mining and Learning with Graphs (MLG'06)},
  year = {2006},
  address = {Berlin, Germany},
  pdf = {http://tucs.fi/publications/attachment.php?fname=inpPaTsBoSa06a.pdf},
  location = {Berlin, Germany}
}
@inproceedings{suominen2006ranking,
  author = {Suominen, Hanna and Pahikkala, Tapio and Hiissa, Marketta and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salanter{\"a}, Sanna and Salakoski, Tapio},
  editor = {Gabrys, Bogdan and Howlett, Robert J. and Jain, Lakhmi C.},
  title = {Relevance ranking of intensive care nursing narratives},
  booktitle = {Knowledge-Based Intelligent Information and Engineering Systems. Proceedings of the 10th International Conference, KES 2006, Part I},
  year = {2006},
  volume = {4251},
  series = {Lecture Notes in Computer Science},
  pages = {720--727},
  address = {Berlin / Heidelberg, Germany},
  url = {http://dx.doi.org/10.1007/11892960_87},
  publisher = {Springer}
}
@inproceedings{tsivtsivadze2005ranking,
  author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and Myll\"{a}ri, Aleksandr and Salakoski, Tapio},
  editor = {Famili, A. Fazel and Kok, Joost N. and Pe{\~n}a, Jos{\'e} Manuel and Siebes, Arno and Feelders, A. J.},
  title = {Regularized Least-Squares for Parse Ranking},
  booktitle = {Proceedings of the 6th International Symposium on Intelligent Data Analysis},
  year = {2005},
  volume = {3646},
  series = {Lecture Notes in Computer Science},
  pages = {464--474},
  address = {Berlin},
  month = {September},
  publisher = {Springer},
  location = {Madrid, Spain}
}
@inproceedings{pahikkala05kernels,
  author = {Pahikkala, Tapio and Pyysalo, Sampo and Ginter, Filip and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  editor = {Russell, Ingrid and Markov, Zdravko},
  title = {Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks},
  booktitle = {Proceedings of the Eighteenth International Florida Artificial Intelligence Research Society Conference},
  year = {2005},
  pages = {442--447},
  address = {Menlo Park, CA, USA},
  month = {May},
  publisher = {AAAI Press},
  isbn = {1-57735-234-3},
  pdf = {www.tucs.fi/publications/attachment.php?fname=inpPaPyGiBoJaSa05a.pdf},
  location = {Clearwater Beach, Florida}
}
@inproceedings{pahikkala05improving,
  author = {Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and Myll{\"a}ri, Aleksandr and Salakoski, Tapio},
  editor = {Honkela, Timo and K{\"o}n{\"o}nen, Ville and P{\"o}ll{\"a}, Matti and Simula, Olli},
  title = {Improving the performance of Bayesian and support vector classifiers in word sense disambiguation using positional information},
  booktitle = {Proceedings of the International and Interdisciplinary Conference on Adaptive Knowledge Representation and Reasoning},
  year = {2005},
  pages = {90--97},
  address = {Espoo, Finland},
  publisher = {Helsinki University of Technology},
  isbn = {951-22-7723-9},
  pdf = {http://tucs.fi/publications/attachment.php?fname=inpPaPyBoMySa05a.pdf}
}
@inproceedings{ginter04extracting,
  author = {Ginter, Filip and Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  editor = {Tsumoto, Husaku and S\l{}owi\'{n}ski, Roman and Komorowski, Jan and Grzymala-Busse, Jerzy W.},
  title = {Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis},
  booktitle = {Proceedings of the Fourth International Conference on Rough Sets and Current Trends in Computing, Uppsala, Sweden},
  year = {2004},
  volume = {3066},
  series = {Lecture Notes in Computer Science},
  pages = {780--785},
  month = {June},
  publisher = {Springer, Heidelberg}
}
@inproceedings{pyysalo04analysis,
  author = {Pyysalo, Sampo and Ginter, Filip and Pahikkala, Tapio and Koivula, Jeppe and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  editor = {Collier, Nigel and Ruch, Patrick and Nazarenko, Adeline},
  title = {Analysis of {Link Grammar} on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions},
  booktitle = {Proceedings of Joint Workshop on Natural Language Processing in Biomedicine and its Applications JNLPBA 04, Geneva, Switzerland},
  year = {2004},
  pages = {15--21},
  month = {August}
}
@incollection{pahikkala2014parallelizedonline,
  author = {Pahikkala, Tapio and Airola, Antti and Xu, Thomas Canhao and Liljeberg, Pasi and Tenhunen, Hannu and Salakoski, Tapio},
  editor = {Virtanen, Seppo},
  title = {On Parallel Online Learning for Adaptive Embedded Systems},
  booktitle = {Advancing Embedded Systems and Real-Time Communications with Emerging Technologies},
  year = {2014},
  publisher = {IGI Global},
  address = {Hershey, PA, USA},
  chapter = {11},
  pages = {262--241}
}
@incollection{tsivtsivadze2010coreg,
  author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio and Heskes, Tom},
  editor = {F{\"u}rnkranz, Johannes and H{\"u}llermeier, Eyke},
  title = {Co-Regularized Least-Squares for Label Ranking},
  booktitle = {Preference Learning},
  year = {2010},
  publisher = {Springer},
  address = {Berlin Heidelberg},
  isbn = {978-3-642-14124-9},
  chapter = {6},
  edition = {1st},
  pages = {107--123},
  doi = {10.1007/978-3-642-14125-6_6},
  url = {http://dx.doi.org/10.1007/978-3-642-14125-6_6}
}
@incollection{suominen08measures,
  author = {Suominen, Hanna and Pyysalo, Sampo and Hiissa, Marketta and Ginter, Filip and Liu, Shuhua and Marghescu, Dorina and Pahikkala, Tapio and Back, Barbro and Karsten, Helena and Salakoski, Tapio},
  editor = {Song, M and Wu, Y-FB},
  title = {Performance Evaluation Measures for Text Mining},
  booktitle = {Handbook of Research on Text and Web Mining Technologies},
  year = {2008},
  pages = {724--747},
  address = {Hershey, Pennsylvania, USA},
  publisher = {IGI Global}
}
@incollection{tsivtsivadze2008kft,
  editor = {Liu, Ying and Sun, Aixin and Loh, Han Tong and Lu, Wen Feng and Lim, Ee-Peng},
  author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
  pages = {81--97},
  title = {Kernel Methods for Text Analysis},
  publisher = {Springer},
  year = {2008},
  volume = {116},
  series = {Studies in Computational Intelligence},
  booktitle = {Advances of Computational Intelligence in Industrial Systems}
}
@inproceedings{linderborg2017milkabstract,
  author = {Linderborg, Kaisa and Nuora, Anu and Tupasela, Tuomo and Tahvonen, Raija and Rokka, Susanna and Viitanen, Matti and M{\"a}kel{\"a}, Petri and Pohjankukka, Jonne and Pahikkala, Tapio and Yang, Baoru and Kallio, Heikki},
  title = {Effect of Homogenisation of Cow’s Milk on Postprandial Lipemia, Gastrointestinal Symptoms and Intestinal Pressure in Sensitive Individuals},
  booktitle = {15th Euro Fed Lipid Congress},
  url = {http://www.eurofedlipid.org/meetings/archive/uppsala2017/index.php},
  year = {2017}
}
@inproceedings{Merisaari2016ismrm,
  author = {Merisaari, Harri and Movahedi, Parisa and Montoya Perez, Ileana and Toivonen, Jussi and Pesola, Marko and Taimen, Pekka and Bostr{\"o}m, Peter and Pahikkala, Tapio and Aronen, Hannu J. and Jambor, Ivan},
  title = {Diffusion weighted imaging of prostate cancer: mathematical modeling of signal obtained using low b values},
  booktitle = {24th Annual Meeting of the International Society for Magnetic Resonance in Medicine},
  year = {2016}
}
@inproceedings{stock2015twostepabstract,
  author = {Stock, Michiel and Pahikkala, Tapio and Airola, Antti and De Baets, Bernard and Waegeman, Willem},
  editor = {Varma, Manik and Ciss{\'e}, Moustapha},
  title = {A two-step method to incorporate task features for large output spaces},
  booktitle = {The NIPS Workshop on Multi-class and Multi-label Learning in Extremely Large Label Spaces (Extreme Classification 2015)},
  year = {2015},
  month = {December}
}
@inproceedings{Nevalainen2014survey,
  author = {Nevalainen, Paavo and Pohjankukka, Jonne and Pahikkala, Tapio and Sutinen, Raimo and Varjo, Jari and Heikkonen, Jukka},
  title = {Open Natural Resource Data in Forecasting Harvester Mobility and Infrastructure Properties},
  booktitle = {Federated Computer Science Event (YTP 2014)},
  year = {2014}
}
@inproceedings{Cichonska2014mlsb,
  author = {Cichonska, Anna and Pahikkala, Tapio and Airola, Antti and Rousu, Juho and Aittokallio, Tero},
  editor = {d'Alch{\'e}-Buc, Florence and Geurts, Pierre},
  title = {Predicting binding affinities between drug compounds and kinase targets},
  booktitle = {The eighth International Workshop on Machine Learning in Systems Biology (MLSB 2014)},
  year = {2014},
  month = {September},
  pages = {82}
}
@inproceedings{stock2014enzyme,
  author = {Stock, Michiel and De Baets, Bernard and Waegeman, Willem and Fober, Thomas and H{\"u}llermeier, Eyke and Pahikkala, Tapio and Airola, Antti},
  editor = {Fr\'{e}enay, Beno\^{i}t and Verleysen, Michel and Dupont, Pierre},
  title = {Enzyme Annotation using Conditional Ranking Algorithms},
  booktitle = {{Proceedings of the 23rd Annual Belgian-Dutch Conference on Machine Learning (Benelearn'14)}},
  year = {2014},
  month = {June}
}
@inproceedings{stock2013pairwisemolecular,
  author = {Stock, Michiel and Pahikkala, Tapio and Airola, Antti and De Baets, Bernard and Waegeman, Willem},
  title = {Pairwise kernel methods for predicting molecular interactions},
  booktitle = {BeNeLux Bioinformatics Conference},
  year = {2013},
  pages = {15},
  month = {December}
}
@inproceedings{waegeman2012objectretrieval,
  author = {Waegeman, Willem and Stock, Michiel and De Baets, Bernard and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  editor = {Demeester, Thomas and Deleu, Johannes and Mertens, Laurent and Plaetinck, Dieter and De Moor, An and Hoang, Thong and Wauters, Tim and Develder, Chris and Vermeulen, Brecht and Demeester, Piet},
  title = {Conditional Ranking Algorithms for Efficient Object Retrieval and Object Querying on Relational Data},
  booktitle = {Proceedings of the 12th Dutch-Belgian Information Retrieval Workshop (DIR 2012)},
  year = {2012},
  publisher = {Ghent University},
  pages = {59-60}
}
@inproceedings{pahikkala2008npref,
  author = {Pahikkala, Tapio and Tsivtsivadze, Evgeni and Airola, Antti and Salakoski, Tapio},
  editor = {Raiko, Tapani and Haikonen, Pentti and V{\"a}yrynen, Jaakko},
  title = {Regularized Least-Squares for Learning Non-Transitive Preferences between Strategies},
  booktitle = {Proceedings of the 13th Finnish Artificial Intelligence Conference and Nokia Workshop on Machine Consciousness},
  year = {2008},
  volume = {24},
  series = {Publications of the Finnish Artificial Intelligence Society},
  pages = {94--98},
  publisher = {Finnish Artificial Intelligence Society}
}
@inproceedings{suominen08challenge,
  author = {Suominen, Hanna and Ginter, Filip and Pyysalo, Sampo and Airola, Antti and Pahikkala, Tapio and Salanter{\"{a}}, Sanna and Salakoski, Tapio},
  editor = {Hauskrecht, Milos and Schuurmans, Dale and Szepesvari, Csaba},
  title = {Machine Learning to Automate the Assignment of Diagnosis Codes to Free-text Radiology Reports: a Method Description},
  booktitle = {Proceedings of the ICML/UAI workshop on Machine Learning in health care applications},
  year = {2008}
}
@inproceedings{ginter05ie,
  author = {Ginter, Filip and Pahikkala, Tapio and Pyysalo, Sampo and Tsivtsivadze, Evgeni and Boberg, Jorma and J{\"a}rvinen, Jouni and Myll{\"a}ri, Aleksandr and Salakoski, Tapio},
  editor = {Langemets, Margit and Priit, Penjam},
  title = {Information Extraction from Biomedical Text: {The} {BioText} Project},
  booktitle = {Proceedings of the Second Baltic Conference on Human Language Technologies HLT 05, Tallinn, Estonia},
  year = {2005},
  pages = {131--136},
  month = {April},
  isbn = {9985-894-83-9},
  publisher = {Institute of Cybernetics (Tallinn University of Technology)}
}
@phdthesis{pahikkala2008phdthesis,
  author = {Pahikkala, Tapio},
  title = {New Kernel Functions and Learning Methods for Text and Data Mining},
  school = {Turku Centre for Computer Science (TUCS)},
  year = {2008},
  address = {Turku, Finland},
  month = {June}
}
@article{Stock2016arXiv160604275S,
  author = {Stock, Michiel and Pahikkala, Tapio and Airola, Antti and De Baets, Bernard and Waegeman, Willem},
  title = {Efficient Pairwise Learning Using Kernel Ridge Regression: an Exact Two-Step Method},
  journal = {ArXiv e-prints},
  year = {2016},
  month = {June}
}
@misc{pahikkala2010spectralarxiv,
  author = {Pahikkala, Tapio and Viljanen, Markus and Airola, Antti and Waegeman, Willem},
  title = {Spectral Analysis of Symmetric and Anti-Symmetric Pairwise Kernels},
  year = {2015},
  eprint = {arXiv:1506.05950},
  note = {http://arxiv.org/abs/1506.05950}
}
@misc{pahikkala2010greedyarxiv,
  author = {Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  title = {Linear Time Feature Selection for Regularized Least-Squares},
  year = {2010},
  eprint = {arXiv:1003.3570},
  note = {http://arxiv.org/abs/1003.3570}
}
@techreport{pahikkala2005tr,
  author = {Pahikkala, Tapio and Nikula, Tuomas and Mykk{\"a}nen, Juha and N{\"a}nt{\"o}-Salonen, Kirsti and Simell, Olli and Lahesmaa, Riitta and Nevalainen, Olli S. and Aittokallio, Tero},
  title = {Considerations when Using Gene Expression Microarray Data to Diagnostic Classification},
  year = {2005},
  number = {719},
  institution = {{TUCS}},
  address = {Turku Centre for Computer Science, Turku, Finland}
}

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