@article{pahikkala2012efficientcv,
author = {Pahikkala, Tapio and Suominen, Hanna and Boberg, Jorma},
publisher = {Springer Netherlands},
doi = {10.1007/s10994-012-5287-6},
title = {Efficient cross-validation for kernelized least-squares regression with sparse basis expansions},
url = {http://dx.doi.org/10.1007/s10994-012-5287-6},
journal = {Machine Learning},
issn = {0885-6125},
number = {3},
month = {June},
volume = {87},
affiliation = {Department of Information Technology and Turku Centre for Computer Science, University of Turku, 20014 Turku, Finland},
year = {2012},
pdf = {CV_postprint.pdf},
pages = {381-407}
}
@article{pahikkala2012wrappergwas,
author = {Pahikkala, Tapio and Okser, Sebastian and Airola, Antti and Salakoski, Tapio and Aittokallio, Tero},
doi = {10.1186/1748-7188-7-11},
title = {Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations},
url = {http://www.almob.org/content/7/1/11},
journal = {Algorithms for Molecular Biology},
issn = {1748-7188},
number = {1},
volume = {7},
year = {2012},
pages = {11}
}
@article{waegeman2012learninggraded,
author = {Waegeman, Willem and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and Stock, Michiel and De Baets, Bernard},
note = {Accepted for publication.},
pdf = {graded_postprint.pdf},
journal = {IEEE Transactions on Fuzzy Systems},
year = {2012},
title = {A Kernel-based Framework for Learning Graded Relations from Data}
}
@article{gieseke2012recurrent,
author = {Gieseke, Fabian and Kramer, Oliver and Airola, Antti and Pahikkala, Tapio},
publisher = {Springer},
doi = {10.1007/s12065-012-0068-5},
title = {Efficient recurrent local search strategies for semi- and unsupervised regularized least-squares classification},
url = {http://dx.doi.org/10.1007/s12065-012-0068-5},
journal = {Evolutionary Intelligence},
issn = {1864-5909},
note = {Accepted for publication},
year = {2012},
pages = {1-17}
}
@article{pahikkala2012parallelizedonline,
author = {Pahikkala, Tapio and Airola, Antti and Xu, Thomas Canhao and Liljeberg, Pasi and Tenhunen, Hannu and Salakoski, Tapio},
publisher = {IGI Global},
doi = {10.4018/jertcs.2012040104},
title = {Parallelized Online Regularized Least-Squares for Adaptive Embedded Systems},
journal = {International Journal of Embedded and Real-Time Communication Systems},
issn = {1947-3176},
number = {2},
month = {April},
volume = {3},
year = {2012},
pages = {73--91}
}
@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},
number = {4},
month = {November},
volume = {27},
year = {2011},
pages = {541--557}
}
@article{airola2011ranksvm,
author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
doi = {10.1016/j.patrec.2011.03.014},
title = {Training linear ranking {SVM}s in linearithmic time using red-black trees},
url = {http://dx.doi.org/10.1016/j.patrec.2011.03.014},
journal = {Pattern Recognition Letters},
number = {9},
month = {July},
volume = {32},
pages = {1328--1336},
year = {2011},
day = {1}
}
@article{airola2011experimental,
author = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
doi = {10.1016/j.csda.2010.11.018},
title = {An experimental comparison of cross-validation techniques for estimating the area under the {ROC} curve},
url = {http://dx.doi.org/10.1016/j.csda.2010.11.018},
journal = {Computational Statistics \& Data Analysis},
number = {4},
month = {April},
volume = {55},
year = {2011},
pages = {1828--1844}
}
@article{airola2011nystromcv,
author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
doi = {10.1007/s11063-010-9159-4},
title = {On learning and cross-validation with decomposed {N}ystr{\"o}m approximation of kernel matrix},
url = {http://dx.doi.org/doi:10.1007/s11063-010-9159-4},
journal = {Neural Processing Letters},
number = {1},
month = {February},
volume = {33},
year = {2011},
pages = {17--30}
}
@article{pahikkala2010reciprocalkm,
author = {Pahikkala, Tapio and Waegeman, Willem and Tsivtsivadze, Evgeni and Salakoski, Tapio and De Baets, Bernard},
doi = {10.1016/j.ejor.2010.03.018},
title = {Learning Intransitive Reciprocal Relations with Kernel Methods},
url = {http://dx.doi.org/10.1016/j.ejor.2010.03.018},
journal = {European Journal of Operational Research},
number = {3},
month = {November},
volume = {206},
year = {2010},
pages = {676--685}
}
@article{karthikeyan2010fuzzy,
author = {Karthikeyan, Rangaswamy and Pahikkala, Tapio and Virtanen, Seppo and Isoaho, Jouni and Manickavasagam, K. and Murthy, K. V. V.},
title = {Fuzzy Logic Based Control for Parallel Cascade Control},
journal = {International Journal on Automatic Control and System Engineering},
number = {2},
volume = {10},
year = {2010},
pages = {39--48}
}
@article{pahikkala2009preferences,
author = {Pahikkala, Tapio and Tsivtsivadze, Evgeni and Airola, Antti and J{\"a}rvinen, Jouni and Boberg, Jorma},
doi = {http://dx.doi.org/10.1007/s10994-008-5097-z},
title = {An Efficient Algorithm for Learning to Rank from Preference Graphs},
url = {http://dx.doi.org/10.1007/s10994-008-5097-z},
journal = {Machine Learning},
number = {1},
month = {April},
volume = {75},
year = {2009},
pdf = {http://staff.cs.utu.fi/~aatapa/publications/jPaTsAiJaBo09a.full.pdf},
pages = {129--165}
}
@article{pahikkala2009matrix,
author = {Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and J\"{a}rvinen, Jouni and Salakoski, Tapio},
publisher = {Kluwer Academic Publishers},
doi = {http://dx.doi.org/10.1007/s10994-008-5082-6},
title = {Matrix representations, linear transformations, and kernels for disambiguation in natural language},
url = {http://dx.doi.org/10.1007/s10994-008-5082-6},
journal = {Machine Learning},
address = {Hingham, MA, USA},
number = {2},
month = {February},
volume = {74},
year = {2009},
pdf = {http://staff.cs.utu.fi/~aatapa/publications/jPaPyBoJaSa08a.pdf},
pages = {133--158},
issn = {0885-6125}
}
@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},
number = {1},
volume = {31},
year = {2009},
pages = {81--88}
}
@article{airola08allpathsbmc,
author = {Airola, Antti and Pyysalo, Sampo and Bj\"{o}rne, Jari and Pahikkala, Tapio and Ginter, Filip and Salakoski, Tapio},
volume = {9 Suppl 11},
journal = {BMC Bioinformatics},
year = {2008},
title = {All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning.}
}
@article{aittokallio2007inspiratory,
author = {Aittokallio, Tero and Malminen, Jani S. and Pahikkala, Tapio and Polo, Olli and Nevalainen, Olli},
doi = {10.1016/j.cmpb.2006.09.012},
title = {Inspiratory Flow Shape Clustering: An Automated Method to Monitor Upper Airway Performance During Sleep},
url = {http://dx.doi.org/10.1016/j.cmpb.2006.09.012},
journal = {Computer Methods and Programs in Biomedicine},
number = {1},
month = {Jan},
volume = {85},
year = {2007},
pages = {8--18}
}
@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},
doi = {http://dx.doi.org/10.1016/j.ijmedinf.2007.03.003},
title = {Towards automated classification of intensive care nursing narratives},
journal = {International Journal of Medical Informatics},
number = {Supplement 3},
month = {December},
volume = {76},
year = {2007},
pages = {S362--S368}
}
@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},
doi = {doi:10.1002/elps.200600424},
title = {Computer-assisted identification of multi-trace electrophoretic patterns in differential display experiments},
url = {http://dx.doi.org/doi:10.1002/elps.200600424},
journal = {Electrophoresis},
number = {6},
volume = {28},
year = {2007},
pages = {879--893}
}
@article{pyysalo06evaluation,
editor = {Baud, Robert and Collier, Nigel and Nazarenko, Adeline and Ruch, Patrick},
author = {Pyysalo, Sampo and Ginter, Filip and Pahikkala, Tapio and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
publisher = {Elsevier},
title = {Evaluation of Two Dependency Parsers on Biomedical Corpus Targeted at Protein-Protein Interactions},
journal = {Recent Advances in Natural Language Processing for Biomedical Applications, special issue of the International Journal of Medical Informatics},
number = {6},
volume = {75},
year = {2006},
pages = {430--442}
}
@article{pahikkala05contextual,
author = {Pahikkala, Tapio and Ginter, Filip and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
doi = {http://dx.doi.org/doi:10.1186/1471-2105-6-157},
title = {Contextual Weighting for Support Vector Machines in Literature Mining: {An} Application to Gene Versus Protein Name Disambiguation},
journal = {BMC Bioinformatics},
number = {1},
volume = {6},
year = {2005},
pages = {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},
url = {http://www.biotechniques.com/multimedia/archive/00010/03341rr02_10316a.pdf},
journal = {BioTechniques},
number = {1},
month = {Jan},
volume = {34},
year = {2003},
pages = {116--122}
}
@proceedings{pahikkala2010step,
editor = {Pahikkala, Tapio and V{\"a}yrynen, Jaakko and Kortela, Jukka and Airola, Antti},
publisher = {Aalto-Print},
title = {Proceedings of the 14th Finnish Artificial Intelligence Conference, STeP 2010},
series = {Publications of the Finnish Artificial Intelligence Society},
address = {Espoo, Finland},
number = {25},
year = {2010},
pages = {86}
}
@proceedings{salakoski06fintal,
editor = {Salakoski, Tapio and Ginter, Filip and Pyysalo, Sampo and Pahikkala, Tapio},
publisher = {Springer},
doi = {10.1007/11816508},
isbn = {3-540-37334-9, 978-3-540-37334-6},
title = {Proceedings of the Fifth International Conference on Natural Language Processing (FinTAL)},
series = {Lecture Notes in Artificial Intelligence},
issn = {0302-9743},
month = {August},
volume = {4139},
location = {Turku, Finland},
year = {2006},
address = {Berlin, Heidelberg}
}
@incollection{tsivtsivadze2010coreg,
editor = {F{\"u}rnkranz, Johannes and H{\"u}llermeier, Eyke},
author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio and Heskes, Tom},
chapter = {6},
publisher = {Springer},
doi = {10.1007/978-3-642-14125-6_6},
isbn = {978-3-642-14124-9},
title = {Co-Regularized Least-Squares for Label Ranking},
url = {http://dx.doi.org/10.1007/978-3-642-14125-6_6},
booktitle = {Preference Learning},
address = {Berlin Heidelberg},
edition = {1st},
year = {2010},
pages = {107--123}
}
@incollection{suominen08measures,
editor = {Song, M and Wu, Y-FB},
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},
publisher = {IGI Global},
title = {Performance Evaluation Measures for Text Mining},
booktitle = {Handbook of Research on Text and Web Mining Technologies},
address = {Hershey, Pennsylvania, USA},
year = {2008},
pages = {724--747}
}
@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},
publisher = {Springer},
title = {Kernel Methods for Text Analysis},
series = {Studies in Computational Intelligence},
booktitle = {Advances of Computational Intelligence in Industrial Systems},
volume = {116},
year = {2008},
pages = {81--97}
}
@inproceedings{gieseke2012sqn,
editor = {Latorre Carmona, Pedro and S{\'a}nchez, J. Salvador and Fred, Ana L. N.},
author = {Gieseke, Fabian and Airola, Antti and Pahikkala, Tapio and Kramer, Oliver},
publisher = {SciTePress},
booktitle = {Proceedings of the 1st International Conference on Pattern Recognition Applications and Methods (ICPRAM)},
year = {2012},
pages = {45-54},
title = {Sparse Quasi-Newton Optimization for Semi-Supervised Support Vector Machines}
}
@inproceedings{xu2012blunoc,
author = {Xu, Thomas Canhao and Pahikkala, Tapio and Airola, Antti and Liljeberg, Pasi and Plosila, Juha and Salakoski, Tapio and Tenhunen, Hannu},
note = {To appear},
publisher = {IEEE},
booktitle = {The 14th IEEE International Conference on High Performance Computing and Communications (HPCC-2012)},
year = {2012},
title = {Implementation and Analysis of Block Dense Matrix Decomposition on Network-on-Chips}
}
@inproceedings{waegeman2011learningvalued,
editor = {Melo-Pinto, Pedro and Couto, Pedro and Ser\^{o}dio, Carlos and Fodor, J\'{a}nos and De Baets, Bernard},
author = {Waegeman, Willem and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and De Baets, Bernard},
publisher = {Springer},
doi = {10.1007/978-3-642-24001-0_24},
title = {Learning Valued Relations from Data},
url = {http://dx.doi.org/10.1007/978-3-642-24001-0_24},
series = {Advances in Intelligent and Soft Computing},
booktitle = {Eurofuse 2011},
volume = {107},
year = {2012},
pages = {257--268}
}
@inproceedings{waegeman2012objectretrieval,
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},
author = {Waegeman, Willem and Stock, Michiel and De Baets, Bernard and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
publisher = {Ghent University},
booktitle = {Proceedings of the 12th Dutch-Belgian Information Retrieval Workshop (DIR 2012)},
year = {2012},
pages = {59-60},
title = {Conditional Ranking Algorithms for Efficient Object Retrieval and Object Querying on Relational Data}
}
@inproceedings{naula2011grlsmultitask,
editor = {Spiliopoulou, Myra and Wang, Haixun and Cook, Diane and Pei, Jian and Wang, Wei and Za{\"i}ane, Osmar and Wu, Xindong},
author = {Naula, Pekka and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
publisher = {IEEE Computer Society},
doi = {10.1109/ICDMW.2011.91},
title = {Greedy Regularized Least-Squares for Multi-Task Learning},
booktitle = {11th IEEE International Conference on Data Mining Workshops (ICDMW'11)},
month = {December},
year = {2011},
pages = {527--533}
}
@inproceedings{okser2011fastgwas,
editor = {Chen, Yidong and Huang, Yufei and Dougherty, Edward},
author = {Okser, Sebastian and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
publisher = {IEEE Signal Processing Society},
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)},
month = {December},
year = {2011},
pages = {214--217}
}
@inproceedings{gieseke2011speedy,
editor = {Bach, Joscha and Edelkamp, Stefan},
author = {Gieseke, Fabian and Kramer, Oliver and Airola, Antti and Pahikkala, Tapio},
publisher = {Springer},
doi = {10.1007/978-3-642-24455-1_8},
title = {Speedy Local Search for Semi-Supervised Regularized Least-Squares},
url = {http://dx.doi.org/10.1007/978-3-642-24455-1_8},
series = {Lecture Notes in Computer Science},
booktitle = {KI 2011: Advances in Artificial Intelligence},
volume = {7006},
location = {Berlin, Germany},
year = {2011},
pages = {87--98}
}
@inproceedings{bjorne2011drugchallenge,
editor = {Segura-Bedmar, Isabel and Martinez, Paloma and Sanchez-Cisneros, Daniel},
author = {Bj\"{o}rne, Jari and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
publisher = {CEUR-WS.org},
title = {Drug-Drug Interaction Extraction with {SVM} and {RLS} Classifiers},
series = {CEUR Workshop Proceedings},
booktitle = {Proceedings of the 1st Challenge Task on Drug-Drug Interaction Extraction 2011},
month = {September},
volume = {761},
year = {2011}
}
@inproceedings{airola2011improvedranksvm,
editor = {Honkela, Timo and Duch, W{\l}odzis{\l}aw and Girolami, Mark and Kaski, Samuel},
author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
publisher = {Springer},
isbn = {978-3-642-21734-0},
title = {An Improved Training Algorithm for the Linear Ranking Support Vector Machine},
series = {Lecture Notes in Computer Science},
booktitle = {Artificial Neural Networks and Machine Learning -- ICANN 2011},
month = {June},
volume = {6791},
location = {Heidelberg},
year = {2011},
pages = {134--141}
}
@inproceedings{naula2011budgeted,
editor = {Kofod-Petersen, Anders and Heintz, Fredrik and Langseth, Helge},
author = {Naula, Pekka and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
publisher = {IOS Press},
isbn = {978-1-60750-753-6},
title = {Learning Multi-Label Predictors under Sparsity Budget},
series = {Frontiers in Artificial Intelligence and Applications},
booktitle = {Eleventh Scandinavian Conference on Artificial Intelligence, SCAI 2011},
month = {May},
volume = {227},
year = {2011},
pages = {30--39}
}
@inproceedings{pahikkala2011parallelonline,
editor = {Benavente-Peces, C{\'e}sar and Filipe, Joaquim},
author = {Pahikkala, Tapio and Airola, Antti and Xu, Thomas Canhao and Liljeberg, Pasi and Tenhunen, Hannu and Salakoski, Tapio},
publisher = {SciTePress},
isbn = {978-989-8425-48-5},
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},
location = {Algarve, Portugal},
year = {2011},
pages = {590--599}
}
@inproceedings{airola2010comparison,
editor = {D\v{z}eroski, Sa\v{s}o and Geurts, Pierre and Rousu, Juho},
author = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
publisher = {Journal of Machine Learning Research},
title = {A comparison of {AUC} estimators in small-sample studies},
url = {http://jmlr.csail.mit.edu/proceedings/papers/v8/airola10a/airola10a.pdf},
series = {JMLR Workshop and Conference Proceedings},
booktitle = {Proceedings of the third International Workshop on Machine Learning in Systems Biology},
volume = {8},
year = {2010},
pages = {3--13}
}
@inproceedings{pahikkala2010conditional,
editor = {Balc{\'a}zar, Jos{\'e} L. and Bonchi, Francesco and Gionis, Aristides and Sebag, Mich{\`e}le},
author = {Pahikkala, Tapio and Waegeman, Willem and Airola, Antti and Salakoski, Tapio and De Baets, Bernard},
publisher = {Springer},
doi = {10.1007/978-3-642-15883-4_32},
title = {Conditional Ranking on Relational Data},
url = {http://dx.doi.org/10.1007/978-3-642-15883-4_32},
series = {Lecture Notes in Computer Science},
booktitle = {Machine Learning and Knowledge Discovery in Databases (ECML PKDD 2010)},
volume = {6322},
location = {Barcelona, Spain},
year = {2010},
pages = {499--514}
}
@inproceedings{pahikkala2010greedyrls,
editor = {Draghici, Sorin and Khoshgoftaar, Taghi M. and Palade, Vasile and Pedrycz, Witold and Wani, M. Arif and Zhu, Xingquan},
author = {Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
publisher = {IEEE},
doi = {10.1109/ICMLA.2010.55},
title = {Speeding up Greedy Forward Selection for Regularized Least-Squares},
url = {http://staff.cs.utu.fi/~aatapa/publications/inpPaAiSa10b.full.pdf},
booktitle = {Proceedings of The Ninth International Conference on Machine Learning and Applications (ICMLA'10)},
month = {December},
year = {2010},
pages = {325--330}
}
@inproceedings{airola2010permutation,
editor = {Draghici, Sorin and Khoshgoftaar, Taghi M. and Palade, Vasile and Pedrycz, Witold and Wani, M. Arif and Zhu, Xingquan},
author = {Airola, Antti and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
publisher = {IEEE},
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)},
month = {December},
year = {2010},
pages = {989--994}
}
@inproceedings{airola2010largescale,
editor = {H{\"u}llermeier, Eyke and F{\"u}rnkranz, Johannes},
author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
booktitle = {Proceedings of the {ECML/PKDD}-Workshop on Preference Learning {(PL-10)}},
year = {2010},
title = {Large scale training methods for linear {RankRLS}}
}
@inproceedings{pahikkala2010fsrls,
editor = {Kaski, Samuel and Miller, David J. and Oja, Erkki and Honkela, Antti},
author = {Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
publisher = {IEEE},
doi = {10.1109/MLSP.2010.5589210},
isbn = {978-1-4244-7876-7},
title = {Feature Selection for Regularized Least-Squares: New Computational Short-Cuts and Fast Algorithmic Implementations},
url = {http://dx.doi.org/10.1109/MLSP.2010.5589210},
booktitle = {Proceedings of the Twentieth IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010)},
location = {Kittil{\"a}, Finland},
year = {2010},
pages = {295--300}
}
@inproceedings{pahikkala2010grankrls,
editor = {Gabrilovich, Evgeniy and Smola, Alexander J. and Tishby, Naftali},
author = {Pahikkala, Tapio and Airola, Antti and Naula, Pekka and Salakoski, Tapio},
publisher = {ACM},
title = {Greedy {RankRLS}: a Linear Time Algorithm for Learning Sparse Ranking Models},
url = {http://alex.smola.org/workshops/sigir10/contrib/Pahikkala.pdf},
booktitle = {SIGIR 2010 Workshop on Feature Generation and Selection for Information Retrieval},
year = {2010},
pages = {11--18}
}
@inproceedings{airola2009comparison,
editor = {D\v{z}eroski, Sa\v{s}o and Geurts, Pierre and Rousu, Juho},
author = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
publisher = {Helsinki University Printing House},
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)},
address = {Helsinki, Finland},
year = {2009},
pages = {15--23}
}
@inproceedings{pahikkala2009beyond,
editor = {H{\"u}llermeier, Eyke and F{\"u}rnkranz, Johannes},
author = {Pahikkala, Tapio and Waegeman, Willem and Tsivtsivadze, Evgeni and Salakoski, Tapio and De Baets, Bernard},
booktitle = {Proceedings of the {ECML/PKDD}-Workshop on Preference Learning {(PL-09)}},
year = {2009},
pages = {84--100},
title = {From Ranking to Intransitive Preference Learning: Rock-Paper-Scissors and beyond}
}
@inproceedings{bjorne09sharedtask,
editor = {Tsujii, Jun'ichi},
author = {Bj\"{o}rne, Jari and Heimonen, Juho and Ginter, Filip and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
publisher = {Association for Computational Linguistics},
isbn = {978-1-932432-44-2},
title = {Extracting Complex Biological Events with Rich Graph-Based Feature Sets},
url = {http://www.aclweb.org/anthology/W09-1402},
booktitle = {Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task},
month = {June},
location = {Boulder, Colorado},
year = {2009},
pages = {10--18}
}
@inproceedings{gieseke2009evolutionary,
editor = {Bottou, L\'{e}on and Littman, Michael},
author = {Gieseke, Fabian and Pahikkala, Tapio and Kramer, Oliver},
publisher = {ACM},
doi = {http://doi.acm.org/10.1145/1553374.1553421},
isbn = {978-1-60558-516-1},
title = {Fast evolutionary maximum margin clustering},
url = {http://doi.acm.org/10.1145/1553374.1553421},
series = {ACM International Conference Proceeding Series},
booktitle = {ICML '09: Proceedings of the 26th Annual International Conference on Machine Learning},
address = {New York, NY, USA},
month = {June},
volume = {382},
location = {Montreal, Quebec, Canada},
year = {2009},
pdf = {http://www.cs.mcgill.ca/~icml2009/papers/245.pdf},
pages = {361--368}
}
@inproceedings{pahikkala2009holdout,
editor = {Kolehmainen, Mikko and Toivanen, Pekka and Beliczynski, Bartlomiej},
author = {Pahikkala, Tapio and Suominen, Hanna and Boberg, Jorma and Salakoski, Tapio},
publisher = {Springer},
doi = {10.1007/978-3-642-04921-7_36},
title = {Efficient Hold-Out for Subset of Regressors},
url = {http://dx.doi.org/10.1007/978-3-642-04921-7_36},
series = {Lecture Notes in Computer Science},
booktitle = {{Proceedings of the 9th International Conference on Adaptive and Natural Computing Algorithms (ICANNGA'09)}},
address = {Berlin, Germany},
volume = {5495},
file = {attachment.php?fname=inpPaSuBoSa09a.full.pdf:http\://www.tucs.fi/publications/attachment.php?fname=inpPaSuBoSa09a.full.pdf:PDF},
year = {2009},
pages = {350--359}
}
@inproceedings{pahikkala2009benelearn,
editor = {van Zaanen, Menno and Stehouwer, Herman and van Erp, Marieke},
author = {Pahikkala, Tapio and Waegeman, Willem and Tsivtsivadze, Evgeni and De Baets, Bernard and Salakoski, Tapio},
publisher = {Tilburg centre for Creative Computing},
title = {Learning Intransitive Reciprocal Relations with Regularized Least-Squares},
booktitle = {{Proceedings of the 18th Annual Belgian-Dutch Conference on Machine Learning (Benelearn 09)}},
address = {Tilburg, The Netherlands},
year = {2009},
pages = {13--20}
}
@incollection{pahikkala2008aucmax,
editor = {Holst, Anders and Kreuger, Per and Funk, Peter},
author = {Pahikkala, Tapio and Airola, Antti and Suominen, Hanna and Boberg, Jorma and Salakoski, Tapio},
publisher = {IOS Press},
title = {Efficient {AUC} Maximization with Regularized Least-Squares},
series = {Frontiers in Artificial Intelligence and Applications},
booktitle = {Tenth Scandinavian Conference on Artificial Intelligence, SCAI 2008},
address = {Amsterdam, Netherlands},
volume = {173},
location = {Stockholm, Sweden},
year = {2008},
pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaAiSuBoSa08a.pdf},
pages = {12--19}
}
@inproceedings{pahikkala2008lpocv,
editor = {Honkela, Timo and P{\"o}ll{\"a}, Matti and Paukkeri, Mari-Sanna and Simula, Olli},
author = {Pahikkala, Tapio and Airola, Antti and Boberg, Jorma and Salakoski, Tapio},
publisher = {Helsinki University of Technology},
isbn = {978-951-22-9525-8},
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)},
address = {Espoo, Finland},
year = {2008},
pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaAiBoSa08a.pdf},
pages = {1--8}
}
@inproceedings{tsivtsivadze2008coreg,
editor = {H{\"u}llermeier, Eyke and F{\"u}rnkranz, Johannes},
author = {Tsivtsivadze, Evgeni and Gieseke, Fabian and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
booktitle = {{ECML/PKDD-Workshop on Preference Learning (PL-08)}},
year = {2008},
pages = {55--62},
title = {Learning Preferences with Co-Regularized Least Squares}
}
@inproceedings{tsivtsivadze08sparse,
editor = {Holst, Anders and Kreuger, Per and Funk, Peter},
author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Airola, Antti and Boberg, Jorma and Salakoski, Tapio},
publisher = {IOS Press},
title = {A Sparse Regularized Least-Squares Preference Learning Algorithm},
series = {Frontiers in Artificial Intelligence and Applications},
booktitle = {Tenth Scandinavian Conference on Artificial Intelligence, SCAI 2008},
volume = {173},
file = {attachment.php?fname=inpTsPaAiBoSa08a.pdf:http\://www.tucs.fi/publications/attachment.php?fname=inpTsPaAiBoSa08a.pdf:PDF},
year = {2008},
pages = {76--83}
}
@inproceedings{SuominenetalAKRR,
editor = {Honkela, Timo and P{\"o}ll{\"a}, Matti and Paukkeri, Mari-Sanna and Simula, Olli},
author = {Suominen, Hanna and Pahikkala, Tapio and Salakoski, Tapio},
publisher = {Helsinki University of Technology},
isbn = {978-951-22-9525-8},
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)},
address = {Espoo, Finland},
year = {2008},
pages = {9--22}
}
@inproceedings{airola08bionlp,
editor = {Demner-Fushman, Dina and Ananiadou, Sophia and Cohen, Kevin Bretonnel and Pestian, John and Tsujii, Jun'ichi and Webber, Bonnie},
author = {Airola, Antti and Pyysalo, Sampo and Bj{\"{o}}rne, Jari and Pahikkala, Tapio and Ginter, Filip and Salakoski, Tapio},
publisher = {Association for Computational Linguistics},
isbn = {978-1-932432-11-4},
title = {A Graph Kernel for Protein-Protein Interaction Extraction},
url = {http://aclweb.org/anthology-new/W/W08/W08-0601.pdf},
booktitle = {Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP'08)},
address = {Stroudsburg, PA, USA},
year = {2008},
pages = {1--9}
}
@inproceedings{suominen08challenge,
editor = {Hauskrecht, Milos and Schuurmans, Dale and Szepesvari, Csaba},
author = {Suominen, Hanna and Ginter, Filip and Pyysalo, Sampo and Airola, Antti and Pahikkala, Tapio and Salanter{\"{a}}, Sanna and Salakoski, Tapio},
booktitle = {Proceedings of the ICML/UAI workshop on Machine Learning in health care applications},
year = {2008},
title = {Machine Learning to Automate the Assignment of Diagnosis Codes to Free-text Radiology Reports: a Method Description}
}
@inproceedings{pahikkala07mlg,
editor = {Frasconi, P and Kersting, K and Tsuda, K},
author = {Pahikkala, Tapio and Suominen, Hanna and Boberg, Jorma and Salakoski, Tapio},
title = {Transductive Ranking via Pairwise Regularized Least-Squares},
booktitle = {The 5th International Workshop on Mining and Learning with Graphs (MLG'07)},
location = {Florence, Italy},
file = {:http\://www.tucs.fi/publications/attachment.php?fname=inpPaSuBoSa07a.pdf:PDF},
year = {2007},
pages = {175--178}
}
@inproceedings{pahikkala2007rankrls,
editor = {Joachims, Thorsten and Li, Hang and Liu, Tie-Yan and Zhai, ChengXiang},
author = {Pahikkala, Tapio and Tsivtsivadze, Evgeni and Airola, Antti and Boberg, Jorma and Salakoski, Tapio},
pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaTsAiBoSa07a.pdf},
booktitle = {SIGIR 2007 Workshop on Learning to Rank for Information Retrieval},
year = {2007},
pages = {27--33},
title = {Learning to Rank with Pairwise Regularized Least-Squares}
}
@inproceedings{hiissa2006towards,
editor = {Hasman, A and Haux, R and Van Der Lei, J and E, De Clercq and Roger France, FH},
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},
publisher = {IOS Press},
title = {Towards automated classification of intensive care nursing narratives},
series = {Studies in Health Technology and Informatics},
booktitle = {Ubiquity: Technologies for Better Health in Aging Societies. Proceedings of MIE 2006, the 20th International Congress of the European Federation of Medical Informatics},
address = {Amsterdam, the Netherlands},
volume = {124},
year = {2006},
pages = {789--794}
}
@inproceedings{pahikkala06ltbayes,
editor = {Salakoski, Tapio and Ginter, Filip and Pyysalo, Sampo and Pahikkala, Tapio},
author = {Pahikkala, Tapio and Boberg, Jorma and Myll\"{a}ri, Aleksandr and Salakoski, Tapio},
publisher = {Springer},
title = {Incorporating External Information in Bayesian Classifiers via Linear Feature Transformations},
series = {Lecture Notes in Artificial Intelligence},
booktitle = {Proceedings of the 5th International Conference on Natural Language Processing FinTAL 06, Turku, Finland},
address = {Heidelberg},
volume = {4139},
year = {2006},
pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaBoMySa06a.pdf},
pages = {399--410}
}
@inproceedings{tsivtsivadze2006locality,
editor = {Ali, Moonis and Dapoigny, Richard},
author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
publisher = {Springer},
title = {Locality-Convolution Kernel and Its Application to Dependency Parse Ranking},
series = {Lecture Notes in Artificial Intelligence},
booktitle = {Proceedings of the The 19th International Conference on Industrial, Engineering {\&} Other Applications of Applied Intelligent Systems},
address = {Berlin},
volume = {4031},
year = {2006},
pages = {610--618}
}
@inproceedings{pahikkala06rls,
editor = {Honkela, Timo and Raiko, Tapani and Kortela, Jukka and Valpola, Harri},
author = {Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
publisher = {Helsinki University of Technology},
isbn = {978-952-5677-00-3},
title = {Fast n-Fold Cross-Validation for Regularized Least-Squares},
series = {Publications of the Finnish Artificial Intelligence Society},
booktitle = {Proceedings of the Ninth Scandinavian Conference on Artificial Intelligence (SCAI 2006)},
address = {Espoo, Finland},
volume = {22},
location = {Espoo, Finland},
year = {2006},
pdf = {http://staff.cs.utu.fi/~aatapa/publications/inpPaBoSa06a.pdf},
pages = {83--90}
}
@inproceedings{pahikkala2006graph,
editor = {G{\"a}rtner, Thomas and Garriga, Gemma C. and Meinl, Thorsten},
author = {Pahikkala, Tapio and Tsivtsivadze, Evgeni and Boberg, Jorma and Salakoski, Tapio},
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)},
address = {Berlin, Germany},
location = {Berlin, Germany},
file = {:http\://www.tucs.fi/publications/attachment.php?fname=inpPaTsBoSa06a.pdf:PDF},
year = {2006}
}
@inproceedings{suominen2006ranking,
editor = {Gabrys, Bogdan and Howlett, Robert J. and Jain, Lakhmi C.},
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},
publisher = {Springer},
title = {Relevance ranking of intensive care nursing narratives},
url = {http://dx.doi.org/10.1007/11892960_87},
series = {Lecture Notes in Computer Science},
booktitle = {Knowledge-Based Intelligent Information and Engineering Systems. Proceedings of the 10th International Conference, KES 2006, Part I},
address = {Berlin / Heidelberg, Germany},
volume = {4251},
year = {2006},
pages = {720--727}
}
@inproceedings{tsivtsivadze2005ranking,
editor = {Famili, A. Fazel and Kok, Joost N. and Pe{\~n}a, Jos{\'e} Manuel and Siebes, Arno and Feelders, A. J.},
author = {Tsivtsivadze, Evgeni and Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and Myll\"{a}ri, Aleksandr and Salakoski, Tapio},
publisher = {Springer},
title = {Regularized Least-Squares for Parse Ranking},
series = {Lecture Notes in Computer Science},
booktitle = {Proceedings of the 6th International Symposium on Intelligent Data Analysis},
address = {Berlin},
month = {September},
volume = {3646},
location = {Madrid, Spain},
year = {2005},
pages = {464--474}
}
@inproceedings{pahikkala05kernels,
editor = {Russell, Ingrid and Markov, Zdravko},
author = {Pahikkala, Tapio and Pyysalo, Sampo and Ginter, Filip and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
publisher = {AAAI Press},
isbn = {1-57735-234-3},
title = {Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks},
booktitle = {Proceedings of the Eighteenth International Florida Artificial Intelligence Research Society Conference},
address = {Menlo Park, CA, USA},
month = {May},
location = {Clearwater Beach, Florida},
file = {attachment.php?fname=inpPaPyGiBoJaSa05a.pdf:http\://www.tucs.fi/publications/attachment.php?fname=inpPaPyGiBoJaSa05a.pdf:PDF},
year = {2005},
pages = {442--447}
}
@inproceedings{pahikkala05improving,
editor = {Honkela, Timo and K{\"o}n{\"o}nen, Ville and P{\"o}ll{\"a}, Matti and Simula, Olli},
author = {Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and Myll{\"a}ri, Aleksandr and Salakoski, Tapio},
publisher = {Helsinki University of Technology},
isbn = {951-22-7723-9},
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},
address = {Espoo, Finland},
file = {:http\://www.tucs.fi/publications/attachment.php?fname=inpPaPyBoMySa05a.pdf:PDF},
year = {2005},
pages = {90--97}
}
@inproceedings{ginter05ie,
editor = {Langemets, Margit and Priit, Penjam},
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},
publisher = {Institute of Cybernetics (Tallinn University of Technology)},
isbn = {9985-894-83-9},
title = {Information Extraction from Biomedical Text: {The} {BioText} Project},
booktitle = {Proceedings of the Second Baltic Conference on Human Language Technologies HLT 05, Tallinn, Estonia},
month = {April},
year = {2005},
pages = {131--136}
}
@inproceedings{ginter04extracting,
editor = {Tsumoto, Husaku and Slowinski, Roman and Komorowski, Jan and Grzymala-Busse, Jerzy W.},
author = {Ginter, Filip and Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
publisher = {Springer, Heidelberg},
title = {Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis},
series = {Lecture Notes in Computer Science},
booktitle = {Proceedings of the Fourth International Conference on Rough Sets and Current Trends in Computing, Uppsala, Sweden},
month = {June},
volume = {3066},
year = {2004},
pages = {780--785}
}
@inproceedings{pyysalo04analysis,
editor = {Collier, Nigel and Ruch, Patrick and Nazarenko, Adeline},
author = {Pyysalo, Sampo and Ginter, Filip and Pahikkala, Tapio and Koivula, Jeppe and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
month = {August},
booktitle = {Proceedings of Joint Workshop on Natural Language Processing in Biomedicine and its Applications JNLPBA 04, Geneva, Switzerland},
year = {2004},
pages = {15--21},
title = {Analysis of {Link Grammar} on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions}
}
@inproceedings{pahikkala2008npref,
editor = {Raiko, Tapani and Haikonen, Pentti and V{\"a}yrynen, Jaakko},
author = {Pahikkala, Tapio and Tsivtsivadze, Evgeni and Airola, Antti and Salakoski, Tapio},
publisher = {Finnish Artificial Intelligence Society},
title = {Regularized Least-Squares for Learning Non-Transitive Preferences between Strategies},
series = {Publications of the Finnish Artificial Intelligence Society},
booktitle = {Proceedings of the 13th Finnish Artificial Intelligence Conference and Nokia Workshop on Machine Consciousness},
volume = {24},
year = {2008},
pages = {94--98}
}
@phdthesis{pahikkala2008phdthesis,
author = {Pahikkala, Tapio},
month = {June},
school = {Turku Centre for Computer Science (TUCS)},
year = {2008},
address = {Turku, Finland},
title = {New Kernel Functions and Learning Methods for Text and Data Mining}
}
@misc{pahikkala2010greedyarxiv,
author = {Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
note = {http://arxiv.org/abs/1003.3570},
year = {2010},
eprint = {arXiv:1003.3570},
title = {Linear Time Feature Selection for Regularized Least-Squares}
}
@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},
address = {Turku Centre for Computer Science, Turku, Finland},
year = {2005},
number = {719},
institution = {{TUCS}},
title = {Considerations when Using Gene Expression Microarray Data to Diagnostic Classification}
}
This file was generated by bibtex2html 1.96.