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    Author Title Year Journal / Proceedings / Book BibTeX type
    Björne, J. & Salakoski, T. UTU at SemEval-2016 Task 10: Binary Classification for Expression Detection (BCED) 2016 Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval-2016) , pp. 925-930   inproceedings
    BibTeX:
    @inproceedings{bjorne2016SemEval,
      author = {Björne, Jari and Salakoski, Tapio},
      title = {UTU at SemEval-2016 Task 10: Binary Classification for Expression Detection (BCED)},
      booktitle = {Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval-2016)},
      publisher = {Association for Computational Linguistics},
      year = {2016},
      pages = {925--930},
      url = {http://www.aclweb.org/anthology/S16-1142}
    }
    					
    Hakala, K.; Kaewphan, S.; Salakoski, T. & Ginter, F. Syntactic analyses and named entity recognition for PubMed and PubMed Central —up-to-the-minute 2016 Proceedings of the 2016 Workshop on Biomedical Natural Language Processing , pp. 102-107   inproceedings
    BibTeX:
    @inproceedings{hakala2016syntactic,
      author = {Hakala, Kai and Kaewphan, Suwisa and Salakoski, Tapio and Ginter, Filip},
      title = {Syntactic analyses and named entity recognition for PubMed and PubMed Central —up-to-the-minute},
      booktitle = {Proceedings of the 2016 Workshop on Biomedical Natural Language Processing},
      year = {2016},
      pages = {102--107}
    }
    					
    Huumo, T.; Kyröläinen, A.-J.; Kanerva, J.; Luotolahti, J.; Salakoski, T.; Ginter, F. & Laippala, V. Distributional Semantics of the Partitive A Argument Construction in Finnish 2016 Empirical approaches to cognitive linguistics: Analysing real-life data.   incollection
    BibTeX:
    @incollection{huumoParA,
      author = {Huumo, Tuomas and Kyröläinen, Aki-Juhani and Kanerva, Jenna and Luotolahti, Juhani and Salakoski, Tapio and Ginter, Filip and Laippala, Veronika},
      editor = {Luodonpaa-Manni, M. and E. Penttila and J. Viimaranta},
      title = {Distributional Semantics of the Partitive A Argument Construction in Finnish},
      booktitle = {Empirical approaches to cognitive linguistics: Analysing real-life data.},
      publisher = {Cambridge Scholars Publishing},
      year = {2016},
      edition = {1st}
    }
    					
    Jiang, Y.; Oron, R.T.; Clark, T.W.; Bankapur, R.A.; D'Andrea, D.; Lepore, R.; Funk, S.C.; Kahanda, I.; Verspoor, M.K.; Ben-Hur, A.; Koo, E.D.C.; Penfold-Brown, D.; Shasha, D.; Youngs, N.; Bonneau, R.; Lin, A.; Sahraeian, E.S.M.; Martelli, L.P.; Profiti, G.; Casadio, R.; Cao, R.; Zhong, Z.; Cheng, J.; Altenhoff, A.; Skunca, N.; Dessimoz, C.; Dogan, T.; Hakala, K.; Kaewphan, S.; Mehryary, F.; Salakoski, T.; Ginter, F.; Fang, H.; Smithers, B.; Oates, M.; Gough, J.; Törönen, P.; Koskinen, P.; Holm, L.; Chen, C.-T.; Hsu, W.-L.; Bryson, K.; Cozzetto, D.; Minneci, F.; Jones, T.D.; Chapman, S.; BKC, D.; Khan, K.I.; Kihara, D.; Ofer, D.; Rappoport, N.; Stern, A.; Cibrian-Uhalte, E.; Denny, P.; Foulger, E.R.; Hieta, R.; Legge, D.; Lovering, C.R.; Magrane, M.; Melidoni, N.A.; Mutowo-Meullenet, P.; Pichler, K.; Shypitsyna, A.; Li, B.; Zakeri, P.; ElShal, S.; Tranchevent, Lé.-C.; Das, S.; Dawson, L.N.; Lee, D.; Lees, G.J.; Sillitoe, I.; Bhat, P.; Nepusz, T.; Romero, E.A.; Sasidharan, R.; Yang, H.; Paccanaro, A.; Gillis, J.; Sedeño-Cortés, E.A.; Pavlidis, P.; Feng, S.; Cejuela, M.J.; Goldberg, T.; Hamp, T.; Richter, L.; Salamov, A.; Gabaldon, T.; Marcet-Houben, M.; Supek, F.; Gong, Q.; Ning, W.; Zhou, Y.; Tian, W.; Falda, M.; Fontana, P.; Lavezzo, E.; Toppo, S.; Ferrari, C.; Giollo, M.; Piovesan, D.; Tosatto, C.S.; del Pozo, A.; Fernández, M.J.; Maietta, P.; Valencia, A.; Tress, L.M.; Benso, A.; Di Carlo, S.; Politano, G.; Savino, A.; Rehman, U.H.; Re, M.; Mesiti, M.; Valentini, G.; Bargsten, W.J.; van Dijk, J.A.D.; Gemovic, B.; Glisic, S.; Perovic, V.; Veljkovic, V.; Veljkovic, N.; Almeida-e-Silva, C.D.; Vencio, N.R.Z.; Sharan, M.; Vogel, Jö.; Kansakar, L.; Zhang, S.; Vucetic, S.; Wang, Z.; Sternberg, E.M.J.; Wass, N.M.; Huntley, P.R.; Martin, J.M.; O'Donovan, C.; Robinson, N.P.; Moreau, Y.; Tramontano, A.; Babbitt, C.P.; Brenner, E.S.; Linial, M.; Orengo, A.C.; Rost, B.; Greene, S.C.; Mooney, D.S.; Friedberg, I. & Radivojac, P. An expanded evaluation of protein function prediction methods shows an improvement in accuracy 2016 Genome Biology
    Vol. 17 (1) , pp. 1-19  
    article
    BibTeX:
    @article{Jiang2016,
      author = {Jiang, Yuxiang and Oron, Ronnen Tal and Clark, T. Wyatt and Bankapur, R. Asma and D'Andrea, Daniel and Lepore, Rosalba and Funk, S. Christopher and Kahanda, Indika and Verspoor, M. Karin and Ben-Hur, Asa and Koo, Emily Da Chen and Penfold-Brown, Duncan and Shasha, Dennis and Youngs, Noah and Bonneau, Richard and Lin, Alexandra and Sahraeian, E. Sayed M. and Martelli, Luigi Pier and Profiti, Giuseppe and Casadio, Rita and Cao, Renzhi and Zhong, Zhaolong and Cheng, Jianlin and Altenhoff, Adrian and Skunca, Nives and Dessimoz, Christophe and Dogan, Tunca and Hakala, Kai and Kaewphan, Suwisa and Mehryary, Farrokh and Salakoski, Tapio and Ginter, Filip and Fang, Hai and Smithers, Ben and Oates, Matt and Gough, Julian and Törönen, Petri and Koskinen, Patrik and Holm, Liisa and Chen, Ching-Tai and Hsu, Wen-Lian and Bryson, Kevin and Cozzetto, Domenico and Minneci, Federico and Jones, T. David and Chapman, Samuel and BKC, Dukka and Khan, K. Ishita and Kihara, Daisuke and Ofer, Dan and Rappoport, Nadav and Stern, Amos and Cibrian-Uhalte, Elena and Denny, Paul and Foulger, E. Rebecca and Hieta, Reija and Legge, Duncan and Lovering, C. Ruth and Magrane, Michele and Melidoni, N. Anna and Mutowo-Meullenet, Prudence and Pichler, Klemens and Shypitsyna, Aleksandra and Li, Biao and Zakeri, Pooya and ElShal, Sarah and Tranchevent, Léon-Charles and Das, Sayoni and Dawson, L. Natalie and Lee, David and Lees, G. Jonathan and Sillitoe, Ian and Bhat, Prajwal and Nepusz, Tamás and Romero, E. Alfonso and Sasidharan, Rajkumar and Yang, Haixuan and Paccanaro, Alberto and Gillis, Jesse and Sedeño-Cortés, E. Adriana and Pavlidis, Paul and Feng, Shou and Cejuela, M. Juan and Goldberg, Tatyana and Hamp, Tobias and Richter, Lothar and Salamov, Asaf and Gabaldon, Toni and Marcet-Houben, Marina and Supek, Fran and Gong, Qingtian and Ning, Wei and Zhou, Yuanpeng and Tian, Weidong and Falda, Marco and Fontana, Paolo and Lavezzo, Enrico and Toppo, Stefano and Ferrari, Carlo and Giollo, Manuel and Piovesan, Damiano and Tosatto, C.E. Silvio and del Pozo, Angela and Fernández, M. José and Maietta, Paolo and Valencia, Alfonso and Tress, L. Michael and Benso, Alfredo and Di Carlo, Stefano and Politano, Gianfranco and Savino, Alessandro and Rehman, Ur Hafeez and Re, Matteo and Mesiti, Marco and Valentini, Giorgio and Bargsten, W. Joachim and van Dijk, J. Aalt D. and Gemovic, Branislava and Glisic, Sanja and Perovic, Vladmir and Veljkovic, Veljko and Veljkovic, Nevena and Almeida-e-Silva, C. Danillo and Vencio, N. Ricardo Z. and Sharan, Malvika and Vogel, Jörg and Kansakar, Lakesh and Zhang, Shanshan and Vucetic, Slobodan and Wang, Zheng and Sternberg, E. Michael J. and Wass, N. Mark and Huntley, P. Rachael and Martin, J. Maria and O'Donovan, Claire and Robinson, N. Peter and Moreau, Yves and Tramontano, Anna and Babbitt, C. Patricia and Brenner, E. Steven and Linial, Michal and Orengo, A. Christine and Rost, Burkhard and Greene, S. Casey and Mooney, D. Sean and Friedberg, Iddo and Radivojac, Predrag},
      title = {An expanded evaluation of protein function prediction methods shows an improvement in accuracy},
      journal = {Genome Biology},
      year = {2016},
      volume = {17},
      number = {1},
      pages = {1--19},
      url = {http://dx.doi.org/10.1186/s13059-016-1037-6},
      doi = {http://dx.doi.org/10.1186/s13059-016-1037-6}
    }
    					
    Laippala, V.; Kyröläinen, A.-J.; Kanerva, J.; Luotolahti, J.; Salakoski, T. & Ginter, F. Dependency profiles as a tool for big data analysis of linguistic constructions: A case study of emoticons (To appear) 2016 Journal of Estonian and Finno-Ugric Linguistics , pp. 1–27   article
    BibTeX:
    @article{laippala2016profilesemoticons,
      author = {Laippala, Veronika and Kyröläinen, Aki-Juhani and Kanerva, Jenna and Luotolahti, Juhani and Salakoski, Tapio and Ginter, Filip},
      editor = {Lindström, Liina and Huumo, Tuomas},
      title = {Dependency profiles as a tool for big data analysis of linguistic constructions: A case study of emoticons},
      journal = {Journal of Estonian and Finno-Ugric Linguistics},
      year = {2016},
      pages = {1–27},
      note = {To appear}
    }
    					
    Laippala, V.; Kyröläinen, A.-J.; Komppa, J.; Vilkuna, M.; Kalliokoski, J. & Ginter, F. Sentence-initial discourse relational devices in the Finnish Internet 2016 Conference handbook: TextLink – Structuring discourse in multilingual Europe. Second Action Conference , pp. 70–73   misc
    Lehti, L.; Isosävi, J.; Luotolahti, J. & Laippala, V. Linguistic analysis of online conflicts: A case study of flaming in Smokahontas comment thread in YouTube 2016 Wider Screen (1)   article
    BibTeX:
    @article{lehti16Smoka,
      author = {Lehti, Lotta and Isosävi, Johanna and Luotolahti, Juhani and Laippala, Veronika},
      title = {Linguistic analysis of online conflicts: A case study of flaming in Smokahontas comment thread in YouTube},
      journal = {Wider Screen},
      year = {2016},
      number = {1}
    }
    					
    Luotolahti, J.; Kanerva, J. & Ginter, F. Cross-Lingual Pronoun Prediction with Deep Recurrent Neural Networks 2016 Proceedings of the First Conference on Machine Translation , pp. 596-601   inproceedings
    BibTeX:
    @inproceedings{luotolahti-kanerva-ginter:2016:WMT,
      author = {Luotolahti, Juhani and Kanerva, Jenna and Ginter, Filip},
      title = {Cross-Lingual Pronoun Prediction with Deep Recurrent Neural Networks},
      booktitle = {Proceedings of the First Conference on Machine Translation},
      publisher = {Association for Computational Linguistics},
      year = {2016},
      pages = {596--601},
      url = {http://www.aclweb.org/anthology/W/W16/W16-2353}
    }
    					
    Mehryary, F.; Björne, J.; Pyysalo, S.; Salakoski, T. & Ginter, F. Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016 2016 Proceedings of the 4th BioNLP Shared Task Workshop , pp. 73-81   inproceedings
    BibTeX:
    @inproceedings{mehryary2016bionlpst,
      author = {Mehryary, Farrokh and Björne, Jari and Pyysalo, Sampo and Salakoski, Tapio and Ginter, Filip},
      title = {Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016},
      booktitle = {Proceedings of the 4th BioNLP Shared Task Workshop},
      publisher = {Association for Computational Linguistics},
      year = {2016},
      pages = {73--81}
    }
    					
    Mehryary, F.; Kaewphan, S.; Hakala, K. & Ginter, F. Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification 2016 Journal of Biomedical Semantics
    Vol. 7 (1) , pp. 1-13  
    article
    BibTeX:
    @article{mehryary2016filtering,
      author = {Mehryary, Farrokh and Kaewphan, Suwisa and Hakala, Kai and Ginter, Filip},
      title = {Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification},
      journal = {Journal of Biomedical Semantics},
      year = {2016},
      volume = {7},
      number = {1},
      pages = {1--13},
      url = {http://dx.doi.org/10.1186/s13326-016-0070-4},
      doi = {http://dx.doi.org/10.1186/s13326-016-0070-4}
    }
    					
    Moen, H.; Peltonen, L.; Heimonen, J.; Airola, A.; Pahikkala, T.; Salakoski, T. & Salanterä, S. Comparison of automatic summarisation methods for clinical free text notes 2016 Artificial Intelligence in Medicine
    Vol. 67 , pp. 25-37  
    article
    BibTeX:
    @article{moen2016aiim,
      author = {Hans Moen and Laura-Maria Peltonen and Juho Heimonen and Antti Airola and Tapio Pahikkala and Tapio Salakoski and Sanna Salanterä},
      title = {Comparison of automatic summarisation methods for clinical free text notes},
      journal = {Artificial Intelligence in Medicine},
      year = {2016},
      volume = {67},
      pages = {25--37},
      url = {http://dx.doi.org/10.1016/j.artmed.2016.01.003},
      doi = {http://dx.doi.org/10.1016/j.artmed.2016.01.003}
    }
    					
    Nivre, J.; de Marneffe, M.-C.; Ginter, F.; Goldberg, Y.; Hajič, J.; Manning, C.D.; McDonald, R.; Petrov, S.; Pyysalo, S.; Silveira, N.; Tsarfaty, R. & Zeman, D. Universal Dependencies v1: A Multilingual Treebank Collection (To appear.) 2016 Proceedings of Language Resources and Evaluation Conference (LREC'16)   inproceedings
    BibTeX:
    @inproceedings{nivre2016udv1,
      author = {Joakim Nivre and Marie-Catherine de Marneffe and Filip Ginter and Yoav Goldberg and Jan Hajič and Christopher D. Manning and Ryan McDonald and Slav Petrov and Sampo Pyysalo and Natalia Silveira and Reut Tsarfaty and Daniel Zeman},
      title = {Universal Dependencies v1: A Multilingual Treebank Collection},
      booktitle = {Proceedings of Language Resources and Evaluation Conference (LREC'16)},
      year = {2016},
      note = {To appear.}
    }
    					
    Tiedemann, J.; Cap, F.; Kanerva, J.; Ginter, F.; Stymne, S.; Östling, R. & Weller-Di Marco, M. Phrase-Based SMT for Finnish with More Data, Better Models and Alternative Alignment and Translation Tools 2016 Proceedings of the First Conference on Machine Translation , pp. 391-398   inproceedings
    BibTeX:
    @inproceedings{tiedemann-EtAl:2016:WMT,
      author = {Tiedemann, Jörg and Cap, Fabienne and Kanerva, Jenna and Ginter, Filip and Stymne, Sara and Östling, Robert and Weller-Di Marco, Marion},
      title = {Phrase-Based SMT for Finnish with More Data, Better Models and Alternative Alignment and Translation Tools},
      booktitle = {Proceedings of the First Conference on Machine Translation},
      publisher = {Association for Computational Linguistics},
      year = {2016},
      pages = {391--398},
      url = {http://www.aclweb.org/anthology/W/W16/W16-2326}
    }
    					
    Björne, J. & Salakoski, T. TEES 2.2: Biomedical Event Extraction for Diverse Corpora 2015 BMC bioinformatics
    Vol. 16 (16) , pp. 1  
    article
    BibTeX:
    @article{bjorne2015tees,
      author = {Björne, Jari and Salakoski, Tapio},
      title = {TEES 2.2: Biomedical Event Extraction for Diverse Corpora},
      journal = {BMC bioinformatics},
      publisher = {BioMed Central},
      year = {2015},
      volume = {16},
      number = {16},
      pages = {1}
    }
    					
    Björne, J. & Salakoski, T. Cancer Progression Classification for Mutation Analysis 2015 The 14th Annual International Conference On Critical Assessment of Massive Data Analysis (CAMDA)   article
    BibTeX:
    @article{bjornecancer,
      author = {Björne, Jari and Salakoski, Tapio},
      title = {Cancer Progression Classification for Mutation Analysis},
      journal = {The 14th Annual International Conference On Critical Assessment of Massive Data Analysis (CAMDA)},
      year = {2015}
    }
    					
    Hakala, K. UTU: Adapting Biomedical Event Extraction System to Disorder Attribute Detection 2015 Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015) , pp. 375-379   inproceedings
    BibTeX:
    @inproceedings{hakala2015semeval,
      author = {Hakala, Kai},
      title = {UTU: Adapting Biomedical Event Extraction System to Disorder Attribute Detection},
      booktitle = {Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015)},
      publisher = {Association for Computational Linguistics},
      year = {2015},
      pages = {375--379},
      url = {https://aclweb.org/anthology/S/S15/S15-2064.pdf}
    }
    					
    Hakala, K.; Van Landeghem, S.; Salakoski, T.; Van de Peer, Y. & Ginter, F. Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis 2015 BMC Bioinformatics
    Vol. 16 (Suppl 16) , pp. S3  
    article
    BibTeX:
    @article{hakala2015stextension,
      author = {Hakala, Kai and Van Landeghem, Sofie and Salakoski, Tapio and Van de Peer, Yves and Ginter, Filip},
      title = {Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis},
      journal = {BMC Bioinformatics},
      year = {2015},
      volume = {16},
      number = {Suppl 16},
      pages = {S3},
      url = {http://www.biomedcentral.com/1471-2105/16/S16/S3},
      doi = {http://dx.doi.org/10.1186/1471-2105-16-S16-S3}
    }
    					
    Haverinen, K.; Kanerva, J.; Kohonen, S.; Missilä, A.; Ojala, S.; Viljanen, T.; Laippala, V. & Ginter, F. The Finnish Proposition Bank 2015 Language Resources and Evaluation
    Vol. 49 (4) , pp. 907-926  
    article
    BibTeX:
    @article{haverinen2015propbank,
      author = {Katri Haverinen and Jenna Kanerva and Samuel Kohonen and Anna Missilä and Stina Ojala and Timo Viljanen and Veronika Laippala and Filip Ginter},
      title = {The Finnish Proposition Bank},
      journal = {Language Resources and Evaluation},
      publisher = {Springer Netherlands},
      year = {2015},
      volume = {49},
      number = {4},
      pages = {907--926},
      url = {http://dx.doi.org/10.1007/s10579-015-9310-y},
      doi = {http://dx.doi.org/10.1007/s10579-015-9310-y}
    }
    					
    Kaewphan, S.; Van Landeghem, S.; Ohta, T.; Van de Peer, Y.; Ginter, F. & Pyysalo, S. Cell line name recognition in support of the identification of synthetic lethality in cancer from text (To appear.) 2015 Bioinformatics   article
    BibTeX:
    @article{kaewphan2015cellline,
      author = {Kaewphan, Suwisa and Van Landeghem, Sofie and Ohta, Tomoko and Van de Peer, Yves and Ginter, Filip and Pyysalo, Sampo},
      title = {Cell line name recognition in support of the identification of synthetic lethality in cancer from text},
      journal = {Bioinformatics},
      year = {2015},
      note = {To appear.}
    }
    					
    Kanerva, J.; Luotolahti, J. & Ginter, F. Turku: Semantic Dependency Parsing as a Sequence Classification 2015 Proceedings of SemEval 2015 , pp. 265-269   inproceedings
    BibTeX:
    @inproceedings{kanerva2015semeval,
      author = {Jenna Kanerva and Juhani Luotolahti and Filip Ginter},
      title = {Turku: Semantic Dependency Parsing as a Sequence Classification},
      booktitle = {Proceedings of SemEval 2015},
      publisher = {Association for Computational Linguistics},
      year = {2015},
      pages = {265--269},
      url = {https://aclweb.org/anthology/S/S15/S15-2161.pdf}
    }
    					
    Laippala, V.; Kanerva, J. & Ginter, F. Syntactic Ngrams as Keystructures Reflecting Typical Syntactic Patterns of Corpora in Finnish 2015 Procedia - Social and Behavioral Sciences. Current Work in Corpus Linguistics: Working Traditionally-conceived Corpora and Beyon. Selected Papers from the 7th International Conference on Corpus Linguistics (CILC2015)
    Vol. 198 , pp. 233-241  
    article
    BibTeX:
    @article{laippala2015syngrams,
      author = {Veronika Laippala and Jenna Kanerva and Filip Ginter},
      title = {Syntactic Ngrams as Keystructures Reflecting Typical Syntactic Patterns of Corpora in Finnish},
      journal = {Procedia -- Social and Behavioral Sciences. Current Work in Corpus Linguistics: Working Traditionally-conceived Corpora and Beyon. Selected Papers from the 7th International Conference on Corpus Linguistics (CILC2015)},
      year = {2015},
      volume = {198},
      pages = {233--241}
    }
    					
    Laippala, V.; Kanerva, J.; Pyysalo, S.; Missilä, A.; Salakoski, T. & Ginter, F. Syntactic N-grams in the Classification of the Finnish Internet Parsebank: Detecting Translations and Informality 2015 Proceedings of NoDaLiDa 2015 , pp. 108-116   inproceedings
    BibTeX:
    @inproceedings{laippala2015synngrams,
      author = {Laippala, Veronika and Kanerva, Jenna and Pyysalo, Sampo and Missilä, Anna and Salakoski, Tapio and Ginter, Filip},
      title = {Syntactic N-grams in the Classification of the Finnish Internet Parsebank: Detecting Translations and Informality},
      booktitle = {Proceedings of NoDaLiDa 2015},
      publisher = {NEALT},
      year = {2015},
      pages = {108--116},
      url = {https://aclweb.org/anthology/W/W15/W15-1815.pdf}
    }
    					
    Luotolahti, J. & Ginter, F. Sentence Compression for Automatic Subtitling 2015 Proceedings of NoDaLiDa 2015 , pp. 135-143   inproceedings
    BibTeX:
    @inproceedings{luotolahti2015compression,
      author = {Luotolahti, Juhani and Ginter, Filip},
      title = {Sentence Compression for Automatic Subtitling},
      booktitle = {Proceedings of NoDaLiDa 2015},
      year = {2015},
      pages = {135--143},
      url = {https://aclweb.org/anthology/W/W15/W15-1818.pdf}
    }
    					
    Luotolahti, J.; Kanerva, J.; Laippala, V.; Pyysalo, S. & Ginter, F. Towards Universal Web Parsebanks 2015 Proceedings of the International Conference on Dependency Linguistics (Depling'15) , pp. 211-220   inproceedings
    BibTeX:
    @inproceedings{luotolahti2015parsebanks,
      author = {Luotolahti, Juhani and Kanerva, Jenna and Laippala, Veronika and Pyysalo, Sampo and Ginter, Filip},
      title = {Towards Universal Web Parsebanks},
      booktitle = {Proceedings of the International Conference on Dependency Linguistics (Depling'15)},
      publisher = {Uppsala University},
      year = {2015},
      pages = {211--220}
    }
    					
    Luotolahti, J.; Kanerva, J.; Pyysalo, S. & Ginter, F. SETS: Scalable and Efficient Tree Search in Dependency Graphs 2015 Proceedings of the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Demonstrations , pp. 51-55   inproceedings
    BibTeX:
    @inproceedings{luotolahti2015sets,
      author = {Juhani Luotolahti and Jenna Kanerva and Sampo Pyysalo and Filip Ginter},
      title = {SETS: Scalable and Efficient Tree Search in Dependency Graphs},
      booktitle = {Proceedings of the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Demonstrations},
      publisher = {Association for Computational Linguistics},
      year = {2015},
      pages = {51--55},
      url = {https://aclweb.org/anthology/N/N15/N15-3011.pdf}
    }
    					
    Moen, H.; Ginter, F.; Marsi, E.; Peltonen, L.-M.; Salakoski, T. & Salanterä, S. Care episode retrieval: distributional semantic models for information retrieval in the clinical domain 2015 BMC Medical Informatics and Decision Making
    Vol. 15 (Suppl 2) , pp. S2  
    article
    BibTeX:
    @article{moen2015care,
      author = {Moen, Hans and Ginter, Filip and Marsi, Erwin and Peltonen, Laura-Maria and Salakoski, Tapio and Salanterä, Sanna},
      title = {Care episode retrieval: distributional semantic models for information retrieval in the clinical domain},
      journal = {BMC Medical Informatics and Decision Making},
      publisher = {BioMed Central Ltd},
      year = {2015},
      volume = {15},
      number = {Suppl 2},
      pages = {S2},
      url = {http://www.biomedcentral.com/1472-6947/15/S2/S2},
      doi = {http://dx.doi.org/10.1186/1472-6947-15-S2-S2}
    }
    					
    Pyysalo, S.; Campos, J.; Cejuela, J.M.; Ginter, F.; Hakala, K.; Li, C.; Stenetorp, P. & Jensen, L.J. Sharing annotations better: RESTful Open Annotation (To appear.) 2015 Proceedings of ACL'15: Demonstrations   inproceedings
    BibTeX:
    @inproceedings{pyysalo2015restful,
      author = {Sampo Pyysalo and Jorge Campos and Cejuela, Juan Miguel and Filip Ginter and Kai Hakala and Chen Li and Pontus Stenetorp and Jensen, Lars Juhl},
      title = {Sharing annotations better: RESTful Open Annotation},
      booktitle = {Proceedings of ACL'15: Demonstrations},
      year = {2015},
      note = {To appear.}
    }
    					
    Pyysalo, S.; Kanerva, J.; Missilä, A.; Laippala, V. & Ginter, F. Universal Dependencies for Finnish 2015 Proceedings of NoDaLiDa 2015 , pp. 163-172   inproceedings
    BibTeX:
    @inproceedings{pyysalo2015udfinnish,
      author = {Pyysalo, Sampo and Kanerva, Jenna and Missilä, Anna and Laippala, Veronika and Ginter, Filip},
      title = {Universal Dependencies for Finnish},
      booktitle = {Proceedings of NoDaLiDa 2015},
      publisher = {NEALT},
      year = {2015},
      pages = {163--172},
      url = {https://aclweb.org/anthology/W/W15/W15-1821.pdf}
    }
    					
    Tiedemann, J.; Ginter, F. & Kanerva, J. Morphological Segmentation and OPUS for Finnish-English Machine Translation 2015 Proceedings of the Tenth Workshop on Statistical Machine Translation , pp. 177-183   inproceedings
    BibTeX:
    @inproceedings{tiedemann2015WMT,
      author = {Tiedemann, Jörg and Ginter, Filip and Kanerva, Jenna},
      title = {Morphological Segmentation and OPUS for Finnish-English Machine Translation},
      booktitle = {Proceedings of the Tenth Workshop on Statistical Machine Translation},
      publisher = {Association for Computational Linguistics},
      year = {2015},
      pages = {177--183},
      url = {http://aclweb.org/anthology/W15-3021}
    }
    					
    Björne, J. Biomedical Event Extraction with Machine Learning 2014 School: TUCS Dissertations   phdthesis
    BibTeX:
    @phdthesis{bjorne2014biomedical,
      author = {Björne, Jari},
      title = {Biomedical Event Extraction with Machine Learning},
      school = {TUCS Dissertations},
      year = {2014}
    }
    					
    de Marneffe, M.-C.; Dozat, T.; Silveira, N.; Haverinen, K.; Ginter, F.; Nivre, J. & Manning, C.D. Universal Stanford Dependencies: a Cross-Linguistic Typology 2014 Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14)   inproceedings
    BibTeX:
    @inproceedings{demarneffe2014usd,
      author = {Marie-Catherine de Marneffe and Timothy Dozat and Natalia Silveira and Katri Haverinen and Filip Ginter and Joakim Nivre and Christopher D. Manning},
      title = {Universal Stanford Dependencies: a Cross-Linguistic Typology},
      booktitle = {Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14)},
      publisher = {European Language Resources Association (ELRA)},
      year = {2014},
      url = {http://www.lrec-conf.org/proceedings/lrec2014/pdf/1062_Paper.pdf}
    }
    					
    Haverinen, K.; Nyblom, J.; Viljanen, T.; Laippala, V.; Kohonen, S.; Missilä, A.; Ojala, S.; Salakoski, T. & Ginter, F. Building the essential resources for Finnish: the Turku Dependency Treebank (Open access) 2014 Language Resources and Evaluation
    Vol. 48 , pp. 493-531  
    article
    BibTeX:
    @article{haverinen2013tdt,
      author = {Haverinen, Katri and Nyblom, Jenna and Viljanen, Timo and Laippala, Veronika and Kohonen, Samuel and Missilä, Anna and Ojala, Stina and Salakoski, Tapio and Ginter, Filip},
      title = {Building the essential resources for Finnish: the Turku Dependency Treebank},
      journal = {Language Resources and Evaluation},
      publisher = {Springer Netherlands},
      year = {2014},
      volume = {48},
      pages = {493-531},
      note = {Open access},
      url = {http://dx.doi.org/10.1007/s10579-013-9244-1},
      doi = {http://dx.doi.org/10.1007/s10579-013-9244-1}
    }
    					
    Kaewphan, S.; Hakala, K. & Ginter, F. UTU: Disease Mention Recognition and Normalization with CRFs and Vector Space Representations 2014 Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014) , pp. 807-811   inproceedings
    BibTeX:
    @inproceedings{kaewphan2014SemEval,
      author = {Kaewphan, Suwisa and Hakala, Kai and Ginter, Filip},
      title = {UTU: Disease Mention Recognition and Normalization with CRFs and Vector Space Representations},
      booktitle = {Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014)},
      publisher = {Association for Computational Linguistics and Dublin City University},
      year = {2014},
      pages = {807--811},
      url = {http://www.aclweb.org/anthology/S/S14/S14-2143.pdf}
    }
    					
    Kanerva, J. & Ginter, F. Post-hoc Manipulations of Vector Space Models with Application to Semantic Role Labeling 2014 Proceedings of the 2nd Workshop on Continuous Vector Space Models and their Compositionality (CVSC) at EACL'14 , pp. 1-10   inproceedings
    BibTeX:
    @inproceedings{kanerva2014post,
      author = {Kanerva, Jenna and Ginter, Filip},
      title = {Post-hoc Manipulations of Vector Space Models with Application to Semantic Role Labeling},
      booktitle = {Proceedings of the 2nd Workshop on Continuous Vector Space Models and their Compositionality (CVSC) at EACL'14},
      year = {2014},
      pages = {1--10},
      url = {https://aclweb.org/anthology/W/W14/W14-1501.pdf}
    }
    					
    Kanerva, J.; Luotolahti, J. & Ginter, F. Turku: Broad-Coverage Semantic Parsing with Rich Features 2014 Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014) , pp. 678-682   inproceedings
    BibTeX:
    @inproceedings{kanerva2014SemEval,
      author = {Kanerva, Jenna and Luotolahti, Juhani and Ginter, Filip},
      title = {Turku: Broad-Coverage Semantic Parsing with Rich Features},
      booktitle = {Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014)},
      publisher = {Association for Computational Linguistics and Dublin City University},
      year = {2014},
      pages = {678--682},
      url = {http://www.aclweb.org/anthology/S/S14/S14-2121.pdf}
    }
    					
    Kanerva, J.; Luotolahti, M.; Laippala, V. & Ginter, F. Syntactic N-gram Collection from a Large-Scale Corpus of Internet Finnish 2014 Proceedings of the Sixth International Conference Baltic HLT 2014 , pp. 184-191   inproceedings
    BibTeX:
    @inproceedings{kanerva2014syn,
      author = {Kanerva, Jenna and Luotolahti, Matti and Laippala, Veronika and Ginter, Filip},
      title = {Syntactic N-gram Collection from a Large-Scale Corpus of Internet Finnish},
      booktitle = {Proceedings of the Sixth International Conference Baltic HLT 2014},
      publisher = {IOS Press},
      year = {2014},
      pages = {184--191},
      url = {http://ebooks.iospress.nl/volumearticle/38025},
      doi = {http://dx.doi.org/10.3233/978-1-61499-442-8-184}
    }
    					
    Laippala, V.; Viljanen, T.; Airola, A.; Kanerva, J.; Salanterä, S.; Salakoski, T. & Ginter, F. Statistical parsing of varieties of clinical Finnish (Text Mining and Information Analysis of Health Documents ) 2014 Artificial Intelligence in Medicine
    Vol. 61 (3) , pp. 131-136  
    article
    BibTeX:
    @article{laippala2014sp,
      author = {Veronika Laippala and Timo Viljanen and Antti Airola and Jenna Kanerva and Sanna Salanterä and Tapio Salakoski and Filip Ginter},
      title = {Statistical parsing of varieties of clinical Finnish},
      journal = {Artificial Intelligence in Medicine},
      year = {2014},
      volume = {61},
      number = {3},
      pages = {131--136},
      note = {Text Mining and Information Analysis of Health Documents },
      url = {http://dx.doi.org/10.1016/j.artmed.2014.02.002},
      doi = {http://dx.doi.org/10.1016/j.artmed.2014.02.002}
    }
    					
    Mehryary, F.; Kaewphan, S.; Hakala, K. & Ginter, F. Eliminating Incorrect Events from Large-Scale Event Networks by Trigger Word Clustering and Pruning 2014 Proceedings of SMBM'14 , pp. 75-79   inproceedings
    BibTeX:
    @inproceedings{mehryary2014clustering,
      author = {Farrokh Mehryary and Suwisa Kaewphan and Kai Hakala and Filip Ginter},
      title = {Eliminating Incorrect Events from Large-Scale Event Networks by Trigger Word Clustering and Pruning},
      booktitle = {Proceedings of SMBM'14},
      year = {2014},
      pages = {75--79},
      url = {http://www.zora.uzh.ch/98982/}
    }
    					
    Moen, H.; Marsi, E.; Ginter, F.; Murtola, L.-M.; Salakoski, T. & Salanterä, S. Care Episode Retrieval 2014 Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi) , pp. 116-124   inproceedings
    BibTeX:
    @inproceedings{moen2014care,
      author = {Moen, Hans and Marsi, Erwin and Ginter, Filip and Murtola, Laura-Maria and Salakoski, Tapio and Salanterä, Sanna},
      title = {Care Episode Retrieval},
      booktitle = {Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi)},
      publisher = {Association for Computational Linguistics},
      year = {2014},
      pages = {116--124},
      url = {http://www.aclweb.org/anthology/W14-1118}
    }
    					
    Björne, J.; Airola, A.; Pahikkala, T. & Salakoski, T. Analyzing the Japanese Toxicogenomics Project Dataset with SVM and RLS Classifiers 2013 13th Annual International Conference on Critical Assessment of Massive Data Analysis (CAMDA 2013)   inproceedings
    BibTeX:
    @inproceedings{bjorne2013analyzing,
      author = {Björne, 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}
    }
    					
    Björne, J.; Kaewphan, S. & Salakoski, T. UTurku: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using SVM Classification and Domain Knowledge 2013 Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013) , pp. 651-659   inproceedings
    BibTeX:
    @inproceedings{bjorne2013uturku,
      author = {Björne, Jari and Kaewphan, Suwisa and Salakoski, Tapio},
      title = {UTurku: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using SVM Classification and Domain Knowledge},
      booktitle = {Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013)},
      year = {2013},
      pages = {651--659}
    }
    					
    Björne, J. & Salakoski, T. TEES 2.1: Automated annotation scheme learning in the BioNLP 2013 Shared Task 2013 Proceedings of the BioNLP Shared Task 2013 Workshop , pp. 16-25   inproceedings
    BibTeX:
    @inproceedings{bjorne2013tees,
      author = {Björne, Jari and Salakoski, Tapio},
      title = {TEES 2.1: Automated annotation scheme learning in the BioNLP 2013 Shared Task},
      booktitle = {Proceedings of the BioNLP Shared Task 2013 Workshop},
      year = {2013},
      pages = {16--25}
    }
    					
    Bohnet, B.; Nivre, J.; Boguslavsky, I.; Farkas, R.; Ginter, F. & Hajič, J. Joint Morphological and Syntactic Analysis for Richly Inflected Languages 2013 Transactions of the Association for Computational Linguistics
    Vol. 1 , pp. 415-428  
    article
    BibTeX:
    @article{bohnet2013joint,
      author = {Bernd Bohnet and Joakim Nivre and Igor Boguslavsky and Richárd Farkas and Filip Ginter and Jan Hajič},
      title = {Joint Morphological and Syntactic Analysis for Richly Inflected Languages},
      journal = {Transactions of the Association for Computational Linguistics},
      year = {2013},
      volume = {1},
      pages = {415--428}
    }
    					
    Ginter, F.; Nyblom, J.; Laippala, V.; Kohonen, S.; Haverinen, K.; Vihjanen, S. & Salakoski, T. Building a Large Automatically Parsed Corpus of Finnish 2013 Proceedings of the 19th Nordic Conference on Computational Linguistics (NoDaLiDa'13) , pp. 291-300   inproceedings
    BibTeX:
    @inproceedings{ginter13ftb3,
      author = {Ginter, Filip and Nyblom, Jenna and Laippala, Veronika and Kohonen, Samuel and Haverinen, Katri and Vihjanen, Simo and Salakoski, Tapio},
      title = {Building a Large Automatically Parsed Corpus of Finnish},
      booktitle = {Proceedings of the 19th Nordic Conference on Computational Linguistics (NoDaLiDa'13)},
      year = {2013},
      pages = {291-300}
    }
    					
    Hakala, K.; Mehryary, F.; Kaewphan, S. & Ginter, F. Hypothesis Generation in Large-Scale Event Networks 2013 Proceedings of the 5th International Symposium on Languages in Biology and Medicine (LBM'13) , pp. 19-28   inproceedings
    BibTeX:
    @inproceedings{hakala2013hypothesis,
      author = {Kai Hakala and Farrokh Mehryary and Suwisa Kaewphan and Filip Ginter},
      title = {Hypothesis Generation in Large-Scale Event Networks},
      booktitle = {Proceedings of the 5th International Symposium on Languages in Biology and Medicine (LBM'13)},
      year = {2013},
      pages = {19--28}
    }
    					
    Hakala, K.; Van Landeghem, S.; Salakoski, T.; Van de Peer, Y. & Ginter, F. EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction 2013 Proceedings of the BioNLP Shared Task 2013 Workshop (BioNLP-ST'13) , pp. 26-34   inproceedings
    BibTeX:
    @inproceedings{hakala2013st,
      author = {Hakala, Kai and Van Landeghem, Sofie and Salakoski, Tapio and Van de Peer, Yves and Ginter, Filip},
      title = {EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction},
      booktitle = {Proceedings of the BioNLP Shared Task 2013 Workshop (BioNLP-ST'13)},
      year = {2013},
      pages = {26--34}
    }
    					
    Haverinen, K.; Ginter, F.; Laippala, V.; Kohonen, S.; Viljanen, T.; Nyblom, J. & Salakoski, T. A Dependency-based Analysis of Treebank Annotation Errors 2013 Computational Dependency Theory   incollection
    BibTeX:
    @incollection{haverinen13errors,
      author = {Katri Haverinen and Filip Ginter and Veronika Laippala and Samuel Kohonen and Timo Viljanen and Jenna Nyblom and Tapio Salakoski},
      editor = {Gerdes, Kim and Hajičová, Eva and Wanner, Leo},
      title = {A Dependency-based Analysis of Treebank Annotation Errors},
      booktitle = {Computational Dependency Theory},
      publisher = {IOS Press},
      year = {2013}
    }
    					
    Haverinen, K.; Laippala, V.; Kohonen, S.; Missilä, A.; Nyblom, J.; Ojala, S.; Viljanen, T.; Salakoski, T. & Ginter, F. Towards a Dependency-based PropBank of General Finnish 2013 Proceedings of the 19th Nordic Conference on Computational Linguistics (NoDaLiDa'13) , pp. 41-57   inproceedings
    BibTeX:
    @inproceedings{haverinen13propbank,
      author = {Haverinen, Katri and Laippala, Veronika and Kohonen, Samuel and Missilä, Anna and Nyblom, Jenna and Ojala, Stina and Viljanen, Timo and Salakoski, Tapio and Ginter, Filip},
      title = {Towards a Dependency-based PropBank of General Finnish},
      booktitle = {Proceedings of the 19th Nordic Conference on Computational Linguistics (NoDaLiDa'13)},
      year = {2013},
      pages = {41--57}
    }
    					
    Laippala, V.; Viljanen, T.; Airola, A.; Nyblom, J.; Salanterä, S.; Salakoski, T. & Ginter, F. Statistical Parsing of Varieties of Clinical Finnish 2013 Proceedings of the 4th International Louhi Workshop on Health Document Text Mining and Information Analysis (Louhi 2013)   inproceedings
    BibTeX:
    @inproceedings{laippala13statparsing,
      author = {Laippala, Veronika and Viljanen, Timo and Airola, Antti and Nyblom, Jenna and Salanterä, Sanna and Salakoski, Tapio and Ginter, Filip},
      editor = {Suominen, Hanna},
      title = {Statistical Parsing of Varieties of Clinical Finnish},
      booktitle = {Proceedings of the 4th International Louhi Workshop on Health Document Text Mining and Information Analysis (Louhi 2013)},
      year = {2013}
    }
    					
    Nyblom, J.; Kohonen, S.; Haverinen, K.; Salakoski, T. & Ginter, F. Predicting conjunct propagation and other extended Stanford Dependencies 2013 Proceedings of the International Conference on Dependency Linguistics (Depling 2013) , pp. 252-261   inproceedings
    BibTeX:
    @inproceedings{nyblom2013ccprop,
      author = {Nyblom, Jenna and Kohonen, Samuel and Haverinen, Katri and Salakoski, Tapio and Ginter, Filip},
      title = {Predicting conjunct propagation and other extended Stanford Dependencies},
      booktitle = {Proceedings of the International Conference on Dependency Linguistics (Depling 2013)},
      year = {2013},
      pages = {252--261}
    }
    					
    Pyysalo, S.; Ginter, F.; Moen, H.; Salakoski, T. & Ananiadou, S. Distributional Semantic Resources for Biomedical Text Mining 2013 Proceedings of the 5th International Symposium on Languages in Biology and Medicine , pp. 39-44   inproceedings
    BibTeX:
    @inproceedings{pyysalo2013dist,
      author = {Sampo Pyysalo and Filip Ginter and Hans Moen and Tapio Salakoski and Sophia Ananiadou},
      title = {Distributional Semantic Resources for Biomedical Text Mining},
      booktitle = {Proceedings of the 5th International Symposium on Languages in Biology and Medicine},
      year = {2013},
      pages = {39--44}
    }
    					
    Radivojac, P.; Clark, W.T.; Oron, T.R.; Schnoes, A.M.; Wittkop, T.; Sokolov, A.; Graim, K.; Funk, C.; Verspoor, K.; Ben-Hur, A. & others A large-scale evaluation of computational protein function prediction 2013 Nature methods
    Vol. 10 (3) , pp. 221-227  
    article
    BibTeX:
    @article{radivojac2013large,
      author = {Radivojac, Predrag and Clark, Wyatt T and Oron, Tal Ronnen and Schnoes, Alexandra M and Wittkop, Tobias and Sokolov, Artem and Graim, Kiley and Funk, Christopher and Verspoor, Karin and Ben-Hur, Asa and others},
      title = {A large-scale evaluation of computational protein function prediction},
      journal = {Nature methods},
      publisher = {Nature Publishing Group},
      year = {2013},
      volume = {10},
      number = {3},
      pages = {221--227}
    }
    					
    Van Landeghem, S.; Björne, J.; Wei, C.-H.; Hakala, K.; Pyysalo, S.; Ananiadou, S.; Kao, H.-Y.; Lu, Z.; Salakoski, T.; Van de Peer, Y. & Ginter, F. Large-scale event extraction from literature with multi-level gene normalization 2013 PLoS ONE
    Vol. 8 (4) , pp. e55814  
    article
    BibTeX:
    @article{vanlandeghem13evex2,
      author = {Van Landeghem, Sofie and Björne, Jari and Wei, Chih-Hsuan and Hakala, Kai and Pyysalo, Sampo and Ananiadou, Sophia and Kao, Hung-Yu and Lu, Zhiyong and Salakoski, Tapio and Van de Peer, Yves and Ginter, Filip},
      title = {Large-scale event extraction from literature with multi-level gene normalization},
      journal = {PLoS ONE},
      year = {2013},
      volume = {8},
      number = {4},
      pages = {e55814},
      doi = {http://dx.doi.org/10.1371/journal.pone.0055814}
    }
    					
    Van Landeghem, S.; Kaewphan, S.; Ginter, F. & Van de Peer, Y. Evaluating large-scale text mining applications beyond the traditional numeric performance measures 2013 Proceedings of the 2013 Workshop on Biomedical Natural Language Processing (BioNLP'13) , pp. 63-71   inproceedings
    BibTeX:
    @inproceedings{vanlandeghem2013eval,
      author = {Van Landeghem, Sofie and Kaewphan, Suwisa and Ginter, Filip and Van de Peer, Yves},
      title = {Evaluating large-scale text mining applications beyond the traditional numeric performance measures},
      booktitle = {Proceedings of the 2013 Workshop on Biomedical Natural Language Processing (BioNLP'13)},
      year = {2013},
      pages = {63--71}
    }
    					
    Airola, A. Machine Learning and Performance Estimation Methods for Ranking Problems 2012 Proceedings of the Federated Computer Science Event , pp. 8-14   inproceedings
    BibTeX:
    @inproceedings{airola2012ranking,
      author = {Airola, Antti},
      editor = {Tarkoma, Sasu and Kämäräinen, Joni-Kristian and Pahikkala, Tapio},
      title = {Machine Learning and Performance Estimation Methods for Ranking Problems},
      booktitle = {Proceedings of the Federated Computer Science Event},
      publisher = {Unigrafia Oy},
      year = {2012},
      pages = {8--14}
    }
    					
    Björne, J.; Van Landeghem, S.; Pyysalo, S.; Ohta, T.; Ginter, F.; Van de Peer, Y.; Ananiadou, S. & Salakoski, T. PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations 2012 BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing , pp. 82-90   inproceedings
    BibTeX:
    @inproceedings{bjorne2012epi,
      author = {Björne, Jari and Van Landeghem, Sofie and Pyysalo, Sampo and Ohta, Tomoko and Ginter, Filip and Van de Peer, Yves and Ananiadou, Sophia and Salakoski, Tapio},
      title = {PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations},
      booktitle = {BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
      publisher = {Association for Computational Linguistics},
      year = {2012},
      pages = {82--90}
    }
    					
    Gieseke, F.; Airola, A.; Pahikkala, T. & Kramer, O. Sparse Quasi-Newton Optimization for Semi-Supervised Support Vector Machines 2012 Proceedings of the 1st International Conference on Pattern Recognition Applications and Methods (ICPRAM) , pp. 45-54   inproceedings
    BibTeX:
    @inproceedings{gieseke2012sqn,
      author = {Gieseke, Fabian and Airola, Antti and Pahikkala, Tapio and Kramer, Oliver},
      editor = {Latorre Carmona, Pedro and Sánchez, 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)},
      publisher = {SciTePress},
      year = {2012},
      pages = {45-54}
    }
    					
    Gieseke, F.; Kramer, O.; Airola, A. & Pahikkala, T. Efficient recurrent local search strategies for semi- and unsupervised regularized least-squares classification 2012 Evolutionary Intelligence
    Vol. 5 (3) , pp. 189-205  
    article
    BibTeX:
    @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},
      year = {2012},
      volume = {5},
      number = {3},
      pages = {189--205},
      url = {http://dx.doi.org/10.1007/s12065-012-0068-5},
      doi = {http://dx.doi.org/10.1007/s12065-012-0068-5}
    }
    					
    Hakala, K.; Van Landeghem, S.; Kaewphan, S.; Salakoski, T.; Van de Peer, Y. & Ginter, F. CyEVEX: Literature-scale network integration and visualization through Cytoscape 2012 Proceedings of SMBM'12, Zurich, Switzerland , pp. 91-96   inproceedings
    BibTeX:
    @inproceedings{hakala2012cyevex,
      author = {Hakala, Kai and Van Landeghem, Sofie and Kaewphan, Suwisa and Salakoski, Tapio and Van de Peer, Yves and Ginter, Filip},
      title = {CyEVEX: Literature-scale network integration and visualization through Cytoscape},
      booktitle = {Proceedings of SMBM'12, Zurich, Switzerland},
      year = {2012},
      pages = {91--96}
    }
    					
    Kaewphan, S.; Kreula, S.; Van Landeghem, S.; Van de Peer, Y.; Jones, P.R. & Ginter, F. Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting NADP(H) Metabolism in E. coli with Event Extraction 2012 Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012) , pp. 8-15   inproceedings
    BibTeX:
    @inproceedings{kaewphan12nadph,
      author = {Kaewphan, Suwisa and Kreula, Sanna and Van Landeghem, Sofie and Van de Peer, Yves and Jones, Patrik R. and Ginter, Filip},
      title = {Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting NADP(H) Metabolism in E. coli with Event Extraction},
      booktitle = {Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012)},
      year = {2012},
      pages = {8--15}
    }
    					
    Pahikkala, T.; Airola, A.; Gieseke, F. & Kramer, O. Unsupervised Multi-Class Regularized Least-Squares Classification 2012 The 12th IEEE International Conference on Data Mining (ICDM 2012) , pp. 585-594   inproceedings
    BibTeX:
    @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},
      year = {2012},
      pages = {585--594},
      url = {http://staff.cs.utu.fi/~aatapa/publications/pdf/icdm2012preprint.pdf},
      doi = {http://dx.doi.org/10.1109/ICDM.2012.71}
    }
    					
    Pahikkala, T.; Airola, A.; Xu, T.C.; Liljeberg, P.; Tenhunen, H. & Salakoski, T. Parallelized Online Regularized Least-Squares for Adaptive Embedded Systems 2012 International Journal of Embedded and Real-Time Communication Systems
    Vol. 3 (2) , pp. 73-91  
    article
    BibTeX:
    @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},
      publisher = {IGI Global},
      year = {2012},
      volume = {3},
      number = {2},
      pages = {73--91},
      doi = {http://dx.doi.org/10.4018/jertcs.2012040104}
    }
    					
    Pahikkala, T.; Okser, S.; Airola, A.; Salakoski, T. & Aittokallio, T. Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations 2012 Algorithms for Molecular Biology
    Vol. 7 (1) , pp. 11  
    article
    BibTeX:
    @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},
      year = {2012},
      volume = {7},
      number = {1},
      pages = {11},
      url = {http://www.almob.org/content/7/1/11},
      doi = {http://dx.doi.org/10.1186/1748-7188-7-11}
    }
    					
    Pahikkala, T.; Suominen, H. & Boberg, J. Efficient cross-validation for kernelized least-squares regression with sparse basis expansions 2012 Machine Learning
    Vol. 87 (3) , pp. 381-407  
    article
    BibTeX:
    @article{pahikkala2012efficientcv,
      author = {Pahikkala, Tapio and Suominen, Hanna and Boberg, Jorma},
      title = {Efficient cross-validation for kernelized least-squares regression with sparse basis expansions},
      journal = {Machine Learning},
      publisher = {Springer Netherlands},
      year = {2012},
      volume = {87},
      number = {3},
      pages = {381-407},
      url = {http://dx.doi.org/10.1007/s10994-012-5287-6},
      doi = {http://dx.doi.org/10.1007/s10994-012-5287-6}
    }
    					
    Stock, M.; Pahikkala, T.; Airola, A.; Salakoski, T.; De Baets, B. & Waegeman, W. Learning Monadic and Dyadic Relations: Three Case Studies in Systems Biology 2012 Proceedings of the ECML/PKDD 2012 Workshop on Learning and Discovery in Symbolic Systems Biology , pp. 74-84   inproceedings
    BibTeX:
    @inproceedings{stock2012monadic,
      author = {Stock, Michiel and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and De Baets, Bernard and Waegeman, Willem},
      editor = {Oliver Ray and Katsumi Inoue},
      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}
    }
    					
    Van Landeghem, S.; Hakala, K.; Rönnqvist, S.; Salakoski, T.; Van de Peer, Y. & Ginter, F. Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology and Indirect Associations 2012 Advances in Bioinformatics, special issue Literature-Mining Solutions for Life Science Research   article
    BibTeX:
    @article{vanlandeghem12evexweb,
      author = {Van Landeghem, Sofie and Hakala, Kai and Rönnqvist, Samuel and Salakoski, Tapio and Van de Peer, Yves and Ginter, Filip},
      title = {Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology and Indirect Associations},
      journal = {Advances in Bioinformatics, special issue Literature-Mining Solutions for Life Science Research},
      year = {2012}
    }
    					
    Waegeman, W.; Pahikkala, T.; Airola, A.; Salakoski, T. & De Baets, B. Learning Valued Relations from Data 2012
    Vol. 107 Eurofuse 2011 , pp. 257-268  
    inproceedings
    BibTeX:
    @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 Serôdio, Carlos and Fodor, János and De Baets, Bernard},
      title = {Learning Valued Relations from Data},
      booktitle = {Eurofuse 2011},
      publisher = {Springer},
      year = {2012},
      volume = {107},
      pages = {257--268},
      url = {http://dx.doi.org/10.1007/978-3-642-24001-0_24},
      doi = {http://dx.doi.org/10.1007/978-3-642-24001-0_24}
    }
    					
    Waegeman, W.; Stock, M.; De Baets, B.; Pahikkala, T.; Airola, A. & Salakoski, T. Conditional Ranking Algorithms for Efficient Object Retrieval and Object Querying on Relational Data 2012 Proceedings of the 12th Dutch-Belgian Information Retrieval Workshop (DIR 2012) , pp. 59-60   inproceedings
    BibTeX:
    @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)},
      publisher = {Ghent University},
      year = {2012},
      pages = {59-60}
    }
    					
    Xu, T.C.; Pahikkala, T.; Airola, A.; Liljeberg, P.; Plosila, J.; Salakoski, T. & Tenhunen, H. Implementation and Analysis of Block Dense Matrix Decomposition on Network-on-Chips 2012 The 14th IEEE International Conference on High Performance Computing and Communications (HPCC-2012) , pp. 516-523   inproceedings
    BibTeX:
    @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)},
      publisher = {IEEE Computer Society},
      year = {2012},
      pages = {516--523},
      doi = {http://dx.doi.org/10.1109/HPCC.2012.76}
    }
    					
    The Federated Computer Science Event 2012   proceedings
    BibTeX:
    @proceedings{tarkoma2012ytp,,
      editor = {Tarkoma, Sasu and Kämäräinen, Joni-Kristian and Pahikkala, Tapio},
      title = {The Federated Computer Science Event},
      publisher = {Unigrafia Oy},
      year = {2012},
      url = {http://www.cs.helsinki.fi/u/starkoma/ytp/YTP-Proceedings-2012.pdf}
    }
    					
    Airola, A. Kernel-Based Ranking: Methods for Learning and Performance Estimation 2011 School: Turku Centre for Computer Science (TUCS)   phdthesis
    BibTeX:
    @phdthesis{airola2011phd,
      author = {Airola, Antti},
      title = {Kernel-Based Ranking: Methods for Learning and Performance Estimation},
      school = {Turku Centre for Computer Science (TUCS)},
      year = {2011}
    }
    					
    Airola, A.; Pahikkala, T. & Salakoski, T. An Improved Training Algorithm for the Linear Ranking Support Vector Machine 2011
    Vol. 6791 Proceedings of the 21st International Conference on Artificial Neural Networks (ICANN 2011) , pp. 134-141  
    inproceedings
    BibTeX:
    @inproceedings{airola2011improved,
      author = {Antti Airola and Tapio Pahikkala and Tapio Salakoski},
      editor = {Timo Honkela and Wlodzislaw Duch and Mark A. Girolami and Samuel Kaski},
      title = {An Improved Training Algorithm for the Linear Ranking Support Vector Machine},
      booktitle = {Proceedings of the 21st International Conference on Artificial Neural Networks (ICANN 2011)},
      publisher = {Springer},
      year = {2011},
      volume = {6791},
      pages = {134-141},
      url = {http://dx.doi.org/10.1007/978-3-642-21735-7_17}
    }
    					
    Airola, A.; Pahikkala, T. & Salakoski, T. On learning and cross-validation with decomposed Nyström approximation of kernel matrix 2011 Neural Processing Letters
    Vol. 33 (1) , pp. 17-30  
    article
    BibTeX:
    @article{airola2011nystromcv,
      author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
      title = {On learning and cross-validation with decomposed Nyström approximation of kernel matrix},
      journal = {Neural Processing Letters},
      year = {2011},
      volume = {33},
      number = {1},
      pages = {17--30},
      url = {http://dx.doi.org/doi:10.1007/s11063-010-9159-4},
      doi = {http://dx.doi.org/10.1007/s11063-010-9159-4}
    }
    					
    Airola, A.; Pahikkala, T. & Salakoski, T. Training linear ranking SVMs in linearithmic time using red-black trees 2011 Pattern Recognition Letters
    Vol. 32 (9) , pp. 1328-1336  
    article
    BibTeX:
    @article{airola2011ranksvm,
      author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
      title = {Training linear ranking SVMs in linearithmic time using red-black trees},
      journal = {Pattern Recognition Letters},
      year = {2011},
      volume = {32},
      number = {9},
      pages = {1328--1336},
      url = {http://dx.doi.org/doi:10.1016/j.patrec.2011.03.014}
    }
    					
    Airola, A.; Pahikkala, T.; Waegeman, W.; De Baets, B. & Salakoski, T. An experimental comparison of cross-validation techniques for estimating the area under the ROC curve 2011 Computational Statistics & Data Analysis
    Vol. 55 (4) , pp. 1828-1844  
    article
    BibTeX:
    @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},
      url = {http://dx.doi.org/10.1016/j.csda.2010.11.018 },
      doi = {http://dx.doi.org/10.1016/j.csda.2010.11.018}
    }
    					
    Björne, J.; Airola, A.; Pahikkala, T. & Salakoski, T. Drug-Drug Interaction Extraction from Biomedical Texts with SVM and RLS Classifiers 2011 Proceedings of the First Challenge task on Drug-Drug Interaction Extraction (DDIExtraction 2011) , pp. 35-42   inproceedings
    BibTeX:
    @inproceedings{bjorne2011ddi,
      author = {Björne, Jari and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
      title = {Drug-Drug Interaction Extraction from Biomedical Texts with SVM and RLS Classifiers},
      booktitle = {Proceedings of the First Challenge task on Drug-Drug Interaction Extraction (DDIExtraction 2011)},
      publisher = {CEUR Workshop Proceedings},
      year = {2011},
      pages = {35--42},
      url = {http://ceur-ws.org/Vol-761/paper4.pdf}
    }
    					
    Björne, J.; Heimonen, J.; Ginter, F.; Airola, A.; Pahikkala, T. & Salakoski, T. Extracting Contextualized Complex Biological Events with Rich Graph-Based Feature Sets (Accepted in 2009) 2011 Computational Intelligence
    Vol. 27 (4) , pp. 541-557  
    article
    BibTeX:
    @article{bjorne2010extractingcontext,
      author = {Björne, 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},
      publisher = {Blackwell Publishing Inc},
      year = {2011},
      volume = {27},
      number = {4},
      pages = {541--557},
      note = {Accepted in 2009},
      url = {http://dx.doi.org/10.1111/j.1467-8640.2011.00399.x},
      doi = {http://dx.doi.org/10.1111/j.1467-8640.2011.00399.x}
    }
    					
    Björne, J. & Salakoski, T. Generalizing Biomedical Event Extraction 2011 Proceedings of BioNLP Shared Task 2011 Workshop , pp. 183-191   inproceedings
    BibTeX:
    @inproceedings{bjorne2011bionlpst,
      author = {Björne, Jari and Salakoski, Tapio},
      title = {Generalizing Biomedical Event Extraction},
      booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop},
      publisher = {Association for Computational Linguistics},
      year = {2011},
      pages = {183--191},
      url = {http://www.aclweb.org/anthology/W11-1828}
    }
    					
    Björne, J. & Salakoski, T. A Machine Learning Model and Evaluation of Text Mining for Protein Function Prediction 2011 Automated Function Prediction Featuring a Critical Assessment of Function Annotations (AFP/CAFA) 2011 , pp. 7-8   inproceedings
    BibTeX:
    @inproceedings{bjorne2011cafa,
      author = {Björne, Jari and Salakoski, Tapio},
      title = {A Machine Learning Model and Evaluation of Text Mining for Protein Function Prediction},
      booktitle = {Automated Function Prediction Featuring a Critical Assessment of Function Annotations (AFP/CAFA) 2011},
      publisher = {Automated Function Prediction -- an ISMB Special Interest Group},
      year = {2011},
      pages = {7--8},
      url = {http://iddo-friedberg.net/afp-cafa-2011-booklet.pdf}
    }
    					
    Gieseke, F.; Kramer, O.; Airola, A. & Pahikkala, T. Speedy Local Search for Semi-Supervised Regularized Least-Squares 2011
    Vol. 7006 KI 2011: Advances in Artificial Intelligence , pp. 87-98  
    inproceedings
    BibTeX:
    @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},
      publisher = {Springer},
      year = {2011},
      volume = {7006},
      pages = {87--98},
      url = {http://dx.doi.org/10.1007/978-3-642-24455-1_8},
      doi = {http://dx.doi.org/10.1007/978-3-642-24455-1_8}
    }
    					
    Haverinen, K.; Ginter, F.; Laippala, V.; Kohonen, S.; Viljanen, T.; Nyblom, J. & Salakoski, T. A Dependency-based Analysis of Treebank Annotation Errors 2011 Proceedings of International Conference on Dependency Linguistics (Depling'11), Barcelona, Spain , pp. 115-124   inproceedings
    BibTeX:
    @inproceedings{haverinen11errors,
      author = {Katri Haverinen and Filip Ginter and Veronika Laippala and Samuel Kohonen and Timo Viljanen and Jenna Nyblom and Tapio Salakoski},
      title = {A Dependency-based Analysis of Treebank Annotation Errors},
      booktitle = {Proceedings of International Conference on Dependency Linguistics (Depling'11), Barcelona, Spain},
      year = {2011},
      pages = {115-124}
    }
    					
    Kano, Y.; Björne, J.; Ginter, F.; Salakoski, T.; Buyko, E.; Hahn, U.; Cohen, K.; Verspoor, K.; Roeder, C.; Hunter, L.; Kilicoglu, H.; Bergler, S.; Landeghem, S.; Parys, T.; Van de Peer, Y.; Miwa, M.; Ananiadou, S.; Neves, M.; Pascual-Montano, A.; Ozgur, A.; Radev, D.; Riedel, S.; Saetre, R.; Chun, H.-W.; Kim, J.-D.; Pyysalo, S.; Ohta, T. & Tsujii, J. U-Compare bio-event meta-service: compatible BioNLP event extraction services 2011 BMC Bioinformatics
    Vol. 12 (1) , pp. 481  
    article
    BibTeX:
    @article{kano2011ucompare,
      author = {Kano, Yoshinobu and Björne, Jari and Ginter, Filip and Salakoski, Tapio and Buyko, Ekaterina and Hahn, Udo and Cohen, Kevin and Verspoor, Karin and Roeder, Christophe and Hunter, Lawrence and Kilicoglu, Halil and Bergler, Sabine and Landeghem, Sofie and Parys, Thomas and Van de Peer, Yves and Miwa, Makoto and Ananiadou, Sophia and Neves, Mariana and Pascual-Montano, Alberto and Ozgur, Arzucan and Radev, Dragomir and Riedel, Sebastian and Saetre, Rune and Chun, Hong-Woo and Kim, Jin-Dong and Pyysalo, Sampo and Ohta, Tomoko and Tsujii, Jun'ichi},
      title = {U-Compare bio-event meta-service: compatible BioNLP event extraction services},
      journal = {BMC Bioinformatics},
      year = {2011},
      volume = {12},
      number = {1},
      pages = {481},
      url = {http://www.biomedcentral.com/1471-2105/12/481},
      doi = {http://dx.doi.org/10.1186/1471-2105-12-481}
    }
    					
    Naula, P.; Pahikkala, T.; Airola, A. & Salakoski, T. Learning Multi-Label Predictors under Sparsity Budget 2011
    Vol. 227 Eleventh Scandinavian Conference on Artificial Intelligence, SCAI 2011 , pp. 30-39  
    inproceedings
    BibTeX:
    @inproceedings{naula2010budgeted,
      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},
      year = {2011},
      volume = {227},
      pages = {30--39}
    }
    					
    Naula, P.; Pahikkala, T.; Airola, A. & Salakoski, T. Greedy Regularized Least-Squares for Multi-Task Learning 2011 11th IEEE International Conference on Data Mining Workshops (ICDMW'11) , pp. 527-533   inproceedings
    BibTeX:
    @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 Zaïane, 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},
      year = {2011},
      pages = {527--533},
      doi = {http://dx.doi.org/10.1109/ICDMW.2011.91}
    }
    					
    Okser, S.; Pahikkala, T.; Airola, A.; Aittokallio, T. & Salakoski, T. Fast and Parallelized Greedy Forward Selection of Genetic Variants in Genome-Wide Association Studies 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'11) , pp. 214-217   inproceedings
    BibTeX:
    @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},
      year = {2011},
      pages = {214--217},
      doi = {http://dx.doi.org/10.1109/GENSiPS.2011.6169483}
    }
    					
    Pahikkala, T.; Airola, A.; Xu, T.C.; Liljeberg, P.; Tenhunen, H. & Salakoski, T. A parallel online regularized least-squares machine learning algorithm for future multi-core processors 2011 Proceedings of the 1st International Conference on Pervasive and Embedded Computing and Communication Systems (PECCS 2011) , pp. 590-599   inproceedings
    BibTeX:
    @inproceedings{pahikkala2011parallelonline,
      author = {Pahikkala, Tapio and Airola, Antti and Xu, Thomas Canhao and Liljeberg, Pasi and Tenhunen, Hannu and Salakoski, Tapio},
      editor = {Benavente-Peces, César 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)},
      publisher = {SciTePress},
      year = {2011},
      pages = {590--599}
    }
    					
    Van Landeghem, S.; Ginter, F.; Van de Peer, Y. & Salakoski, T. EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions 2011 Proceedings of BioNLP'11 Workshop , pp. 28-37   inproceedings
    BibTeX:
    @inproceedings{vanlandeghem2011evex,
      author = {Van Landeghem, Sofie and Ginter, Filip and Van de Peer, Yves and Salakoski, Tapio},
      title = {EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions},
      booktitle = {Proceedings of BioNLP'11 Workshop},
      publisher = {Association for Computational Linguistics},
      year = {2011},
      pages = {28--37}
    }
    					
    Airola, A.; Pahikkala, T.; Boberg, J. & Salakoski, T. Applying permutation tests for assessing the statistical significance of wrapper based feature selection 2010 Proceedings of The Ninth International Conference on Machine Learning and Applications (ICMLA'10) , pp. 989-994   inproceedings
    BibTeX:
    @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},
      pages = {989--994},
      url = {http://dx.doi.org/10.1109/ICMLA.2010.158}
    }
    					
    Airola, A.; Pahikkala, T. & Salakoski, T. Large scale training methods for linear RankRLS 2010 Proceedings of the ECML/PKDD-Workshop on Preference Learning (PL-10)   inproceedings
    BibTeX:
    @inproceedings{airola2010largescale,
      author = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
      editor = {Eyke Hüllermeier and Johannes Fürnkranz},
      title = {Large scale training methods for linear RankRLS},
      booktitle = {Proceedings of the ECML/PKDD-Workshop on Preference Learning (PL-10)},
      year = {2010},
      url = {www.ke.tu-darmstadt.de/events/PL-10/papers/11-Airola.pdf}
    }
    					
    Airola, A.; Pahikkala, T.; Waegeman, W.; De Baets, B. & Salakoski, T. A comparison of AUC estimators in small-sample studies 2010 JMLR Workshop and Conference Proceedings: Machine Learning in Systems Biology , pp. 3-13   incollection
    BibTeX:
    @incollection{airola2010comparison,
      author = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
      editor = {Džeroski, Sašo and Geurts, Pierre and Rousu, Juho},
      title = {A comparison of AUC estimators in small-sample studies},
      booktitle = {JMLR Workshop and Conference Proceedings: Machine Learning in Systems Biology},
      year = {2010},
      pages = {3--13}
    }
    					
    Björne, J.; Ginter, F.; Pyysalo, S.; Tsujii, J. & Salakoski, T. Complex Event Extraction at PubMed Scale 2010 Bioinformatics (ISMB'2010 proceedings volume)
    Vol. 26 , pp. i382-i390  
    article
    BibTeX:
    @article{bjorne2010complex,
      author = {Björne, Jari and Ginter, Filip and Pyysalo, Sampo and Tsujii, Jun'ichi and Salakoski, Tapio},
      title = {Complex Event Extraction at PubMed Scale},
      journal = {Bioinformatics (ISMB'2010 proceedings volume)},
      year = {2010},
      volume = {26},
      pages = {i382--i390},
      url = {http://bioinformatics.oxfordjournals.org/cgi/content/full/btq180?ijkey=41vpyrHIQkfr2dP&keytype=ref}
    }
    					
    Björne, J.; Ginter, F.; Pyysalo, S.; Tsujii, J. & Salakoski, T. Scaling up Biomedical Event Extraction to the Entire PubMed 2010 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing (BioNLP'10) , pp. 28-36   inproceedings
    BibTeX:
    @inproceedings{bjorne2010scalingup,
      author = {Björne, Jari and Ginter, Filip and Pyysalo, Sampo and Tsujii, Jun'ichi and Salakoski, Tapio},
      title = {Scaling up Biomedical Event Extraction to the Entire PubMed},
      booktitle = {Proceedings of the 2010 Workshop on Biomedical Natural Language Processing (BioNLP'10)},
      publisher = {ACL},
      year = {2010},
      pages = {28--36}
    }
    					
    Haverinen, K.; Ginter, F.; Laippala, V.; Viljanen, T. & Salakoski, T. Dependency-based PropBanking of Clinical Finnish 2010 Proceedings of The Fourth Linguistic Annotation Workshop (LAW IV) , pp. 137-141   inproceedings
    BibTeX:
    @inproceedings{haverinen2010propbanking,
      author = {Haverinen, Katri and Ginter, Filip and Laippala, Veronika and Viljanen, Timo and Salakoski, Tapio},
      title = {Dependency-based PropBanking of Clinical Finnish},
      booktitle = {Proceedings of The Fourth Linguistic Annotation Workshop (LAW IV)},
      publisher = {ACL},
      year = {2010},
      pages = {137--141}
    }
    					
    Haverinen, K.; Viljanen, T.; Laippala, V.; Kohonen, S.; Ginter, F. & Salakoski, T. Treebanking Finnish 2010 Proceedings of the Ninth International Workshop on Treebanks and Linguistic Theories (TLT9) , pp. 79-90   inproceedings
    BibTeX:
    @inproceedings{haverinen2010treebankingfinnish,
      author = {Katri Haverinen and Timo Viljanen and Veronika Laippala and Samuel Kohonen and Filip Ginter and Tapio Salakoski},
      editor = {Dickinson, Markus and Müürisep, Kaili and Passarotti, Marco},
      title = {Treebanking Finnish},
      booktitle = {Proceedings of the Ninth International Workshop on Treebanks and Linguistic Theories (TLT9)},
      year = {2010},
      pages = {79--90},
      url = {http://hdl.handle.net/10062/15936}
    }
    					
    Heimonen, J.; Björne, J. & Salakoski, T. Reconstruction of semantic relationships from their projections in biomolecular domain 2010 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing , pp. 108-116   inproceedings
    BibTeX:
    @inproceedings{heimonen2010reconstruction,
      author = {Heimonen, Juho and Björne, Jari and Salakoski, Tapio},
      title = {Reconstruction of semantic relationships from their projections in biomolecular domain},
      booktitle = {Proceedings of the 2010 Workshop on Biomedical Natural Language Processing},
      year = {2010},
      pages = {108--116}
    }
    					
    Pahikkala, T.; Airola, A.; Naula, P. & Salakoski, T. Greedy RankRLS: a Linear Time Algorithm for Learning Sparse Ranking Models 2010 SIGIR 2010 Workshop on Feature Generation and Selection for Information Retrieval , pp. 11-18   inproceedings
    BibTeX:
    @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},
      publisher = {ACM},
      year = {2010},
      pages = {11--18}
    }
    					
    Pahikkala, T.; Airola, A. & Salakoski, T. Feature Selection for Regularized Least-Squares: New Computational Short-Cuts and Fast Algorithmic Implementations 2010 Proceedings of the Twentieth IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010) , pp. 295-300   inproceedings
    BibTeX:
    @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},
      year = {2010},
      pages = {295--300},
      url = {http://dx.doi.org/10.1109/MLSP.2010.5589210},
      doi = {http://dx.doi.org/10.1109/MLSP.2010.5589210}
    }
    					
    Pahikkala, T.; Airola, A. & Salakoski, T. Speeding up Greedy Forward Selection for Regularized Least-Squares 2010 Proceedings of The Ninth International Conference on Machine Learning and Applications (ICMLA'10) , pp. 325-330   inproceedings
    BibTeX:
    @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},
      year = {2010},
      pages = {325--330},
      url = {http://staff.cs.utu.fi/~aatapa/publications/inpPaAiSa10b.full.pdf},
      doi = {http://dx.doi.org/10.1109/ICMLA.2010.55}
    }
    					
    Pahikkala, T.; Waegeman, W.; Airola, A.; Salakoski, T. & De Baets, B. Conditional Ranking on Relational Data 2010
    Vol. 6322 Machine Learning and Knowledge Discovery in Databases, European Conference, ECML PKDD 2010, Barcelona, Spain, September 20-24, 2010, Proceedings, Part II , pp. 499-514  
    inproceedings
    BibTeX:
    @inproceedings{pahikkala2010conditional,
      author = {Pahikkala, Tapio and Waegeman, Willem and Airola, Antti and Salakoski, Tapio and De Baets, Bernard},
      editor = {José L. Balcázar and Francesco Bonchi and Aristides Gionis and Michèle Sebag},
      title = {Conditional Ranking on Relational Data},
      booktitle = {Machine Learning and Knowledge Discovery in Databases, European Conference, ECML PKDD 2010, Barcelona, Spain, September 20-24, 2010, Proceedings, Part II},
      publisher = {Springer},
      year = {2010},
      volume = {6322},
      pages = {499-514},
      url = {http://dx.doi.org/10.1007/978-3-642-15883-4_32},
      doi = {http://dx.doi.org/10.1007/978-3-642-15883-4_32}
    }
    					
    Pahikkala, T.; Waegeman, W.; Tsivtsivadze, E.; Salakoski, T. & Baets, B.D. Learning Intransitive Reciprocal Relations with Kernel Methods 2010 European Journal of Operational Research
    Vol. 206 (3) , pp. 676-685  
    article
    BibTeX:
    @article{pahikkala2010reciprocalkm,
      author = {Tapio Pahikkala and Willem Waegeman and Evgeni Tsivtsivadze and Tapio Salakoski and Bernard De Baets},
      title = {Learning Intransitive Reciprocal Relations with Kernel Methods},
      journal = {European Journal of Operational Research},
      year = {2010},
      volume = {206},
      number = {3},
      pages = {676--685},
      url = {http://dx.doi.org/10.1016/j.ejor.2010.03.018},
      doi = {http://dx.doi.org/10.1016/j.ejor.2010.03.018}
    }
    					
    Tsivtsivadze, E.; Pahikkala, T.; Boberg, J.; Salakoski, T. & Heskes, T. 6 ( Co-Regularized Least-Squares for Label Ranking ) 2010 Co-Regularized Least-Squares for Label Ranking Preference Learning , pp. 107-123   incollection
    BibTeX:
    @incollection{tsivtsivadze2010coreg,
      author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski and Tom Heskes},
      editor = {Johannes Fürnkranz and Eyke Hüllermeier},
      title = {Co-Regularized Least-Squares for Label Ranking},
      booktitle = {Preference Learning},
      publisher = {Springer},
      year = {2010},
      pages = {107--123},
      edition = {1st},
      url = {http://dx.doi.org/10.1007/978-3-642-14125-6_6},
      doi = {http://dx.doi.org/10.1007/978-3-642-14125-6_6}
    }
    					
    Proceedings of the 14th Finnish Artificial Intelligence Conference, STeP 2010 2010 (25)   proceedings
    BibTeX:
    @proceedings{pahikkala2010step,,
      editor = {Pahikkala, Tapio and Väyrynen, Jaakko and Kortela, Jukka and Airola, Antti},
      title = {Proceedings of the 14th Finnish Artificial Intelligence Conference, STeP 2010},
      publisher = {Aalto--Print},
      year = {2010},
      number = {25}
    }
    					
    Airola, A.; Pahikkala, T.; Waegeman, W.; De Baets, B. & Salakoski, T. A comparison of AUC estimators in small-sample studies 2009 Proceedings of the Third International Workshop on Machine Learning in Systems Biology (MLSB'09) , pp. 15-23   incollection
    BibTeX:
    @incollection{airola2009comparison,
      author = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
      editor = {Džeroski, Sašo 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}
    }
    					
    Björne, J.; Ginter, F.; Heimonen, J.; Pyysalo, S. & Salakoski, T. Learning to Extract Biological Event and Relation Graphs 2009 Proceedings of NODALIDA'09, Odense, Denmark , pp. 18-25   inproceedings
    BibTeX:
    @inproceedings{bjorne09learning,
      author = {Björne, Jari and Ginter, Filip and Heimonen, Juho and Pyysalo, Sampo and Salakoski, Tapio},
      editor = {Jokinen, Kristiina and Bick, Eckhard},
      title = {Learning to Extract Biological Event and Relation Graphs},
      booktitle = {Proceedings of NODALIDA'09, Odense, Denmark},
      year = {2009},
      pages = {18--25}
    }
    					
    Björne, J.; Heimonen, J.; Ginter, F.; Airola, A.; Pahikkala, T. & Salakoski, T. Extracting Complex Biological Events with Rich Graph-Based Feature Sets 2009 Proceedings of the BioNLP'09 Shared Task on Event Extraction , pp. 10-18   inproceedings
    BibTeX:
    @inproceedings{bjorne09sharedtask,
      author = {Björne, Jari and Heimonen, Juho and Ginter, Filip and Airola,Antti and Pahikkala, Tapio and Salakoski, Tapio},
      title = {Extracting Complex Biological Events with Rich Graph-Based Feature Sets},
      booktitle = {Proceedings of the BioNLP'09 Shared Task on Event Extraction},
      year = {2009},
      pages = {10--18}
    }
    					
    Gieseke, F.; Pahikkala, T. & Kramer, O. Fast evolutionary maximum margin clustering 2009
    Vol. 382 ICML '09: Proceedings of the 26th Annual International Conference on Machine Learning , pp. 361-368  
    inproceedings
    BibTeX:
    @inproceedings{gieseke2009evolutionary,
      author = {Gieseke, Fabian and Pahikkala, Tapio and Kramer, Oliver},
      editor = {Léon Bottou and Michael Littman},
      title = {Fast evolutionary maximum margin clustering},
      booktitle = {ICML '09: Proceedings of the 26th Annual International Conference on Machine Learning},
      publisher = {ACM},
      year = {2009},
      volume = {382},
      pages = {361--368},
      url = {http://doi.acm.org/10.1145/1553374.1553421},
      doi = {http://doi.acm.org/10.1145/1553374.1553421}
    }
    					
    Ginter, F.; Suominen, H.; Pyysalo, S. & Salakoski, T. Combining Hidden Markov Models and Latent Semantic Analysis for Topic Segmentation and Labeling: Method and Clinical Application 2009 International Journal of Medical Informatics, Special Issue on Mining of Clinical and Biomedical Text and Data
    Vol. 78 (12) , pp. e1-e6  
    article
    BibTeX:
    @article{ginter09combiningjournal,
      author = {Filip Ginter and Hanna Suominen and Sampo Pyysalo and Tapio Salakoski},
      title = {Combining Hidden Markov Models and Latent Semantic Analysis for Topic Segmentation and Labeling: Method and Clinical Application},
      journal = {International Journal of Medical Informatics, Special Issue on Mining of Clinical and Biomedical Text and Data},
      publisher = {Elsevier},
      year = {2009},
      volume = {78},
      number = {12},
      pages = {e1--e6},
      url = {http://dx.doi.org/10.1016/j.ijmedinf.2009.02.003}
    }
    					
    Haverinen, K.; Ginter, F.; Laippala, V. & Salakoski, T. Parsing Clinical Finnish: Experiments with Rule-Based and Statistical Dependency Parsers 2009 Proceedings of NODALIDA'09, Odense, Denmark , pp. 65-72   inproceedings
    BibTeX:
    @inproceedings{haverinen09parsing,
      author = {Haverinen, Katri and Ginter, Filip and Laippala, Veronika and Salakoski, Tapio},
      editor = {Jokinen, Kristiina and Bick, Eckhard},
      title = {Parsing Clinical Finnish: Experiments with Rule-Based and Statistical Dependency Parsers},
      booktitle = {Proceedings of NODALIDA'09, Odense, Denmark},
      year = {2009},
      pages = {65--72}
    }
    					
    Haverinen, K.; Ginter, F.; Laippala, V.; Viljanen, T. & Salakoski, T. Dependency Annotation of Wikipedia: First Steps towards a Finnish Treebank 2009 Proceedings of The Eighth International Workshop on Treebanks and Linguistic Theories (TLT8) , pp. 95-105   inproceedings
    BibTeX:
    @inproceedings{haverinen2009wiki,
      author = {Haverinen, Katri and Ginter, Filip and Laippala, Veronika and Viljanen, Timo and Salakoski, Tapio},
      editor = {Passarotti, Marco and Przepiórkowski, Adam and Raynaud, Sabina and van Eynde, Frank},
      title = {Dependency Annotation of Wikipedia: First Steps towards a Finnish Treebank},
      booktitle = {Proceedings of The Eighth International Workshop on Treebanks and Linguistic Theories (TLT8)},
      year = {2009},
      pages = {95--105}
    }
    					
    Laippala, V.; Ginter, F.; Pyysalo, S. & Salakoski, T. Towards Automated Processing of Clinical Finnish: A Sublanguage Analysis and a Rule-Based Parser 2009 International Journal of Medical Informatics, Special Issue on Mining of Clinical and Biomedical Text and Data
    Vol. 78 (12) , pp. e7-e12  
    article
    BibTeX:
    @article{laippala09parserjournal,
      author = {Veronika Laippala and Filip Ginter and Sampo Pyysalo and Tapio Salakoski},
      title = {Towards Automated Processing of Clinical Finnish: A Sublanguage Analysis and a Rule-Based Parser},
      journal = {International Journal of Medical Informatics, Special Issue on Mining of Clinical and Biomedical Text and Data},
      publisher = {Elsevier},
      year = {2009},
      volume = {78},
      number = {12},
      pages = {e7--e12}
    }
    					
    Lundgrén-Laine, H.; Suominen, H.; Kontio, E.; Salanterä, S. & Salakoski, T. Intensive care admission and discharge -- critical decision-making points 2009
    Vol. 146 Connecting Health and Humans. Proceedings of NI2009, the 10th International Congress of Nursing Informatics , pp. 358-361  
    inproceedings
    BibTeX:
    @inproceedings{LLSuominenetal2009,
      author = {Lundgrén-Laine, Heljä and Suominen, Hanna and Kontio, Elina and Salanterä, Sanna and Salakoski, Tapio},
      editor = {Saranto, K and Flatley Brennan, P and Park, H-A and Tallberg, M and Ensio, A},
      title = {Intensive care admission and discharge --- critical decision-making points},
      booktitle = {Connecting Health and Humans. Proceedings of NI2009, the 10th International Congress of Nursing Informatics},
      publisher = {IOS Press},
      year = {2009},
      volume = {146},
      pages = {358--361}
    }
    					
    Pahikkala, T.; Pyysalo, S.; Boberg, J.; Järvinen, J. & Salakoski, T. Matrix representations, linear transformations, and kernels for disambiguation in natural language 2009 Machine Learning
    Vol. 74 (2) , pp. 133-158  
    article
    BibTeX:
    @article{pahikkala2009matrix,
      author = {Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and Järvinen, Jouni and Salakoski, Tapio},
      title = {Matrix representations, linear transformations, and kernels for disambiguation in natural language},
      journal = {Machine Learning},
      publisher = {Kluwer Academic Publishers},
      year = {2009},
      volume = {74},
      number = {2},
      pages = {133--158},
      url = {http://dx.doi.org/10.1007/s10994-008-5082-6},
      doi = {http://dx.doi.org/10.1007/s10994-008-5082-6}
    }
    					
    Pahikkala, T.; Suominen, H.; Boberg, J. & Salakoski, T. Efficient Hold-Out for Subset of Regressors 2009
    Vol. 5495 Proceedings of the 9th International Conference on Adaptive and Natural Computing Algorithms (ICANNGA'09) , pp. 350-359  
    inproceedings
    BibTeX:
    @inproceedings{pahikkala2009holdout,
      author = {Tapio Pahikkala and Hanna Suominen and Jorma Boberg and Tapio Salakoski},
      editor = {Mikko Kolehmainen and Pekka Toivanen and Bartlomiej Beliczynski},
      title = {Efficient Hold-Out for Subset of Regressors},
      booktitle = {Proceedings of the 9th International Conference on Adaptive and Natural Computing Algorithms (ICANNGA'09)},
      publisher = {Springer},
      year = {2009},
      volume = {5495},
      pages = {350--359},
      url = {http://dx.doi.org/DOI:10.1007/978-3-642-04921-7_36},
      doi = {http://dx.doi.org/10.1007/978-3-642-04921-7_36}
    }
    					
    Pahikkala, T.; Tsivtsivadze, E.; Airola, A.; Järvinen, J. & Boberg, J. An Efficient Algorithm for Learning to Rank from Preference Graphs 2009 Machine Learning
    Vol. 75 (1) , pp. 129-165  
    article
    BibTeX:
    @article{pahikkala2009preferences,
      author = {Tapio Pahikkala and Evgeni Tsivtsivadze and Antti Airola and Jouni Järvinen and Jorma Boberg},
      title = {An Efficient Algorithm for Learning to Rank from Preference Graphs},
      journal = {Machine Learning},
      year = {2009},
      volume = {75},
      number = {1},
      pages = {129--165},
      url = {http://dx.doi.org/10.1007/s10994-008-5097-z},
      doi = {http://dx.doi.org/10.1007/s10994-008-5097-z}
    }
    					
    Pahikkala, T.; Waegeman, W.; Tsivtsivadze, E.; Baets, B.D. & Salakoski, T. Learning Intransitive Reciprocal Relations with Regularized Least-Squares 2009 Proceedings of the 18th Annual Belgian-Dutch Conference on Machine Learning (Benelearn 09) , pp. 13-20   inproceedings
    BibTeX:
    @inproceedings{pahikkala2009benelearn,
      author = {Tapio Pahikkala and Willem Waegeman and Evgeni Tsivtsivadze and Bernard De Baets and Tapio Salakoski},
      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}
    }
    					
    Pahikkala, T.; Waegeman, W.; Tsivtsivadze, E.; Baets, B.D. & Salakoski, T. From Ranking to Intransitive Preference Learning: Rock-Paper-Scissors and beyond 2009 Proceedings of the ECML/PKDD-Workshop on Preference Learning (PL-09) , pp. 84-100   inproceedings
    BibTeX:
    @inproceedings{pahikkala2009beyond,
      author = {Tapio Pahikkala and Willem Waegeman and Evgeni Tsivtsivadze and Bernard De Baets and Tapio Salakoski},
      editor = {Eyke Hüllermeier and Johannes Fürnkranz},
      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}
    }
    					
    Suominen, H.; Lundgrén-Laine, H.; Salakoski, T. & Salanterä, S. Evaluating pain in intensive care 2009
    Vol. 146 Connecting Health and Humans. Proceedings of NI2009, the 10th International Congress of Nursing Informatics , pp. 191-196  
    inproceedings
    BibTeX:
    @inproceedings{SuominenetalNI2009,
      author = {Suominen, Hanna and Lundgrén-Laine, Heljä and Salakoski, Tapio and Salanterä, Sanna},
      editor = {Saranto, K and Flatley Brennan, P and Park, H-A and Tallberg, M and Ensio, A},
      title = {Evaluating pain in intensive care},
      booktitle = {Connecting Health and Humans. Proceedings of NI2009, the 10th International Congress of Nursing Informatics},
      publisher = {IOS Press},
      year = {2009},
      volume = {146},
      pages = {191-196}
    }
    					
    Suominen, H.; Lundgrén-Laine, H.; Salanterä, S.; Karsten, H. & Salakoski, T. Information flow in intensive care narratives 2009 Proceedings of IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBM 2009 , pp. 325-330   inproceedings
    BibTeX:
    @inproceedings{suominen09informationflow,
      author = {Suominen, Hanna and Lundgrén-Laine, Heljä and Salanterä, Sanna and Karsten, Helena and Salakoski, Tapio},
      title = {Information flow in intensive care narratives},
      booktitle = {Proceedings of IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBM 2009},
      year = {2009},
      pages = {325--330}
    }
    					
    Suominen, H. & Salakoski, T. Information retrieval and personal health records: user needs and domain tailoring (In Press) 2009 SPIRE 2009 Workshop on Task-based Information Access   inproceedings
    BibTeX:
    @inproceedings{SuominenetalSPIRE,
      author = {Suominen, Hanna and Salakoski, Tapio},
      title = {Information retrieval and personal health records: user needs and domain tailoring},
      booktitle = {SPIRE 2009 Workshop on Task-based Information Access},
      year = {2009},
      note = {In Press}
    }
    					
    Tsivtsivadze, E.; Pahikkala, T.; Boberg, J. & Salakoski, T. Locality Kernels for Sequential Data and Their Applications to Parse Ranking 2009 Applied Intelligence
    Vol. 31 (1) , pp. 81-88  
    article
    BibTeX:
    @article{tsivtsivadze2009localityjournal,
      author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
      title = {Locality Kernels for Sequential Data and Their Applications to Parse Ranking},
      journal = {Applied Intelligence},
      year = {2009},
      volume = {31},
      number = {1},
      pages = {81--88}
    }
    					
    Airola, A.; Pyysalo, S.; Björne, J.; Pahikkala, T.; Ginter, F. & Salakoski, T. A Graph Kernel for Protein-Protein Interaction Extraction 2008 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP'08) , pp. 1-9   inproceedings
    BibTeX:
    @inproceedings{airola08bionlp,
      author = {Airola, Antti and Pyysalo, Sampo and Björne, Jari and Pahikkala, Tapio and Ginter, Filip and Salakoski, Tapio},
      title = {A Graph Kernel for Protein-Protein Interaction Extraction},
      booktitle = {Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP'08)},
      publisher = {Association for Computational Linguistics},
      year = {2008},
      pages = {1--9}
    }
    					
    Airola, A.; Pyysalo, S.; Björne, J.; Pahikkala, T.; Ginter, F. & Salakoski, T. All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning 2008 BMC Bioinformatics
    Vol. 9 Suppl 11  
    article
    BibTeX:
    @article{airola08allpathsbmc,
      author = {Airola, Antti and Pyysalo, Sampo and Björne, 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}
    }
    					
    Björne, J.; Pyysalo, S.; Ginter, F. & Salakoski, T. How Complex are Complex Protein-protein Interactions? 2008 Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland , pp. 125-128   inproceedings
    BibTeX:
    @inproceedings{bjorne08how,
      author = {Jari Björne and Sampo Pyysalo and Filip Ginter and Tapio Salakoski},
      editor = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
      title = {How Complex are Complex Protein-protein Interactions?},
      booktitle = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
      publisher = {Turku Centre for Computer Science (TUCS)},
      year = {2008},
      pages = {125--128}
    }
    					
    Ginter, F.; Suominen, H.; Pyysalo, S. & Salakoski, T. Combining Hidden Markov Models and Latent Semantic Analysis for Topic Segmentation and Labeling: Method and Clinical Application 2008 Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland , pp. 37-44   inproceedings
    BibTeX:
    @inproceedings{ginter08combining,
      author = {Filip Ginter and Hanna Suominen and Sampo Pyysalo and Tapio Salakoski},
      editor = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
      title = {Combining Hidden Markov Models and Latent Semantic Analysis for Topic Segmentation and Labeling: Method and Clinical Application},
      booktitle = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
      publisher = {Turku Centre for Computer Science (TUCS)},
      year = {2008},
      pages = {37--44}
    }
    					
    Haverinen, K.; Ginter, F.; Pyysalo, S. & Salakoski, T. Accurate Conversion of Dependency Parses: Targeting the Stanford Scheme 2008 Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland , pp. 133-136   inproceedings
    BibTeX:
    @inproceedings{haverinen08accurrate,
      author = {Katri Haverinen and Filip Ginter and Sampo Pyysalo and Tapio Salakoski},
      editor = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
      title = {Accurate Conversion of Dependency Parses: Targeting the Stanford Scheme},
      booktitle = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
      publisher = {Turku Centre for Computer Science (TUCS)},
      year = {2008},
      pages = {133--136}
    }
    					
    Heimonen, J.; Pyysalo, S.; Ginter, F. & Salakoski, T. Complex-to-Pairwise Mapping of Biological Relationships using a Semantic Network Representation 2008 Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland , pp. 45-52   inproceedings
    BibTeX:
    @inproceedings{heimonen08complex,
      author = {Juho Heimonen and Sampo Pyysalo and Filip Ginter and Tapio Salakoski},
      editor = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
      title = {Complex-to-Pairwise Mapping of Biological Relationships using a Semantic Network Representation},
      booktitle = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
      publisher = {Turku Centre for Computer Science (TUCS)},
      year = {2008},
      pages = {45--52}
    }
    					
    Laippala, V.; Ginter, F.; Pyysalo, S. & Salakoski, T. Resource-efficient construction of a full parser for Finnish nursing narratives 2008 Proceedings of the First Louhi Conference on Text and Data Mining of Clinical Documents (Louhi'08), Turku, Finland , pp. 34-53   inproceedings
    BibTeX:
    @inproceedings{laippala08resource2,
      author = {Laippala, Veronika and Ginter, Filip and Pyysalo, Sampo and Salakoski, Tapio},
      editor = {Karsten, Helena and Back, Barbro and Salakoski, Tapio and Salanterä, Sanna},
      title = {Resource-efficient construction of a full parser for Finnish nursing narratives},
      booktitle = {Proceedings of the First Louhi Conference on Text and Data Mining of Clinical Documents (Louhi'08), Turku, Finland},
      publisher = {Turku Centre for Computer Science (TUCS)},
      year = {2008},
      pages = {34--53}
    }
    					
    Pahikkala, T. New Kernel Functions and Learning Methods for Text and Data Mining 2008 School: Turku Centre for Computer Science (TUCS)   phdthesis
    BibTeX:
    @phdthesis{pahikkala2008phdthesis,
      author = {Tapio Pahikkala},
      title = {New Kernel Functions and Learning Methods for Text and Data Mining},
      school = {Turku Centre for Computer Science (TUCS)},
      year = {2008}
    }
    					
    Pahikkala, T.; Airola, A.; Boberg, J. & Salakoski, T. Exact and Efficient Leave-Pair-Out Cross-Validation for Ranking RLS 2008 Proceedings of the 2nd International and Interdisciplinary Conference on Adaptive Knowledge Representation and Reasoning (AKRR'08) , pp. 1-8   inproceedings
    BibTeX:
    @inproceedings{pahikkala2008lpocv,
      author = {Pahikkala, Tapio and Airola, Antti and Boberg, Jorma and Salakoski, Tapio},
      editor = {Timo Honkela and Matti Pöllä and Mari-Sanna Paukkeri and Olli Simula},
      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)},
      publisher = {Helsinki University of Technology},
      year = {2008},
      pages = {1--8}
    }
    					
    Pahikkala, T.; Airola, A.; Suominen, H.; Boberg, J. & Salakoski, T. Efficient AUC Maximization with Regularized Least-Squares 2008
    Vol. 173 Proceedings of the 10th Scandinavian Conference on Artificial Intelligence (SCAI 2008) , pp. 12-19  
    incollection
    BibTeX:
    @incollection{pahikkala2008aucmax,
      author = {Pahikkala, Tapio and Airola, Antti and Suominen, Hanna and Boberg, Jorma and Salakoski, Tapio},
      editor = {Anders Holst and Per Kreuger and Peter Funk},
      title = {Efficient AUC Maximization with Regularized Least-Squares},
      booktitle = {Proceedings of the 10th Scandinavian Conference on Artificial Intelligence (SCAI 2008)},
      publisher = {IOS Press},
      year = {2008},
      volume = {173},
      pages = {12--19}
    }
    					
    Pahikkala, T.; Tsivtsivadze, E.; Airola, A. & Salakoski, T. Regularized Least-Squares for Learning Non-Transitive Preferences between Strategies 2008
    Vol. 24 Proceedings of the 13th Finnish Artificial Intelligence Conference and Nokia Workshop on Machine Consciousness , pp. 94-98  
    inproceedings
    BibTeX:
    @inproceedings{pahikkala2008npref,
      author = {Tapio Pahikkala and Evgeni Tsivtsivadze and Antti Airola and Tapio Salakoski},
      editor = {Tapani Raiko and Pentti Haikonen and Jaakko Väyrynen},
      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},
      publisher = {Finnish Artificial Intelligence Society},
      year = {2008},
      volume = {24},
      pages = {94--98}
    }
    					
    Pyysalo, S.; Airola, A.; Heimonen, J.; Björne, J.; Ginter, F. & Salakoski, T. Comparative Analysis of Five Protein-protein Interaction Corpora 2008 BMC Bioinformatics, special issue
    Vol. 9 (Suppl 3) , pp. S6  
    article
    BibTeX:
    @article{pyysalo08comparative,
      author = {Pyysalo, Sampo and Airola, Antti and Heimonen, Juho and Björne, Jari and Ginter, Filip and Salakoski, Tapio},
      title = {Comparative Analysis of Five Protein-protein Interaction Corpora},
      journal = {BMC Bioinformatics, special issue},
      year = {2008},
      volume = {9},
      number = {Suppl 3},
      pages = {S6}
    }
    					
    Pyysalo, S.; Sætre, R.; Tsujii, J. & Salakoski, T. Why Biomedical Relation Extraction Results are Incomparable and What to do about it 2008 Proceedings of the Third International Symposium on Semantic Mining in Biomedicine , pp. 149-152   inproceedings
    BibTeX:
    @inproceedings{pyysalo08why,
      author = {Pyysalo, Sampo and Sætre, Rune and Tsujii, Jun'ichi and Salakoski, Tapio},
      editor = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
      title = {Why Biomedical Relation Extraction Results are Incomparable and What to do about it},
      booktitle = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine},
      publisher = {Turku Centre for Computer Science (TUCS)},
      year = {2008},
      pages = {149--152}
    }
    					
    Suominen, H.; Ginter, F.; Pyysalo, S.; Airola, A.; Pahikkala, T.; Salanterä, S. & Salakoski, T. Machine Learning to Automate the Assignment of Diagnosis Codes to Free-text Radiology Reports: a Method Description 2008 Proceedings of the ICML/UAI workshop on Machine Learning in health care applications   inproceedings
    BibTeX:
    @inproceedings{suominen08challenge,
      author = {Suominen, Hanna and Ginter, Filip and Pyysalo, Sampo and Airola, Antti and Pahikkala, Tapio and Salanterä, Sanna and Salakoski, Tapio},
      editor = {M Hauskrecht and D Schuurmans and D Szepesvari},
      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}
    }
    					
    Suominen, H.; Lundgren-Laine, H.; Perttiä, J.; Salakoski, T. & Salanterä, S. Tehohoidon elektroniset potilasasiakirjat - hyödyntämätön voimavara (Electronic intensive care patient records; an untapped resource]) 2008 The Finnish Medical Convention 2008   inproceedings
    BibTeX:
    @inproceedings{suominen08laakaripaivat,
      author = {Suominen, Hanna and Lundgren-Laine, Heljä and Perttiä, Juha and Salakoski, Tapio and Salanterä, Sanna},
      title = {Tehohoidon elektroniset potilasasiakirjat -- hyödyntämätön voimavara (Electronic intensive care patient records; an untapped resource])},
      booktitle = {The Finnish Medical Convention 2008},
      year = {2008}
    }
    					
    Suominen, H.; Pahikkala, T. & Salakoski, T. Critical points in assessing learning performance via cross-validation 2008 Proceedings of the 2nd International and Interdiciplinary Conference on Adaptive Knowledge Representation and Reasoning (AKRR 2008) , pp. 9-22   inproceedings
    BibTeX:
    @inproceedings{SuominenetalAKRR,
      author = {Suominen, Hanna and Pahikkala, Tapio and Salakoski, Tapio},
      editor = {Honkela, T and Pöllä, M and Paukkeri, MS and Simula O},
      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)},
      publisher = {Multiprint},
      year = {2008},
      pages = {9--22}
    }
    					
    Suominen, H.; Pyysalo, S.; Ginter, F. & Salakoski, T. Automated text segmentation and topic labeling of clinical narratives 2008
    Vol. 52 Proceedings of the First Louhi Conference on Text and Data Mining of Clinical Documents (Louhi'08), Turku, Finland , pp. 99-103  
    inproceedings
    BibTeX:
    @inproceedings{suominen08segposter,
      author = {Suominen, Hanna and Pyysalo, Sampo and Ginter, Filip and Salakoski, Tapio},
      editor = {Karsten, Helena and Back, Barbro and Salakoski, Tapio and Salanterä, Sanna},
      title = {Automated text segmentation and topic labeling of clinical narratives},
      booktitle = {Proceedings of the First Louhi Conference on Text and Data Mining of Clinical Documents (Louhi'08), Turku, Finland},
      publisher = {Turku Centre for Computer Science (TUCS)},
      year = {2008},
      volume = {52},
      pages = {99--103}
    }
    					
    Suominen, H.; Pyysalo, S.; Hiissa, M.; Ginter, F.; Liu, S.; Marghescu, D.; Pahikkala, T.; Back, B.; Karsten, H. & Salakoski, T. Performance Evaluation Measures for Text Mining 2008 Handbook of Research on Text and Web Mining Technologies , pp. 724-747   incollection
    BibTeX:
    @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 = {M Song and Y-FB Wu},
      title = { Performance Evaluation Measures for Text Mining},
      booktitle = {Handbook of Research on Text and Web Mining Technologies},
      publisher = {IGI Global},
      year = {2008},
      pages = {724--747}
    }
    					
    Tsivtsivadze, E.; Gieseke, F.; Pahikkala, T.; Boberg, J. & Salakoski, T. Learning Preferences with Co-Regularized Least Squares 2008 ECML/PKDD-Workshop on Preference Learning (PL-08) , pp. 55-62   inproceedings
    BibTeX:
    @inproceedings{tsivtsivadze2008coreg,
      author = {Evgeni Tsivtsivadze and Fabian Gieseke and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
      editor = {Eyke Hüllermeier and Johannes Fürnkranz},
      title = {Learning Preferences with Co-Regularized Least Squares},
      booktitle = {ECML/PKDD-Workshop on Preference Learning (PL-08)},
      year = {2008},
      pages = {55--62}
    }
    					
    Tsivtsivadze, E.; Pahikkala, T.; Airola, A.; Boberg, J. & Salakoski, T. A Sparse Regularized Least-Squares Preference Learning Algorithm 2008
    Vol. 173 Proceedings of the 10th Scandinavian Conference on Artificial Intelligence (SCAI 2008) , pp. 76-83  
    inproceedings
    BibTeX:
    @inproceedings{tsivtsivadze08sparse,
      author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Antti Airola and Jorma Boberg and Tapio Salakoski},
      editor = {Anders Holst and Per Kreuger and Peter Funk},
      title = {A Sparse Regularized Least-Squares Preference Learning Algorithm},
      booktitle = {Proceedings of the 10th Scandinavian Conference on Artificial Intelligence (SCAI 2008)},
      publisher = {IOS Press},
      year = {2008},
      volume = {173},
      pages = {76--83}
    }
    					
    Tsivtsivadze, E.; Pahikkala, T.; Boberg, J. & Salakoski, T. Kernel Methods for Text Analysis 2008
    Vol. 116 Advances of Computational Intelligence in Industrial Systems , pp. 81-97  
    incollection
    BibTeX:
    @incollection{tsivtsivadze2008kft,
      author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
      editor = {Ying Liu and Aixin Sun and Han Tong Loh and Wen Feng Lu and Ee-Peng Lim},
      title = {Kernel Methods for Text Analysis},
      booktitle = {Advances of Computational Intelligence in Industrial Systems},
      publisher = {Springer},
      year = {2008},
      volume = {116},
      pages = {81--97}
    }
    					
    Proceedings of the First Conference on Text and Data Mining of Clinical Documents (Louhi'08) 2008
    Vol. 52  
    proceedings
    BibTeX:
    @proceedings{Louhi,,
      editor = {Karsten, Helena and Back, Barbro and Salakoski, Tapio and Salanterä, Sanna and Suominen, Hanna},
      title = {Proceedings of the First Conference on Text and Data Mining of Clinical Documents (Louhi'08)},
      publisher = {Turku Centre for Computer Science},
      year = {2008},
      volume = {52}
    }
    					
    Aittokallio, T.; Malminen, J.S.; Pahikkala, T.; Polo, O. & Nevalainen, O. Inspiratory Flow Shape Clustering: An Automated Method to Monitor Upper Airway Performance During Sleep 2007 Computer Methods and Programs in Biomedicine
    Vol. 85 (1) , pp. 8-18  
    article
    BibTeX:
    @article{aittokallio2007inspiratory,
      author = {Tero Aittokallio and Jani S. Malminen and Tapio Pahikkala and Olli Polo and Olli Nevalainen},
      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},
      number = {1},
      pages = {8--18},
      url = {http://dx.doi.org/10.1016/j.cmpb.2006.09.012},
      doi = {http://dx.doi.org/10.1016/j.cmpb.2006.09.012}
    }
    					
    Ginter, F. Information Extraction in the Biomedical Domain: Methods and Resources 2007 School: Turku Centre for Computer Science (TUCS)   phdthesis
    BibTeX:
    @phdthesis{ginter07phd,
      author = {Ginter, Filip},
      title = {Information Extraction in the Biomedical Domain: Methods and Resources},
      school = {Turku Centre for Computer Science (TUCS)},
      year = {2007}
    }
    					
    Ginter, F.; Pyysalo, S.; Björne, J.; Heimonen, J. & Salakoski, T. BioInfer Relationship Annotation Manual 2007 (TR 806)   techreport
    BibTeX:
    @techreport{ginter06manual,
      author = {Ginter, Filip and Pyysalo, Sampo and Björne, Jari and Heimonen, Juho and Salakoski, Tapio},
      title = {BioInfer Relationship Annotation Manual},
      year = {2007},
      number = {TR 806}
    }
    					
    Ginter, F.; Pyysalo, S. & Salakoski, T. Document Classification Using Semantic Networks with An Adaptive Similarity Measure 2007 Recent Advances in Natural Language Processing IV: Selected papers from RANLP 2005 , pp. 137-146   incollection
    BibTeX:
    @incollection{ginter06docclas,
      author = {Ginter, Filip and Pyysalo, Sampo and Salakoski, Tapio},
      editor = {Nicolov, Nicolas and Bontcheva, Kalina and Angelova, Galia and Mitkov, Ruslan},
      title = {Document Classification Using Semantic Networks with An Adaptive Similarity Measure},
      booktitle = {Recent Advances in Natural Language Processing IV: Selected papers from RANLP 2005},
      publisher = {John Benjamins},
      year = {2007},
      pages = {137--146}
    }
    					
    Hiissa, M.; Pahikkala, T.; Suominen, H.; Lehtikunnas, T.; Back, B.; Karsten, H.; Salanterä, S. & Salakoski, T. Towards automated classification of intensive care nursing narratives 2007 International Journal of Medical Informatics
    Vol. 76S3 , pp. S362-S368  
    article
    BibTeX:
    @article{hiissa07,
      author = {Hiissa, Marketta and Pahikkala, Tapio and Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salanterä, Sanna and Salakoski, Tapio},
      title = {Towards automated classification of intensive care nursing narratives},
      journal = {International Journal of Medical Informatics},
      year = {2007},
      volume = {76S3},
      pages = {S362--S368},
      doi = {http://dx.doi.org/10.1016/j.ijmedinf.2007.03.003}
    }
    					
    Pahikkala, T.; Suominen, H.; Boberg, J. & Salakoski, T. Transductive Ranking via Pairwise Regularized Least-Squares 2007 The 5th International Workshop on Mining and Learning with Graphs (MLG'07) , pp. 175-178   inproceedings
    BibTeX:
    @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}
    }
    					
    Pahikkala, T.; Tsivtsivadze, E.; Airola, A.; Boberg, J. & Salakoski, T. Learning to Rank with Pairwise Regularized Least-Squares 2007 SIGIR 2007 Workshop on Learning to Rank for Information Retrieval , pp. 27-33   inproceedings
    BibTeX:
    @inproceedings{pahikkala2007rankrls,
      author = {Tapio Pahikkala and Evgeni Tsivtsivadze and Antti Airola and Jorma Boberg and Tapio Salakoski},
      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}
    }
    					
    Pyysalo, S.; Ginter, F.; Heimonen, J.; Björne, J.; Boberg, J.; Järvinen, J. & Salakoski, T. BioInfer: A Corpus for Information Extraction in the Biomedical Domain 2007 BMC Bioinformatics
    Vol. 8 , pp. 50  
    article
    BibTeX:
    @article{pyysalo06corpus,
      author = {Sampo Pyysalo and Filip Ginter and Juho Heimonen and Jari Björne and Jorma Boberg and Jouni Järvinen and Tapio Salakoski},
      title = {BioInfer: A Corpus for Information Extraction in the Biomedical Domain},
      journal = {BMC Bioinformatics},
      year = {2007},
      volume = {8},
      pages = {50}
    }
    					
    Pyysalo, S.; Ginter, F.; Laippala, V.; Haverinen, K.; Heimonen, J. & Salakoski, T. On the unification of syntactic annotations under the Stanford dependency scheme: A case study on BioInfer and GENIA 2007 ACL'07 workshop on Biological, translational, and clinical language processing (BioNLP'07) , pp. 25-32   inproceedings
    BibTeX:
    @inproceedings{pyysalo07unification,
      author = {Pyysalo, Sampo and Ginter, Filip and Laippala, Veronika and Haverinen, Katri and Heimonen, Juho and Salakoski, Tapio},
      title = {On the unification of syntactic annotations under the Stanford dependency scheme: A case study on BioInfer and GENIA},
      booktitle = {ACL'07 workshop on Biological, translational, and clinical language processing (BioNLP'07)},
      publisher = {Association for Computational Linguistics},
      year = {2007},
      pages = {25--32}
    }
    					
    Suominen, H. Kieliteknologian menetelmien soveltaminen potilasdokumentaation hyödyntämiseen (Applying human language technology to utilization of patient documentation) 2007 Tietojenkäsittelytieteen päivät 2007 , pp. 46-50   inproceedings
    BibTeX:
    @inproceedings{suominen07tktp,
      author = {Suominen, Hanna},
      editor = {Koskinen, M and Jauhiainen, E},
      title = {Kieliteknologian menetelmien soveltaminen potilasdokumentaation hyödyntämiseen (Applying human language technology to utilization of patient documentation)},
      booktitle = {Tietojenkäsittelytieteen päivät 2007},
      publisher = {Jyväskylän yliopistopaino, Jyväskylä},
      year = {2007},
      pages = {46--50}
    }
    					
    Suominen, H.; Lehtikunnas, T.; Back, B.; Karsten, H.; Salakoski, T. & Salanterä, S. Applying language technology to nursing documents: pros and cons with a focus on ethics 2007 International Journal of Medical Informatics
    Vol. 76S2 , pp. S293-S301  
    article
    BibTeX:
    @article{suominen07ethicsjournal,
      author = {Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salakoski, Tapio and Salanterä, Sanna},
      title = {Applying language technology to nursing documents: pros and cons with a focus on ethics},
      journal = {International Journal of Medical Informatics},
      year = {2007},
      volume = {76S2},
      pages = {S293--S301}
    }
    					
    Tsivtsivadze, E.; Boberg, J. & Salakoski, T. Locality Kernels for Protein Classification 2007
    Vol. 4645 Algorithms in Bioinformatics, 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings , pp. 2-11  
    inproceedings
    BibTeX:
    @inproceedings{tsivtsivadze2007prot,
      author = {Evgeni Tsivtsivadze and Jorma Boberg and Tapio Salakoski},
      editor = {Raffaele Giancarlo and Sridhar Hannenhalli},
      title = {Locality Kernels for Protein Classification},
      booktitle = {Algorithms in Bioinformatics, 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings},
      publisher = {Springer},
      year = {2007},
      volume = {4645},
      pages = {2-11}
    }
    					
    Vähämaa, H.; Ojala, P.; Pahikkala, T.; Nevalainen, O.S.; Lahesmaa, R. & Aittokallio, T. Computer-assisted identification of multi-trace electrophoretic patterns in differential display experiments 2007 Electrophoresis
    Vol. 28 (6) , pp. 879-893  
    article
    BibTeX:
    @article{vahamaa2007dd,
      author = {Heidi Vähämaa and Pekka Ojala and Tapio Pahikkala and Olli S. Nevalainen and Riitta Lahesmaa and Tero Aittokallio},
      title = {Computer-assisted identification of multi-trace electrophoretic patterns in differential display experiments},
      journal = {Electrophoresis},
      year = {2007},
      volume = {28},
      number = {6},
      pages = {879--893},
      url = {http://dx.doi.org/doi:10.1002/elps.200600424},
      doi = {http://dx.doi.org/10.1002/elps.200600424}
    }
    					
    Ginter, F.; Mylläri, A. & Salakoski, T. A Probabilistic Search for the Best Solution Among Partially Completed Candidates 2006 Proceedings of the HLT/NAACL'06 Workshop on Computationally Hard Problems and Joint Inference in Speech and Language Processing , pp. 33-40   inproceedings
    BibTeX:
    @inproceedings{ginter06psearch,
      author = {Filip Ginter and Aleksandr Mylläri and Tapio Salakoski},
      editor = {McDonald, Ryan and Sutton, Charles and Daumé, Hal and McCallum, Andrew and Bilmes, Jeff and Pereira, Fernando},
      title = {A Probabilistic Search for the Best Solution Among Partially Completed Candidates},
      booktitle = {Proceedings of the HLT/NAACL'06 Workshop on Computationally Hard Problems and Joint Inference in Speech and Language Processing},
      publisher = {ACL},
      year = {2006},
      pages = {33--40}
    }
    					
    Ginter, F.; Pyysalo, S.; Boberg, J. & Salakoski, T. Regular Approximation of Link Grammar 2006
    Vol. 4139 Proceedings of the 5th International Conference on Natural Language Processing FinTAL 06, Turku, Finland , pp. 564-575  
    inproceedings
    BibTeX:
    @inproceedings{ginter06fslg,
      author = {Ginter, Filip and Pyysalo, Sampo and Boberg, Jorma and Salakoski, Tapio},
      editor = {Salakoski, Tapio and Ginter, Filip and Pyysalo, Sampo and Pahikkala, Tapio},
      title = {Regular Approximation of Link Grammar},
      booktitle = {Proceedings of the 5th International Conference on Natural Language Processing FinTAL 06, Turku, Finland},
      publisher = {Springer, Heidelberg},
      year = {2006},
      volume = {4139},
      pages = {564--575}
    }
    					
    Hiissa, M.; Pahikkala, T.; Suominen, H.; Lehtikunnas, T.; Back, B.; Karsten, E.H.; Salanterä, S. & Salakoski, T. Towards automated classification of intensive care nursing narratives 2006
    Vol. 124 Ubiquity: Technologies for Better Health in Aging Societies. Proceedings of MIE 2006, the 20th International Congress of the European Federation of Medical Informatics , pp. 789-794  
    inproceedings
    BibTeX:
    @inproceedings{hiissa2006towards,
      author = {Marketta Hiissa and Tapio Pahikkala and Hanna Suominen and Tuija Lehtikunnas and Barbro Back and Eija Helena Karsten and Sanna Salanterä and Tapio Salakoski},
      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},
      publisher = {IOS Press},
      year = {2006},
      volume = {124},
      pages = {789--794}
    }
    					
    Hiissa, M.; Pahikkala, T.; Suominen, H.; Lehtikunnas, T.; Back, B.; Karsten, H.; Salanterä, S. & Salakoski, T. Towards automated classification of intensive care nursing narratives 2006
    Vol. 739  
    techreport
    BibTeX:
    @techreport{hiissa06tr,
      author = {Hiissa, Marketta and Pahikkala, Tapio and Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salanterä, Sanna and Salakoski, Tapio},
      title = {Towards automated classification of intensive care nursing narratives},
      year = {2006},
      volume = {739}
    }
    					
    Hiissa, M.; Suominen, H.; Back, B.; Karsten, H.; Salakoski, T. & Salanterä, S. Kohti tehohoitotyön narratiivien tehokkaampaa hyödyntämistä luonnollisen kielen käsittelyn avulla (Towards more efficient use of intensive care narratives through natural language processing) 2006 Sosiaali- ja terveydenhuollon tietotekniikan ja tiedonhallinnan tutkimuspäivät, Tutkimuspaperit 2006 , pp. 17-23   inproceedings
    BibTeX:
    @inproceedings{hiissa06sotetite,
      author = {Hiissa, Marketta and Suominen, Hanna and Back, Barbro and Karsten, Helena and Salakoski, Tapio and Salanterä, Sanna},
      editor = {Häyrinen, Kristiina},
      title = {Kohti tehohoitotyön narratiivien tehokkaampaa hyödyntämistä luonnollisen kielen käsittelyn avulla (Towards more efficient use of intensive care narratives through natural language processing)},
      booktitle = {Sosiaali- ja terveydenhuollon tietotekniikan ja tiedonhallinnan tutkimuspäivät, Tutkimuspaperit 2006},
      publisher = {Valopaino Oy, Helsinki},
      year = {2006},
      pages = {17--23}
    }
    					
    Lundgren-Laine, H.; Hiissa, M.; Suominen, H.; Lehtikunnas, T. & Salanterä, S. Tehohoidon elektroninen kirjaaminen - kohti narratiivien automaattista luokittelua (Electronic intensive care documentation; towards automated classification of narratives) 2006 IX Kansallinen hoitotieteellinen konferenssi ''Viisas vaikuttaja'' , pp. 98   inproceedings
    BibTeX:
    @inproceedings{LundgrenLaine06,
      author = {Lundgren-Laine, Heljä and Hiissa, Marketta and Suominen, Hanna and Lehtikunnas, Tuija and Salanterä, Sanna},
      title = {Tehohoidon elektroninen kirjaaminen -- kohti narratiivien automaattista luokittelua (Electronic intensive care documentation; towards automated classification of narratives)},
      booktitle = {IX Kansallinen hoitotieteellinen konferenssi ''Viisas vaikuttaja''},
      year = {2006},
      pages = {98}
    }
    					
    Pahikkala, T.; Boberg, J.; Mylläri, A. & Salakoski, T. Incorporating External Information in Bayesian Classifiers via Linear Feature Transformations 2006
    Vol. 4139 Proceedings of the 5th International Conference on Natural Language Processing FinTAL 06, Turku, Finland , pp. 399-410  
    inproceedings
    BibTeX:
    @inproceedings{pahikkala06ltbayes,
      author = {Tapio Pahikkala and Jorma Boberg and Aleksandr Mylläri and Tapio Salakoski},
      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},
      publisher = {Springer, Heidelberg},
      year = {2006},
      volume = {4139},
      pages = {399--410}
    }
    					
    Pahikkala, T.; Boberg, J. & Salakoski, T. Fast n-Fold Cross-Validation for Regularized Least-Squares 2006 Proceedings of the Ninth Scandinavian Conference on Artificial Intelligence (SCAI 2006) , pp. 83-90   inproceedings
    BibTeX:
    @inproceedings{pahikkala06rls,
      author = {Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
      editor = {Timo Honkela and Tapani Raiko and Jukka Kortela and Harri Valpola},
      title = {Fast n-Fold Cross-Validation for Regularized Least-Squares},
      booktitle = {Proceedings of the Ninth Scandinavian Conference on Artificial Intelligence (SCAI 2006)},
      publisher = {Otamedia Oy},
      year = {2006},
      pages = {83-90}
    }
    					
    Pahikkala, T.; Tsivtsivadze, E.; Boberg, J. & Salakoski, T. Graph Kernels versus Graph Representations: a Case Study in Parse Ranking 2006 Proceedings of the ECML/PKDD'06 workshop on Mining and Learning with Graphs (MLG'06)   inproceedings
    BibTeX:
    @inproceedings{pahikkala2006graph,
      author = {Tapio Pahikkala and Evgeni Tsivtsivadze and Jorma Boberg and Tapio Salakoski},
      editor = {Thomas Gärtner and Gemma C. Garriga and Thorsten Meinl},
      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}
    }
    					
    Pyysalo, S.; Aubin, S.; Nazarenko, A. & Salakoski, T. Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches 2006 Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM'06) , pp. 60-67   inproceedings
    BibTeX:
    @inproceedings{pyysalo06lexical,
      author = {Sampo Pyysalo and Sophie Aubin and Adeline Nazarenko and Tapio Salakoski},
      title = {Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches},
      booktitle = {Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM'06)},
      year = {2006},
      pages = {60--67}
    }
    					
    Pyysalo, S.; Aubin, S.; Nazarenko, A. & Salakoski, T. Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches 2006 BMC Bioinformatics
    Vol. 7(Suppl 3) , pp. S2  
    article
    BibTeX:
    @article{pyysalo06lexicalBMC,
      author = {Sampo Pyysalo and Sophie Aubin and Adeline Nazarenko and Tapio Salakoski},
      title = {Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches},
      journal = {BMC Bioinformatics},
      year = {2006},
      volume = {7(Suppl 3)},
      pages = {S2}
    }
    					
    Pyysalo, S.; Ginter, F.; Pahikkala, T.; Boberg, J.; Järvinen, J. & Salakoski, T. Evaluation of Two Dependency Parsers on Biomedical Corpus Targeted at Protein-Protein Interactions 2006 Recent Advances in Natural Language Processing for Biomedical Applications, special issue of the International Journal of Medical Informatics
    Vol. 75 (6) , pp. 430-442  
    article
    BibTeX:
    @article{pyysalo06evaluation,
      author = {Pyysalo, Sampo and Ginter, Filip and Pahikkala, Tapio and Boberg, Jorma and Järvinen, Jouni and Salakoski, Tapio},
      editor = {Robert Baud and Nigel Collier and Adeline Nazarenko and Patrick Ruch},
      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},
      publisher = {Elsevier},
      year = {2006},
      volume = {75},
      number = {6},
      pages = {430--442}
    }
    					
    Suominen, H.; Lehtikunnas, T.; Back, B.; Karsten, H.; Salakoski, T. & Salanterä, S. Theoretical considerations of ethics in text mining of nursing documents 2006
    Vol. 122 Consumer-Centered Computer-Supported Care for Healthy People, Proceedings of NI2006, The 9th International Congress on Nursing Informatics , pp. 353-364  
    inproceedings
    BibTeX:
    @inproceedings{suominen06ethics,
      author = {Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salakoski, Tapio and Salanterä, Sanna},
      editor = {Park, HA and Murray, P and Delaney, C},
      title = {Theoretical considerations of ethics in text mining of nursing documents},
      booktitle = {Consumer-Centered Computer-Supported Care for Healthy People, Proceedings of NI2006, The 9th International Congress on Nursing Informatics},
      publisher = {IOS Press, Amsterdam, Netherlands},
      year = {2006},
      volume = {122},
      pages = {353--364}
    }
    					
    Suominen, H.; Pahikkala, T.; Hiissa, M.; Lehtikunnas, T.; Back, B.; Karsten, E.H.; Salanterä, S. & Salakoski, T. Relevance ranking of intensive care nursing narratives 2006
    Vol. 4251 Knowledge-Based & Intelligent Information & Engineering Systems. Proceedings of the 10th International Conference, KES 2006, Part I , pp. 720-727  
    inproceedings
    BibTeX:
    @inproceedings{suominen2006ranking,
      author = {Hanna Suominen and Tapio Pahikkala and Marketta Hiissa and Tuija Lehtikunnas and Barbro Back and Eija Helena Karsten and Sanna Salanterä and Tapio Salakoski},
      editor = {Gabrys, B and Howlett, RJ and and Jain, LC},
      title = {Relevance ranking of intensive care nursing narratives},
      booktitle = {Knowledge-Based & Intelligent Information & Engineering Systems. Proceedings of the 10th International Conference, KES 2006, Part I},
      publisher = { Springer},
      year = {2006},
      volume = {4251},
      pages = {720--727}
    }
    					
    Suominen, H.; Pahikkala, T.; Hiissa, M.; Lehtikunnas, T.; Back, B.; Karsten, H.; Salanterä, S. & Salakoski, T. Relevance Ranking of Intensive Care Nursing Narratives 2006
    Vol. 740  
    techreport
    BibTeX:
    @techreport{suominen06tr,
      author = {Suominen, Hanna and Pahikkala, Tapio and Hiissa, Marketta and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salanterä, Sanna and Salakoski, Tapio},
      title = {Relevance Ranking of Intensive Care Nursing Narratives},
      year = {2006},
      volume = {740}
    }
    					
    Tsivtsivadze, E.; Pahikkala, T.; Boberg, J. & Salakoski, T. Locality-Convolution Kernel and Its Application to Dependency Parse Ranking 2006
    Vol. 4031 Proceedings of the The 19th International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems , pp. 610-618  
    inproceedings
    BibTeX:
    @inproceedings{tsivtsivadze2006locality,
      author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
      editor = {Moonis Ali and Richard Dapoigny},
      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},
      publisher = {Springer},
      year = {2006},
      volume = {4031},
      pages = {610--618}
    }
    					
    Proceedings of the Fifth International Conference on Natural Language Processing FinTAL 06, Turku, Finland 2006
    Vol. 4139  
    proceedings
    BibTeX:
    @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 06, Turku, Finland},
      publisher = {Springer, Heidelberg},
      year = {2006},
      volume = {4139}
    }
    					
    Ginter, F.; Pahikkala, T.; Pyysalo, S.; Tsivtsivadze, E.; Boberg, J.; Järvinen, J.; Mylläri, A. & Salakoski, T. Information Extraction from Biomedical Text: The BioText Project 2005 Proceedings of the Second Baltic Conference on Human Language Technologies HLT 05, Tallinn, Estonia , pp. 131-136   inproceedings
    BibTeX:
    @inproceedings{ginter05ie,
      author = {Ginter, Filip and Pahikkala, Tapio and Pyysalo, Sampo and Tsivtsivadze, Evgeni and Boberg, Jorma and Järvinen, Jouni and Mylläri, 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}
    }
    					
    Ginter, F.; Pyysalo, S. & Salakoski, T. Document Classification Using Semantic Networks with An Adaptive Similarity Measure 2005 Proceedings of the International Conference on Recent Advances in Natural Language Processing RANLP 05, Borovets, Bulgaria , pp. 204-211   inproceedings
    BibTeX:
    @inproceedings{ginter05docclas,
      author = {Ginter, Filip and Pyysalo, Sampo and Salakoski, Tapio},
      editor = {Angelova, Galia and Bontcheva, Kalina and Mitkov, Ruslan and Nicolov, Nicolas and Nikolov, Nikolai},
      title = {Document Classification Using Semantic Networks with An Adaptive Similarity Measure},
      booktitle = {Proceedings of the International Conference on Recent Advances in Natural Language Processing RANLP 05, Borovets, Bulgaria},
      publisher = {Incoma, Bulgaria},
      year = {2005},
      pages = {204--211}
    }
    					
    Pahikkala, T.; Ginter, F.; Boberg, J.; Järvinen, J. & Salakoski, T. Contextual Weighting for Support Vector Machines in Literature Mining: An Application to Gene Versus Protein Name Disambiguation 2005 BMC Bioinformatics
    Vol. 6 (1) , pp. 157  
    article
    BibTeX:
    @article{pahikkala05contextual,
      author = {Pahikkala, Tapio and Ginter, Filip and Boberg, Jorma and Järvinen, 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},
      number = {1},
      pages = {157},
      doi = {http://dx.doi.org/doi:10.1186/1471-2105-6-157}
    }
    					
    Pahikkala, T.; Pyysalo, S.; Boberg, J.; Mylläri, A. & Salakoski, T. Improving the performance of Bayesian and support vector classifiers in word sense disambiguation using positional information 2005 Proceedings of the International and Interdisciplinary Conference on Adaptive Knowledge Representation and Reasoning , pp. 90-97   inproceedings
    BibTeX:
    @inproceedings{pahikkala05improving,
      author = {Tapio Pahikkala and Sampo Pyysalo and Jorma Boberg and Aleksandr Mylläri and Tapio Salakoski},
      editor = {Timo Honkela and Ville Könönen and Matti Pöllä and Olli Simula},
      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},
      publisher = {Helsinki University of Technology},
      year = {2005},
      pages = {90--97}
    }
    					
    Pahikkala, T.; Pyysalo, S.; Ginter, F.; Boberg, J.; Järvinen, J. & Salakoski, T. Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks (Copyright AAAI Press, http://www.aaai.org/) 2005 Proceedings of the Eighteenth International Florida Artificial Intelligence Research Society Conference , pp. 442-447   inproceedings
    BibTeX:
    @inproceedings{pahikkala05kernels,
      author = {Pahikkala, Tapio and Pyysalo, Sampo and Ginter, Filip and Boberg, Jorma and Järvinen, 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},
      publisher = {AAAI Press},
      year = {2005},
      pages = {442--447},
      note = {Copyright AAAI Press, http://www.aaai.org/}
    }
    					
    Suominen, H.J.; Lehtikunnas, T.; Hiissa, M.; Back, B.; Karsten, H.; Salakoski, T. & Salanterä, S. Natural language processing for nursing documentation 2005 Proceedings of the 2nd International Conference on Computational Intelligence in Medicine and Healthcare (CIMED 2005) , pp. 147-154   inproceedings
    BibTeX:
    @inproceedings{suominen05,
      author = {Suominen, Hanna J and Lehtikunnas, Tuija and Hiissa, Marketta and Back, Barbro and Karsten, Helena and Salakoski, Tapio and Salanterä, Sanna},
      editor = {JM Fonseca},
      title = {Natural language processing for nursing documentation},
      booktitle = {Proceedings of the 2nd International Conference on Computational Intelligence in Medicine and Healthcare (CIMED 2005)},
      year = {2005},
      pages = {147--154}
    }
    					
    Tsivtsivadze, E.; Pahikkala, T.; Pyysalo, S.; Boberg, J.; Mylläri, A. & Salakoski, T. Regularized Least-Squares for Parse Ranking 2005
    Vol. 3646 Proceedings of the 6th International Symposium on Intelligent Data Analysis , pp. 464-474  
    inproceedings
    BibTeX:
    @inproceedings{tsivtsivadze2005ranking,
      author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Sampo Pyysalo and Jorma Boberg and Aleksandr Mylläri and Tapio Salakoski},
      editor = {A. Fazel Famili and Joost N. Kok and José Manuel Peña and Arno Siebes and A. J. Feelders},
      title = {Regularized Least-Squares for Parse Ranking},
      booktitle = {Proceedings of the 6th International Symposium on Intelligent Data Analysis},
      publisher = {Springer},
      year = {2005},
      volume = {3646},
      pages = {464--474}
    }
    					
    Ginter, F.; Boberg, J.; Järvinen, J. & Salakoski, T. New Techniques for Disambiguation in Natural Language and Their Application to Biological Text 2004 Journal of Machine Learning Research
    Vol. 5 , pp. 605-621  
    article
    BibTeX:
    @article{ginter04disambiguation,
      author = {Ginter, Filip and Boberg, Jorma and Järvinen, Jouni and Salakoski, Tapio},
      title = {New Techniques for Disambiguation in Natural Language and Their Application to Biological Text},
      journal = {Journal of Machine Learning Research},
      publisher = {MIT Press, Cambridge, Massachusetts},
      year = {2004},
      volume = {5},
      pages = {605--621}
    }
    					
    Ginter, F.; Pahikkala, T.; Pyysalo, S.; Boberg, J.; Järvinen, J. & Salakoski, T. Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis 2004
    Vol. 3066 Proceedings of the Fourth International Conference on Rough Sets and Current Trends in Computing, Uppsala, Sweden , pp. 780-785  
    inproceedings
    BibTeX:
    @inproceedings{ginter04extracting,
      author = {Ginter, Filip and Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and Järvinen, Jouni and Salakoski, Tapio},
      editor = {Tsumoto, Husaku and Slowinski, 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},
      publisher = {Springer, Heidelberg},
      year = {2004},
      volume = {3066},
      pages = {780--785}
    }
    					
    Ginter, F.; Pyysalo, S.; Boberg, J.; Järvinen, J. & Salakoski, T. Ontology-Based Feature Transformations: A Data-Driven Approach 2004
    Vol. 3230 Proceedings of the 4th International Conference EsTAL 04, Alicante, Spain , pp. 279-290  
    inproceedings
    BibTeX:
    @inproceedings{ginter04ontology,
      author = {Ginter, Filip and Pyysalo, Sampo and Boberg, Jorma and Järvinen, Jouni and Salakoski, Tapio},
      editor = {Vicedo, Jose Luis and Martnez-Barco, Patricio and Muñoz, Rafael and Saiz Noeda, Maximiliano},
      title = {Ontology-Based Feature Transformations: A Data-Driven Approach},
      booktitle = {Proceedings of the 4th International Conference EsTAL 04, Alicante, Spain},
      publisher = {Springer, Heidelberg},
      year = {2004},
      volume = {3230},
      pages = {279--290}
    }
    					
    Pyysalo, S.; Ginter, F.; Pahikkala, T.; Koivula, J.; Boberg, J.; Järvinen, J. & Salakoski, T. Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions 2004 Proceedings of Joint Workshop on Natural Language Processing in Biomedicine and its Applications JNLPBA 04, Geneva, Switzerland , pp. 15-21   inproceedings
    BibTeX:
    @inproceedings{pyysalo04analysis,
      author = {Pyysalo, Sampo and Ginter, Filip and Pahikkala, Tapio and Koivula, Jeppe and Boberg, Jorma and Järvinen, 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}
    }
    					
    Aittokallio, T.; Pahikkala, T.; Ojala, P.; Nevalainen, T.J. & Nevalainen, O. Electrophoretic Signal Comparison Applied to mRNA Differential Display Analysis 2003 BioTechniques
    Vol. 34 (1) , pp. 116-122  
    article
    BibTeX:
    @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},
      number = {1},
      pages = {116-122}
    }
    					

    Created by JabRef on 26/09/2016.