Tapio Salakoski

Sofie Van Landeghem, Kai Hakala, Samuel Rönnqvist, Tapio Salakoski, Yves Van de Peer, Filip Ginter: Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations. Adv. Bioinformatics 2012 (2012)

Tapio Pahikkala, Sebastian Okser, Antti Airola, Tapio Salakoski, Tero Aittokallio: Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations. Algorithms for Molecular Biology 7: 11 (2012)

Jari Björne, Filip Ginter, Tapio Salakoski: University of Turku in the BioNLP'11 Shared Task. BMC Bioinformatics 13(S-11): S4 (2012)

Sofie Van Landeghem, Jari Björne, Thomas Abeel, Bernard De Baets, Tapio Salakoski, Yves Van de Peer: Semantically linking molecular entities in literature through entity relationships. BMC Bioinformatics 13(S-11): S6 (2012)

Tapio Pahikkala, Antti Airola, Thomas Canhao Xu, Pasi Liljeberg, Hannu Tenhunen, Tapio Salakoski: Parallelized Online Regularized Least-Squares for Adaptive Embedded Systems. IJERTCS 3(2): 73-91 (2012)

Willem Waegeman, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Michiel Stock, Bernard De Baets: A Kernel-Based Framework for Learning Graded Relations From Data. IEEE T. Fuzzy Systems 20(6): 1090-1101 (2012)

Juho Heimonen, Tapio Salakoski, Sanna Salanterä: An Ontology to Improve Accessibility and Quality of Patient Instructions. CLEF (Online Working Notes/Labs/Workshop) 2012

Veronika Laippala, Riitta Danielsson-Ojala, Heljä Lundgrén-Laine, Sanna Salanterä, Tapio Salakoski: Vocabulary In Discharge Documents The Patient's Perspective. CLEF (Online Working Notes/Labs/Workshop) 2012

Thomas Canhao Xu, Tapio Pahikkala, Antti Airola, Pasi Liljeberg, Juha Plosila, Tapio Salakoski, Hannu Tenhunen: Implementation and Analysis of Block Dense Matrix Decomposition on Network-on-Chips. HPCC-ICESS 2012: 516-523

Johannes Holvitie, Teemu Rajala, Riku Haavisto, Erkki Kaila, Mikko-Jussi Laakso, Tapio Salakoski: Breaking the Programming Language Barrier: Using Program Visualizations to Transfer Programming Knowledge in One Programming Language to Another. ICALT 2012: 116-120

Sebastian Okser, Antti Airola, Tero Aittokallio, Tapio Salakoski, Tapio Pahikkala: Parallel Feature Selection for Regularized Least-Squares. PARA 2012: 280-294

Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics 12: 481 (2011)

Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapio Salakoski: Extracting Contextualized Complex Biological Events with Rich Graph-Based Feature Sets. Computational Intelligence 27(4): 541-557 (2011)

Antti Airola, Tapio Pahikkala, Willem Waegeman, Bernard De Baets, Tapio Salakoski: An experimental comparison of cross-validation techniques for estimating the area under the ROC curve. Computational Statistics & Data Analysis 55(4): 1828-1844 (2011)

Antti Airola, Tapio Pahikkala, Tapio Salakoski: On Learning and Cross-Validation with Decomposed Nyström Approximation of Kernel Matrix. Neural Processing Letters 33(1): 17-30 (2011)

Antti Airola, Tapio Pahikkala, Tapio Salakoski: Training linear ranking SVMs in linearithmic time using red-black trees. Pattern Recognition Letters 32(9): 1328-1336 (2011)

Sebastian Okser, Tapio Pahikkala, Antti Airola, Tero Aittokallio, Tapio Salakoski: Fast and parallelized greedy forward selection of genetic variants in Genome-wide association studies. GENSiPS 2011: 214-217

Antti Airola, Tapio Pahikkala, Tapio Salakoski: An Improved Training Algorithm for the Linear Ranking Support Vector Machine. ICANN (1) 2011: 134-141

Pekka Naula, Tapio Pahikkala, Antti Airola, Tapio Salakoski: Greedy Regularized Least-Squares for Multi-task Learning. ICDM Workshops 2011: 527-533

Tapio Pahikkala, Antti Airola, Thomas Canhao Xu, Pasi Liljeberg, Hannu Tenhunen, Tapio Salakoski: A Parallel Online Regularized Least-squares Machine Learning Algorithm for Future Multi-core Processors. PECCS 2011: 590-599

Pekka Naula, Tapio Pahikkala, Antti Airola, Tapio Salakoski: Learning Multi-Label Predictors under Sparsity Budget. SCAI 2011: 30-39

Willem Waegeman, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Michiel Stock, Bernard De Baets: A kernel-based framework for learning graded relations from data. CoRR abs/1111.6473 (2011)

Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski: Complex event extraction at PubMed scale. Bioinformatics [ISMB] 26(12): 382-390 (2010)

Tapio Pahikkala, Willem Waegeman, Evgeni Tsivtsivadze, Tapio Salakoski, Bernard De Baets: Learning intransitive reciprocal relations with kernel methods. European Journal of Operational Research 206(3): 676-685 (2010)

Satu Jääskeläinen, Pentti Riikonen, Tapio Salakoski, Mauno Vihinen: Accuracy of protein hydropathy predictions. IJDMB 4(6): 735-754 (2010)

Antti Airola, Tapio Pahikkala, Willem Waegeman, Bernard De Baets, Tapio Salakoski: A comparison of AUC estimators in small-sample studies. Journal of Machine Learning Research - Proceedings Track 8: 3-13 (2010)

Denis Shestakov, Tapio Salakoski: Host-IP Clustering Technique for Deep Web Characterization. APWeb 2010: 378-380

Tapio Pahikkala, Antti Airola, Tapio Salakoski: Speeding Up Greedy Forward Selection for Regularized Least-Squares. ICMLA 2010: 325-330

Antti Airola, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski: Applying Permutation Tests for Assessing the Statistical Significance of Wrapper Based Feature Selection. ICMLA 2010: 989-994

Tapio Pahikkala, Willem Waegeman, Antti Airola, Tapio Salakoski, Bernard De Baets: Conditional Ranking on Relational Data. ECML/PKDD (2) 2010: 499-514

Denis Shestakov, Tapio Salakoski: Host-IP clustering technique for deep web characterization. SAC 2010: 874-875

Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski: Locality kernels for sequential data and their applications to parse ranking. Appl. Intell. 31(1): 81-88 (2009)

Erkki Kaila, Teemu Rajala, Mikko-Jussi Laakso, Tapio Salakoski: Effects, Experiences and Feedback from Studies of a Program Visualization Tool. Informatics in Education 8(1): 17-34 (2009)

Filip Ginter, Hanna Suominen, Sampo Pyysalo, Tapio Salakoski: Combining hidden Markov models and latent semantic analysis for topic segmentation and labeling: Method and clinical application. I. J. Medical Informatics 78(12): 1-6 (2009)

Veronika Laippala, Filip Ginter, Sampo Pyysalo, Tapio Salakoski: Towards automated processing of clinical Finnish: Sublanguage analysis and a rule-based parser. I. J. Medical Informatics 78(12): 7-12 (2009)

Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: Matrix representations, linear transformations, and kernels for disambiguation in natural language. Machine Learning 74(2): 133-158 (2009)

Mika Laaksonen, Barbara Simell, Tapio Salakoski, Olli Simell: Integrated Data Management and Analysis Environment for Medical Longitudinal Research with Machine Learning Based Prediction Models. CSIE (1) 2009: 552-556

Tapio Pahikkala, Hanna Suominen, Jorma Boberg, Tapio Salakoski: Efficient Hold-Out for Subset of Regressors. ICANNGA 2009: 350-359

Hanna Suominen, Heljä Lundgrén-Laine, Sanna Salanterä, Tapio Salakoski: Evaluating Pain in Intensive Care. Nursing Informatics 2009: 192-196

Chang Sik Kim, Pentti Riikonen, Tapio Salakoski: Detecting biological associations between genes based on the theory of phase synchronization. Biosystems 92(2): 99-113 (2008)

Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski: All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinformatics 9(S-11) (2008)

Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski: Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics 9(S-3) (2008)

Teemu Rajala, Mikko-Jussi Laakso, Erkki Kaila, Tapio Salakoski: Effectiveness of Program Visualization: A Case Study with the ViLLE Tool. JITE 7: 15-32 (2008)

Mikko-Jussi Laakso, Erkki Kaila, Teemu Rajala, Tapio Salakoski: Define and Visualize Your First Programming Language. ICALT 2008: 324-326

Tuomo Saarni, Jussi Hakokari, Jouni Isoaho, Tapio Salakoski: Utterance-level normalization for relative articulation rate analysis. INTERSPEECH 2008: 538-541

Jussi Hakokari, Tuomo Saarni, Jouni Isoaho, Tapio Salakoski: Correlation of utterance length and segmental duration in Finnish is questionable. INTERSPEECH 2008: 881-884

Stina Ojala, Olli Aaltonen, Tapio Salakoski: Investigating perception of places of articulation in sign and speech. INTERSPEECH 2008: 1969

Tapio Pahikkala, Antti Airola, Hanna Suominen, Jorma Boberg, Tapio Salakoski: Efficient AUC Maximization with Regularized Least-Squares. SCAI 2008: 12-19

Evgeni Tsivtsivadze, Tapio Pahikkala, Antti Airola, Jorma Boberg, Tapio Salakoski: A Sparse Regularized Least-Squares Preference Learning Algorithm. SCAI 2008: 76-83

Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: BioInfer: a corpus for information extraction in the biomedical domain. BMC Bioinformatics 8 (2007)

Satu Jääskeläinen, Pentti Riikonen, Tapio Salakoski, Mauno Vihinen: Evaluation of Protein Hydropathy Scales. BIBM 2007: 245-251

Denis Shestakov, Tapio Salakoski: On Estimating the Scale of National Deep Web. DEXA 2007: 780-789

Evgeni Tsivtsivadze, Jorma Boberg, Tapio Salakoski: Locality Kernels for Protein Classification. WABI 2007: 2-11

Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko: Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches. BMC Bioinformatics 7(S-3) (2006)

Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: Evaluation of two dependency parsers on biomedical corpus targeted at protein-protein interactions. I. J. Medical Informatics 75(6): 430-442 (2006)

Tuomo Saarni, Jyri Paakkulainen, Tuomas Mäkilä, Jussi Hakokari, Olli Aaltonen, Jouni Isoaho, Tapio Salakoski: Implementing a Rule-Based Speech Synthesizer on a Mobile Platform. FinTAL 2006: 349-355

Tapio Pahikkala, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski: Incorporating External Information in Bayesian Classifiers Via Linear Feature Transformations. FinTAL 2006: 399-410

Filip Ginter, Sampo Pyysalo, Jorma Boberg, Tapio Salakoski: Regular Approximation of Link Grammar. FinTAL 2006: 564-575

Tuomo Saarni, Jussi Hakokari, Jouni Isoaho, Olli Aaltonen, Tapio Salakoski: Segmental Duration in Utterance-Initial Environment: Evidence from Finnish Speech Corpora. FinTAL 2006: 576-584

Annu Paganus, Vesa-Petteri Mikkonen, Tomi Mäntylä, Sami Nuuttila, Jouni Isoaho, Olli Aaltonen, Tapio Salakoski: The Vowel Game: Continuous Real-Time Visualization for Pronunciation Learning with Vowel Charts. FinTAL 2006: 696-703

Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski: Locality-Convolution Kernel and Its Application to Dependency Parse Ranking. IEA/AIE 2006: 610-618

Hanna Suominen, Tapio Pahikkala, Marketta Hiissa, Tuija Lehtikunnas, Barbro Back, Helena Karsten, Sanna Salanterä, Tapio Salakoski: Relevance Ranking of Intensive Care Nursing Narratives. KES (1) 2006: 720-727

Marketta Hiissa, Tapio Pahikkala, Hanna Suominen, Tuija Lehtikunnas, Barbro Back, Helena Karsten, Sanna Salanterä, Tapio Salakoski: Towards Automated Classification of Intensive Care Nursing Narratives. MIE 2006: 789-794

Tapio Salakoski, Filip Ginter, Sampo Pyysalo, Tapio Pahikkala (Eds.): Advances in Natural Language Processing, 5th International Conference on NLP, FinTAL 2006, Turku, Finland, August 23-25, 2006, Proceedings. Lecture Notes in Computer Science 4139, Springer 2006, isbn 3-540-37334-9

Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko: Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches. CoRR abs/cs/0606119 (2006)

Tapio Pahikkala, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation. BMC Bioinformatics 6: 157 (2005)

Mikko-Jussi Laakso, Tapio Salakoski, Linda Grandell, Xuemei Qiu, Ari Korhonen, Lauri Malmi: Multi-Perspective Study of Novice Learners Adopting the Visual Algorithm Simulation Exercise System TRAKLA2. Informatics in Education 4(1): 49-68 (2005)

Denis Shestakov, Tapio Salakoski: Web Services for DNA Sequence Analysis. DEXA Workshops 2005: 600-604

Tapio Pahikkala, Sampo Pyysalo, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks. FLAIRS Conference 2005: 442-448

Mikko-Jussi Laakso, Tapio Salakoski, Ari Korhonen: The Feasibility of Automatic Assessment and Feedback. CELDA 2005: 113-122

Evgeni Tsivtsivadze, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski: Regularized Least-Squares for Parse Ranking. IDA 2005: 464-474

Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: New Techniques for Disambiguation in Natural Language and Their Application to Biological Text. Journal of Machine Learning Research 5: 605-621 (2004)

Filip Ginter, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis. Rough Sets and Current Trends in Computing 2004: 780-785

Filip Ginter, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: Ontology-Based Feature Transformations: A Data-Driven Approach. EsTAL 2004: 280-291

Pentti Riikonen, Jorma Boberg, Tapio Salakoski, Mauno Vihinen: Mobile access to biological databases on the Internet. IEEE Trans. Biomed. Engineering 49(12): 1477-1479 (2002)

Pentti Riikonen, Jorma Boberg, Tapio Salakoski, Mauno Vihinen: BioWAP, mobile Internet service for bioinformatics. Bioinformatics 17(9): 855-856 (2001)

Jorma Boberg, Tapio Salakoski: Representative noise-free complete-link classification with application to protein structures. Pattern Recognition 30(3): 467-482 (1997)

Jorma Boberg, Tapio Salakoski: General formulation and evaluation of agglomerative clustering methods with metric and non-metric distances. Pattern Recognition 26(9): 1395-1406 (1993)