publications.bib

@article{Hb14ISME
  author =  {Borgdorff, Hanneke and Tsivtsivadze, Evgeni and Verhelst, Rita and Marzorati, Massimo and Jurriaans, Suzanne and Ndayisaba, Gilles F and Schuren, Frank H and van de Wijgert, Janneke Hhm}
  title = {Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women.},
  journal = {ISME Journal},
  year = {2014},
  url = {http://www.biomedsearch.com/nih/Lactobacillus-dominated-cervicovaginal-microbiota-associated/24599071.html},
  pubmedid = {24599071},
  issm = {1751-7370},
}

@article{Im13IEEE,
 author = {Sultan Imangaliyev, Bart Keijser, Wim Crielaard, and Evgeni Tsivtsivadze},
 title = {Online semi-supervised learning: Algorithm and application in metagenomics},
 journal ={2013 IEEE International Conference on Bioinformatics and Biomedicine},
 year = {2013},
 pages = {521-525},
 publisher = {IEEE Computer Society},
 address = {Los Alamitos, CA, USA},
}
@article{ts13arx,
  author    = {Evgeni Tsivtsivadze and Tom Heskes},
  title     = {Semi-supervised Ranking Pursuit},
  note  	= {Preprint},
  url       = {http://arxiv.org/abs/1307.0846}
}
@article{al12,
  author = {Jesse Alama and Daniel K{\"u}hlwein and Evgeni Tsivtsivadze and Josef Urban and Tom Heskes},
  title = {Premise Selection for Mathematics by Corpus Analysis and Kernel Methods},
  journal = {Journal of Automated Reasoning},
  url = {http://arxiv.org/abs/1108.3446}
}
@article{cl12,
  author = {Lennart Niels Cornelisse and Evgeni Tsivtsivadze and Marieke Meijer and Tjeerd M.D. Dijkstra and Tom Heskes and Matthijs Verhage},
  title = {Molecular Machines in the Synapse: Overlapping Protein Sets Control Distinct Steps in Neurosecretion},
  journal = {PLoS Computation Biology},
  year = {2012},
  note = {Minor revisions pending}
}
@article{pahik10,
  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},
  pages = {676-685},
  volume = {206},
  number = {3},
  publisher = {Springer},
  url = {http://www.sciencedirect.com/science/article/pii/S0377221710002171}
}
@inproceedings{ts10,
  author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski and Tom Heskes},
  title = {Co-Regularized Least-Squares for Label Ranking},
  booktitle = {Preference Learning},
  editor = {Eyke H{\"u}llermeier and Johannes F{\"u}rnkranz},
  year = {2010},
  pages = {107-123},
  url = {http://www.springer.com/computer/ai/book/978-3-642-14124-9}
}
@article{ts08b,
  author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
  title = {Kernels for Text Analysis},
  journal = {Advances of Computational Intelligence},
  month = {May},
  year = {2008},
  publisher = {Springer Berlin / Heidelberg},
  editor = {Ying Liu and Aixin Sun and Han Tong Loh and Wen Feng Lu and Ee-Peng Lim},
  volume = {116},
  pages = {81-97},
  series = {Studies in Computational Intelligence},
  url = {http://www.springerlink.com/content/v536117084857075/}
}
@article{ts09a,
  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},
  pages = {81-88},
  volume = {31},
  number = {1},
  publisher = {Springer},
  url = {http://www.springerlink.com/content/v536117084857075/}
}
@article{pahik08,
  author = {Tapio Pahikkala and Evgeni Tsivtsivadze and Antti Airola and Jouni J{\"a}rvinen and Jorma Boberg},
  title = {An Efficient Algorithm for Learning to Rank from Preference Graphs},
  journal = {Machine Learning},
  volume = {75},
  number = {1},
  pages = {129--165},
  publisher = {Springer},
  year = {2009},
  url = {http://www.springerlink.com/content/h2t2056225h85696/}
}
@inproceedings{ts13a,
  author    = {Evgeni Tsivtsivadze, Hanneke Borgdorff, Janneke van de Wijgert, Frank Schuren, Rita Verhelst, and Tom Heskes},
  title     = {Neighborhood Co-regularized Multi-view Spectral Clustering of Microbiome Data},
  booktitle = {Partially Supervised Learning},
  editor    = {Zhi-Hua Zhou and Friedhelm Schwenker},
  year      = {2013},
  url       = {publications/mvcoreg.pdf}
}
@inproceedings{ts13b,
  author    = {Evgeni Tsivtsivadze, Eveline Lommen, Roy Montijn, and Jos van der Vossen},
  title     = {Semi-supervised Multi-view Gaussian Processes for Microbial Growth Prediction},
  booktitle = {Intelligent Systems for Molecular Biology (ISMB/ECCB)},
  url       = {http://www.iscb.org/cms_addon/conferences/ismbeccb2013/posterlist.php?cat=I}
  year      = {2013},

}
@inproceedings{ts13c,
  author    = {Evgeni Tsivtsivadze, Tom Heskes and Armand Paauw},
  title     = {Multi-view Multi-class Classification for Identification of Pathogenic Bacterial Strains},
  booktitle = {Multiple Classifier Systems},
  editor    = {Zhi-Hua Zhou, Fabio Roli, and Josef Kittler},
  year      = {2013},
  url       = {publications/mvcoreg.pdf}
}
@inproceedings{ts12,
  author    = {Evgeni Tsivtsivadze and Katja Hoffman and Tom Heskes},
  title     = {Large Scale Co-regularized Ranking},
  booktitle = {ECAI Workshop on Preference Learning},
  editor    = {Johannes F{\"u}rnkranz and Eyke H{\"u}llermeier},
  year      = {2012},
  url       = {publications/lcra.pdf}
}
@inproceedings{Ru12,
  author    = {Tom de Ruijter and Evgeni Tsivtsivadze and Tom Heskes},
  title     = {Online Co-regularized Algorithms},
  booktitle = {Proceedings of the 15th International Conference on Discovery Science},
  editor    = {Philippe Lenca and Jean-Marc Petit},
  year      = {2012},
  url       = {publications/lcra.pdf}
}
@inproceedings{kh12,
  author    = {Daniel K{\"u}hlwein and Twan van Laarhoven and Evgeni Tsivtsivadze and Josef Urban and Tom Heskes},
  title     = {Overview and Evaluation of Premise Selection Techniques for Large Theory Mathematics},
  booktitle = {Proceedings of the 6th International Joint Conference on Automated Reasoning},
  year      = {2012},
  url       = {http://www.springerlink.com/content/ak12113233488700/}
}
@inproceedings{kh11c,
  author = {Daniel K{\"u}hlwein and Josef Urban and Evgeni Tsivtsivadze and Herman Geuvers and Tom Heskes},
  title = {Multi-Output Ranking for Automated Reasoning},
  booktitle = {International Conference on Knowledge Discovery and Information Retrieval},
  year = {2011},
  url = {publications/kdir11.pdf}
}
@inproceedings{kh11b,
  author = {Daniel K{\"u}hlwein and Evgeni Tsivtsivadze and Josef Urban and Tom Heskes},
  title = {Learning Semantics for Automated Reasoning},
  booktitle = {NIPS Workshop on Learning Semantics},
  editor = {Antoine Bordes and Jason Weston and Ronan Collobert and Leon Bottou},
  year = {2011},
  url = {publications/l2r_semantics.pdf}
}
@inproceedings{ts11,
  author = {Evgeni Tsivtsivadze and Josef Urban and Herman Geuvers and Tom Heskes},
  title = {Semantic Graph Kernels for Automated Reasoning},
  booktitle = {SIAM International Conference on Data Mining},
  year = {2011},
  url = {http://siam.omnibooksonline.com/2011datamining/data/papers/231.pdf}
}
@inproceedings{kh11a,
  author = {Daniel K{\"u}hlwein and Josef Urban and Evgeni Tsivtsivadze and Herman Geuvers and  Tom Heskes},
  title = {Learning2Reason},
  booktitle = {Calculemus/MKM},
  year = {2011},
  pages = {298-300},
  editor = {James H. Davenport and  William M. Farmer and Josef Urban and Florian Rabe},
  series = {Lecture Notes in Computer Science},
  volume = {6824},
  year = {2011},
  url = {http://www.springerlink.com/content/h08t8k1048374761/}
}
@article{al11,
  author = {Jesse Alama and  Daniel K{\"u}hlwein and  Evgeni Tsivtsivadze and  Josef Urban and  Tom Heskes},
  title = {Premise Selection for Mathematics by Corpus Analysis and Kernel Methods},
  journal = {CoRR},
  volume = {abs/1108.3446},
  year = {2011},
  url = {http://arxiv.org/abs/1108.3446}
}
@inproceedings{ts10a,
  author = {Evgeni Tsivtsivadze and Tom Heskes},
  title = {Sparse Preference Learning},
  booktitle = {NIPS Workshop on Practical Application of Sparse Modeling: Open Issues and New Directions},
  editor = {Irina Rish and Alexandru Niculescu-Mizil and Guillermo Cecchi and Aurelie Lozano},
  year = {2010},
  url = {publications/spl.pdf}
}
@proceedings{td10,
  editor = {Tjeerd Dijkstra and Evgeni Tsivtsivadze and  Elena Marchiori and  Tom Heskes},
  title = {Pattern Recognition in Bioinformatics - 5th IAPR International
               Conference, PRIB 2010, Nijmegen, The Netherlands, September
               22-24, 2010. Proceedings},
  booktitle = {PRIB},
  publisher = {Springer},
  series = {Lecture Notes in Computer Science},
  volume = {6282},
  year = {2010},
  isbn = {978-3-642-16000-4},
  url = {http://www.springer.com/computer/bioinformatics/book/978-3-642-16000-4}
}
@inproceedings{ja10,
  author = {Antolin Janssen and Evgeni Tsivtsivadze and Jorma Boberg and Tjeerd Dijkstra and Tom Heskes},
  title = {Efficient Remote Homology Detection},
  booktitle = {Pattern Recognition in Bioinformatics},
  editor = {Tjeerd Dijkstra and  Evgeni Tsivtsivadze and Elena Marchiori and Tom Heskes},
  year = {2010},
  url = {publications/49Janssen.pdf}
}
@inproceedings{ts09b,
  author = {Evgeni Tsivtsivadze and Botond Cseke and Tom Heskes},
  title = {Kernel Principal Component Ranking: Robust Ranking on Noisy Data},
  booktitle = {ECML/PKDD-Workshop on Preference Learning (PL-09)},
  editor = {Eyke H{\"u}llermeier and Johannes F{\"u}rnkranz},
  year = {2009},
  url = {publications/kpcr.pdf}
}
@inproceedings{Cor09,
  author = { Niels Cornelisse and Evgeni Tsivtsivadze and Marieke Meijer and Tjeerd Dijkstra and Tom Heskes and Matthijs Verhage },
  title = {Identification of Presynaptic Gene Clusters in Synaptic Signaling using Functional Data from Genetic Perturbation Studies in Hippocampal Autapses},
  booktitle = {2nd INCF Congress of Neuroinformatics, Frontiers in Neuroinformatics},
  year = {2009},
  url = {http://www.frontiersin.org/10.3389/conf.neuro.11.2009.08.035/155/neuroinformatics_2009/all_events/event_abstract}
}
@inproceedings{pahik09,
  author = {Tapio Pahikkala and Willem Waegeman and Evgeni Tsivtsivadze and Tapio Salakoski and Bernard De Baets},
  title = {From Ranking to Intransitive Preference Learning: Rock-Paper-Scissors and beyond},
  booktitle = {ECML/PKDD-Workshop on Preference Learning (PL-09)},
  editor = {Eyke H{\"u}llermeier and Johannes F{\"u}rnkranz},
  year = {2009},
  url = {http://www.ke.tu-darmstadt.de/events/PL-09/02-Pahikkala.pdf}
}
@inproceedings{ts08d,
  author = {Evgeni Tsivtsivadze and Fabian Gieseke and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
  title = {Leanring Preferences with Co-Regularized Least Squares},
  booktitle = {ECML/PKDD-Workshop on Preference Learning (PL-08)},
  editor = {Eyke H{\"u}llermeier and Johannes F{\"u}rnkranz},
  year = {2008},
  pages = {55--62},
  url = {http://www.mathematik.uni-marburg.de/~kebi/ws-ecml-08/5.pdf}
}
@inproceedings{ts08c,
  author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Antti Airola and Jorma Boberg and Tapio Salakoski},
  title = {A Sparse Regularized Least-Squares Preference Learning Algorithm},
  booktitle = {Proceedings of the 10th Scandinavian Conference on Artificial Intelligence (SCAI 2008)},
  publisher = {IOS Press},
  editor = {Anders Holst and Per Kreuger and Peter Funk},
  volume = {173},
  pages = {76--83},
  year = {2008},
  url = {publications/srls.pdf}
}
@inproceedings{pahi08a,
  author = {Tapio Pahikkala and Evgeni Tsivtsivadze and Antti Airola and Jorma Boberg and Tapio Salakoski},
  title = {Regularized Least-Squares for Learning Non-Transitive Preferences between Strategies},
  booktitle = {Proceedings of the 13th Finnish Artificial Intelligence Conference (STeP 2008)},
  publisher = {IOS Press},
  editor = {Tapani Raiko and Pentti Haikonen and Jaakko Vyrynen},
  pages = {94--98},
  year = {2008},
  month = {August},
  address = {Espoo}
}
@inproceedings{ts07,
  author = {Evgeni Tsivtsivadze and Jorma Boberg and Tapio Salakoski},
  title = {Locality Kernels for Protein Classification},
  booktitle = {Proceedings of the 7th International Workshop on  Algorithms in Bioinformatics, (WABI 2007)},
  editor = {Raffaele Giancarlo and Sridhar Hannenhalli},
  year = {2007},
  pages = {2-11},
  publisher = {Springer}
}
@inproceedings{pahik07,
  author = {Tapio Pahikkala and Evgeni Tsivtsivadze and Antti Airola and Jorma Boberg and Tapio Salakoski},
  title = {Learning to Rank with Pairwise Regularized Least-Squares},
  booktitle = {Proceedings of the SIGIR 2007 Workshop on Learning to Rank for Information Retrieval},
  editor = {Joachims, Thorsten and Li, Hang and Liu, Tie-Yan and Zhai, ChengXiang},
  pages = {27-33},
  year = {2007},
  url = {publications/rrls.pdf}
}
@inproceedings{ts06,
  author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
  title = {Locality-Convolution Kernel and Its Application to Dependency Parse Ranking},
  year = {2006},
  pages = {610-618},
  editor = {Moonis Ali and Richard Dapoigny},
  booktitle = {Proceedings of the IEA/AIE 2006, Annecy, France},
  publisher = {Springer},
  series = {Lecture Notes in Computer Science},
  volume = {4031},
  url = {publications/LCK_kernel.pdf}
}
@inproceedings{pahik06,
  author = {Tapio Pahikkala and Evgeni Tsivtsivadze and Jorma Boberg and Tapio Salakoski},
  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 2006)},
  editor = {Thomas G{\"a}rtner and Gemma C. Garriga and Thorsten Meinl},
  year = {2006},
  address = {Berlin, Germany},
  url = {http://www.inf.uni-konstanz.de/mlg2006/MLG2006.pdf}
}
@inproceedings{ts05,
  author = {Evgeni Tsivtsivadze and Tapio Pahikkala and Sampo Pyysalo and Jorma Boberg and Aleksandr Myll\"{a}ri and Tapio Salakoski},
  title = {Regularized Least-Squares for Parse Ranking},
  booktitle = {Proceedings of the Advances in Intelligent Data Analysis VI (IDA 2005)},
  editor = {A. Fazel Famili and Joost N. Kok and Jos{\'e} Manuel Pe{\~n}a and Arno Siebes and A. J. Feelders},
  pages = {464--474},
  publisher = {Springer},
  year = {2005},
  url = {publications/inpTsPaPyBoMySa05a.pdf}
}
@inproceedings{gint05,
  author = {Ginter, Filip and Pahikkala, Tapio and Pyysalo, Sampo and Tsivtsivadze, Evgeni and Boberg, Jorma and Jarvinen, Jouni and Myllari, Aleksandr and Salakoski, Tapio},
  title = {Information Extraction from  Biomedical Text: The BioText Project},
  booktitle = {Proceedings of the Second Baltic Conference on Human Language Technologies (HLT 2005)},
  publisher = {Institute of Cybernetics, Tallinn University of Technology and Institute of the Estonian Language},
  editor = {Langemets, Margit and Penjam, Priit},
  pages = {131--136},
  year = {2005},
  url = {publications/biotext.pdf}
}

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