Patrick Ruch - RankMe

160 papers A* 1A 1B 8Misc 14Journal 45Unranked 89

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	TransBERT: A Framework for Synthetic Translation in Domain-Specific Language Modeling. EMNLP (Findings) Julien Knafou, Luc Mottin, Anaïs Mottaz, Alexandre Flament, Patrick Ruch
2024	—	`conf`	Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants. MIE Luc Mottin, Nona Naderi, Anaïs Mottaz, Pierre-André Michel, Lennart F. Johansson, Morris A. Swertz, Andrew Stubbs, Emilie Pasche, Julien Gobeill, Patrick Ruch
2024	—	`conf`	SIB Text-Mining at TREC PLABA 2024. TREC Luc Mottin, Anaïs Mottaz, Julien Knafou, Alexandre Flament, Julien Gobeill, Patrick Ruch
2023	J	`jnl`	Assessing the use of supplementary materials to improve genomic variant discovery. Database J. Biol. Databases Curation Emilie Pasche, Anaïs Mottaz, Julien Gobeill, Pierre-André Michel, Déborah Caucheteur, Nona Naderi, Patrick Ruch
2023	J	`jnl`	COVoc and COVTriage: novel resources to support literature triage. Bioinform. Déborah Caucheteur, Zoë May Pendlington, Paola Roncaglia, Julien Gobeill, Luc Mottin, Nicolas Matentzoglu, Donat Agosti, David Osumi-Sutherland, Helen E. Parkinson, Patrick Ruch
2023	J	`jnl`	Multilingual RECIST classification of radiology reports using supervised learning. Frontiers Digit. Health Luc Mottin, Jean-Philippe Goldman, Christoph Jäggli, Rita Achermann, Julien Gobeill, Julien Knafou, Julien Ehrsam, Alexandre Wicky, Camille L. Gerard, Tanja Schwenk, Mélinda Charrier, Petros Tsantoulis, Christian Lovis, Alexander B. Leichtle, Michael Kiessling, Olivier Michielin, Sylvain Pradervand, Vasiliki Foufi, Patrick Ruch
2022	—	`conf`	Analyzing the Information Content of Text-Based Files in Supplementary Materials of Biomedical Literature. MIE Nona Naderi, Anaïs Mottaz, Douglas Teodoro, Patrick Ruch
2022	—	`conf`	Classification of Oncology Treatment Responses from French Radiology Reports with Supervised Machine Learning. MIE Jean-Philippe Goldman, Luc Mottin, Jamil Zaghir, Daniel Keszthelyi, Belinda Lokaj, Hugues Turbé, Julien Gobeill, Patrick Ruch, Julien Ehrsam, Christian Lovis
2022	Misc	`conf`	Classification of oncology treatment responses from radiology reports with supervised machine learning. AMIA Luc Mottin, Jean-Philippe Goldman, Christoph Jäggli, Rita Achermann, Julien Gobeill, Julien Knafou, Julien Ehrsam, Alexandre Wicky, Camille L. Gerard, Tanja Schwenk, Mélinda Charrier, Petros Tsantoulis, Christian Lovis, Alexander B. Leichtle, Michael Kiessling, Olivier Michielin, Sylvain Pradervand, Vasiliki Foufi, Patrick Ruch
2022	—	`conf`	Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service. MIE Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Douglas Teodoro, Patrick Ruch
2022	J	`jnl`	Variomes: a high recall search engine to support the curation of genomic variants. Bioinform. Emilie Pasche, Anaïs Mottaz, Déborah Caucheteur, Julien Gobeill, Pierre-André Michel, Patrick Ruch
2021	J	`jnl`	Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora. Frontiers Res. Metrics Anal. Nona Naderi, Julien Knafou, Jenny Copara, Patrick Ruch, Douglas Teodoro
2021	—	`conf`	Progress With Improving Preservation and Reuse of Scientific Research Data. iPRES Peter Cornwell, Donat Agosti, Laurence Benichou, Jose Benito Gonzalez Lopez, Madeleine Herren, Patrick Ruch
2021	—	`conf`	SIB Text Mining at TREC Clinical Trials 2021. TREC Déborah Caucheteur, Emilie Pasche, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch
2021	J	`jnl`	UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan W. Sousa da Silva, Paul Denny, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Leyla Jael García Castro, Penelope Garmiri, George E. Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodríguez-López, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan J. Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard De Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Béatrice A. Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh, Jian Zhang, Patrick Ruch, Douglas Teodoro
2020	—	`conf`	An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. CLEF (Working Notes) Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Jingqi Wang, Yuankai Ren, Zhi Zhang, Yaoyun Zhang, Mai Hoang Dao, Pedro Ruas, Andre Lamurias, Francisco M. Couto, Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro, Daniel M. Lowe, John Mayfield, Abdullatif Köksal, Hilal Dönmez, Elif Özkirimli, Arzucan Özgür, Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes, C. S. Malarkodi, Pattabhi R. K. Rao, Sobha Lalitha Devi, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor
2020	—	`conf`	BiTeM at WNUT 2020 Shared Task-1: Named Entity Recognition over Wet Lab Protocols using an Ensemble of Contextual Language Models. W-NUT@EMNLP Julien Knafou, Nona Naderi, Jenny Copara, Douglas Teodoro, Patrick Ruch
2020	—	`conf`	Contextualized French Language Models for Biomedical Named Entity Recognition. JEP-TALN-RECITAL (DEFT) Jenny Copara, Julien Knafou, Nona Naderi, Claudia Moro, Patrick Ruch, Douglas Teodoro
2020	J	`jnl`	DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. András Hatos, Borbála Hajdu-Soltész, Alexander Miguel Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykaç Fas, Claudio Bassot, Guillermo I. Benítez, Martina Bevilacqua, Anastasia Chasapi, Lucía B. Chemes, Norman E. Davey, Radoslav Davidovic, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S. González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamás Horváth, Valentin Iglesias, Andrey V. Kajava, Orsolya P. Kovács, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A. Manso, Cristina Marino Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Micetic, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo D. Parisi, Emilie Pasche, Pedro J. Barbosa Pereira, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Éva Schád, Beáta Szabó, Tamás Szaniszló, Stella Tamana, Ágnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
2020	—	`conf`	Machine Learning for Automatic Encoding of French Electronic Medical Records: Is More Data Better? MIE Julien Gobeill, Patrick Ruch, Rodolphe Meyer
2020	—	`conf`	Named Entity Recognition in Chemical Patents using Ensemble of Contextual Language Models. CLEF (Working Notes) Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro
2020	J	`jnl`	Named entity recognition in chemical patents using ensemble of contextual language models. CoRR Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro
2020	J	`jnl`	SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. Nucleic Acids Res. Julien Gobeill, Déborah Caucheteur, Pierre-André Michel, Luc Mottin, Emilie Pasche, Patrick Ruch
2020	—	`conf`	SIB Text Mining at TREC 2020 Deep Learning Track. TREC Julien Knafou, Matthew Jeffryes, Sohrab Ferdowsi, Patrick Ruch
2020	—	`conf`	SIB Text Mining at TREC Precision Medicine 2020. TREC Emilie Pasche, Déborah Caucheteur, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch
2020	—	`conf`	Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. MIE Déborah Caucheteur, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Daniel J. Stekhoven, Valérie Barbié, Patrick Ruch
2020	J	`jnl`	UPCLASS: a deep learning-based classifier for UniProtKB entry publications. Database J. Biol. Databases Curation Douglas Teodoro, Julien Knafou, Nona Naderi, Emilie Pasche, Julien Gobeill, Cecilia N. Arighi, Patrick Ruch
2019	—	`conf`	A Baseline Approach for Early Detection of Signs of Anorexia and Self-harm in Reddit Posts. CLEF (Working Notes) Nona Naderi, Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch
2019	—	`conf`	A Data-Driven Approach for Measuring the Severity of the Signs of Depression using Reddit Posts. CLEF (Working Notes) Paul Van Rijen, Douglas Teodoro, Nona Naderi, Luc Mottin, Julien Knafou, Matt Jeffryes, Patrick Ruch
2019	—	`conf`	Designing retrieval models to contrast precision-driven ad hoc search vs. recall-driven treatment extraction in Precision Medicine. TREC Déborah Caucheteur, Emilie Pasche, Julien Gobeill, Anaïs Mottaz, Luc Mottin, Patrick Ruch
2019	—	`conf`	Retrieving the Evidence of a Free Text Annotation in a Scientific Article: A Data Free Approach. CICLing (1) Julien Gobeill, Emilie Pasche, Patrick Ruch
2019	—	`conf`	SIB Text Mining at TREC 2019 Deep Learning Track: Working Note. TREC Julien Knafou, Matt Jeffryes, Luc Mottin, Douglas Teodoro, Patrick Ruch
2018	J	`jnl`	Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. Database J. Biol. Databases Curation Aurore Britan, Isabelle Cusin, Valérie Hinard, Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Daniel Dinis Teixeira, Pierre-André Michel, Patrick Ruch, Pascale Gaudet
2018	—	`conf`	Instance-based Learning for ICD10 Categorization. CLEF (Working Notes) Julien Gobeill, Patrick Ruch
2018	J	`jnl`	Overview of the BioCreative VI text-mining services for Kinome Curation Track. Database J. Biol. Databases Curation Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch
2017	—	`conf`	Customizing a Variant Annotation-Support Tool: an Inquiry into Probability Ranking Principles for TREC Precision Medicine. TREC Emilie Pasche, Julien Gobeill, Luc Mottin, Anaïs Mottaz, Douglas Teodoro, Paul Van Rijen, Patrick Ruch
2017	J	`jnl`	Global picture of OAI-PMH repositories through the analysis of 6 key open archive meta-catalogs. CoRR Arnaud Gaudinat, Jonas Beausire, Megan Fuss, Elisa Banfi, Julien Gobeill, Patrick Ruch
2017	J	`jnl`	Improving average ranking precision in user searches for biomedical research datasets. Database J. Biol. Databases Curation Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch
2017	J	`jnl`	Improving average ranking precision in user searches for biomedical research datasets. CoRR Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch
2017	J	`jnl`	Triage by ranking to support the curation of protein interactions. Database J. Biol. Databases Curation Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Pierre-André Michel, Amos Bairoch, Pascale Gaudet, Patrick Ruch
2016	—	`conf`	BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction. CLEF (Working Notes) Luc Mottin, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Arnaud Gaudinat, Patrick Ruch
2016	—	`conf`	Effect of the Named Entity Recognition and Sliding Window on the HONcode Automated Detection of HONcode Criteria for Mass Health Online Content. HEALTHINF Célia Boyer, Ljiljana Dolamic, Patrick Ruch, Gilles Falquet
2016	—	`conf`	Tools to Retrieve Reliable Health Information on the Internet - Improvements of the Automated Detection of HONcode Criteria for Mass Health Online Content. EPS Célia Boyer, Allan Hanbury, Patrick Ruch, Gilles Falquet
2016	J	`jnl`	neXtA Database J. Biol. Databases Curation Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, Patrick Ruch
2015	J	`jnl`	Deep Question Answering for protein annotation. Database J. Biol. Databases Curation Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Dina Vishnyakova, Pascale Gaudet, Amos Bairoch, Patrick Ruch
2015	—	`conf`	Exploiting incoming and outgoing citations for improving Information Retrieval in the TREC 2015 Clinical Decision Support Track. TREC Julien Gobeill, Arnaud Gaudinat, Patrick Ruch
2015	—	`conf`	Instance-Based Learning for Tweet Monitoring and Categorization. CLEF Julien Gobeill, Arnaud Gaudinat, Patrick Ruch
2014	J	`jnl`	Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. Database J. Biol. Databases Curation Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch
2014	J	`jnl`	Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinform. Emilie Pasche, Julien Gobeill, Olivier Kreim, Fatma Oezdemir-Zaech, Thérèse Vachon, Christian Lovis, Patrick Ruch
2014	—	`conf`	Electronic Processing of Informed Consents in a Global Pharmaceutical Company Environment. MIE Dina Vishnyakova, Julien Gobeill, Fatma Oezdemir-Zaech, Olivier Kreim, Thérèse Vachon, Thierry Cladé, Xavier Haenning, Dmitri Mikhailov, Patrick Ruch
2014	—	`conf`	Full-texts representation with Medical Subject Headings, and co-citations network rerank- ing strategies for TREC 2014 Clinical Decision Support Track. TREC Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Patrick Ruch
2014	—	`conf`	Instance-based Learning for Tweet Categorization in CLEF RepLab 2014. CLEF (Working Notes) Julien Gobeill, Arnaud Gaudinat, Patrick Ruch
2014	J	`jnl`	Overview of the gene ontology task at BioCreative IV. Database J. Biol. Databases Curation Yuqing Mao, Kimberly Van Auken, Donghui Li, Cecilia N. Arighi, Peter McQuilton, G. Thomas Hayman, Susan Tweedie, Mary L. Schaeffer, Stanley J. F. Laulederkind, Shur-Jen Wang, Julien Gobeill, Patrick Ruch, Anh Tuan Luu, Jung-Jae Kim, Jung-Hsien Chiang, Yu-De Chen, Chia-Jung Yang, Hongfang Liu, Dongqing Zhu, Yanpeng Li, Hong Yu, Ehsan Emadzadeh, Graciela Gonzalez, Jian-Ming Chen, Hong-Jie Dai, Zhiyong Lu
2013	J	`jnl`	Application of text-mining for updating protein post-translational modification annotation in UniProtKB. BMC Bioinform. Anne-Lise Veuthey, Alan J. Bridge, Julien Gobeill, Patrick Ruch, Johanna R. McEntyre, Lydie Bougueleret, Ioannis Xenarios
2013	—	`conf`	Khresmoi - Multilingual Semantic Search of Medical Text and Images. MedInfo Niraj Aswani, Thomas Beckers, Erich Birngruber, Célia Boyer, Andreas Burner, Jakub Bystron, Khalid Choukri, Sarah Cruchet, Hamish Cunningham, Jan Dedek, Ljiljana Dolamic, René Donner, Sebastian Dungs, Ivan Eggel, Antonio Foncubierta-Rodríguez, Norbert Fuhr, Adam Funk, Alba Garcia Seco de Herrera, Arnaud Gaudinat, Georgi Georgiev, Julien Gobeill, Lorraine Goeuriot, Paz Gomez, Robert Mark Greenwood, Manfred Gschwandtner, Allan Hanbury, Jan Hajic, Jaroslava Hlavácová, Markus Holzer, Gareth J. F. Jones, Blanca Jordan, Matthias Jordan, Klemens Kaderk, Franz Kainberger, Liadh Kelly, Sascha Kriewel, Marlene Kritz, Georg Langs, Nolan Lawson, Dimitrios Markonis, Iván Martínez, Vassil Momtchev, Alexandre Masselot, Hélène Mazo, Henning Müller, João R. M. Palotti, Pavel Pecina, Konstantin Pentchev, Deyan Peychev, Natalia Pletneva, Diana Pottecher, Angus Roberts, Patrick Ruch, Alexander Sachs, Matthias Samwald, Priscille Schneller, Veronika Stefanov, Miguel Angel Tinte, Zdenka Uresová, Alejandro Vargas, Dina Vishnyakova
2013	J	`jnl`	Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database J. Biol. Databases Curation Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch
2013	—	`conf`	Use of Controlled Vocabularies to Improve Biomedical Information Retrieval Tasks. MedInfo Emilie Pasche, Julien Gobeill, Dina Vishnyakova, Patrick Ruch, Christian Lovis
2013	—	`conf`	Using a Question-Answering Approach in Machine Reading Task of Biomedical Texts about the Alzheimer Disease. CLEF (Working Notes) Dina Vishnyakova, Julien Gobeill, Patrick Ruch
2013	—	`conf`	Utilization of Ontology Look-Up Services in Information Retrieval for Biomedical Literature. EFMI-STC Dina Vishnyakova, Emilie Pasche, Christian Lovis, Patrick Ruch
2012	—	`conf`	A User-Friendly Tool for Medical-Related Patent Retrieval. EFMI-STC Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch
2012	—	`conf`	An advanced search engine for patent analytics in medicinal chemistry. MIE Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch
2012	—	`conf`	BiTeM Site Report for the Claims to Passage Task in CLEF-IP 2012. CLEF (Online Working Notes/Labs/Workshop) Julien Gobeill, Patrick Ruch
2012	—	`conf`	Classification and Prioritization of Biomedical Literature for the Comparative Toxicogenomics Database. MIE Dina Vishnyakova, Emilie Pasche, Julien Gobeill, Arnaud Gaudinat, Christian Lovis, Patrick Ruch
2012	—	`conf`	Pathogens and Gene Product Normalization in the Biomedical Literature. EFMI-STC Dina Vishnyakova, Emilie Pasche, Douglas Teodoro, Christian Lovis, Patrick Ruch
2012	J	`jnl`	Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database. Database J. Biol. Databases Curation Dina Vishnyakova, Emilie Pasche, Patrick Ruch
2011	—	`conf`	BiTeM Group Report for TREC Chemical IR Track 2011. TREC Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova
2011	—	`conf`	BiTeM Group Report for TREC Medical Records Track 2011. TREC Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova
2011	—	`conf`	Interoperability Driven Integration of Biomedical Data Sources. MIE Douglas Teodoro, Rémy Choquet, Daniel Schober, Giovanni Mels, Emilie Pasche, Patrick Ruch, Christian Lovis
2011	J	`jnl`	The gene normalization task in BioCreative III. BMC Bioinform. Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sérgio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, W. John Wilbur
2011	—	`conf`	Using Multimodal Mining to Drive Clinical Guidelines Development. MIE Emilie Pasche, Julien Gobeill, Douglas Teodoro, Dina Vishnyakova, Arnaud Gaudinat, Patrick Ruch, Christian Lovis
2010	—	`conf`	Automatic IPC Encoding and Novelty Tracking for Effective Patent Mining. NTCIR Douglas Teodoro, Emilie Pasche, Dina Vishnyakova, Julien Gobeill, Patrick Ruch, Christian Lovis
2010	—	`conf`	Automatic Prior Art Searching and Patent Encoding at CLEF-IP '10. CLEF (Notebook Papers/LABs/Workshops) Douglas Teodoro, Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch, Christian Lovis
2010	—	`conf`	BiTeM site Report for TREC Chemistry 2010: Impact of Citations Feeback for Patent Prior Art Search and Chemical Compounds Expansion for Ad Hoc Retrieval. TREC Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova
2010	J	`jnl`	Literature-based Discovery. J. Assoc. Inf. Sci. Technol. Patrick Ruch
2010	—	`conf`	Partage de Données Biomédicales sur le Web Sémantique. WSM@IC Rémy Choquet, Douglas Teodoro, Giovanni Mels, Ariane Assélé Kama, Emilie Pasche, Patrick Ruch, Christian Lovis, Marie-Christine Jaulent
2009	—	`conf`	Automatic Medical Knowledge Acquisition Using Question-Answering. MIE Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis
2009	—	`conf`	Biomedical Data Management: A Proposal Framework. MIE Douglas Teodoro, Rémy Choquet, Emilie Pasche, Julien Gobeill, Christel Daniel, Patrick Ruch, Christian Lovis
2009	J	`jnl`	Comparing a rule-based versus statistical system for automatic categorization of MEDLINE documents according to biomedical specialty. J. Assoc. Inf. Sci. Technol. Susanne M. Humphrey, Aurélie Névéol, Allen C. Browne, Julien Gobeill, Patrick Ruch, Stéfan Jacques Darmoni
2009	—	`conf`	Exploring a Wide Range of Simple Pre and Post Processing Strategies for Patent Searching in CLEF IP 2009. CLEF (Working Notes) Julien Gobeill, Douglas Theodoro, Patrick Ruch
2009	Misc	`conf`	QA-driven Guidelines Generation for Bacteriotherapy. AMIA Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis
2009	—	`conf`	Report on the TREC 2009 Experiments: Chemical IR Track. TREC Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch
2009	—	`conf`	Simple Pre and Post Processing Strategies for Patent Searching in CLEF Intellectual Property Track 2009. CLEF (1) Julien Gobeill, Emilie Pasche, Douglas Teodoro, Patrick Ruch
2009	—	`conf`	Taking Benefit of Query and Document Expansion using MeSH Descriptors in Medical ImageCLEF 2009. CLEF (Working Notes) Julien Gobeill, Douglas Theodoro, Emilie Pasche, Patrick Ruch
2008	J	`jnl`	Automatic medical encoding with SNOMED categories. BMC Medical Informatics Decis. Mak. Patrick Ruch, Julien Gobeill, Christian Lovis, Antoine Geissbühler
2008	—	`conf`	First Participation of University and Hospitals of Geneva to Domain-Specific Track in CLEF 2008. CLEF (Working Notes) Julien Gobeill, Patrick Ruch
2008	Misc	`conf`	From Episodes of Care to Diagnosis Codes: Automatic Text Categorization for Medico-Economic Encoding. AMIA Patrick Ruch, Julien Gobeill, Imad Tbahriti, Antoine Geissbühler
2008	J	`jnl`	Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. BMC Bioinform. Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Anaïs Mottaz, Anne-Lise Veuthey, Patrick Ruch
2008	J	`jnl`	Mapping proteins to disease terminologies: from UniProt to MeSH. BMC Bioinform. Anaïs Mottaz, Yum Lina Yip, Patrick Ruch, Anne-Lise Veuthey
2008	—	`conf`	Query and Document Expansion with Medical Subject Headings Terms at Medical Imageclef 2008. CLEF Julien Gobeill, Patrick Ruch, Xin Zhou
2008	—	`conf`	Text-only Cross-language Image Search at Medical ImageCLEF 2008. CLEF (Working Notes) Julien Gobeill, Patrick Ruch, Xin Zhou
2007	—	`conf`	Challenges and Methodology for Indexing the Computerized Patient Record. MedInfo Frédéric Ehrler, Patrick Ruch, Antoine Geissbühler, Christian Lovis
2007	—	`conf`	Combining Resources to Find Answers to Biomedical Questions. TREC Dina Demner-Fushman, Susanne M. Humphrey, Nicholas C. Ide, Russell F. Loane, James G. Mork, Patrick Ruch, Miguel E. Ruiz, Lawrence H. Smith, W. John Wilbur, Alan R. Aronson
2007	—	`conf`	Design of a Decentralized Reusable Research Database Architecture to Support Data Acquisition in Large Research Projects. MedInfo Jimison Iavindrasana, Adrien Depeursinge, Patrick Ruch, Stéphane Spahni, Antoine Geissbühler, Henning Müller
2007	J	`jnl`	Mapping protein information to disease terminologies. J. Integr. Bioinform. Anaïs Mottaz, Yum Lina Yip, Patrick Ruch, Anne-Lise Veuthey
2007	J	`jnl`	Recherche d'information dans MEDLINE. Document Numérique Samir Abdou, Patrick Ruch, Jacques Savoy
2007	—	`conf`	Recherche d'information et analyse bibliographique appliquées à la mise à jour automatique de Swiss-Prot. CORIA Imad Tbahriti, Anne-Lise Veuthey, Patrick Ruch, Julien Gobeill
2007	—	`conf`	Reconciliation of Ontology and Terminology to Cope with Linguistics. MedInfo Robert H. Baud, Werner Ceusters, Patrick Ruch, Anne-Marie Rassinoux, Christian Lovis, Antoine Geissbühler
2007	—	`conf`	University and Hospitals of Geneva Participating at ImageCLEF 2007. CLEF Xin Zhou, Julien Gobeill, Patrick Ruch, Henning Müller
2007	—	`conf`	University and Hospitals of Geneva at ImageCLEF 2007. CLEF (Working Notes) Xin Zhou, Julien Gobeill, Patrick Ruch, Henning Müller
2007	B	`conf`	Unsupervised Documents Categorization Using New Threshold-Sensitive Weighting Technique. AIME Frédéric Ehrler, Patrick Ruch
2007	—	`conf`	Using Discourse Analysis to Improve Text Categorization in MEDLINE. MedInfo Patrick Ruch, Antoine Geissbühler, Julien Gobeill, Frédéric Lisacek, Imad Tbahriti, Anne-Lise Veuthey, Alan R. Aronson
2007	J	`jnl`	Using argumentation to extract key sentences from biomedical abstracts. Int. J. Medical Informatics Patrick Ruch, Célia Boyer, Christine Chichester, Imad Tbahriti, Antoine Geissbühler, Paul Fabry, Julien Gobeill, Violaine Pillet, Dietrich Rebholz-Schuhmann, Christian Lovis, Anne-Lise Veuthey
2007	—	`conf`	Vocabulary-Driven Passage Retrieval for Question-Answering in Genomics. TREC Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Patrick Ruch
2006	A*	`conf`	Argumentative Feedback: A Linguistically-Motivated Term Expansion for Information Retrieval. ACL Patrick Ruch, Imad Tbahriti, Julien Gobeill, Alan R. Aronson
2006	J	`jnl`	Automatic assignment of biomedical categories: toward a generic approach. Bioinform. Patrick Ruch
2006	—	`conf`	Dépister efficacement de l'information dans une banque documentaire : L'exemple de MEDLINE. INFORSID Samir Abdou, Jacques Savoy, Patrick Ruch
2006	—	`conf`	Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort. TREC Dina Demner-Fushman, Susanne M. Humphrey, Nicholas C. Ide, Russell F. Loane, Patrick Ruch, Miguel E. Ruiz, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Alan R. Aronson
2006	J	`jnl`	Health search engine with e-document analysis for reliable search results. Int. J. Medical Informatics Arnaud Gaudinat, Patrick Ruch, Michel Joubert, Philippe Uziel, Anne Strauss, Michèle Thonnet, Robert H. Baud, Stéphane Spahni, Patrick Weber, Juan Bonal, Célia Boyer, Marius Fieschi, Antoine Geissbühler
2006	J	`jnl`	Methodology to ease the construction of a terminology of problems. Int. J. Medical Informatics Paul Fabry, Robert H. Baud, Patrick Ruch, Christelle Despont-Gros, Christian Lovis
2006	J	`jnl`	Model Formulation: Advancing Biomedical Image Retrieval: Development and Analysis of a Test Collection. J. Am. Medical Informatics Assoc. William R. Hersh, Henning Müller, Jeffery R. Jensen, Jianji Yang, Paul N. Gorman, Patrick Ruch
2006	—	`conf`	Query and Document Translation by Automatic Text Categorization: A Simple Approach to Establish a Strong Textual Baseline for ImageCLEFmed 2006. CLEF (Working Notes) Julien Gobeill, Henning Müller, Patrick Ruch
2006	J	`jnl`	Recent advances in natural language processing for biomedical applications. Int. J. Medical Informatics Nigel Collier, Adeline Nazarenko, Robert H. Baud, Patrick Ruch
2006	—	`conf`	Report on the TREC 2006 Experiment: Genomics Track. TREC Patrick Ruch, Frédéric Ehrler, Julien Gobeill, Imad Tbahriti, Antonio Jimeno-Yepes
2006	—	`conf`	Translation by Text Categorisation: Medical Image Retrieval in ImageCLEFmed 2006. CLEF Julien Gobeill, Henning Müller, Patrick Ruch
2006	J	`jnl`	Using argumentation to retrieve articles with similar citations: An inquiry into improving related articles search in the MEDLINE digital library. Int. J. Medical Informatics Imad Tbahriti, Christine Chichester, Frédérique Lisacek, Patrick Ruch
2005	J	`jnl`	Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot. BMC Bioinform. Frédéric Ehrler, Antoine Geissbühler, Antonio Jimeno-Yepes, Patrick Ruch
2005	—	`conf`	Evaluation of Stemming, Query Expansion and Manual Indexing Approaches for the Genomic Task. TREC Samir Abdou, Jacques Savoy, Patrick Ruch
2005	—	`conf`	Extracting Key Sentences with Latent Argumentative Structuring. MIE Patrick Ruch, Robert H. Baud, Christine Chichester, Antoine Geissbühler, Frédérique Lisacek, Johan Marty, Dietrich Rebholz-Schuhmann, Imad Tbahriti, Anne-Lise Veuthey
2005	A	`conf`	Features Combination for Extracting Gene Functions from MEDLINE. ECIR Patrick Ruch, Laura Perret, Jacques Savoy
2005	—	`conf`	Fusion of Knowledge-Intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents. TREC Alan R. Aronson, Dina Demner-Fushman, Susanne M. Humphrey, Jimmy Lin, Patrick Ruch, Miguel E. Ruiz, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Hongfang Liu
2005	B	`conf`	Latent Argumentative Pruning for Compact MEDLINE Indexing. AIME Patrick Ruch, Robert H. Baud, Johan Marty, Antoine Geissbühler, Imad Tbahriti, Anne-Lise Veuthey
2005	Misc	`conf`	Model Selection for Support Vector Classifiers via Direct Simplex Search. FLAIRS Gilles Cohen, Patrick Ruch, Melanie Hilario
2005	—	`conf`	Report on the TREC 2005 Experiment: Genomics Track. TREC Patrick Ruch, Frédéric Ehrler, Samir Abdou, Jacques Savoy
2005	—	`conf`	The Use of MedGIFT and EasyIR for ImageCLEF 2005. CLEF Henning Müller, Antoine Geissbühler, Johan Marty, Christian Lovis, Patrick Ruch
2005	J	`jnl`	UMLF: a unified medical lexicon for French. Int. J. Medical Informatics Pierre Zweigenbaum, Robert H. Baud, Anita Burgun, Fiammetta Namer, Éric Jarrousse, Natalia Grabar, Patrick Ruch, Franck Le Duff, Jean-François Forget, Magaly Douyère, Stéfan Jacques Darmoni
2005	—	`conf`	Using medGIFT and easyIR for the ImageCLEF 2005 Evaluation Tasks. CLEF (Working Notes) Henning Müller, Antoine Geissbühler, Johan Marty, Christian Lovis, Patrick Ruch
2004	B	`conf`	An Argumentative Annotation Schema for Meeting Discussions. LREC Vincenzo Pallotta, Hatem Ghorbel, Patrick Ruch, Giovanni Coray
2004	J	`jnl`	An argumentative annotation schema for meeting discussions CoRR Vincenzo Pallotta, Hatem Ghorbel, Patrick Ruch, Giovanni Coray
2004	—	`conf`	Coping with the Variability of Medical Terms. MedInfo Robert H. Baud, Patrick Ruch, Arnaud Gaudinat, Paul Fabry, Christian Lovis, Antoine Geissbühler
2004	—	`conf`	ImageCLEF 2004: Combining Image and Multi-lingual Search for Medical Image Retrieval. CLEF Henning Müller, Antoine Geissbühler, Patrick Ruch
2004	—	`ed.`	Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications, NLPBA/BioNLP 2004, Geneva, Switzerland, August 28-29, 2004 NLPBA/BioNLP Nigel Collier, Patrick Ruch, Adeline Nazarenko
2004	B	`conf`	Query Translation by Text Categorization. COLING Patrick Ruch
2004	—	`conf`	Report on the CLEF Experiment: Combining Image and Multilingual Search for Medical Image Retrieval. CLEF (Working Notes) Henning Müller, Antoine Geissbühler, Patrick Ruch
2004	—	`conf`	Report on the ImageCLEF Experiment: How to Visually Retrieve Images from the St. Andrews Collection using GIFT. CLEF (Working Notes) Henning Müller, Antoine Geissbühler, Patrick Ruch
2004	—	`conf`	Report on the TREC 2004 Experiment: Genomics Track. TREC Patrick Ruch, Christine Chichester, Gilles Cohen, Frédéric Ehrler, Paul Fabry, Johan Marty, Henning Müller, Antoine Geissbühler
2004	—	`conf`	Using Argumentation to Retrieve Articles with Similar Citations from MEDLINE. NLPBA/BioNLP Imad Tbahriti, Christine Chichester, Frédérique Lisacek, Patrick Ruch
2003	—	`conf`	A Frame-based Representation of ICD-10. MIE Paul Fabry, Robert H. Baud, Patrick Ruch, Pierre Le Beux, Christian Lovis
2003	B	`conf`	Learning-Free Text Categorization. AIME Patrick Ruch, Robert H. Baud, Antoine Geissbühler
2003	—	`conf`	Report on the TREC 2003 Experiment: Genomic Track. TREC Patrick Ruch, Gilles Cohen, Frédéric Ehrler, Henning Müller, Giovanni Coray, Hatem Ghorbel, Vincenzo Pallotta, Christine Chichester
2003	—	`ed.`	The New Navigators: from Professionals to Patients - Proceedings of MIE2003, Saint Malo, France. MIE Robert H. Baud, Marius Fieschi, Pierre Le Beux, Patrick Ruch
2003	—	`conf`	Towards a Unified Medical Lexicon for French. MIE Pierre Zweigenbaum, Robert H. Baud, Anita Burgun, Fiammetta Namer, Éric Jarrousse, Natalia Grabar, Patrick Ruch, Franck Le Duff, Benoît Thirion, Stéfan Jacques Darmoni
2003	Misc	`conf`	UMLF: a Unified Medical Lexicon for French. AMIA Pierre Zweigenbaum, Robert H. Baud, Anita Burgun, Fiammetta Namer, Éric Jarrousse, Natalia Grabar, Patrick Ruch, Franck Le Duff, Benoît Thirion, Stéfan Jacques Darmoni
2003	J	`jnl`	Using lexical disambiguation and named-entity recognition to improve spelling correction in the electronic patient record. Artif. Intell. Medicine Patrick Ruch, Robert H. Baud, Antoine Geissbühler
2002	Misc	`conf`	Controlling the vocabulary for anatomy. AMIA Robert H. Baud, Christian Lovis, Anne-Marie Rassinoux, Patrick Ruch, Antoine Geissbühler
2002	J	`jnl`	Evaluating and reducing the effect of data corruption when applying bag of words approaches to medical records. Int. J. Medical Informatics Patrick Ruch, Robert H. Baud, Antoine Geissbühler
2002	Misc	`conf`	Information retrieval and spelling correction: an inquiry into lexical disambiguation. SAC Patrick Ruch
2002	J	`jnl`	The future of natural language processing for biomedical applications. Int. J. Medical Informatics Robert H. Baud, Patrick Ruch
2002	B	`conf`	Using Contextual Spelling Correction to Improve Retrieval Effectiveness in Degraded Text Collections. COLING Patrick Ruch
2001	Misc	`conf`	A light knowledge model for linguistic applications. AMIA Robert H. Baud, Christian Lovis, Patrick Ruch, Anne-Marie Rassinoux
2001	—	`conf`	Comparing General and Medical Texts for Information Retrieval Based on Natural Language Processing: An Inquiry into Lexical Disambiguation. MedInfo Patrick Ruch, Robert H. Baud, Antoine Geissbühler, Anne-Marie Rassinoux
2001	—	`conf`	Conceptual Search in Electronic Patient Record. MedInfo Robert H. Baud, Christian Lovis, Patrick Ruch, Anne-Marie Rassinoux
2001	Misc	`conf`	Looking back or looking all around: comparing two spell checking strategies for documents edition in an electronic patient record. AMIA Patrick Ruch, Robert H. Baud, Antoine Geissbühler, Christian Lovis, Anne-Marie Rassinoux, Alain Rivière
2001	B	`conf`	Toward filling the gap between interactive and fully-automatic spelling correction using the linguistic context. SMC Patrick Ruch, Robert H. Baud, Antoine Geissbühler
2001	B	`conf`	Using Part-of-Speech and Word-Sense Disambiguation for Boosting String-Edit Distance Spelling Correction. AIME Patrick Ruch, Robert H. Baud, Antoine Geissbühler, Christian Lovis, Anne-Marie Rassinoux, Alain Rivière
2000	Misc	`conf`	Medical document anonymization with a semantic lexicon. AMIA Patrick Ruch, Robert H. Baud, Anne-Marie Rassinoux, Pierrette Bouillon, Gilbert Robert
2000	—	`conf`	Minimal Commitment and Full Lexical Disambiguation: Balancing Rules and Hidden Markov Models. CoNLL/LLL Patrick Ruch, Robert H. Baud, Pierrette Bouillon, Gilbert Robert
2000	Misc	`conf`	Semantic handling of medical compound words through sound analysis and generation processes. AMIA Anne-Marie Rassinoux, Patrick Ruch, Robert H. Baud, Christian Lovis
1999	Misc	`conf`	MEDTAG: tag-like semantics for medical document indexing. AMIA Patrick Ruch, Judith C. Wagner, Pierrette Bouillon, Robert H. Baud, Anne-Marie Rassinoux, Jean-Raoul Scherrer
1999	Misc	`conf`	Model-based semantic dictionaries for medical language understanding. AMIA Anne-Marie Rassinoux, Robert H. Baud, Patrick Ruch, Béatrice Trombert Paviot, Jean Marie Rodrigues
1999	Misc	`conf`	The power and limits of a rule-based morpho-semantic parser. AMIA Robert H. Baud, Anne-Marie Rassinoux, Patrick Ruch, Christian Lovis, Jean-Raoul Scherrer