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2020 – today
- 2024
[c111]Luc Mottin
, Nona Naderi, Anaïs Mottaz, Pierre-André Michel, Lennart F. Johansson, Morris A. Swertz, Andrew Stubbs, Emilie Pasche, Julien Gobeill, Patrick Ruch:
Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants. MIE 2024: 1684-1688- 2023
- [j40]Emilie Pasche, Anaïs Mottaz, Julien Gobeill, Pierre-André Michel, Déborah Caucheteur, Nona Naderi, Patrick Ruch:
Assessing the use of supplementary materials to improve genomic variant discovery. Database J. Biol. Databases Curation 2023 (2023) - [j39]Déborah Caucheteur, Zoë May Pendlington, Paola Roncaglia, Julien Gobeill, Luc Mottin, Nicolas Matentzoglu, Donat Agosti, David Osumi-Sutherland, Helen E. Parkinson, Patrick Ruch:
COVoc and COVTriage: novel resources to support literature triage. Bioinform. 39(1) (2023) - [j38]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:
Multilingual RECIST classification of radiology reports using supervised learning. Frontiers Digit. Health 5 (2023) - 2022
- [c110]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:
Classification of oncology treatment responses from radiology reports with supervised machine learning. AMIA 2022 - [c109]Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Douglas Teodoro, Patrick Ruch:
Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service. MIE 2022: 839-843 - [c108]Jean-Philippe Goldman, Luc Mottin, Jamil Zaghir, Daniel Keszthelyi, Belinda Lokaj, Hugues Turbé, Julien Gobeill, Patrick Ruch, Julien Ehrsam, Christian Lovis:
Classification of Oncology Treatment Responses from French Radiology Reports with Supervised Machine Learning. MIE 2022: 849-853 - [c107]Nona Naderi, Anaïs Mottaz, Douglas Teodoro, Patrick Ruch:
Analyzing the Information Content of Text-Based Files in Supplementary Materials of Biomedical Literature. MIE 2022: 876-877 - 2021
- [j37]Nona Naderi, Julien Knafou, Jenny Copara, Patrick Ruch, Douglas Teodoro:
Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora. Frontiers Res. Metrics Anal. 6: 689803 (2021) - [j36]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:
UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49(Database-Issue): D480-D489 (2021) - [c106]Peter Cornwell, Donat Agosti, Laurence Benichou, Jose Benito Gonzalez Lopez, Madeleine Herren, Patrick Ruch:
Progress With Improving Preservation and Reuse of Scientific Research Data. iPRES 2021 - [c105]Déborah Caucheteur, Emilie Pasche, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch:
SIB Text Mining at TREC Clinical Trials 2021. TREC 2021 - 2020
- [j35]Douglas Teodoro, Julien Knafou, Nona Naderi, Emilie Pasche, Julien Gobeill, Cecilia N. Arighi, Patrick Ruch:
UPCLASS: a deep learning-based classifier for UniProtKB entry publications. Database J. Biol. Databases Curation 2020 (2020) - [j34]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:
DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 48(Database-Issue): D269-D276 (2020) - [j33]Julien Gobeill, Déborah Caucheteur, Pierre-André Michel, Luc Mottin, Emilie Pasche, Patrick Ruch:
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. Nucleic Acids Res. 48(Webserver-Issue): W12-W16 (2020) - [c104]Julien Knafou, Nona Naderi, Jenny Copara, Douglas Teodoro, Patrick Ruch:
BiTeM at WNUT 2020 Shared Task-1: Named Entity Recognition over Wet Lab Protocols using an Ensemble of Contextual Language Models. W-NUT@EMNLP 2020: 305-313 - [c103]Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro:
Named Entity Recognition in Chemical Patents using Ensemble of Contextual Language Models. CLEF (Working Notes) 2020 - [c102]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 Rk Rao, Sobha Lalitha Devi, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor:
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. CLEF (Working Notes) 2020 - [c101]Julien Gobeill, Patrick Ruch, Rodolphe Meyer:
Machine Learning for Automatic Encoding of French Electronic Medical Records: Is More Data Better? MIE 2020: 312-316 - [c100]Déborah Caucheteur, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Daniel J. Stekhoven, Valérie Barbié, Patrick Ruch:
Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. MIE 2020: 884-888 - [c99]Jenny Copara, Julien Knafou, Nona Naderi, Claudia Moro, Patrick Ruch, Douglas Teodoro:
Contextualized French Language Models for Biomedical Named Entity Recognition. JEP-TALN-RECITAL (DEFT) 2020: 36-48 - [c98]Julien Knafou, Matthew Jeffryes, Sohrab Ferdowsi, Patrick Ruch:
SIB Text Mining at TREC 2020 Deep Learning Track. TREC 2020 - [c97]Emilie Pasche, Déborah Caucheteur, Luc Mottin, Anaïs Mottaz, Julien Gobeill, Patrick Ruch:
SIB Text Mining at TREC Precision Medicine 2020. TREC 2020 - [i4]Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro:
Named entity recognition in chemical patents using ensemble of contextual language models. CoRR abs/2007.12569 (2020)
2010 – 2019
- 2019
- [c96]Julien Gobeill, Emilie Pasche, Patrick Ruch:
Retrieving the Evidence of a Free Text Annotation in a Scientific Article: A Data Free Approach. CICLing (1) 2019: 233-246 - [c95]Nona Naderi, Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch:
A Baseline Approach for Early Detection of Signs of Anorexia and Self-harm in Reddit Posts. CLEF (Working Notes) 2019 - [c94]Paul Van Rijen, Douglas Teodoro, Nona Naderi, Luc Mottin, Julien Knafou, Matt Jeffryes, Patrick Ruch:
A Data-Driven Approach for Measuring the Severity of the Signs of Depression using Reddit Posts. CLEF (Working Notes) 2019 - [c93]Déborah Caucheteur, Emilie Pasche, Julien Gobeill, Anaïs Mottaz, Luc Mottin, Patrick Ruch:
Designing retrieval models to contrast precision-driven ad hoc search vs. recall-driven treatment extraction in Precision Medicine. TREC 2019 - [c92]Julien Knafou, Matt Jeffryes, Luc Mottin, Douglas Teodoro, Patrick Ruch:
SIB Text Mining at TREC 2019 Deep Learning Track: Working Note. TREC 2019 - 2018
- [j32]Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch:
Overview of the BioCreative VI text-mining services for Kinome Curation Track. Database J. Biol. Databases Curation 2018: bay104 (2018) - [j31]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:
Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. Database J. Biol. Databases Curation 2018: bay129 (2018) - [c91]Julien Gobeill, Patrick Ruch:
Instance-based Learning for ICD10 Categorization. CLEF (Working Notes) 2018 - 2017
- [j30]Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Pierre-André Michel, Amos Bairoch, Pascale Gaudet, Patrick Ruch:
Triage by ranking to support the curation of protein interactions. Database J. Biol. Databases Curation 2017: bax040 (2017) - [j29]Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch:
Improving average ranking precision in user searches for biomedical research datasets. Database J. Biol. Databases Curation 2017: bax083 (2017) - [c90]Emilie Pasche, Julien Gobeill, Luc Mottin, Anaïs Mottaz, Douglas Teodoro, Paul Van Rijen, Patrick Ruch:
Customizing a Variant Annotation-Support Tool: an Inquiry into Probability Ranking Principles for TREC Precision Medicine. TREC 2017 - [i3]Arnaud Gaudinat, Jonas Beausire, Megan Fuss, Elisa Banfi, Julien Gobeill, Patrick Ruch:
Global picture of OAI-PMH repositories through the analysis of 6 key open archive meta-catalogs. CoRR abs/1708.08669 (2017) - [i2]Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch:
Improving average ranking precision in user searches for biomedical research datasets. CoRR abs/1709.03061 (2017) - 2016
- [j28]Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, Patrick Ruch:
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. Database J. Biol. Databases Curation 2016 (2016) - [c89]Célia Boyer, Ljiljana Dolamic, Patrick Ruch, Gilles Falquet:
Effect of the Named Entity Recognition and Sliding Window on the HONcode Automated Detection of HONcode Criteria for Mass Health Online Content. HEALTHINF 2016: 151-158 - [c88]Luc Mottin, Julien Gobeill, Anaïs Mottaz, Emilie Pasche, Arnaud Gaudinat, Patrick Ruch:
BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction. CLEF (Working Notes) 2016: 94-102 - [c87]Célia Boyer, Allan Hanbury, Patrick Ruch, Gilles Falquet:
Tools to Retrieve Reliable Health Information on the Internet - Improvements of the Automated Detection of HONcode Criteria for Mass Health Online Content. EPS 2016 - 2015
- [j27]Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Dina Vishnyakova, Pascale Gaudet, Amos Bairoch, Patrick Ruch:
Deep Question Answering for protein annotation. Database J. Biol. Databases Curation 2015 (2015) - [c86]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch:
Instance-Based Learning for Tweet Monitoring and Categorization. CLEF 2015: 235-240 - [c85]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch:
Exploiting incoming and outgoing citations for improving Information Retrieval in the TREC 2015 Clinical Decision Support Track. TREC 2015 - 2014
- [j26]Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch:
Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. Database J. Biol. Databases Curation 2014 (2014) - [j25]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:
Overview of the gene ontology task at BioCreative IV. Database J. Biol. Databases Curation 2014 (2014) - [j24]Emilie Pasche, Julien Gobeill, Olivier Kreim, Fatma Oezdemir-Zaech, Thérèse Vachon, Christian Lovis, Patrick Ruch:
Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinform. 15(S-1): S15 (2014) - [c84]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch:
Instance-based Learning for Tweet Categorization in CLEF RepLab 2014. CLEF (Working Notes) 2014: 1491-1499 - [c83]Dina Vishnyakova, Julien Gobeill, Fatma Oezdemir-Zaech, Olivier Kreim, Thérèse Vachon, Thierry Cladé, Xavier Haenning, Dmitri Mikhailov, Patrick Ruch:
Electronic Processing of Informed Consents in a Global Pharmaceutical Company Environment. MIE 2014: 995-999 - [c82]Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Patrick Ruch:
Full-texts representation with Medical Subject Headings, and co-citations network rerank- ing strategies for TREC 2014 Clinical Decision Support Track. TREC 2014 - 2013
- [j23]Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch:
Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database J. Biol. Databases Curation 2013 (2013) - [j22]Anne-Lise Veuthey, Alan J. Bridge, Julien Gobeill, Patrick Ruch, Johanna R. McEntyre, Lydie Bougueleret, Ioannis Xenarios:
Application of text-mining for updating protein post-translational modification annotation in UniProtKB. BMC Bioinform. 14: 104 (2013) - [c81]Dina Vishnyakova, Julien Gobeill, Patrick Ruch:
Using a Question-Answering Approach in Machine Reading Task of Biomedical Texts about the Alzheimer Disease. CLEF (Working Notes) 2013 - [c80]Dina Vishnyakova, Emilie Pasche, Christian Lovis, Patrick Ruch:
Utilization of Ontology Look-Up Services in Information Retrieval for Biomedical Literature. EFMI-STC 2013: 155-159 - [c79]Emilie Pasche, Julien Gobeill, Dina Vishnyakova, Patrick Ruch, Christian Lovis:
Use of Controlled Vocabularies to Improve Biomedical Information Retrieval Tasks. MedInfo 2013: 1068 - [c78]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:
Khresmoi - Multilingual Semantic Search of Medical Text and Images. MedInfo 2013: 1266 - 2012
- [j21]Dina Vishnyakova, Emilie Pasche, Patrick Ruch:
Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database. Database J. Biol. Databases Curation 2012 (2012) - [c77]Julien Gobeill, Patrick Ruch:
BiTeM Site Report for the Claims to Passage Task in CLEF-IP 2012. CLEF (Online Working Notes/Labs/Workshop) 2012 - [c76]Dina Vishnyakova, Emilie Pasche, Douglas Teodoro, Christian Lovis, Patrick Ruch:
Pathogens and Gene Product Normalization in the Biomedical Literature. EFMI-STC 2012: 89-93 - [c75]Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch:
A User-Friendly Tool for Medical-Related Patent Retrieval. EFMI-STC 2012: 121-125 - [c74]Emilie Pasche, Julien Gobeill, Douglas Teodoro, Arnaud Gaudinat, Dina Vishnyakova, Christian Lovis, Patrick Ruch:
An advanced search engine for patent analytics in medicinal chemistry. MIE 2012: 204-209 - [c73]Dina Vishnyakova, Emilie Pasche, Julien Gobeill, Arnaud Gaudinat, Christian Lovis, Patrick Ruch:
Classification and Prioritization of Biomedical Literature for the Comparative Toxicogenomics Database. MIE 2012: 210-214 - 2011
- [j20]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:
The gene normalization task in BioCreative III. BMC Bioinform. 12(S-8): S2 (2011) - [c72]Douglas Teodoro, Rémy Choquet, Daniel Schober, Giovanni Mels, Emilie Pasche, Patrick Ruch, Christian Lovis:
Interoperability Driven Integration of Biomedical Data Sources. MIE 2011: 185-189 - [c71]Emilie Pasche, Julien Gobeill, Douglas Teodoro, Dina Vishnyakova, Arnaud Gaudinat, Patrick Ruch, Christian Lovis:
Using Multimodal Mining to Drive Clinical Guidelines Development. MIE 2011: 477-481 - [c70]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM Group Report for TREC Chemical IR Track 2011. TREC 2011 - [c69]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM Group Report for TREC Medical Records Track 2011. TREC 2011 - 2010
- [j19]Patrick Ruch:
Literature-based Discovery. J. Assoc. Inf. Sci. Technol. 61(7): 1506-1508 (2010) - [c68]Douglas Teodoro, Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch, Christian Lovis:
Automatic Prior Art Searching and Patent Encoding at CLEF-IP '10. CLEF (Notebook Papers/LABs/Workshops) 2010 - [c67]Rémy Choquet, Douglas Teodoro, Giovanni Mels, Ariane Assélé Kama, Emilie Pasche, Patrick Ruch, Christian Lovis, Marie-Christine Jaulent:
Partage de Données Biomédicales sur le Web Sémantique. WSM@IC 2010: 3-12 - [c66]Douglas Teodoro, Emilie Pasche, Dina Vishnyakova, Julien Gobeill, Patrick Ruch, Christian Lovis:
Automatic IPC Encoding and Novelty Tracking for Effective Patent Mining. NTCIR 2010: 309-317 - [c65]Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
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 2010
2000 – 2009
- 2009
- [j18]Susanne M. Humphrey, Aurélie Névéol, Allen C. Browne, Julien Gobeill, Patrick Ruch, Stéfan Jacques Darmoni:
Comparing a rule-based versus statistical system for automatic categorization of MEDLINE documents according to biomedical specialty. J. Assoc. Inf. Sci. Technol. 60(12): 2530-2539 (2009) - [c64]Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis:
QA-driven Guidelines Generation for Bacteriotherapy. AMIA 2009 - [c63]Julien Gobeill, Emilie Pasche, Douglas Teodoro, Patrick Ruch:
Simple Pre and Post Processing Strategies for Patent Searching in CLEF Intellectual Property Track 2009. CLEF (1) 2009: 444-451 - [c62]Julien Gobeill, Douglas Theodoro, Emilie Pasche, Patrick Ruch:
Taking Benefit of Query and Document Expansion using MeSH Descriptors in Medical ImageCLEF 2009. CLEF (Working Notes) 2009 - [c61]Julien Gobeill, Douglas Theodoro, Patrick Ruch:
Exploring a Wide Range of Simple Pre and Post Processing Strategies for Patent Searching in CLEF IP 2009. CLEF (Working Notes) 2009 - [c60]Douglas Teodoro, Rémy Choquet, Emilie Pasche, Julien Gobeill, Christel Daniel, Patrick Ruch, Christian Lovis:
Biomedical Data Management: A Proposal Framework. MIE 2009: 175-179 - [c59]Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis:
Automatic Medical Knowledge Acquisition Using Question-Answering. MIE 2009: 569-573 - [c58]Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch:
Report on the TREC 2009 Experiments: Chemical IR Track. TREC 2009 - 2008
- [j17]Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Anaïs Mottaz, Anne-Lise Veuthey, Patrick Ruch:
Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. BMC Bioinform. 9(S-3) (2008) - [j16]Anaïs Mottaz, Yum Lina Yip, Patrick Ruch, Anne-Lise Veuthey:
Mapping proteins to disease terminologies: from UniProt to MeSH. BMC Bioinform. 9(S-5) (2008) - [j15]Patrick Ruch, Julien Gobeill, Christian Lovis, Antoine Geissbühler:
Automatic medical encoding with SNOMED categories. BMC Medical Informatics Decis. Mak. 8(S-1): S6 (2008) - [c57]Patrick Ruch, Julien Gobeill, Imad Tbahriti, Antoine Geissbühler:
From Episodes of Care to Diagnosis Codes: Automatic Text Categorization for Medico-Economic Encoding. AMIA 2008 - [c56]Julien Gobeill, Patrick Ruch:
First Participation of University and Hospitals of Geneva to Domain-Specific Track in CLEF 2008. CLEF (Working Notes) 2008 - [c55]Julien Gobeill, Patrick Ruch, Xin Zhou:
Query and Document Expansion with Medical Subject Headings Terms at Medical Imageclef 2008. CLEF 2008: 736-743 - [c54]Julien Gobeill, Patrick Ruch, Xin Zhou:
Text-only Cross-language Image Search at Medical ImageCLEF 2008. CLEF (Working Notes) 2008 - 2007
- [j14]Samir Abdou, Patrick Ruch, Jacques Savoy:
Recherche d'information dans MEDLINE. Document Numérique 10(1): 131-151 (2007) - [j13]Patrick Ruch, Célia Boyer, Christine Chichester, Imad Tbahriti, Antoine Geissbühler, Paul Fabry, Julien Gobeill, Violaine Pillet, Dietrich Rebholz-Schuhmann, Christian Lovis, Anne-Lise Veuthey:
Using argumentation to extract key sentences from biomedical abstracts. Int. J. Medical Informatics 76(2-3): 195-200 (2007) - [j12]Anaïs Mottaz, Yum Lina Yip, Patrick Ruch, Anne-Lise Veuthey:
Mapping protein information to disease terminologies. J. Integr. Bioinform. 4(3) (2007) - [c53]Frédéric Ehrler, Patrick Ruch:
Unsupervised Documents Categorization Using New Threshold-Sensitive Weighting Technique. AIME 2007: 247-251 - [c52]Xin Zhou, Julien Gobeill, Patrick Ruch, Henning Müller:
University and Hospitals of Geneva Participating at ImageCLEF 2007. CLEF 2007: 649-656 - [c51]Xin Zhou, Julien Gobeill, Patrick Ruch, Henning Müller:
University and Hospitals of Geneva at ImageCLEF 2007. CLEF (Working Notes) 2007 - [c50]Imad Tbahriti, Anne-Lise Veuthey, Patrick Ruch, Julien Gobeill:
Recherche d'information et analyse bibliographique appliquées à la mise à jour automatique de Swiss-Prot. CORIA 2007: 319-334 - [c49]Jimison Iavindrasana, Adrien Depeursinge, Patrick Ruch, Stéphane Spahni, Antoine Geissbühler, Henning Müller:
Design of a Decentralized Reusable Research Database Architecture to Support Data Acquisition in Large Research Projects. MedInfo 2007: 325-329 - [c48]Frédéric Ehrler, Patrick Ruch, Antoine Geissbühler, Christian Lovis:
Challenges and Methodology for Indexing the Computerized Patient Record. MedInfo 2007: 417-421 - [c47]Patrick Ruch, Antoine Geissbühler, Julien Gobeill, Frédéric Lisacek, Imad Tbahriti, Anne-Lise Veuthey, Alan R. Aronson:
Using Discourse Analysis to Improve Text Categorization in MEDLINE. MedInfo 2007: 710-715 - [c46]Robert H. Baud, Werner Ceusters, Patrick Ruch, Anne-Marie Rassinoux, Christian Lovis, Antoine Geissbühler:
Reconciliation of Ontology and Terminology to Cope with Linguistics. MedInfo 2007: 796-801 - [c45]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:
Combining Resources to Find Answers to Biomedical Questions. TREC 2007 - [c44]Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Patrick Ruch:
Vocabulary-Driven Passage Retrieval for Question-Answering in Genomics. TREC 2007 - 2006
- [j11]Patrick Ruch:
Automatic assignment of biomedical categories: toward a generic approach. Bioinform. 22(6): 658-664 (2006) - [j10]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:
Health search engine with e-document analysis for reliable search results. Int. J. Medical Informatics 75(1): 73-85 (2006) - [j9]Nigel Collier, Adeline Nazarenko, Robert H. Baud, Patrick Ruch:
Recent advances in natural language processing for biomedical applications. Int. J. Medical Informatics 75(6): 413-417 (2006) - [j8]Imad Tbahriti, Christine Chichester, Frédérique Lisacek, Patrick Ruch:
Using argumentation to retrieve articles with similar citations: An inquiry into improving related articles search in the MEDLINE digital library. Int. J. Medical Informatics 75(6): 488-495 (2006) - [j7]Paul Fabry, Robert H. Baud, Patrick Ruch, Christelle Despont-Gros, Christian Lovis:
Methodology to ease the construction of a terminology of problems. Int. J. Medical Informatics 75(8): 624-632 (2006) - [j6]William R. Hersh, Henning Müller, Jeffery R. Jensen, Jianji Yang, Paul N. Gorman, Patrick Ruch:
Model Formulation: Advancing Biomedical Image Retrieval: Development and Analysis of a Test Collection. J. Am. Medical Informatics Assoc. 13(5): 488-496 (2006) - [c43]Patrick Ruch, Imad Tbahriti, Julien Gobeill, Alan R. Aronson:
Argumentative Feedback: A Linguistically-Motivated Term Expansion for Information Retrieval. ACL 2006 - [c42]Julien Gobeill, Henning Müller, Patrick Ruch:
Translation by Text Categorisation: Medical Image Retrieval in ImageCLEFmed 2006. CLEF 2006: 706-710 - [c41]Julien Gobeill, Henning Müller, Patrick Ruch:
Query and Document Translation by Automatic Text Categorization: A Simple Approach to Establish a Strong Textual Baseline for ImageCLEFmed 2006. CLEF (Working Notes) 2006 - [c40]Samir Abdou, Jacques Savoy, Patrick Ruch:
Dépister efficacement de l'information dans une banque documentaire : L'exemple de MEDLINE. INFORSID 2006: 129-143 - [c39]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:
Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort. TREC 2006 - [c38]Patrick Ruch, Frédéric Ehrler, Julien Gobeill, Imad Tbahriti, Antonio Jimeno-Yepes:
Report on the TREC 2006 Experiment: Genomics Track. TREC 2006 - 2005
- [j5]Frédéric Ehrler, Antoine Geissbühler, Antonio Jimeno-Yepes, Patrick Ruch:
Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot. BMC Bioinform. 6(S-1) (2005) - [j4]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:
UMLF: a unified medical lexicon for French. Int. J. Medical Informatics 74(2-4): 119-124 (2005) - [c37]Patrick Ruch, Robert H. Baud, Johan Marty, Antoine Geissbühler, Imad Tbahriti, Anne-Lise Veuthey:
Latent Argumentative Pruning for Compact MEDLINE Indexing. AIME 2005: 246-250 - [c36]Henning Müller, Antoine Geissbühler, Johan Marty, Christian Lovis, Patrick Ruch:
The Use of MedGIFT and EasyIR for ImageCLEF 2005. CLEF 2005: 724-732 - [c35]Henning Müller, Antoine Geissbühler, Johan Marty, Christian Lovis, Patrick Ruch:
Using medGIFT and easyIR for the ImageCLEF 2005 Evaluation Tasks. CLEF (Working Notes) 2005 - [c34]Patrick Ruch, Laura Perret, Jacques Savoy:
Features Combination for Extracting Gene Functions from MEDLINE. ECIR 2005: 112-126 - [c33]Gilles Cohen, Patrick Ruch, Melanie Hilario:
Model Selection for Support Vector Classifiers via Direct Simplex Search. FLAIRS 2005: 431-435 - [c32]Patrick Ruch, Robert H. Baud, Christine Chichester, Antoine Geissbühler, Frédérique Lisacek, Johan Marty, Dietrich Rebholz-Schuhmann, Imad Tbahriti, Anne-Lise Veuthey:
Extracting Key Sentences with Latent Argumentative Structuring. MIE 2005: 835-840 - [c31]Samir Abdou, Jacques Savoy, Patrick Ruch:
Evaluation of Stemming, Query Expansion and Manual Indexing Approaches for the Genomic Task. TREC 2005 - [c30]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:
Fusion of Knowledge-Intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents. TREC 2005 - [c29]Patrick Ruch, Frédéric Ehrler, Samir Abdou, Jacques Savoy:
Report on the TREC 2005 Experiment: Genomics Track. TREC 2005 - 2004
- [c28]Imad Tbahriti, Christine Chichester, Frédérique Lisacek, Patrick Ruch:
Using Argumentation to Retrieve Articles with Similar Citations from MEDLINE. NLPBA/BioNLP 2004 - [c27]Henning Müller, Antoine Geissbühler, Patrick Ruch:
Report on the ImageCLEF Experiment: How to Visually Retrieve Images from the St. Andrews Collection using GIFT. CLEF (Working Notes) 2004 - [c26]Henning Müller, Antoine Geissbühler, Patrick Ruch:
Report on the CLEF Experiment: Combining Image and Multilingual Search for Medical Image Retrieval. CLEF (Working Notes) 2004 - [c25]Henning Müller, Antoine Geissbühler, Patrick Ruch:
ImageCLEF 2004: Combining Image and Multi-lingual Search for Medical Image Retrieval. CLEF 2004: 718-727 - [c24]Patrick Ruch:
Query Translation by Text Categorization. COLING 2004 - [c23]Vincenzo Pallotta, Hatem Ghorbel, Patrick Ruch, Giovanni Coray:
An Argumentative Annotation Schema for Meeting Discussions. LREC 2004 - [c22]Robert H. Baud, Patrick Ruch, Arnaud Gaudinat, Paul Fabry, Christian Lovis, Antoine Geissbühler:
Coping with the Variability of Medical Terms. MedInfo 2004: 322-326 - [c21]Patrick Ruch, Christine Chichester, Gilles Cohen, Frédéric Ehrler, Paul Fabry, Johan Marty, Henning Müller, Antoine Geissbühler:
Report on the TREC 2004 Experiment: Genomics Track. TREC 2004 - [e2]Nigel Collier, Patrick Ruch, Adeline Nazarenko:
Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications, NLPBA/BioNLP 2004, Geneva, Switzerland, August 28-29, 2004. 2004 [contents] - [i1]Vincenzo Pallotta, Hatem Ghorbel, Patrick Ruch, Giovanni Coray:
An argumentative annotation schema for meeting discussions. CoRR cs.CL/0410061 (2004) - 2003
- [j3]Patrick Ruch, Robert H. Baud, Antoine Geissbühler:
Using lexical disambiguation and named-entity recognition to improve spelling correction in the electronic patient record. Artif. Intell. Medicine 29(1-2): 169-184 (2003) - [c20]Patrick Ruch, Robert H. Baud, Antoine Geissbühler:
Learning-Free Text Categorization. AIME 2003: 199-208 - [c19]Pierre Zweigenbaum, Robert H. Baud, Anita Burgun, Fiammetta Namer, Éric Jarrousse, Natalia Grabar, Patrick Ruch, Franck Le Duff, Benoît Thirion, Stéfan Jacques Darmoni:
UMLF: a Unified Medical Lexicon for French. AMIA 2003 - [c18]Pierre Zweigenbaum, Robert H. Baud, Anita Burgun, Fiammetta Namer, Éric Jarrousse, Natalia Grabar, Patrick Ruch, Franck Le Duff, Benoît Thirion, Stéfan Jacques Darmoni:
Towards a Unified Medical Lexicon for French. MIE 2003: 415-420 - [c17]Paul Fabry, Robert H. Baud, Patrick Ruch, Pierre Le Beux, Christian Lovis:
A Frame-based Representation of ICD-10. MIE 2003: 433-438 - [c16]Patrick Ruch, Gilles Cohen, Frédéric Ehrler, Henning Müller, Giovanni Coray, Hatem Ghorbel, Vincenzo Pallotta, Christine Chichester:
Report on the TREC 2003 Experiment: Genomic Track. TREC 2003: 756-761 - [e1]Robert H. Baud, Marius Fieschi, Pierre Le Beux, Patrick Ruch:
The New Navigators: from Professionals to Patients - Proceedings of MIE2003, Saint Malo, France. Studies in Health Technology and Informatics 95, IOS Press 2003, ISBN 978-1-58603-347-7 [contents] - 2002
- [j2]Robert H. Baud, Patrick Ruch:
The future of natural language processing for biomedical applications. Int. J. Medical Informatics 67(1-3): 1-5 (2002) - [j1]Patrick Ruch, Robert H. Baud, Antoine Geissbühler:
Evaluating and reducing the effect of data corruption when applying bag of words approaches to medical records. Int. J. Medical Informatics 67(1-3): 75-83 (2002) - [c15]Robert H. Baud, Christian Lovis, Anne-Marie Rassinoux, Patrick Ruch, Antoine Geissbühler:
Controlling the vocabulary for anatomy. AMIA 2002 - [c14]Patrick Ruch:
Using Contextual Spelling Correction to Improve Retrieval Effectiveness in Degraded Text Collections. COLING 2002 - [c13]Patrick Ruch:
Information retrieval and spelling correction: an inquiry into lexical disambiguation. SAC 2002: 699-703 - 2001
- [c12]Patrick Ruch, Robert H. Baud, Antoine Geissbühler, Christian Lovis, Anne-Marie Rassinoux, Alain Rivière:
Using Part-of-Speech and Word-Sense Disambiguation for Boosting String-Edit Distance Spelling Correction. AIME 2001: 249-257 - [c11]Robert H. Baud, Christian Lovis, Patrick Ruch, Anne-Marie Rassinoux:
A light knowledge model for linguistic applications. AMIA 2001 - [c10]Patrick Ruch, Robert H. Baud, Antoine Geissbühler, Christian Lovis, Anne-Marie Rassinoux, Alain Rivière:
Looking back or looking all around: comparing two spell checking strategies for documents edition in an electronic patient record. AMIA 2001 - [c9]Robert H. Baud, Christian Lovis, Patrick Ruch, Anne-Marie Rassinoux:
Conceptual Search in Electronic Patient Record. MedInfo 2001: 156-160 - [c8]Patrick Ruch, Robert H. Baud, Antoine Geissbühler, Anne-Marie Rassinoux:
Comparing General and Medical Texts for Information Retrieval Based on Natural Language Processing: An Inquiry into Lexical Disambiguation. MedInfo 2001: 261-265 - [c7]Patrick Ruch, Robert H. Baud, Antoine Geissbühler:
Toward filling the gap between interactive and fully-automatic spelling correction using the linguistic context. SMC 2001: 199-204 - 2000
- [c6]Anne-Marie Rassinoux, Patrick Ruch, Robert H. Baud, Christian Lovis:
Semantic handling of medical compound words through sound analysis and generation processes. AMIA 2000 - [c5]Patrick Ruch, Robert H. Baud, Anne-Marie Rassinoux, Pierrette Bouillon, Gilbert Robert:
Medical document anonymization with a semantic lexicon. AMIA 2000 - [c4]Patrick Ruch, Robert H. Baud, Pierrette Bouillon, Gilbert Robert:
Minimal Commitment and Full Lexical Disambiguation: Balancing Rules and Hidden Markov Models. CoNLL/LLL 2000: 111-114
1990 – 1999
- 1999
- [c3]Robert H. Baud, Anne-Marie Rassinoux, Patrick Ruch, Christian Lovis, Jean-Raoul Scherrer:
The power and limits of a rule-based morpho-semantic parser. AMIA 1999 - [c2]Anne-Marie Rassinoux, Robert H. Baud, Patrick Ruch, Béatrice Trombert Paviot, Jean Marie Rodrigues:
Model-based semantic dictionaries for medical language understanding. AMIA 1999 - [c1]Patrick Ruch, Judith C. Wagner, Pierrette Bouillon, Robert H. Baud, Anne-Marie Rassinoux, Jean-Raoul Scherrer:
MEDTAG: tag-like semantics for medical document indexing. AMIA 1999
Coauthor Index
[c111] [j40] [j39] [j38] [c110] [c108] [c105] [j35] [j34] [j33] [c101] [c100] [c97] [c96] [c95] [c93] [j32] [j31] [c91] [j30] [j29] [c90] [i3] [i2] [j28] [c88] [j27] [c86] [c85] [j26] [j25] [j24] [c84] [c83] [c82] [j23] [j22] [c81] [c79] [c78] [c77] [c75] [c74] [c73] [c71] [c70] [c69] [c68] [c66] [c65] [j18] [c64] [c63] [c62] [c61] [c60] [c59] [c58] [j17] [j15] [c57] [c56] [c55] [c54] [j13] [c52] [c51] [c50] [c47] [c44] [c43] [c42] [c41] [c38]
Douglas Teodoro
aka: Douglas Theodoro
aka: Douglas Theodoro
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