The power and limits of a rule-based morpho-semantic parser. - Robert H. Baud; Anne-Marie Rassinoux; Patrick Ruch; Christian Lovis; Jean-Raoul Scherrer (AMIA, 1999)

Model-based semantic dictionaries for medical language understanding. - Anne-Marie Rassinoux; Robert H. Baud; Patrick Ruch; Béatrice Trombert Paviot; Jean Marie Rodrigues (AMIA, 1999)

MEDTAG: tag-like semantics for medical document indexing. - Patrick Ruch; Judith C. Wagner; Pierrette Bouillon; Robert H. Baud; Anne-Marie Rassinoux; Jean-Raoul Scherrer (AMIA, 1999)

Semantic handling of medical compound words through sound analysis and generation processes. - Anne-Marie Rassinoux; Patrick Ruch; Robert H. Baud; Christian Lovis (AMIA, 2000)

Medical document anonymization with a semantic lexicon. - Patrick Ruch; Robert H. Baud; Anne-Marie Rassinoux; Pierrette Bouillon; Gilbert Robert (AMIA, 2000)

Minimal Commitment and Full Lexical Disambiguation: Balancing Rules and Hidden Markov Models. - Patrick Ruch; Robert H. Baud; Pierrette Bouillon; Gilbert Robert (CoNLL/LLL, 2000)

Using Part-of-Speech and Word-Sense Disambiguation for Boosting String-Edit Distance Spelling Correction. - Patrick Ruch; Robert H. Baud; Antoine Geissbühler; Christian Lovis; Anne-Marie Rassinoux; Alain Rivière (AIME, 2001)

A light knowledge model for linguistic applications. - Robert H. Baud; Christian Lovis; Patrick Ruch; Anne-Marie Rassinoux (AMIA, 2001)

Looking back or looking all around: comparing two spell checking strategies for documents edition in an electronic patient record. - Patrick Ruch; Robert H. Baud; Antoine Geissbühler; Christian Lovis; Anne-Marie Rassinoux; Alain Rivière (AMIA, 2001)

Conceptual Search in Electronic Patient Record. - Robert H. Baud; Christian Lovis; Patrick Ruch; Anne-Marie Rassinoux (MedInfo, 2001)

Comparing General and Medical Texts for Information Retrieval Based on Natural Language Processing: An Inquiry into Lexical Disambiguation. - Patrick Ruch; Robert H. Baud; Antoine Geissbühler; Anne-Marie Rassinoux (MedInfo, 2001)

Toward filling the gap between interactive and fully-automatic spelling correction using the linguistic context. - Patrick Ruch; Robert H. Baud; Antoine Geissbühler (SMC, 2001)

Controlling the vocabulary for anatomy. - Robert H. Baud; Christian Lovis; Anne-Marie Rassinoux; Patrick Ruch; Antoine Geissbühler (AMIA, 2002)

Using Contextual Spelling Correction to Improve Retrieval Effectiveness in Degraded Text Collections. - Patrick Ruch (COLING, 2002)

Information retrieval and spelling correction: an inquiry into lexical disambiguation. - Patrick Ruch (SAC, 2002)

The future of natural language processing for biomedical applications. - Robert H. Baud; Patrick Ruch (Int. J. Medical Informatics, 2002)

Evaluating and reducing the effect of data corruption when applying bag of words approaches to medical records. - Patrick Ruch; Robert H. Baud; Antoine Geissbühler (Int. J. Medical Informatics, 2002)

Learning-Free Text Categorization. - Patrick Ruch; Robert H. Baud; Antoine Geissbühler (AIME, 2003)

UMLF: a Unified Medical Lexicon for French. - Pierre Zweigenbaum; Robert H. Baud; Anita Burgun; Fiammetta Namer; Éric Jarrousse; Natalia Grabar; Patrick Ruch; Franck Le Duff; Benoît Thirion; Stéfan Jacques Darmoni (AMIA, 2003)

A Frame-based Representation of ICD-10. - Paul Fabry; Robert H. Baud; Patrick Ruch; Pierre Le Beux; Christian Lovis (MIE, 2003)

Towards a Unified Medical Lexicon for French. - Pierre Zweigenbaum; Robert H. Baud; Anita Burgun; Fiammetta Namer; Éric Jarrousse; Natalia Grabar; Patrick Ruch; Franck Le Duff; Benoît Thirion; Stéfan Jacques Darmoni (MIE, 2003)

Report on the TREC 2003 Experiment: Genomic Track. - Patrick Ruch; Gilles Cohen; Frédéric Ehrler; Henning Müller; Giovanni Coray; Hatem Ghorbel; Vincenzo Pallotta; Christine Chichester (TREC, 2003)

Using lexical disambiguation and named-entity recognition to improve spelling correction in the electronic patient record. - Patrick Ruch; Robert H. Baud; Antoine Geissbühler (Artif. Intell. Medicine, 2003)

Using Argumentation to Retrieve Articles with Similar Citations from MEDLINE. - Imad Tbahriti; Christine Chichester; Frédérique Lisacek; Patrick Ruch (NLPBA/BioNLP, 2004)

Report on the ImageCLEF Experiment: How to Visually Retrieve Images from the St. Andrews Collection using GIFT. - Henning Müller; Antoine Geissbühler; Patrick Ruch (CLEF (Working Notes), 2004)

Report on the CLEF Experiment: Combining Image and Multilingual Search for Medical Image Retrieval. - Henning Müller; Antoine Geissbühler; Patrick Ruch (CLEF (Working Notes), 2004)

ImageCLEF 2004: Combining Image and Multi-lingual Search for Medical Image Retrieval. - Henning Müller; Antoine Geissbühler; Patrick Ruch (CLEF, 2004)

Query Translation by Text Categorization. - Patrick Ruch (COLING, 2004)

An Argumentative Annotation Schema for Meeting Discussions. - Vincenzo Pallotta; Hatem Ghorbel; Patrick Ruch; Giovanni Coray (LREC, 2004)

Coping with the Variability of Medical Terms. - Robert H. Baud; Patrick Ruch; Arnaud Gaudinat; Paul Fabry; Christian Lovis; Antoine Geissbühler (MedInfo, 2004)

Report on the TREC 2004 Experiment: Genomics Track. - Patrick Ruch; Christine Chichester; Gilles Cohen; Frédéric Ehrler; Paul Fabry; Johan Marty; Henning Müller; Antoine Geissbühler (TREC, 2004)

Latent Argumentative Pruning for Compact MEDLINE Indexing. - Patrick Ruch; Robert H. Baud; Johan Marty; Antoine Geissbühler; Imad Tbahriti; Anne-Lise Veuthey (AIME, 2005)

The Use of MedGIFT and EasyIR for ImageCLEF 2005. - Henning Müller; Antoine Geissbühler; Johan Marty; Christian Lovis; Patrick Ruch (CLEF, 2005)

Using medGIFT and easyIR for the ImageCLEF 2005 Evaluation Tasks. - Henning Müller; Antoine Geissbühler; Johan Marty; Christian Lovis; Patrick Ruch (CLEF (Working Notes), 2005)

Features Combination for Extracting Gene Functions from MEDLINE. - Patrick Ruch; Laura Perret; Jacques Savoy (ECIR, 2005)

Model Selection for Support Vector Classifiers via Direct Simplex Search. - Gilles Cohen; Patrick Ruch; Melanie Hilario (FLAIRS, 2005)

Extracting Key Sentences with Latent Argumentative Structuring. - Patrick Ruch; Robert H. Baud; Christine Chichester; Antoine Geissbühler; Frédérique Lisacek; Johan Marty; Dietrich Rebholz-Schuhmann; Imad Tbahriti; Anne-Lise Veuthey (MIE, 2005)

Evaluation of Stemming, Query Expansion and Manual Indexing Approaches for the Genomic Task. - Samir Abdou; Jacques Savoy; Patrick Ruch (TREC, 2005)

Fusion of Knowledge-Intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents. - 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 (TREC, 2005)

Report on the TREC 2005 Experiment: Genomics Track. - Patrick Ruch; Frédéric Ehrler; Samir Abdou; Jacques Savoy (TREC, 2005)

Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot. - Frédéric Ehrler; Antoine Geissbühler; Antonio Jimeno-Yepes; Patrick Ruch (BMC Bioinform., 2005)

UMLF: a unified medical lexicon for French. - 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 (Int. J. Medical Informatics, 2005)

Argumentative Feedback: A Linguistically-Motivated Term Expansion for Information Retrieval. - Patrick Ruch; Imad Tbahriti; Julien Gobeill; Alan R. Aronson (ACL, 2006)

Translation by Text Categorisation: Medical Image Retrieval in ImageCLEFmed 2006. - Julien Gobeill; Henning Müller; Patrick Ruch (CLEF, 2006)

Query and Document Translation by Automatic Text Categorization: A Simple Approach to Establish a Strong Textual Baseline for ImageCLEFmed 2006. - Julien Gobeill; Henning Müller; Patrick Ruch (CLEF (Working Notes), 2006)

Dépister efficacement de l'information dans une banque documentaire : L'exemple de MEDLINE. - Samir Abdou; Jacques Savoy; Patrick Ruch (INFORSID, 2006)

Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort. - 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 (TREC, 2006)

Report on the TREC 2006 Experiment: Genomics Track. - Patrick Ruch; Frédéric Ehrler; Julien Gobeill; Imad Tbahriti; Antonio Jimeno-Yepes (TREC, 2006)

Automatic assignment of biomedical categories: toward a generic approach. - Patrick Ruch (Bioinform., 2006)

Recent advances in natural language processing for biomedical applications. - Nigel Collier; Adeline Nazarenko; Robert H. Baud; Patrick Ruch (Int. J. Medical Informatics, 2006)

Methodology to ease the construction of a terminology of problems. - Paul Fabry; Robert H. Baud; Patrick Ruch; Christelle Despont-Gros; Christian Lovis (Int. J. Medical Informatics, 2006)

Health search engine with e-document analysis for reliable search results. - 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; et al. (Int. J. Medical Informatics, 2006)

Using argumentation to retrieve articles with similar citations: An inquiry into improving related articles search in the MEDLINE digital library. - Imad Tbahriti; Christine Chichester; Frédérique Lisacek; Patrick Ruch (Int. J. Medical Informatics, 2006)

Model Formulation: Advancing Biomedical Image Retrieval: Development and Analysis of a Test Collection. - William R. Hersh; Henning Müller; Jeffery R. Jensen; Jianji Yang; Paul N. Gorman; Patrick Ruch (J. Am. Medical Informatics Assoc., 2006)

Unsupervised Documents Categorization Using New Threshold-Sensitive Weighting Technique. - Frédéric Ehrler; Patrick Ruch (AIME, 2007)

University and Hospitals of Geneva Participating at ImageCLEF 2007. - Xin Zhou 002; Julien Gobeill; Patrick Ruch; Henning Müller (CLEF, 2007)

University and Hospitals of Geneva at ImageCLEF 2007. - Xin Zhou 002; Julien Gobeill; Patrick Ruch; Henning Müller (CLEF (Working Notes), 2007)

Recherche d'information et analyse bibliographique appliquées à la mise à jour automatique de Swiss-Prot. - Imad Tbahriti; Anne-Lise Veuthey; Patrick Ruch; Julien Gobeill (CORIA, 2007)

Reconciliation of Ontology and Terminology to Cope with Linguistics. - Robert H. Baud; Werner Ceusters; Patrick Ruch; Anne-Marie Rassinoux; Christian Lovis; Antoine Geissbühler (MedInfo, 2007)

Challenges and Methodology for Indexing the Computerized Patient Record. - Frédéric Ehrler; Patrick Ruch; Antoine Geissbühler; Christian Lovis (MedInfo, 2007)

Design of a Decentralized Reusable Research Database Architecture to Support Data Acquisition in Large Research Projects. - Jimison Iavindrasana; Adrien Depeursinge; Patrick Ruch; Stéphane Spahni; Antoine Geissbühler; Henning Müller (MedInfo, 2007)

Using Discourse Analysis to Improve Text Categorization in MEDLINE. - Patrick Ruch; Antoine Geissbühler; Julien Gobeill; Frédéric Lisacek; Imad Tbahriti; Anne-Lise Veuthey; Alan R. Aronson (MedInfo, 2007)

Combining Resources to Find Answers to Biomedical Questions. - 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 (TREC, 2007)

Vocabulary-Driven Passage Retrieval for Question-Answering in Genomics. - Julien Gobeill; Imad Tbahriti; Frédéric Ehrler; Patrick Ruch (TREC, 2007)

Recherche d'information dans MEDLINE. - Samir Abdou; Patrick Ruch; Jacques Savoy (Document Numérique, 2007)

Using argumentation to extract key sentences from biomedical abstracts. - Patrick Ruch; Célia Boyer; Christine Chichester; Imad Tbahriti; Antoine Geissbühler; Paul Fabry; Julien Gobeill; Violaine Pillet; Dietrich Rebholz-Schuhmann; Christian Lovis; Anne-Lise Veuthey (Int. J. Medical Informatics, 2007)

Mapping protein information to disease terminologies. - Anaïs Mottaz; Yum Lina Yip; Patrick Ruch; Anne-Lise Veuthey (J. Integr. Bioinform., 2007)

From Episodes of Care to Diagnosis Codes: Automatic Text Categorization for Medico-Economic Encoding. - Patrick Ruch; Julien Gobeill; Imad Tbahriti; Antoine Geissbühler (AMIA, 2008)

First Participation of University and Hospitals of Geneva to Domain-Specific Track in CLEF 2008. - Julien Gobeill; Patrick Ruch (CLEF (Working Notes), 2008)

Query and Document Expansion with Medical Subject Headings Terms at Medical Imageclef 2008. - Julien Gobeill; Patrick Ruch; Xin Zhou 002 (CLEF, 2008)

Text-only Cross-language Image Search at Medical ImageCLEF 2008. - Julien Gobeill; Patrick Ruch; Xin Zhou 002 (CLEF (Working Notes), 2008)

Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. - Julien Gobeill; Imad Tbahriti; Frédéric Ehrler; Anaïs Mottaz; Anne-Lise Veuthey; Patrick Ruch (BMC Bioinform., 2008)

Mapping proteins to disease terminologies: from UniProt to MeSH. - Anaïs Mottaz; Yum Lina Yip; Patrick Ruch; Anne-Lise Veuthey (BMC Bioinform., 2008)

Automatic medical encoding with SNOMED categories. - Patrick Ruch; Julien Gobeill; Christian Lovis; Antoine Geissbühler (BMC Medical Informatics Decis. Mak., 2008)

QA-driven Guidelines Generation for Bacteriotherapy. - Emilie Pasche; Douglas Teodoro; Julien Gobeill; Patrick Ruch; Christian Lovis (AMIA, 2009)

Simple Pre and Post Processing Strategies for Patent Searching in CLEF Intellectual Property Track 2009. - Julien Gobeill; Emilie Pasche; Douglas Teodoro; Patrick Ruch (CLEF (1), 2009)

Taking Benefit of Query and Document Expansion using MeSH Descriptors in Medical ImageCLEF 2009. - Julien Gobeill; Douglas Theodoro; Emilie Pasche; Patrick Ruch (CLEF (Working Notes), 2009)

Exploring a Wide Range of Simple Pre and Post Processing Strategies for Patent Searching in CLEF IP 2009. - Julien Gobeill; Douglas Theodoro; Patrick Ruch (CLEF (Working Notes), 2009)

Automatic Medical Knowledge Acquisition Using Question-Answering. - Emilie Pasche; Douglas Teodoro; Julien Gobeill; Patrick Ruch; Christian Lovis (MIE, 2009)

Biomedical Data Management: A Proposal Framework. - Douglas Teodoro; Rémy Choquet; Emilie Pasche; Julien Gobeill; Christel Daniel; Patrick Ruch; Christian Lovis (MIE, 2009)

Report on the TREC 2009 Experiments: Chemical IR Track. - Julien Gobeill; Douglas Teodoro; Emilie Pasche; Patrick Ruch (TREC, 2009)

Comparing a rule-based versus statistical system for automatic categorization of MEDLINE documents according to biomedical specialty. - Susanne M. Humphrey; Aurélie Névéol; Allen C. Browne; Julien Gobeill; Patrick Ruch; Stéfan Jacques Darmoni (J. Assoc. Inf. Sci. Technol., 2009)

Automatic Prior Art Searching and Patent Encoding at CLEF-IP '10. - Douglas Teodoro; Julien Gobeill; Emilie Pasche; Dina Vishnyakova; Patrick Ruch; Christian Lovis (CLEF (Notebook Papers/LABs/Workshops), 2010)

Partage de Données Biomédicales sur le Web Sémantique. - Rémy Choquet; Douglas Teodoro; Giovanni Mels; Ariane Assélé Kama; Emilie Pasche; Patrick Ruch; Christian Lovis; Marie-Christine Jaulent (WSM@IC, 2010)

Automatic IPC Encoding and Novelty Tracking for Effective Patent Mining. - Douglas Teodoro; Emilie Pasche; Dina Vishnyakova; Julien Gobeill; Patrick Ruch; Christian Lovis (NTCIR, 2010)

BiTeM site Report for TREC Chemistry 2010: Impact of Citations Feeback for Patent Prior Art Search and Chemical Compounds Expansion for Ad Hoc Retrieval. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch; Emilie Pasche; Douglas Teodoro; Dina Vishnyakova (TREC, 2010)

Literature-based Discovery. - Patrick Ruch (J. Assoc. Inf. Sci. Technol., 2010)

Using Multimodal Mining to Drive Clinical Guidelines Development. - Emilie Pasche; Julien Gobeill; Douglas Teodoro; Dina Vishnyakova; Arnaud Gaudinat; Patrick Ruch; Christian Lovis (MIE, 2011)

Interoperability Driven Integration of Biomedical Data Sources. - Douglas Teodoro; Rémy Choquet; Daniel Schober; Giovanni Mels; Emilie Pasche; Patrick Ruch; Christian Lovis (MIE, 2011)

BiTeM Group Report for TREC Chemical IR Track 2011. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch; Emilie Pasche; Douglas Teodoro; Dina Vishnyakova (TREC, 2011)

BiTeM Group Report for TREC Medical Records Track 2011. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch; Emilie Pasche; Douglas Teodoro; Dina Vishnyakova (TREC, 2011)

The gene normalization task in BioCreative III. - 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; et al. (BMC Bioinform., 2011)

BiTeM Site Report for the Claims to Passage Task in CLEF-IP 2012. - Julien Gobeill; Patrick Ruch (CLEF (Online Working Notes/Labs/Workshop), 2012)

A User-Friendly Tool for Medical-Related Patent Retrieval. - Emilie Pasche; Julien Gobeill; Douglas Teodoro; Arnaud Gaudinat; Dina Vishnyakova; Christian Lovis; Patrick Ruch (EFMI-STC, 2012)

Pathogens and Gene Product Normalization in the Biomedical Literature. - Dina Vishnyakova; Emilie Pasche; Douglas Teodoro; Christian Lovis; Patrick Ruch (EFMI-STC, 2012)

An advanced search engine for patent analytics in medicinal chemistry. - Emilie Pasche; Julien Gobeill; Douglas Teodoro; Arnaud Gaudinat; Dina Vishnyakova; Christian Lovis; Patrick Ruch (MIE, 2012)

Classification and Prioritization of Biomedical Literature for the Comparative Toxicogenomics Database. - Dina Vishnyakova; Emilie Pasche; Julien Gobeill; Arnaud Gaudinat; Christian Lovis; Patrick Ruch (MIE, 2012)

Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database. - Dina Vishnyakova; Emilie Pasche; Patrick Ruch (Database J. Biol. Databases Curation, 2012)

Using a Question-Answering Approach in Machine Reading Task of Biomedical Texts about the Alzheimer Disease. - Dina Vishnyakova; Julien Gobeill; Patrick Ruch (CLEF (Working Notes), 2013)

Utilization of Ontology Look-Up Services in Information Retrieval for Biomedical Literature. - Dina Vishnyakova; Emilie Pasche; Christian Lovis; Patrick Ruch (EFMI-STC, 2013)

Khresmoi - Multilingual Semantic Search of Medical Text and Images. - Niraj Aswani; Thomas Beckers 002; Erich Birngruber; Célia Boyer; Andreas Burner; Jakub Bystron; Khalid Choukri; Sarah Cruchet; Hamish Cunningham; Jan Dedek; Ljiljana Dolamic; René Donner; et al. (MedInfo, 2013)

Use of Controlled Vocabularies to Improve Biomedical Information Retrieval Tasks. - Emilie Pasche; Julien Gobeill; Dina Vishnyakova; Patrick Ruch; Christian Lovis (MedInfo, 2013)

Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. - Julien Gobeill; Emilie Pasche; Dina Vishnyakova; Patrick Ruch (Database J. Biol. Databases Curation, 2013)

Application of text-mining for updating protein post-translational modification annotation in UniProtKB. - Anne-Lise Veuthey; Alan J. Bridge; Julien Gobeill; Patrick Ruch; Johanna R. McEntyre; Lydie Bougueleret; Ioannis Xenarios (BMC Bioinform., 2013)

Instance-based Learning for Tweet Categorization in CLEF RepLab 2014. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch (CLEF (Working Notes), 2014)

Electronic Processing of Informed Consents in a Global Pharmaceutical Company Environment. - Dina Vishnyakova; Julien Gobeill; Fatma Oezdemir-Zaech; Olivier Kreim; Thérèse Vachon; Thierry Cladé; Xavier Haenning; Dmitri Mikhailov; Patrick Ruch (MIE, 2014)

Full-texts representation with Medical Subject Headings, and co-citations network rerank- ing strategies for TREC 2014 Clinical Decision Support Track. - Julien Gobeill; Arnaud Gaudinat; Emilie Pasche; Patrick Ruch (TREC, 2014)

Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. - Julien Gobeill; Emilie Pasche; Dina Vishnyakova; Patrick Ruch (Database J. Biol. Databases Curation, 2014)

Overview of the gene ontology task at BioCreative IV. - 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; et al. (Database J. Biol. Databases Curation, 2014)

Development and tuning of an original search engine for patent libraries in medicinal chemistry. - Emilie Pasche; Julien Gobeill; Olivier Kreim; Fatma Oezdemir-Zaech; Thérèse Vachon; Christian Lovis; Patrick Ruch (BMC Bioinform., 2014)

Instance-Based Learning for Tweet Monitoring and Categorization. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch (CLEF, 2015)

Exploiting incoming and outgoing citations for improving Information Retrieval in the TREC 2015 Clinical Decision Support Track. - Julien Gobeill; Arnaud Gaudinat; Patrick Ruch (TREC, 2015)

Deep Question Answering for protein annotation. - Julien Gobeill; Arnaud Gaudinat; Emilie Pasche; Dina Vishnyakova; Pascale Gaudet; Amos Bairoch; Patrick Ruch (Database J. Biol. Databases Curation, 2015)

Effect of the Named Entity Recognition and Sliding Window on the HONcode Automated Detection of HONcode Criteria for Mass Health Online Content. - Célia Boyer; Ljiljana Dolamic; Patrick Ruch; Gilles Falquet (HEALTHINF, 2016)

BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction. - Luc Mottin; Julien Gobeill; Anaïs Mottaz; Emilie Pasche; Arnaud Gaudinat; Patrick Ruch (CLEF (Working Notes), 2016)

Tools to Retrieve Reliable Health Information on the Internet - Improvements of the Automated Detection of HONcode Criteria for Mass Health Online Content. - Célia Boyer; Allan Hanbury; Patrick Ruch; Gilles Falquet (EPS, 2016)

neXtA5: accelerating annotation of articles via automated approaches in neXtProt. - Luc Mottin; Julien Gobeill; Emilie Pasche; Pierre-André Michel; Isabelle Cusin; Pascale Gaudet; Patrick Ruch (Database J. Biol. Databases Curation, 2016)

Customizing a Variant Annotation-Support Tool: an Inquiry into Probability Ranking Principles for TREC Precision Medicine. - Emilie Pasche; Julien Gobeill; Luc Mottin; Anaïs Mottaz; Douglas Teodoro; Paul Van Rijen; Patrick Ruch (TREC, 2017)

Triage by ranking to support the curation of protein interactions. - Luc Mottin; Emilie Pasche; Julien Gobeill; Valentine Rech de Laval; Anne Gleizes; Pierre-André Michel; Amos Bairoch; Pascale Gaudet; Patrick Ruch (Database J. Biol. Databases Curation, 2017)

Improving average ranking precision in user searches for biomedical research datasets. - Douglas Teodoro; Luc Mottin; Julien Gobeill; Arnaud Gaudinat; Thérèse Vachon; Patrick Ruch (Database J. Biol. Databases Curation, 2017)

Global picture of OAI-PMH repositories through the analysis of 6 key open archive meta-catalogs. - Arnaud Gaudinat; Jonas Beausire; Megan Fuss; Elisa Banfi; Julien Gobeill; Patrick Ruch (CoRR, 2017)

Instance-based Learning for ICD10 Categorization. - Julien Gobeill; Patrick Ruch (CLEF (Working Notes), 2018)

Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. - 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 (Database J. Biol. Databases Curation, 2018)

Overview of the BioCreative VI text-mining services for Kinome Curation Track. - Julien Gobeill; Pascale Gaudet; Daniel Dopp; Adam Morrone; Indika Kahanda; Yi-Yu Hsu; Chih-Hsuan Wei; Zhiyong Lu; Patrick Ruch (Database J. Biol. Databases Curation, 2018)

Retrieving the Evidence of a Free Text Annotation in a Scientific Article: A Data Free Approach. - Julien Gobeill; Emilie Pasche; Patrick Ruch (CICLing (1), 2019)

A Baseline Approach for Early Detection of Signs of Anorexia and Self-harm in Reddit Posts. - Nona Naderi; Julien Gobeill; Douglas Teodoro; Emilie Pasche; Patrick Ruch (CLEF (Working Notes), 2019)

A Data-Driven Approach for Measuring the Severity of the Signs of Depression using Reddit Posts. - Paul Van Rijen; Douglas Teodoro; Nona Naderi; Luc Mottin; Julien Knafou; Matt Jeffryes; Patrick Ruch (CLEF (Working Notes), 2019)

Designing retrieval models to contrast precision-driven ad hoc search vs. recall-driven treatment extraction in Precision Medicine. - Déborah Caucheteur; Emilie Pasche; Julien Gobeill; Anaïs Mottaz; Luc Mottin; Patrick Ruch (TREC, 2019)

SIB Text Mining at TREC 2019 Deep Learning Track: Working Note. - Julien Knafou; Matt Jeffryes; Luc Mottin; Douglas Teodoro; Patrick Ruch (TREC, 2019)

BiTeM at WNUT 2020 Shared Task-1: Named Entity Recognition over Wet Lab Protocols using an Ensemble of Contextual Language Models. - Julien Knafou; Nona Naderi; Jenny Copara; Douglas Teodoro; Patrick Ruch (W-NUT@EMNLP, 2020)

Named Entity Recognition in Chemical Patents using Ensemble of Contextual Language Models. - Jenny Copara; Nona Naderi; Julien Knafou; Patrick Ruch; Douglas Teodoro (CLEF (Working Notes), 2020)

An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. - Jiayuan He 002; Dat Quoc Nguyen; Saber A. Akhondi; Christian Druckenbrodt; Camilo Thorne; Ralph Hoessel; Zubair Afzal; Zenan Zhai; Biaoyan Fang; Hiyori Yoshikawa; Ameer Albahem; Jingqi Wang; et al. (CLEF (Working Notes), 2020)

Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. - Déborah Caucheteur; Julien Gobeill; Anaïs Mottaz; Emilie Pasche; Pierre-André Michel; Luc Mottin; Daniel J. Stekhoven; Valérie Barbié; Patrick Ruch (MIE, 2020)

Machine Learning for Automatic Encoding of French Electronic Medical Records: Is More Data Better? - Julien Gobeill; Patrick Ruch; Rodolphe Meyer (MIE, 2020)

Contextualized French Language Models for Biomedical Named Entity Recognition. - Jenny Copara; Julien Knafou; Nona Naderi; Claudia Moro 001; Patrick Ruch; Douglas Teodoro (JEP-TALN-RECITAL (DEFT), 2020)

SIB Text Mining at TREC 2020 Deep Learning Track. - Julien Knafou; Matthew Jeffryes; Sohrab Ferdowsi; Patrick Ruch (TREC, 2020)

SIB Text Mining at TREC Precision Medicine 2020. - Emilie Pasche; Déborah Caucheteur; Luc Mottin; Anaïs Mottaz; Julien Gobeill; Patrick Ruch (TREC, 2020)

UPCLASS: a deep learning-based classifier for UniProtKB entry publications. - Douglas Teodoro; Julien Knafou; Nona Naderi; Emilie Pasche; Julien Gobeill; Cecilia N. Arighi; Patrick Ruch (Database J. Biol. Databases Curation, 2020)

SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. - Julien Gobeill; Déborah Caucheteur; Pierre-André Michel; Luc Mottin; Emilie Pasche; Patrick Ruch (Nucleic Acids Res., 2020)

DisProt: intrinsic protein disorder annotation in 2020. - 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; et al. (Nucleic Acids Res., 2020)

Progress With Improving Preservation and Reuse of Scientific Research Data. - Peter Cornwell; Donat Agosti; Laurence Benichou; Jose Benito Gonzalez Lopez; Madeleine Herren; Patrick Ruch (iPRES, 2021)

SIB Text Mining at TREC Clinical Trials 2021. - Déborah Caucheteur; Emilie Pasche; Luc Mottin; Anaïs Mottaz; Julien Gobeill; Patrick Ruch (TREC, 2021)

Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora. - Nona Naderi; Julien Knafou; Jenny Copara; Patrick Ruch; Douglas Teodoro (Frontiers Res. Metrics Anal., 2021)

UniProt: the universal protein knowledgebase in 2021. - 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; et al. (Nucleic Acids Res., 2021)

Classification of oncology treatment responses from radiology reports with supervised machine learning. - 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; et al. (AMIA, 2022)

Classification of Oncology Treatment Responses from French Radiology Reports with Supervised Machine Learning. - Jean-Philippe Goldman; Luc Mottin; Jamil Zaghir; Daniel Keszthelyi; Belinda Lokaj; Hugues Turbé; Julien Gobeill; Patrick Ruch; Julien Ehrsam; Christian Lovis (MIE, 2022)

Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service. - Anaïs Mottaz; Emilie Pasche; Pierre-André Michel; Luc Mottin; Douglas Teodoro; Patrick Ruch (MIE, 2022)

Analyzing the Information Content of Text-Based Files in Supplementary Materials of Biomedical Literature. - Nona Naderi; Anaïs Mottaz; Douglas Teodoro; Patrick Ruch (MIE, 2022)

Variomes: a high recall search engine to support the curation of genomic variants. - Emilie Pasche; Anaïs Mottaz; Déborah Caucheteur; Julien Gobeill; Pierre-André Michel; Patrick Ruch (Bioinform., 2022)

Assessing the use of supplementary materials to improve genomic variant discovery. - Emilie Pasche; Anaïs Mottaz; Julien Gobeill; Pierre-André Michel; Déborah Caucheteur; Nona Naderi; Patrick Ruch (Database J. Biol. Databases Curation, 2023)

COVoc and COVTriage: novel resources to support literature triage. - Déborah Caucheteur; Zoë May Pendlington; Paola Roncaglia; Julien Gobeill; Luc Mottin; Nicolas Matentzoglu; Donat Agosti; David Osumi-Sutherland; Helen E. Parkinson; Patrick Ruch (Bioinform., 2023)

Multilingual RECIST classification of radiology reports using supervised learning. - 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; et al. (Frontiers Digit. Health, 2023)

Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants. - Luc Mottin; Nona Naderi; Anaïs Mottaz; Pierre-André Michel; Lennart F. Johansson; Morris A. Swertz; Andrew Stubbs; Emilie Pasche; Julien Gobeill; Patrick Ruch (MIE, 2024)