BITEM Biblio

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2020
Knafou J, Naderi N, Copara J, Teodoro D, Ruch P. BiTeM at WNUT 2020 Shared Task-1: Named Entity Recognition over Wet Lab Protocols using an Ensemble of Contextual Language Models. In: Proceedings of the Sixth Workshop on Noisy User-generated Text (W-NUT 2020). Proceedings of the Sixth Workshop on Noisy User-generated Text (W-NUT 2020). Online: Association for Computational Linguistics; 2020. Available from: https://www.aclweb.org/anthology/2020.wnut-1.40PDF icon 2020.wnut-1.40.pdf (842.21 KB)
Copara J, Knafou J, Naderi N, Moro C, Ruch P, Teodoro D. Contextualized French Language Models for Biomedical Named Entity Recognition. In: Actes de la 6e conférence conjointe Journées d'Études sur la Parole (JEP, 31e édition), Traitement Automatique des Langues Naturelles (TALN, 27e édition), Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues. Actes de la 6e conférence conjointe Journées d'Études sur la Parole (JEP, 31e édition), Traitement Automatique des Langues Naturelles (TALN, 27e édition), Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues. ATALA; 2020.
He J, Nguyen DQuoc, Akhondi SA, Druckenbrodt C, Thorne C, Hoessel R, Afzal Z, Zhai Z, Fang B, Yoshikawa H, et al. An extended overview of the CLEF 2020 ChEMU Lab : information extraction of chemical reactions from patents. Proceedings of the CLEF 2020 conference [Internet]. 2020 :31 p. Available from: http://hesso.tind.io/record/6175
Copara J, Naderi N, Knafou J, Ruch P, Teodoro D. Named entity recognition in chemical patents using ensemble of contextual language models. Working Notes of CLEF2020—Conference and Labs of the Evaluation Forum (2020). 2020 .
Gobeill J, Caucheteur D, Michel P-A, Mottin L, Pasche E, Ruch P. SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. Nucleic Acids Res. 2020 ;48(W1):W12-W16.
Pasche E, Caucheteur D, Mottin L, Mottaz A, Gobeill J, Ruch P. SIB text mining at TREC precision medicine 2020. In: Proceedings of the Twenty-Ninth Text REtrieval Conference (TREC 2020). Proceedings of the Twenty-Ninth Text REtrieval Conference (TREC 2020). 16-20 November 2020; 2020.PDF icon bitem.pm_.pdf (358.89 KB)
Caucheteur D, Gobeill J, Mottaz A, Pasche E, Michel P-A, Mottin L, Stekhoven DJ, Barbié V, Ruch P. Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. Stud Health Technol Inform. 2020 ;270:884-888.
Teodoro D, Knafou J, Naderi N, Pasche E, Gobeill J, Arighi CN, Ruch P. UPCLASS: a deep learning-based classifier for UniProtKB entry publications. Database [Internet]. 2020 ;2020. Available from: https://doi.org/10.1093/database/baaa026
2019
Mottin L. Assistance à la curation de publications scientifiques par des méthodes de triage et d’annotation automatiques. [Internet]. 2019 . Available from: https://archive-ouverte.unige.ch/unige:118269PDF icon these_luc_mottin.pdf (4.27 MB)
Naderi N, Gobeill J, Teodoro D, Pasche E, Ruch P. A Baseline Approach for Early Detection of Signs of Anorexia and Self-harm in Reddit Posts. In: Working Notes of CLEF 2019 - Conference and Labs of the Evaluation Forum, Lugano, Switzerland, September 9-12, 2019. Working Notes of CLEF 2019 - Conference and Labs of the Evaluation Forum, Lugano, Switzerland, September 9-12, 2019. ; 2019. Available from: http://ceur-ws.org/Vol-2380/paper_111.pdf
Van Rijen P, Teodoro D, Naderi N, Mottin L, Knafou J, Jeffryes M, Ruch P. A Data-Driven Approach for Measuring the Severity of the Signs of Depression using Reddit Posts. In: Working Notes of CLEF 2019 - Conference and Labs of the Evaluation Forum, Lugano, Switzerland, September 9-12, 2019. Working Notes of CLEF 2019 - Conference and Labs of the Evaluation Forum, Lugano, Switzerland, September 9-12, 2019. ; 2019. Available from: http://ceur-ws.org/Vol-2380/paper_79.pdf
Caucheteur D, Pasche E, Gobeill J, Mottaz A, Mottin L, Ruch P. Designing retrieval models to contrast precision-driven ad hoc search vs. recall-driven treatment extraction in Precision Medicine. In: TREC. TREC. ; 2019.PDF icon bitem_pm.pm_.pdf (365.41 KB)
2015
Gobeill J, Gaudinat A, Pasche E, Vishnyakova D, Gaudet P, Bairoch A, Ruch P. Deep Question Answering for protein annotation. Database (Oxford). 2015 ;2015.PDF icon Database-2015-Gobeill-database_bav081.pdf (587.33 KB)
Gobeill J, Gaudinat A, Ruch P. Instance-Based Learning for Tweet Monitoring and Categorization. In: Experimental IR Meets Multilinguality, Multimodality, and Interaction. Experimental IR Meets Multilinguality, Multimodality, and Interaction. Springer; 2015. pp. 235–240.PDF icon 370583_1_En_22_Chapter_OnlinePDF.pdf (294.92 KB)

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