Variomes: a high recall search engine to support the curation of genomic variants

ruch — Thu, 17 Jun 2021 21:22:15 +0000

Pasche E, Mottaz A, Caucheteur D, Gobeill J, Michel P-A, Ruch P. Variomes: a high recall search engine to support the curation of genomic variants. [Internet]. 2021 . Available from: https://doi.org/10.1101/2021.05.29.446224

Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora

naderi — Fri, 19 Nov 2021 20:15:44 +0000

Naderi N, Knafou J, Copara J, Ruch P, Teodoro D. Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora. Frontiers in Research Metrics and Analytics [Internet]. 2021 ;6:67. Available from: https://www.frontiersin.org/article/10.3389/frma.2021.689803

CINECA synthetic cohort Europe CH SIB [CC-BY-NC- SA]

naderi — Wed, 01 Dec 2021 10:11:50 +0000

Naderi N, Tanzer R, Teodoro D, Copara J, Mottin L, Ruch P. CINECA synthetic cohort Europe CH SIB [CC-BY-NC- SA]. [Internet]. 2021 . Available from: https://doi.org/10.5281/zenodo.5082689

Analyzing the information content of text-based files in supplementary materials of biomedical literature

naderi — Tue, 07 Dec 2021 14:04:11 +0000

Naderi N, Mottaz A, Teodoro D, Ruch P. Analyzing the information content of text-based files in supplementary materials of biomedical literature. 2021 .

Contextualized French Language Models for Biomedical Named Entity Recognition

naderi — Tue, 23 Jun 2020 12:44:04 +0000

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.

BiTeM at WNUT 2020 Shared Task-1: Named Entity Recognition over Wet Lab Protocols using an Ensemble of Contextual Language Models

naderi — Thu, 12 Nov 2020 10:08:56 +0000

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-1.40

SIB text mining at TREC precision medicine 2020

pasche — Thu, 01 Jul 2021 12:43:41 +0000

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.

An extended overview of the CLEF 2020 ChEMU Lab : information extraction of chemical reactions from patents

naderi — Wed, 21 Oct 2020 13:10:23 +0000

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

Named entity recognition in chemical patents using ensemble of contextual language models

naderi — Thu, 24 Sep 2020 11:08:57 +0000

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 .

SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts.

pasche — Thu, 01 Jul 2021 12:34:48 +0000

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.