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)

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)

Ensuring HL7-based information model requirements within an ontology framework. - David Ouagne; Nadia Nadah; Daniel Schober; Rémy Choquet; Douglas Teodoro; Dirk Colaert; Stefan Schulz 001; Marie-Christine Jaulent; Christel Daniel (MedInfo, 2010)

The DebugIT Core Ontology: semantic integration of antibiotics resistance patterns. - Daniel Schober; Martin Boeker; Jessica Bullenkamp; Csaba Huszka; Kristof Depraetere; Douglas Teodoro; Nadia Nadah; Rémy Choquet; Christel Daniel; Stefan Schulz 001 (MedInfo, 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)

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)

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)

Data Definition Ontology for clinical data integration and querying. - Ariane Assélé Kama; Audi Primadhanty; Rémy Choquet; Douglas Teodoro; Frank Enders; Catherine Duclos; Marie-Christine Jaulent (MIE, 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)

Data integration and trend analysis for surveillance of antimicrobial resistance. - Douglas Teodoro (2012)

DebugIT: Ontology-mediated Layered Data Integration for Real-time Antibiotics Resistance Surveillance. - Daniel Schober; Rémy Choquet; Kristof Depraetere; Frank Enders; Philipp Daumke; Marie-Christine Jaulent; Douglas Teodoro; Emilie Pasche; Christian Lovis; Martin Boeker (SWAT4LS, 2014)

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)

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)

Design of an Integrated Analytics Platform for Healthcare Assessment Centered on the Episode of Care. - Douglas Teodoro; Nils Rotgans; Lucas Oliveira; Lilian Correia (CoRR, 2017)

Archetypes for Representing Data about the Brazilian Public Hospital Information System and Outpatient High Complexity Procedures System. - Sérgio Miranda Freire; Luciana Tricai Cavalini; Douglas Teodoro; Erik Sundvall (CoRR, 2017)

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)

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

BioBERTpt - A Portuguese Neural Language Model for Clinical Named Entity Recognition. - Elisa Terumi Rubel Schneider; João Vitor Andrioli de Souza; Julien Knafou; Lucas Emanuel Silva e Oliveira; Jenny Copara; Yohan Bonescki Gumiel; Lucas Ferro Antunes de Oliveira; Emerson Cabrera Paraiso; Douglas Teodoro; Claudia Maria Cabral Moro Barra (ClinicalNLP@EMNLP, 2020)

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)

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)

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)

Classification of hierarchical text using geometric deep learning: the case of clinical trials corpus. - Sohrab Ferdowsi; Nikolay Borissov; Julien Knafou; Poorya Amini; Douglas Teodoro (EMNLP (1), 2021)

DS4DH at TREC Health Misinformation 2021: Multi-Dimensional Ranking Models with Transfer Learning and Rank Fusion. - Boya Zhang; Nona Naderi; Fernando Jaume-Santero; Douglas Teodoro (TREC, 2021)

Vaccine Development in the Time of COVID-19: The Relevance of the Risklick AI to Assist in Risk Assessment and Optimize Performance. - Quentin Haas; Nikolay Borisov; David Vicente Alvarez; Sohrab Ferdowsi; Leonhard von Mayenn; Douglas Teodoro; Poorya Amini (Frontiers Digit. Health, 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)

On Graph Construction for Classification of Clinical Trials Protocols Using Graph Neural Networks. - Sohrab Ferdowsi; Jenny Copara; Racha Gouareb; Nikolay Borissov; Fernando Jaume-Santero; Poorya Amini; Douglas Teodoro (AIME, 2022)

Cluster Analysis of Low-Dimensional Medical Concept Representations from Electronic Health Records. - Fernando Jaume-Santero; Boya Zhang; Dimitrios Proios; Anthony Yazdani; Racha Gouareb; Mina Bjelogrlic; Douglas Teodoro (HIS, 2022)

Efficient Joint Learning for Clinical Named Entity Recognition and Relation Extraction Using Fourier Networks: A Use Case in Adverse Drug Events. - Anthony Yazdani; Dimitrios Proios; Hossein Rouhizadeh; Douglas Teodoro (ICON, 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)

Vessel Destination Prediction Using a Graph-Based Machine Learning Model. - Racha Gouareb; Francois Can; Sohrab Ferdowsi; Douglas Teodoro (NetSci-X, 2022)

DS4DH at SemEval-2022 Task 11: Multilingual Named Entity Recognition Using an Ensemble of Transformer-based Language Models. - Hossein Rouhizadeh; Douglas Teodoro (SemEval@NAACL, 2022)

DS4DH at MEDIQA-Chat 2023: Leveraging SVM and GPT-3 Prompt Engineering for Medical Dialogue Classification and Summarization. - Boya Zhang; Rahul Mishra 004; Douglas Teodoro (ClinicalNLP@ACL, 2023)

CardioBERTpt: Transformer-based Models for Cardiology Language Representation in Portuguese. - Elisa Terumi Rubel Schneider; Yohan Bonescki Gumiel; João Vitor Andrioli de Souza; Lilian Mie Mukai Cintho; Lucas Emanuel Silva e Oliveira; Marina de Sá Rebelo; Marco Antonio Gutierrez 001; José Eduardo Krieger; Douglas Teodoro; Claudia Maria Cabral Moro; Emerson Cabrera Paraiso (CBMS, 2023)

Leveraging patient similarities via graph neural networks to predict phenotypes from temporal data. - Dimitrios Proios; Anthony Yazdani; Alban Bornet; Julien Ehrsam; Islem Rekik; Douglas Teodoro (DSAA, 2023)

DS4DH at #SMM4H 2023: Zero-Shot Adverse Drug Events Normalization using Sentence Transformers and Reciprocal-Rank Fusion. - Anthony Yazdani; Hossein Rouhizadeh; David Vicente Alvarez; Douglas Teodoro (CoRR, 2023)

Deep learning-based risk prediction for interventional clinical trials based on protocol design: A retrospective study. - Sohrab Ferdowsi; Julien Knafou; Nikolay Borissov; David Vicente Alvarez; Rahul Mishra 004; Poorya Amini; Douglas Teodoro (Patterns, 2023)

Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios. - Fernando Jaume-Santero; Alban Bornet; Alain Valery; Nona Naderi; David Vicente Alvarez; Dimitrios Proios; Anthony Yazdani; Colin Bournez; Thomas Fessard; Douglas Teodoro (J. Chem. Inf. Model., 2023)

CT-ADE: An Evaluation Benchmark for Adverse Drug Event Prediction from Clinical Trial Results. - Anthony Yazdani; Alban Bornet; Boya Zhang; Philipp Khlebnikov; Poorya Amini; Douglas Teodoro (CoRR, 2024)

A data-driven assessment of biomedical terminology evolution using information theoretical and network analysis approaches. - Jenny Copara; Nona Naderi; Gilles Falquet; Douglas Teodoro (CoRR, 2024)

PRIMIS: Privacy-preserving medical image sharing via deep sparsifying transform learning with obfuscation. - Isaac Shiri; Behrooz Razeghi; Sohrab Ferdowsi; Yazdan Salimi; Deniz Gündüz; Douglas Teodoro; Slava Voloshynovskiy; Habib Zaidi (J. Biomed. Informatics, 2024)

STM-GNN: Space-Time-and-Memory Graph Neural Networks for Predicting Multi-Drug Resistance Risks in Dynamic Patient Networks. - Damien Geissbuhler; Alban Bornet; Catarina Marques; André Anjos; Sónia Pereira; Douglas Teodoro (AIME (1), 2025)

ICU-TSB: A Benchmark for Temporal Patient Representation Learning for Unsupervised Stratification Into Patient Cohorts. - Dimitrios Proios; Alban Bornet; Anthony Yazdani; Jose F. Rodrigues; Douglas Teodoro (CBMS, 2025)

Comparing neural language models for medical concept representation and patient trajectory prediction. - Alban Bornet; Dimitrios Proios; Anthony Yazdani; Fernando Jaume-Santero; Guy Haller; Edward Choi; Douglas Teodoro (Artif. Intell. Medicine, 2025)

Analysis of eligibility criteria clusters based on large language models for clinical trial design. - Alban Bornet; Philipp Khlebnikov; Florian Meer; Quentin Haas; Anthony Yazdani; Boya Zhang; Poorya Amini; Douglas Teodoro (J. Am. Medical Informatics Assoc., 2025)

A scoping review of artificial intelligence applications in clinical trial risk assessment. - Douglas Teodoro; Nona Naderi; Anthony Yazdani; Boya Zhang; Alban Bornet (npj Digit. Medicine, 2025)

MMLU-ProX: A Multilingual Benchmark for Advanced Large Language Model Evaluation. - Weihao Xuan; Rui Yang; Heli Qi; Qingcheng Zeng; Yunze Xiao; Yun Xing; Junjue Wang; Huitao Li; Xin Li 079; Kunyu Yu; Nan Liu 003; Qingyu Chen 001; et al. (CoRR, 2025)

MKG-Rank: Enhancing Large Language Models with Knowledge Graph for Multilingual Medical Question Answering. - Feiyang Li; Yingjian Chen; Haoran Liu; Rui Yang; Han Yuan; Yuang Jiang; Tianxiao Li; Edison Marrese-Taylor; Hossein Rouhizadeh; Yusuke Iwasawa; Douglas Teodoro; Yutaka Matsuo; et al. (CoRR, 2025)

GLiNER-biomed: A Suite of Efficient Models for Open Biomedical Named Entity Recognition. - Anthony Yazdani; Ihor Stepanov; Douglas Teodoro (CoRR, 2025)

The Evolving Landscape of Generative Large Language Models and Traditional Natural Language Processing in Medicine. - Rui Yang; Huitao Li; Matthew Yu Heng Wong; Yuhe Ke; Xin Li 079; Kunyu Yu; Jingchi Liao; Jonathan Chong Kai Liew; Sabarinath Vinod Nair; Jasmine Chiat Ling Ong; Irene Li; Douglas Teodoro; et al. (CoRR, 2025)

ICU-TSB: A Benchmark for Temporal Patient Representation Learning for Unsupervised Stratification into Patient Cohorts. - Dimitrios Proios; Alban Bornet; Anthony Yazdani; Jose F. Rodrigues Jr.; Douglas Teodoro (CoRR, 2025)