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Douglas Teodoro

Douglas Theodoro

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2020 – today

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2024
[j8]
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Isaac Shiri, Behrooz Razeghi, Sohrab Ferdowsi, Yazdan Salimi, Deniz Gündüz, Douglas Teodoro, Slava Voloshynovskiy, Habib Zaidi:
PRIMIS: Privacy-preserving medical image sharing via deep sparsifying transform learning with obfuscation. J. Biomed. Informatics 150: 104583 (2024)
[i10]
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  - journals/corr/abs-2404-12827
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Anthony Yazdani, Alban Bornet, Boya Zhang, Philipp Khlebnikov, Poorya Amini, Douglas Teodoro:
CT-ADE: An Evaluation Benchmark for Adverse Drug Event Prediction from Clinical Trial Results. CoRR abs/2404.12827 (2024)
[i9]
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  - journals/corr/abs-2406-18792
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Jenny Copara, Nona Naderi, Gilles Falquet, Douglas Teodoro:
A data-driven assessment of biomedical terminology evolution using information theoretical and network analysis approaches. CoRR abs/2406.18792 (2024)
2023
[j7]
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  - journals/jcisd/JaumeSanteroBVNAPYBFT23
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Fernando Jaume-Santero, Alban Bornet, Alain Valery, Nona Naderi, David Vicente Alvarez, Dimitrios Proios, Anthony Yazdani, Colin Bournez, Thomas Fessard, Douglas Teodoro:
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios. J. Chem. Inf. Model. 63(7): 1914-1924 (2023)
[j6]
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  - journals/patterns/FerdowsiKBAMAT23
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Sohrab Ferdowsi, Julien Knafou, Nikolay Borissov, David Vicente Alvarez, Rahul Mishra, Poorya Amini, Douglas Teodoro:
Deep learning-based risk prediction for interventional clinical trials based on protocol design: A retrospective study. Patterns 4(3): 100689 (2023)
[c43]
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  - conf/acl-clinicalnlp/ZhangMT23
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Boya Zhang, Rahul Mishra, Douglas Teodoro:
DS4DH at MEDIQA-Chat 2023: Leveraging SVM and GPT-3 Prompt Engineering for Medical Dialogue Classification and Summarization. ClinicalNLP@ACL 2023: 536-545
[c42]
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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, José Eduardo Krieger, Douglas Teodoro, Claudia Maria Cabral Moro, Emerson Cabrera Paraiso:
CardioBERTpt: Transformer-based Models for Cardiology Language Representation in Portuguese. CBMS 2023: 378-381
[c41]
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Dimitrios Proios, Anthony Yazdani, Alban Bornet, Julien Ehrsam, Islem Rekik, Douglas Teodoro:
Leveraging patient similarities via graph neural networks to predict phenotypes from temporal data. DSAA 2023: 1-10
[i8]
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  - journals/corr/abs-2302-04185
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Anthony Yazdani, Dimitrios Proios, Hossein Rouhizadeh, Douglas Teodoro:
Efficient Joint Learning for Clinical Named Entity Recognition and Relation Extraction Using Fourier Networks: A Use Case in Adverse Drug Events. CoRR abs/2302.04185 (2023)
[i7]
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  - journals/corr/abs-2308-12877
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Anthony Yazdani, Hossein Rouhizadeh, David Vicente Alvarez, Douglas Teodoro:
DS4DH at #SMM4H 2023: Zero-Shot Adverse Drug Events Normalization using Sentence Transformers and Reciprocal-Rank Fusion. CoRR abs/2308.12877 (2023)
2022
[c40]
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Sohrab Ferdowsi, Jenny Copara, Racha Gouareb, Nikolay Borissov, Fernando Jaume-Santero, Poorya Amini, Douglas Teodoro:
On Graph Construction for Classification of Clinical Trials Protocols Using Graph Neural Networks. AIME 2022: 249-259
[c39]
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  - conf/his2/Jaume-SanteroZP22
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Fernando Jaume-Santero, Boya Zhang, Dimitrios Proios, Anthony Yazdani, Racha Gouareb, Mina Bjelogrlic, Douglas Teodoro:
Cluster Analysis of Low-Dimensional Medical Concept Representations from Electronic Health Records. HIS 2022: 313-324
[c38]
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Anthony Yazdani, Dimitrios Proios, Hossein Rouhizadeh, Douglas Teodoro:
Efficient Joint Learning for Clinical Named Entity Recognition and Relation Extraction Using Fourier Networks: A Use Case in Adverse Drug Events. ICON 2022: 212-223
[c37]
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  - conf/mie/MottazPMMTR22
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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
[c36]
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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
[c35]
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  - conf/netscix/GouarebCFT22
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Racha Gouareb, Francois Can, Sohrab Ferdowsi, Douglas Teodoro:
Vessel Destination Prediction Using a Graph-Based Machine Learning Model. NetSci-X 2022: 80-93
[c34]
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  - conf/semeval/RouhizadehT22
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Hossein Rouhizadeh, Douglas Teodoro:
DS4DH at SemEval-2022 Task 11: Multilingual Named Entity Recognition Using an Ensemble of Transformer-based Language Models. SemEval@NAACL 2022: 1543-1548
[i6]
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  - journals/corr/abs-2202-06771
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Boya Zhang, Nona Naderi, Fernando Jaume-Santero, Douglas Teodoro:
DS4DH at TREC Health Misinformation 2021: Multi-Dimensional Ranking Models with Transfer Learning and Rank Fusion. CoRR abs/2202.06771 (2022)
2021
[j5]
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  - journals/fdgth/HaasBAFMTA21
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Quentin Haas, Nikolay Borisov, David Vicente Alvarez, Sohrab Ferdowsi, Leonhard von Mayenn, Douglas Teodoro, Poorya Amini:
Vaccine Development in the Time of COVID-19: The Relevance of the Risklick AI to Assist in Risk Assessment and Optimize Performance. Frontiers Digit. Health 3: 745674 (2021)
[j4]
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  - journals/frma/NaderiKCRT21
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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)
[j3]
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  - journals/nar/BatemanMOMAAABB21
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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)
[c33]
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Sohrab Ferdowsi, Nikolay Borissov, Julien Knafou, Poorya Amini, Douglas Teodoro:
Classification of hierarchical text using geometric deep learning: the case of clinical trials corpus. EMNLP (1) 2021: 608-618
[c32]
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Boya Zhang, Nona Naderi, Fernando Jaume-Santero, Douglas Teodoro:
DS4DH at TREC Health Misinformation 2021: Multi-Dimensional Ranking Models with Transfer Learning and Rank Fusion. TREC 2021
[i5]
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  - journals/corr/abs-2110-15710
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Sohrab Ferdowsi, Nikolay Borissov, Julien Knafou, Poorya Amini, Douglas Teodoro:
Classification of hierarchical text using geometric deep learning: the case of clinical trials corpus. CoRR abs/2110.15710 (2021)
2020
[j2]
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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)
[c31]
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  - conf/acl-clinicalnlp/SchneiderSKOCGO20
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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:
BioBERTpt - A Portuguese Neural Language Model for Clinical Named Entity Recognition. ClinicalNLP@EMNLP 2020: 65-72
[c30]
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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
[c29]
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  - conf/clef/CoparaNKRT20
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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
[c28]
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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
[c27]
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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
[i4]
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  - journals/corr/abs-2007-12569
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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

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2019
[c26]
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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
[c25]
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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
[c24]
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Julien Knafou, Matt Jeffryes, Luc Mottin, Douglas Teodoro, Patrick Ruch:
SIB Text Mining at TREC 2019 Deep Learning Track: Working Note. TREC 2019
2017
[j1]
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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)
[c23]
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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]
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  - journals/corr/abs-1709-03061
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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)
[i2]
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  - journals/corr/abs-1711-09729
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Douglas Teodoro, Nils Rotgans, Lucas Oliveira, Lilian Correia:
Design of an Integrated Analytics Platform for Healthcare Assessment Centered on the Episode of Care. CoRR abs/1711.09729 (2017)
[i1]
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  - journals/corr/abs-1711-09731
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Sérgio Miranda Freire, Luciana Tricai Cavalini, Douglas Teodoro, Erik Sundvall:
Archetypes for Representing Data about the Brazilian Public Hospital Information System and Outpatient High Complexity Procedures System. CoRR abs/1711.09731 (2017)
2014
[c22]
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Daniel Schober, Rémy Choquet, Kristof Depraetere, Frank Enders, Philipp Daumke, Marie-Christine Jaulent, Douglas Teodoro, Emilie Pasche, Christian Lovis, Martin Boeker:
DebugIT: Ontology-mediated Layered Data Integration for Real-time Antibiotics Resistance Surveillance. SWAT4LS 2014
2012
[b1]
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Douglas Teodoro:
Data integration and trend analysis for surveillance of antimicrobial resistance. University of Geneva, Switzerland, 2012
[c21]
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Dina Vishnyakova, Emilie Pasche, Douglas Teodoro, Christian Lovis, Patrick Ruch:
Pathogens and Gene Product Normalization in the Biomedical Literature. EFMI-STC 2012: 89-93
[c20]
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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
[c19]
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Ariane Assélé Kama, Audi Primadhanty, Rémy Choquet, Douglas Teodoro, Frank Enders, Catherine Duclos, Marie-Christine Jaulent:
Data Definition Ontology for clinical data integration and querying. MIE 2012: 38-42
[c18]
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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
2011
[c17]
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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
[c16]
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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
[c15]
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Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM Group Report for TREC Chemical IR Track 2011. TREC 2011
[c14]
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Julien Gobeill, Arnaud Gaudinat, Patrick Ruch, Emilie Pasche, Douglas Teodoro, Dina Vishnyakova:
BiTeM Group Report for TREC Medical Records Track 2011. TREC 2011
2010
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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
[c12]
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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
[c11]
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David Ouagne, Nadia Nadah, Daniel Schober, Rémy Choquet, Douglas Teodoro, Dirk Colaert, Stefan Schulz, Marie-Christine Jaulent, Christel Daniel:
Ensuring HL7-based information model requirements within an ontology framework. MedInfo 2010: 912-916
[c10]
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Daniel Schober, Martin Boeker, Jessica Bullenkamp, Csaba Huszka, Kristof Depraetere, Douglas Teodoro, Nadia Nadah, Rémy Choquet, Christel Daniel, Stefan Schulz:
The DebugIT Core Ontology: semantic integration of antibiotics resistance patterns. MedInfo 2010: 1060-1064
[c9]
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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
[c8]
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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

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2009
[c7]
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Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis:
QA-driven Guidelines Generation for Bacteriotherapy. AMIA 2009
[c6]
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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
[c5]
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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
[c4]
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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
[c3]
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Douglas Teodoro, Rémy Choquet, Emilie Pasche, Julien Gobeill, Christel Daniel, Patrick Ruch, Christian Lovis:
Biomedical Data Management: A Proposal Framework. MIE 2009: 175-179
[c2]
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Emilie Pasche, Douglas Teodoro, Julien Gobeill, Patrick Ruch, Christian Lovis:
Automatic Medical Knowledge Acquisition Using Question-Answering. MIE 2009: 569-573
[c1]
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Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch:
Report on the TREC 2009 Experiments: Chemical IR Track. TREC 2009

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