Alexis Allot

31 papers Misc 3Journal 26Unranked 1
YearRankTypeTitle / Venue / Authors
2024 J jnl
PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge.
CoRR
Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu
2024 J jnl
Towards Accountable AI-Assisted Eye Disease Diagnosis: Workflow Design, External Validation, and Continual Learning.
CoRR
Qingyu Chen, Tiarnan D. L. Keenan, Elvira Agrón, Alexis Allot, Emily Guan, Bryant Duong, Amr S. Elsawy, Benjamin Hou, Cancan Xue, Sanjeeb Bhandari, Geoff Broadhead, Chantal Cousineau-Krieger, Ellen Davis, William G. Gensheimer, David Grasic, Seema Gupta, Luis Haddock, Eleni Konstantinou, Tania Lamba, Michele Maiberger, Dimosthenis Mantopoulos, Mitul C. Mehta, Ayman G. Nahri, Mutaz AL-Nawaflh, Arnold Oshinsky, Brittany E. Powell, Boonkit Purt, Soo Shin, Hillary Stiefel, Alisa T. Thavikulwat, Keith Wroblewski, Tham Yih Chung, Chui Ming Gemmy Cheung, Ching-Yu Cheng, Emily Y. Chew, Michelle R. Hribar, Michael F. Chiang, Zhiyong Lu
2023 J jnl
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning.
Patterns
Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2023 J jnl
LitCovid in 2022: an information resource for the COVID-19 literature.
Nucleic Acids Res.
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
2022 Misc conf
Automated and Accessible Diagnosis of Age-related Macular Degeneration: a Comparative Analysis of the impact of machine learning models in clinical diagnostic Workflows.
AMIA
Qingyu Chen, Tiarnan D. Keenan, Alexis Allot, Sanjeeb Bhandari, Geoff Broadhead, Chantal Cousineau-Krieger, Ellen Davis, William G. Gensheimer, David Grasic, Seema Gupta, Eleni Konstantinou, Tania Lamba, Michele Maiberger, Arnold Oshinsky, Brittany E. Powell, Boonkit Purt, Soo Shin, Hillary Steifel, Alisa T. Thavikulwat, Keith Wroblewski, Sirisha Koirala, Tom Murickan, Michael F. Chiang, Michelle R. Hribar, Emily Y. Chew, Zhiyong Lu
2022 J jnl
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning.
CoRR
Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2022 J jnl
LitCovid in 2022: an information resource for the COVID-19 literature.
CoRR
Qingyu Chen, Alexis Allot, Robert Leaman, Chih-Hsuan Wei, Elaheh Aghaarabi, John J. Guerrerio, Lilly Xu, Zhiyong Lu
2022 J jnl
LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation.
IEEE ACM Trans. Comput. Biol. Bioinform.
Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
2022 J jnl
LitMC-BERT: transformer-based multi-label classification of biomedical literature with an application on COVID-19 literature curation.
CoRR
Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
2022 J jnl
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
Database J. Biol. Databases Curation
Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep Vg, Zhiyong Lu
2022 J jnl
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
CoRR
Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj Dogan, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Zhiyong Lu
2022 J jnl
tmVar 3.0: an improved variant concept recognition and normalization tool.
Bioinform.
Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu
2022 J jnl
tmVar 3.0: an improved variant concept recognition and normalization tool.
CoRR
Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu
2021 Misc conf
AM2BERT: attention guided and regularized transformer-based multi-label classification model for COVID-19 literature curation.
AMIA
Qingyu Chen, Jingcheng Du, Alexis Allot, Zhiyong Lu
2021 J jnl
LitCovid: an open database of COVID-19 literature.
Nucleic Acids Res.
Qingyu Chen, Alexis Allot, Zhiyong Lu
2021 J jnl
LitSuggest: a web-based system for literature recommendation and curation using machine learning.
Nucleic Acids Res.
Alexis Allot, Kyubum Lee, Qingyu Chen, Ling Luo, Zhiyong Lu
2021 Misc conf
Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors.
AMIA
Robert Leaman, Qingyu Chen, Alexis Allot, Zhiyong Lu
2021 J jnl
Multimodal, multitask, multiattention (M3) deep learning detection of reticular pseudodrusen: Toward automated and accessible classification of age-related macular degeneration.
J. Am. Medical Informatics Assoc.
Qingyu Chen, Tiarnan D. L. Keenan, Alexis Allot, Yifan Peng, Elvira Agrón, Amitha Domalpally, Caroline C. W. Klaver, Daniel T. Luttikhuizen, Marcus H. Colyer, Catherine A. Cukras, Henry E. Wiley, M. Teresa Magone, Chantal Cousineau-Krieger, Wai T. Wong, Yingying Zhu, Emily Y. Chew, Zhiyong Lu
2020 J jnl
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP).
CoRR
Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
2020 J jnl
Multi-modal, multi-task, multi-attention (M3) deep learning detection of reticular pseudodrusen: towards automated and accessible classification of age-related macular degeneration.
CoRR
Qingyu Chen, Tiarnan D. L. Keenan, Alexis Allot, Yifan Peng, Elvira Agrón, Amitha Domalpally, Caroline C. W. Klaver, Daniel T. Luttikhuizen, Marcus H. Colyer, Catherine A. Cukras, Henry E. Wiley, M. Teresa Magone, Chantal Cousineau-Krieger, Wai T. Wong, Yingying Zhu, Emily Y. Chew, Zhiyong Lu
2020 J jnl
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view.
CoRR
Lana Yeganova, Rezarta Islamaj Dogan, Qingyu Chen, Robert Leaman, Alexis Allot, Chih-Hsuan Wei, Donald C. Comeau, Won Kim, Yifan Peng, W. John Wilbur, Zhiyong Lu
2020 J jnl
Predicting risk of late age-related macular degeneration using deep learning.
CoRR
Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2020 J jnl
Predicting risk of late age-related macular degeneration using deep learning.
npj Digit. Medicine
Yifan Peng, Tiarnan D. Keenan, Qingyu Chen, Elvira Agrón, Alexis Allot, Wai T. Wong, Emily Y. Chew, Zhiyong Lu
2019 — conf
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles.
BCB
Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu
2019 J jnl
LitSense: making sense of biomedical literature at sentence level.
Nucleic Acids Res.
Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2019 J jnl
PubTator central: automated concept annotation for biomedical full text articles.
Nucleic Acids Res.
Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu
2018 J jnl
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
Nucleic Acids Res.
Paul Julian Kersey, James E. Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu, Thomas Maurel, Benjamin Moore, Mark D. McDowall, Uma Maheswari, Guy Naamati, Victoria Newman, Chuang Kee Ong, Michael Paulini, Helder Pedro, Emily Perry, Matthew Russell, Helen Sparrow, Electra Tapanari, Kieron R. Taylor, Alessandro Vullo, Gareth Williams, Amonida Zadissa, Andrew Olson, Joshua C. Stein, Sharon Wei, Marcela K. Tello-Ruiz, Doreen Ware, Aurelien Luciani, Simon C. Potter, Robert D. Finn, Martin Urban, Kim E. Hammond-Kosack, Dan M. Bolser, Nishadi De Silva, Kevin L. Howe, Nicholas Langridge, Gareth Maslen, Daniel Michael Staines, Andrew D. Yates
2018 J jnl
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.
Nucleic Acids Res.
Alexis Allot, Yifan Peng, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, Zhiyong Lu
2015 — —
MyGeneFriends : vers un nouveau rapport entre chercheurs et mégadonnées. (MyGeneFriends : towards a new relationship between researchers and big data).
Alexis Allot
2015 J jnl
OrthoInspector 2.0: Software and database updates.
Bioinform.
Benjamin Linard, Alexis Allot, Raphael Schneider, Can Morel, Raymond Ripp, Marc Bigler, Julie Dawn Thompson, Olivier Poch, Odile Lecompte
2013 J jnl
PARSEC: PAtteRn SEarch and Contextualization.
Bioinform.
Alexis Allot, Yannick-Noël Anno, Laetitia Poidevin, Raymond Ripp, Olivier Poch, Odile Lecompte