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Research

My primary research interests lie in the areas of biomedical informatics, applications of natural language processing to biomedical and scientific text, biomedical ontologies and KR, open access, and meta-science. My ORCID is: 0000-0001-8752-6635

All Publications & Preprints || Organized Shared Tasks & Workshops || Talks & Panels || Teaching || Selected Press Coverage

 

Quick Nav to Latest work

thumbnail of preprint of S2-VILA, a project that experiments with injecting document visual layout features into language models for scientific text classification
thumbnail of preprint of SciA11y, a prototype system for creating accessible HTML renders of scientific papers from PDF
thumbnail of preprint of MS2, a multi-document summarization dataset for medical papers
thumbnail of paper on accessibility research literature review published in CHI 2021
thumbnail of paper on gender trends in CS publishing published in CACM 2021
thumbnail of paper on covid-19 text mining published in Briefings in Bioinformatics in 2020
thumbnail of paper on scientific fact checking published in EMNLP 2020
thumbnail of paper on kidney ontologies for the kidney precision medicine project published in Nature Reviews Nephrology in 2020

All Publications & Preprints

Incorporating visual layout structures for scientific text classification
Zejiang Shen, Kyle Lo, Lucy Lu Wang, Bailey Kuehl, Daniel S. Weld, Doug Downey
arXiv  

Improving the accessibility of scientific documents: current state, user needs, and a system solution to enhance scientific PDF accessibility for blind and low vision users
Lucy Lu Wang, Isabel Cachola, Jonathan Bragg, Evie Yu-Yen Cheng, Chelsea Haupt, Matt Latzke, Bailey Kuehl, Madeleine van Zuylen, Linda Wagner, Daniel S. Weld
arXiv   Demo  

MS^2: Multi-document summarization of medical studies
Jay DeYoung, Iz Beltagy, Madeleine van Zuylen, Bailey Kuehl, Lucy Lu Wang
EMNLP 2021
arXiv   GitHub  

Searching for scientific evidence in a pandemic: an overview of TREC-COVID
Kirk Roberts, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, Kyle Lo, Ian Soboroff, Ellen Voorhees, Lucy Lu Wang, William R Hersh
Journal of Biomedical Informatics
DOI: 10.1016/j.jbi.2021.103865; PMID: 34245913
arXiv  

Harnessing the power of smart and connected health to tackle COVID-19: IoT, AI, robotics, and blockchain for a better world
Farshad Firouzi, Bahar Farahani, Mahmoud Daneshmand, Kathy Grise, Jae Seung Song, Roberto Saracco, Lucy Lu Wang, Kyle Lo, Plamen Angelov, Eduardo Soares, Po-Shen Loh, Zeynab Talebpour, Reza Moradi, Mohsen Goodarzi, Haleh Ashraf, Mohammad Talebpour, Alireza Talebpour, Luca Romeo, Rupam Das, Hadi Heidari, Dana Pasquale, James Moody, Chris Woods, Erich S Huang, Payam Barnaghi, Majid Sarrafzadeh, Ron Li, Kristen L Beck, Olexandr Isayev, Nakmyoung Sung, Alan Luo
IEEE Internet of Things
DOI: 10.1109/JIOT.2021.3073904

A bibliometric analysis of citation diversity in accessibility and HCI research
Lucy Lu Wang, Kelly Mack, Emma McDonnell, Dhruv Jain, Leah Findlater, Jon E. Froehlich
CHI LBW 2021
DOI: 10.1145/3411763.3451618
arXiv   Supplement   GitHub

What do we mean by "accessibility research"? A literature survey of accessibility papers in CHI and ASSETS from 1994 to 2019
Kelly Mack, Emma McDonnell, Dhruv Jain, Lucy Lu Wang, Jon E. Froehlich, Leah Findlater
CHI 2021
DOI: 10.1145/3411764.3445412
arXiv   GitHub

Gender trends in computer science authorship
Lucy Lu Wang, Gabriel Stanovsky, Luca Weihs, Oren Etzioni
Communications of the ACM
DOI: 10.1145/3430803
ACM   arXiv

Text mining approaches for dealing with the rapidly expanding literature on COVID-19
Lucy Lu Wang and Kyle Lo
Briefings in Bioinformatics
DOI: 10.1093/bib/bbaa296; PMID: 33279995

Fact or Fiction: Verifying Scientific Claims
David Wadden, Shanchuan Lin, Kyle Lo, Lucy Lu Wang, Madeleine van Zuylen, Arman Cohan, Hannaneh Hajishirzi
EMNLP 2020
DOI: 10.18653/v1/2020.emnlp-main.609
ACL   arXiv   GitHub   Demo

MedICaT: A Dataset of Medical Images, Captions, and Textual References
Sanjay Subramanian, Lucy Lu Wang, Sachin Mehta, Ben Bogin, Madeleine van Zuylen, Sravanthi Parasa, Sameer Singh, Matt Gardner, Hannaneh Hajishirzi
EMNLP Findings 2020
DOI: 10.18653/v1/2020.findings-emnlp.191
ACL   arXiv   GitHub

Mitigating Biases in CORD-19 for Analyzing COVID-19 Literature
Anshul Kanakia, Kuansan Wang, Yuxiao Dong, Boya Xie, Kyle Lo, Zhihong Shen, Lucy Lu Wang, Chiyuan Huang, Darrin Eide, Sebastian Kohlmeier, Chieh-Han Wu
To appear: Frontiers in Research Metrics and Analytics
DOI: 10.3389/frma.2020.596624

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project
Edison Ong*, Lucy Lu Wang*, Jennifer Schaub, John F O’Toole, Becky Steck, Avi Z Rosenberg, Frederick Dowd, Jens Hansen, Laura Barisoni, Sanjay Jain, Ian H de Boer, M Todd Valerius, Sushrut S Waikar, Christopher Park, Dana C Crawford, Theodore Alexandrov, Christopher R Anderton, Christian Stoeckert, Chunhua Weng, Alexander D Diehl, Christopher J Mungall, Melissa Haendel, Peter N Robinson, Jonathan Himmelfarb, Ravi Iyengar, Matthias Kretzler, Sean Mooney, Yongqun He
Nature Reviews Nephrology
DOI: 10.1038/s41581-020-00335-w; PMID: 32939051

CORD-19: The Covid-19 Open Research Dataset.
Lucy Lu Wang*, Kyle Lo*, Yoganand Chandrasekhar, Russell Reas, Jiangjiang Yang, Darrin Eide, Kathryn Funk, Rodney Kinney, Ziyang Liu, William Merrill, Paul Mooney, Dewey Murdick, Devvret Rishi, Jerry Sheehan, Zhihong Shen, Brandon Stilson, Alex D Wade, Kuansan Wang, Chris Wilhelm, Boya Xie, Douglas Raymond, Daniel S Weld, Oren Etzioni, Sebastian Kohlmeier
NLP-COVID Workshop at ACL 2020
PMID: 32510522
ACL   arXiv   GitHub   Download

S2ORC: The Semantic Scholar Open Research Corpus
Kyle Lo*, Lucy Lu Wang*, Mark Neumann, Rodney Kinney, Daniel S Weld
ACL 2020
DOI: 10.18653/v1/2020.acl-main.447
ACL   arXiv   GitHub

SUPP.AI: finding evidence for supplement-drug interactions
Lucy Lu Wang, Oyvind Tafjord, Arman Cohan, Sarthak Jain, Sam Skjonsberg, Carissa Schoenick, Nick Botner, Waleed Ammar
ACL: System Demonstrations 2020
DOI: 10.18653/v1/2020.acl-demos.41
ACL   arXiv   Demo

TREC-COVID: Constructing a Pandemic Information Retrieval Test Collection
Ellen Voorhees, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, William R Hersh, Kyle Lo, Kirk Roberts, Ian Soboroff, Lucy Lu Wang
SIGIR Forum
arXiv

TREC-COVID: Rationale and Structure of an Information Retrieval Shared Task for COVID-19
Kirk Roberts, Tasmeer Alam, Steven Bedrick, Dina Demner-Fushman, Kyle Lo, Ian Soboroff, Ellen Voorhees, Lucy Lu Wang, William R Hersh
Journal of the American Medical Informatics Association
DOI: 10.1093/jamia/ocaa091; PMID: 32365190

Predicting instances of Pathway Ontology classes for pathway integration
Lucy Lu Wang, G Thomas Hayman, Jennifer R Smith, Monika Tutaj, Mary E Shimoyama, John Gennari
Journal of Biomedical Semantics
DOI: 10.1186/s13326-019-0202-8; PMID: 31196182

Ontology alignment in the biomedical domain using entity definitions and context
Lucy Lu Wang, Chandra Bhagavatula, Mark Neumann, Kyle Lo, Chris Wilhelm, Waleed Ammar
BioNLP at ACL 2018
DOI: 10.18653/v1/W18-2306
ACL   arXiv   GitHub

Construction of the literature graph in Semantic Scholar
Waleed Ammar, Dirk Groeneveld, Chandra Bhagavatula, Iz Beltagy, Miles Crawford, Doug Downey, Jason Dunkelberger, Ahmed Elgohary, Sergey Feldman, Vu Ha, Rodney Kinney, Sebastian Kohlmeier, Kyle Lo, Tyler Murray, Hsu-Han Ooi, Matthew Peters, Joanna Power, Sam Skjonsberg, Lucy Lu Wang, Chris Wilhelm, Zheng Yuan, Madeleine van Zuylen, Oren Etzioni
NAACL 2018
DOI: 10.18653/v1/N18-3011
ACL   arXiv   Download

PhenotypeXpression: sub-classification of disease states using public gene expression data and literature
Lucy Lu Wang, Huaiying Lin, Xiaojun Bao, Subhajit Sengupta, Ben Busby, Robert R Butler III
DOI: 10.1101/461301
Preprint

Similarity metrics for determining overlap among biological pathways
Lucy Lu Wang and John H Gennari
ICBO 2017

Fluctuation analysis of peak expiratory flow and its associations with treatment failure in asthma
David A Kaminsky, Lucy Lu Wang, Jason HT Bates, Cindy Thamrin, David M Shade, Anne E Dixon, Robert A Wise, Stephen Peters, Charles G Irvin
American Journal of Respiratory and Critical Care Medicine
DOI: 10.1164/rccm.201601-0076OC; PMID: 27814453

An analysis of differences in biological pathway resources
Lucy Lu Wang, John H Gennari, Neil F Abernethy
ICBO and BioCreative 2016

Development of a novel Markov chain model for the prediction of head and neck squamous cell carcinoma dissemination
Hyunggu Jung, Anthony Law, Eli Grunblatt, Lucy Lu Wang, Aaron Kusano, Jose LV Mejino Jr, Mark E Whipple
AMIA Annual Sympsium 2016
PMID: 28269942

Biological model development as an opportunity to provide content auditing for the foundational model of anatomy ontology
Lucy Lu Wang, Eli Grunblatt, Hyunggu Jung, Ira Kalet, Mark Whipple
AMIA Annual Sympsium 2015
PMID: 26958311

Electrical impedance myography in Duchenne muscular dystrophy and health controls: a multi-center study of reliability and validity
Craig M Zaidman, Lucy Lu Wang, Anne M Connolly, Julaine Florence, Brenda L Wong, Julie A Parsons, Susan Apkon, Namita Goyal, Eugene Williams, Diana Escolar, Seward B Rutkove, Jose L Bohorquez, DART‐EIM Clinical Evaluators Consortium
Muscle & Nerve
DOI: 10.1002/mus.24611; PMID: 25702806

Electrical impedance myography for monitoring motor neuron loss in the SOD1 G93A amyotrophic lateral sclerosis rat
Lucy Lu Wang, Andrew J Spieker, Jia Li, Seward B Rutkove
Clinical Neurophysiology
DOI: 10.1016/j.clinph.2011.04.021; PMID: 21612980

Assessment of alterations in the electrical impedance of muscle after experimental nerve injury via finite-element analysis
Lucy Lu Wang, Mohammad Ahad, Alistair McEwan, Jia Li, Mina Jafarpoor, Seward B Rutkove
IEEE Transactions on Biomedical Engineering
DOI: 10.1109/TBME.2011.2104957; PMID: 21224171


Organized Shared Tasks & Workshops

SciNLP Workshop at AKBC 2021
2nd Workshop on Natural Language Processing for Scientific Text

Scholarly Document Processing (SDP) Workshop at NAACL 2021
Improve scholarly document understanding and NLP for scientific text

EPIC-QA Challenge at TAC 2020
Epidemic question-answering track challenge on COVID-19

1st SciNLP Workshop at AKBC 2020
Natural language processing and data mining for scientific text

TREC-COVID Challenge at TREC 2020
COVID-19 ad-hoc document retrieval challenge


Talks & Panels

2021 Sep 7. "Mathematics in the Scholarly Literature." Invited talk. AI and Theorem Proving. Aussois, France and Online. Link.

2021 Jul 13. "The Power of AI: A Discussion on COVID-19 & the Future of Industries." Panel. LegalWeek. Online. Link.

2021 Jun 22. "Biomedical Informatics Career Development." Panel. National Library of Medicine Informatics Training Conference. Online. Link.

2021 May 7. "Scientific NLP for COVID-19 and Beyond." Invited talk. Machine Learning for Preventing and Combating Pandemics Workshop at ICLR 2021. Online. Link.

2021 Apr 22. "The Power of AI: A Discussion on COVID-19 & the Future of Industries." Panel. Relativity Pandemic Short Film Event. Online. Video.

2021 Apr 1. "Text Mining Insights from the COVID-19 Pandemic." Keynote. Bibliometric-enhanced Information Retrieval Workshop at ECIR 2021. Online. Link. Video.

2021 Mar 8. "Practical NLP for Biomedicine: Synthesizing Knowledge from Scientific Literature." Invited talk. CS Colloquium, Northwestern University. Online.

2021 Feb 18. "Fast-track Learning: Growing Insights from Text-mining COVID-19 Data." Invited talk and panel. 1st GTM2021 Virtual Forum. Online.

2020 Nov 13. "CORD-19: The COVID-19 Open Research Dataset." Invited talk. Global Tech Mining Conference. Online. Link.

2020 Nov 11. "Open Publishing and Publications as Data." Panel. Neuro-Gairdner Open Science in Action Symposium. Online. Link.

2020 Oct 19. "CORD-19: The COVID-19 Open Research Dataset." Invited talk and panel. AI for Data Discovery and Reuse + Open Science Symposium. Online. Link.

2020 Jul 29. "CORD-19 Search: Using Machine Learning to Explore COVID-19 Scientific Literature." Invited talk. AWS Education: Research Seminar Series. Online. Video.

2020 Jun 18. "Improving Access to Scientific Literature for NLP." Invited talk. Microsoft Research Project Hanover Group. Online.

2020 Jun 12. "The COVID-19 Open Research Dataset." Invited talk. Connected Health and COVID-19: Now and Beyond the Great Lockdown. Online.

2020 May 27. "The COVID-19 Open Research Dataset." Invited talk. Centre for Science and Technology Studies, Leiden University. Online.

2020 Apr 27. "CORD-19: The COVID-19 Open Research Dataset." Invited talk. NLP Meetup (NY-NLP, A2D-NLP, DC-NLP, Hungarian NLP, London Text Analytics). Online. Video.

2020 Apr 14. "The COVID-19 Open Research Dataset." Keynote. Semantic Indexing and Information Retrieval for Health Workshop at ECIR. Online. Video.

2019 May 22. "Ontology-based Integration of Biological Pathway Data." Invited talk. Scientific Literature Knowledge Bases Workshop at AKBC. Amherst, MA.

2018 Oct 11. "Ontologies and Algorithms for Integrating Biological Pathway Data." Invited talk. BIME 590: Departmental Seminar. Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA.

2018 Oct 10. "Learning from Biomedical Knowledge." Invited talk. The Allen Institute for AI, Seattle, WA. Video.


Teaching & Tutorials

"Practical NLP for Scientific Text Mining: Extracting and Synthesizing Knowledge from the Literature." Science of Science Summer School. Online.

"A SPARQL Tutorial." Guest lecture. BIME 550: Knowledge Representation. Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA. PDF

"A Brief Introduction to Ontology." Tutorial talk. Kidney Precision Medicine Project Ontology Workshop. PDF

2017. "Biological Pathway Analysis: Trends and Applications." BIME 591: Winter 2017 Seminar Course. Course website.

Note: You're welcome to reuse these materials, but I'd appreciate a credit.


Selected Press Coverage

Practical AI: Exploring the COVID-19 Open Research Dataset (Podcast)
Roll Call: AI researchers seeking COVID-19 answers face hurdles
Geekwire: Software tools for mining COVID-19 research studies go viral among scientists
King5: Free online tool identifies dangerous drug/supplement combinations
Geekwire: How do drugs interact with supplements? Supp.AI search engine tracks down clues
VentureBeat: Supp AI uses machine learning to identify supplement interactions
Axios: Another century of gender inequality in computer science
NYTimes: The Gender Gap in Computer Science Research Won’t Close for 100 Years
Geekwire: A study about studies suggests men will still prevail in computer science in 2100

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