Publications

Graves RL, Perrone J, Al-Garadi MA, Yang YC, Love JS, O’Connor K, Gonzalez-Hernandez G, Sarker A. Thematic Analysis of Reddit Content About Buprenorphine-naloxone Using Manual Annotation and Natural Language Processing Techniques. Journal of addiction medicine. 2021 Dec 3.

Sarker A, Al-Garadi MA, Yang Y, Choi J, Quyyumi AA, Martin GS. Defining Patient-Oriented Natural Language Processing: A New Paradigm for Research and Development to Facilitate Adoption and Use by Medical Experts. JMIR Med Inform 2021;9(9):e18471

Sarker A, Ge Y. Mining long-COVID symptoms from Reddit: characterizing post-COVID syndrome from patient reports. JAMIA open. 2021 Jul;4(3):ooab075.

Yang YC, Al-Garadi MA, Love JS, Perrone J, Sarker A. Automatic gender detection in Twitter profiles for health-related cohort studies. JAMIA Open. 2021 Apr;4(2):ooab042.

Guo Y, Ge Y, Al-Garadi MA, Sarker A. Pre-Trained Transformer-Based Classification and Span Detection Models for Social Media Health Applications. Proceedings of the Sixth Social Media Mining for Health (#SMM4H) Workshop and Shared Task. Association for Computational Linguistics. 2021; 52-57. Mexico City, Mexico.

Magge A, Klein A, Miranda-Escalada, Al-Garadi MA, Alimova I, Miftahutdinov Z, Farre E, Lopez SL, Flores I, O’Connor K, Weissenbacher D, Tutubalina E, Sarker A, Banda J, Krallinger M, Gonzalez-Hernandez G. Overview of the Sixth Social Media Mining for Health Applications (#SMM4H) Shared Tasks at NAACL 2021. Proceedings of the Sixth Social Media Mining for Health (#SMM4H) Workshop and Shared Task. Association for Computational Linguistics. 2021; 21 – 32. Mexico City, Mexico.

Yang YC, Al-Garadi MA, Bremer W, Zhu JM, Grande D, Sarker A. Developing an Automatic System for Classifying Chatter About Health Services on Twitter: Case Study for Medicaid. J Med Internet Res. 2021 May 3;23(5):e26616. doi: 10.2196/26616. PMID: 33938807; PMCID: PMC8129876.

Yang YC, Al-Garadi MA, Love J, Perrone J, Sarker A. Gender Differences in Nonmedical Use of Prescription Opioids, Tranquilizers and Stimulant Medications Using Machine Learning and Social Media. Proceedings of the ACMT Annual Summit [meeting abstract]. 2021 (virtual).

Chenworth M, Perrone J, Love JS, Graves R, Hogg-Bremer W, Sarker A. Methadone and Suboxone® Mentions on Twitter: Thematic and Sentiment Analysis. Clin Toxicol (Phila). 2021 Apr 6:1-14. doi: 10.1080/15563650.2021.1893742. Epub ahead of print. PMID: 33821724.

Lakamana S, Al-Garadi MA, Yang YC, Sarker A. CoviDash-SM: A Public COVID19 Dashboard for Social Media Data-Based Research and Surveillance. Proceedings of the AMIA Informatics Summit (posters). 2021 (virtual). doi: 10.13140/RG.2.2.23784.80644.

Leslie A, Lakamana S, Sarker A. Syndromic Surveillance for COVID19 from Reddit using Multi-Platform Lexicons. AMIA Informatics Summit (posters). March 22 – 25 (virtual).

Fodeh, S. J., Al-Garadi, M., Elsankary, O., Perrone, J., Becker, W., Sarker, A. Utilizing a Multi-Class Classification Approach to Detect Therapeutic and Recreational Misuse of Opioids on Twitter. Computers in Biology and Medicine, 129 (2021), 104132.

Al-Garadi MA, Yang YC, Cai H, Ruan Y, O'Connor K, Graciela GH, Perrone J, Sarker A. Text Classification Models for the Automatic Detection of Nonmedical Prescription Medication Use from Social Media. BMC Med Inform Decis Mak. 2021 Jan 26;21(1):27. doi: 10.1186/s12911-021-01394-0. PMID: 33499852; PMCID: PMC7835447.

Sarker A, Yang YC, Al-Garadi MA. A Light-Weight Text Summarization System for Fast Access to Medical Evidence. Front Digit Health. 2020 Dec 04; 3:585559. doi: 10.3389/fdgth.2020.585559.

Guo Y, Dong X, Al-Garadi MA, Sarker A, Paris C, Molla-Aliod D. Benchmarking of Transformer-Based Pre-Trained Models on Social Media Text Classification Datasets. Proceedings of the The 18th Annual Workshop of the Australasian Language Technology Association (virtual). 2020; 86 – 91.

Sarker A. LexExp: A System for Automatically Expanding Concept Lexicons for Noisy Biomedical Texts. Bioinformatics. 2020 Nov 27:btaa995. doi: 10.1093/bioinformatics/btaa995. Epub ahead of print. PMID: 33244602.

Fodeh SJ, Al-Garadi M, Elsankary O, Perrone J, Becker W, Sarker A. Utilizing a Multi-Class Classification Approach to Detect Therapeutic and Recreational Misuse of Opioids on Twitter. Comput Biol Med. 2021 Feb;129:104132. doi: 10.1016/j.compbiomed.2020.104132. Epub 2020 Nov 20. PMID: 33290931; PMCID: PMC7855783.

Guo Y, Al-Garadi MA, Sarker A. Emory at WNUT-2020 Task 2: Combining Pretrained Deep Learning Models and Feature Enrichment for Informative Tweet Identification. Proceedings of the 2020 EMNLP Workshop W-NUT: The Sixth Workshop on Noisy User-generated Text. 2020; 388-393. Association for Computational Linguistics (virtual).

Tofighi B, El Shahawy O, Segoshi A, Moreno KP, Badiei B, Sarker A, Krawczyk N. Assessing Perceptions about Medications for Opioid Use Disorder and Naloxone on Twitter. J Addict Dis. 2020 Aug 24:1-9. doi: 10.1080/10550887.2020.1811456. Epub ahead of print. PMID: 32835641.

Zhu JM, Sarker A, Gollust S, Merchant R, Grande D. Characteristics of Twitter Use by State Medicaid Programs in the United States: Machine Learning Approach. J Med Internet Res. 2020 Aug 17;22(8):e18401. doi: 10.2196/18401. PMID: 32804085; PMCID: PMC7459428.

Sarker A, Lakamana S, Hogg-Bremer W, Xie A, Al-Garadi MA, Yang YC. Self-Reported COVID-19 Symptoms on Twitter: An Analysis and a Research Resource. J Am Med Inform Assoc. 2020 Aug 1;27(8):1310-1315. doi: 10.1093/jamia/ocaa116. PMID: 32620975; PMCID: PMC7337747.

Zhu JM, Sarker A, Gollust S, Merchant R, Grande D. Characteristics of Twitter Use by State Medicaid Programs in the United States: A Machine Learning Application. Proceedings of the AcademyHealth Annual Research Meeting. 2020 (virtual).

Davoudi A, Klein AZ, Sarker A, Gonzalez-Hernandez G. Towards Automatic Bot Detection in Twitter for Health-related Tasks. AMIA Jt Summits Transl Sci Proc. 2020; 136-141. PMID: 32477632; PMCID: PMC7233076.

Al-Garadi MA, Yang YC, Lakamana S, Lin J, Li S, Xie A, Hogg-Bremer W, Torres M, Banerjee I, Sarker A. Automatic Breast Cancer Cohort Detection from Social Media for Studying Factors Affecting Patient Centered Outcomes. Proceedings of the Conference on Artificial Intelligence in Medicine (AIME). 2020. Minneapolis, Minnesota. doi: 10.1101/2020.05.17.20104778.

O’Connor K, Sarker A, Perrone J, Gonzalez-Hernandez G. Promoting Reproducible Research for Characterizing Nonmedical Use of Medications Through Data Annotation: Description of a Twitter Corpus and Guidelines. Journal of Medical Internet Research. 2020;22(2): e15861. PMID: 32130117 PMCID: PMC7066507.

A Sarker, A DeRoos, J Perrone. Mining Social Media for Prescription Medication Abuse Monitoring: A Review and Proposal for a Data-Centric Framework. J Am Med Inform Assoc. 2020 Feb 1; 27(2):315-329. doi: 10.1093/jamia/ocz162. PMID: 31584645; PMCID: PMC7025330.

Chenworth M, Perrone J, Love JS, Greller HA, Sarker A, Chai PR. Buprenorphine Initiation in the Emergency Department: A Thematic Content Analysis of a #firesidetox Tweetchat. J Med Toxicol. 2020 Jul;16(3):262-268. doi: 10.1007/s13181-019-00754-7. Epub 2020 Jan 2. PMID: 31898154; PMCID: PMC7320102.

Weissenbacher, Davy, Abeed Sarker, Ari Klein, Karen O'Connor, Arjun Magge Ranganatha, and Graciela Gonzalez-Hernandez. Deep Neural Networks Ensemble for Detecting Medication Mentions in Tweets. J Am Med Inform Assoc. 2019 Dec 1; 26(12):1618-1626. doi: 10.1093/jamia/ocz156. PMID: 31562510; PMCID: PMC6857507.

A Sarker, G Gonzalez-Hernandez, Y Ruan, J Perrone. Machine Learning and Natural Language Processing for Geolocation-Centric Monitoring and Characterization of Opioid-Related Social Media Chatter. JAMA Netw Open. 2019 Nov 1;2(11):e1914672. doi: 10.1001/jamanetworkopen.2019.14672. PMID: 31693125; PMCID: PMC6865282.

Klein, Ari Z., Abeed Sarker, Davy Weissenbacher, and Graciela Gonzalez-Hernandez. Towards Scaling Twitter for Digital Epidemiology of Birth Defects. NPJ Digit Med. 2019 Oct 1; 2:96. doi: 10.1038/s41746-019-0170-5. PMID: 31583284; PMCID: PMC6773753.

Sarker A, Gonzalez-Hernandez G, Perrone J. Towards Automating Location-Specific Opioid Toxicosurveillance from Twitter via Data Science Methods. Stud Health Technol Inform. 2019 Aug 21;264:333-337. doi: 10.3233/SHTI190238. PMID: 31437940; PMCID: PMC6774610.

Dirkson, Anne, Suzan Verberne, Abeed Sarker, and Wessel Kraaij. Data-Driven Lexical Normalization for Medical Social Media. Multimodal Technologies and Interaction. 2019 Aug 20; 3(3):60. DOI: 10.3390/mti3030060.

Sarker A, Klein AZ, Mee J, Harik P, Gonzalez-Hernandez G. An Interpretable Natural Language Processing System for Written Medical Examination Assessment. J Biomed Inform. 2019 Oct;98:103268. doi: 10.1016/j.jbi.2019.103268. Epub 2019 Aug 14. PMID: 31421211.

Weissenbacher, Davy, Abeed Sarker, Arjun Magge, Ashlynn Daughton, Karen O’Connor, Michael Paul, and Graciela Gonzalez. Overview of the Fourth Social Media Mining for Health (SMM4H) Shared Tasks at ACL 2019. Proceedings of the 4th Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task. 2019; 21-30. Florence, Italy. doi: 10.18653/v1/W19-3203.

Magge, Arjun, Abeed Sarker, Azadeh Nikfarjam, and Graciela Gonzalez-Hernandez. Comment on: "Deep Learning for Pharmacovigilance: Recurrent Neural Network Architectures for Labeling Adverse Drug Reactions in Twitter Posts". J Am Med Inform Assoc. 2019 Jun 1; 26(6):577-579. doi: 10.1093/jamia/ocz013. PMID: 31087070; PMCID: PMC6515520.

A Sarker, G Gonzalez-Hernandez, F DeRoos, J Perrone. Towards Real-Time Opioid Abuse Surveillance: Machine Learning for Automatic Characterization of Opioid-Related Tweets. Proceedings of the 39th International Congress of the European Association of Poisons Centres and Clinical Toxicologists (EAPCCT). 2019. Naples, Italy.

Sarker A, Gonzalez G, DeRoos F, Perrone J. Characterizing Opioid-Related Tweets: A Comparison Between Prescription and Illicit Opioid Chatter. Proceedings of the 39th International Congress of the European Association of Poisons Centres and Clinical Toxicologists (EAPCCT). 2019. Naples, Italy.

Klein AZ, Sarker A, Weissenbacher D, Gonzalez G. An Analysis of a Twitter Corpus for Training a Medication Intake Classifier. Proceedings of the AMIA Joint Summits on Translational Science. 2019; 102-106. San Francisco, USA.

J Love, J Perrone, R Graves, Abeed Sarker. Sentiment, Themes, and Analyses in Tweets about Suboxone. Proceedings of the ACMT Annual Summit [meeting abstract]. 2019; 58-59. San Francisco, USA. doi: https://doi.org/10.1007/s13181-019-00699-x.

R Graves, J Perrone, J Love, Abeed Sarker. Can Reddit Reveal Unique Facets of Suboxone Use and Misuse? Proceedings of the ACMT Annual Summit [meeting abstract]. 2019. San Francisco, USA. doi: 10.1007/s13181-019-00699-x.

Magge A, Weissenbacher D, Sarker A, Scotch M, Gonzalez G. Bi-Directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature. Proceedings of the Pacific Symposium on Biocomputing (PSB 2019). 2019; 100-111. Hawaii, USA.