Abeed Sarker, PhD

Research Program

Cancer Prevention and Control
Phone Number

404-712-0055
Email Address

abeed.sarker@emory.edu

Biography

Abeed Sarker, PhD, is an associate professor in the Department of Biomedical Informatics at Emory University School of Medicine. Dr. Sarker holds secondary appointments as associate professor in the Department of Computer Science of the College of Arts and Sciences at Emory University, and associate professor in the Department of Biomedical Engineering at Georgia Institute of Technology and Emory University.

Dr. Sarker is a member of the Cancer Prevention and Control Research Program at Winship Cancer Institute of Emory University in Atlanta, Georgia.

Education

Dr. Sarker earned his PhD in Computer Science at Macquarie University in Sydney, Australia. He completed his postdoctoral training in Biomedical Informatics at Arizona State University in Scottsdale, Arizona.

Titles & Roles

Associate Professor, Department of Biomedical Informatics

Emory University School of Medicine
Associate Professor, Department of Computer Science

College of Arts and Sciences, Emory University
Associate Professor, Wallace H. Coulter Department of Biomedical Engineering

Georgia Institute of Technology and Emory University

Research

Dr. Sarker's research interests and expertise lie at the intersection of natural language processing (NLP), applied machine learning, social media mining and the application of innovations in these fields to solve problems in the broader health domain. His research primarily focuses on developing data-centric solutions that utilize biomedical natural language data from various domains such as social media, clinical notes and medical literature. He is particularly interested in designing, developing and deploying end-to-end NLP and machine learning systems that can extract useful knowledge that is encapsulated within large free text data.

Publications

Dr. Sarker has authored over 50 peer-reviewed publications in journals, conferences and workshops. He currently serves as an associate editor for BMC Medical Informatics and Decision Making and is an editorial board member for Digital Health: Frontiers in Public Health.

Title/Journal	Authors	Publication Date
Risk Factors for Adverse Outcomes in a Fontan Population. Pediatric cardiology	G Licitra, LC Ivey, CL Raskind-Hood, FH Rodriguez, Y Guo, A Sarker, WM Book	06/06/2025
Building community through data: the value of a researcher driven open science ecosystem. Pain medicine (Malden, Mass.)	MCB Adams, CM Bann, EO Bayman, M Chao, GW Hergenroeder, C Knott, MA Lindquist, ZD Luo, R Martin, ME Martone, J McCarthy, M McCumber, SB Meropol, TA Ridenour, LM Saavedra, A Sarker, KJ Anstrom, WK Thompson	06/01/2025
The Digital Narrative: Chronic Pain Self-Management Insights from Reddit in Systemic Lupus Erythematosus. Studies in health technology and informatics	S Bozkurt, A Walker, T Park, N Le, A Sarker, A Irani, T Falasinnu	04/08/2025
Machine Learning and Natural Language Processing to Improve Classification of Atrial Septal Defects in Electronic Health Records. Birth defects research	Y Guo, H Shi, WM Book, LC Ivey, FH Rodriguez, R Sameni, C Raskind-Hood, C Robichaux, KF Downing, A Sarker	03/01/2025
CARE-SD: classifier-based analysis for recognizing provider stigmatizing and doubt marker labels in electronic health records: model development and validation. Journal of the American Medical Informatics Association : JAMIA	A Walker, A Thorne, S Das, J Love, HLF Cooper, M Livingston, A Sarker	02/01/2025
Applications of Natural Language Processing and Large Language Models for Social Determinants of Health: Protocol for a Systematic Review. JMIR research protocols	S Rajwal, Z Zhang, Y Chen, H Rogers, A Sarker, Y Xiao	01/21/2025
Two-Layer Retrieval-Augmented Generation Framework for Low-Resource Medical Question Answering Using Reddit Data: Proof-of-Concept Study. Journal of medical Internet research	S Das, Y Ge, Y Guo, S Rajwal, J Hairston, J Powell, D Walker, S Peddireddy, S Lakamana, S Bozkurt, M Reyna, R Sameni, Y Xiao, S Kim, R Chandler, N Hernandez, D Mowery, R Wightman, J Love, A Spadaro, J Perrone, A Sarker	01/06/2025
"I Been Taking Adderall Mixing it With Lean, Hope I Don't Wake Up Out My Sleep": Harnessing Twitter to Understand Nonmedical Prescription Stimulant Use among Black Women and Men Subscribers. medRxiv : the preprint server for health sciences	JL Webster, S Lakamana, Y Ge, A Sarker	12/05/2024
MultiADE: A Multi-domain benchmark for Adverse Drug Event extraction. Journal of biomedical informatics	X Dai, S Karimi, A Sarker, B Hachey, C Paris	12/01/2024
Evaluating large language models for health-related text classification tasks with public social media data. Journal of the American Medical Informatics Association : JAMIA	Y Guo, A Ovadje, MA Al-Garadi, A Sarker	10/01/2024
Natural Language Processing for Digital Health in the Era of Large Language Models. Yearbook of medical informatics	A Sarker, R Zhang, Y Wang, Y Xiao, S Das, D Schutte, D Oniani, Q Xie, H Xu	08/01/2024
Emerging Trends of Self-Harm Using Sodium Nitrite in an Online Suicide Community: Observational Study Using Natural Language Processing Analysis. JMIR mental health	S Das, D Walker, S Rajwal, S Lakamana, SA Sumner, KA Mack, W Kaczkowski, A Sarker	05/02/2024
Overview of the 8th Social Media Mining for Health Applications (#SMM4H) shared tasks at the AMIA 2023 Annual Symposium. Journal of the American Medical Informatics Association : JAMIA	AZ Klein, JM Banda, Y Guo, AL Schmidt, D Xu, I Flores Amaro, R Rodriguez-Esteban, A Sarker, G Gonzalez-Hernandez	04/03/2024
A large language model-based generative natural language processing framework fine-tuned on clinical notes accurately extracts headache frequency from electronic health records. Headache	CC Chiang, M Luo, G Dumkrieger, S Trivedi, YC Chen, CJ Chao, TJ Schwedt, A Sarker, I Banerjee	04/01/2024
Data Augmentation with Nearest Neighbor Classifier for Few-Shot Named Entity Recognition. Studies in health technology and informatics	Y Ge, MA Al-Garadi, A Sarker	01/25/2024
Detection of Medication Mentions and Medication Change Events in Clinical Notes Using Transformer-Based Models. Studies in health technology and informatics	Y Guo, Y Ge, A Sarker	01/25/2024
Area-level Measures of the Social Environment: Operationalization, Pitfalls, and Ways Forward. Current topics in behavioral neurosciences	M Helbich, Y Zeng, A Sarker	01/01/2024
Overview of the 8^th Social Media Mining for Health Applications (#SMM4H) Shared Tasks at the AMIA 2023 Annual Symposium. medRxiv : the preprint server for health sciences	AZ Klein, JM Banda, Y Guo, AL Schmidt, D Xu, JIF Amaro, R Rodriguez-Esteban, A Sarker, G Gonzalez-Hernandez	11/08/2023
Public Perceptions About Monkeypox on Twitter: Thematic Analysis. JMIR formative research	A Leslie, O Okunromade, A Sarker	11/03/2023
Self-reported Xylazine Experiences: A Mixed-methods Study of Reddit Subscribers. Journal of addiction medicine	A Spadaro, K O'Connor, S Lakamana, A Sarker, R Wightman, JS Love, J Perrone	11/01/2023
A Large Language Model-Based Generative Natural Language Processing Framework Finetuned on Clinical Notes Accurately Extracts Headache Frequency from Electronic Health Records. medRxiv : the preprint server for health sciences	CC Chiang, M Luo, G Dumkrieger, S Trivedi, YC Chen, CJ Chao, TJ Schwedt, A Sarker, I Banerjee	10/03/2023
An aspect-level sentiment analysis dataset for therapies on Twitter. Data in brief	Y Guo, S Das, S Lakamana, A Sarker	10/01/2023
Automatic Detection of Twitter Users Who Express Chronic Stress Experiences via Supervised Machine Learning and Natural Language Processing. Computers, informatics, nursing : CIN	YC Yang, A Xie, S Kim, J Hair, M Al-Garadi, A Sarker	09/01/2023
Characteristics of Intimate Partner Violence and Survivor's Needs During the COVID-19 Pandemic: Insights From Subreddits Related to Intimate Partner Violence. Journal of interpersonal violence	S Kim, E Warren, T Jahangir, M Al-Garadi, Y Guo, YC Yang, S Lakamana, A Sarker	09/01/2023
Self-reported Xylazine Experiences: A Mixed-methods Study of Reddit Subscribers. Journal of addiction medicine	A Spadaro, K O'Connor, S Lakamana, A Sarker, R Wightman, JS Love, J Perrone	08/10/2023
Few-shot learning for medical text: A review of advances, trends, and opportunities. Journal of biomedical informatics	Y Ge, Y Guo, S Das, MA Al-Garadi, A Sarker	08/01/2023
Supervised Text Classification System Detects Fontan Patients in Electronic Records With Higher Accuracy Than ICD Codes. Journal of the American Heart Association	Y Guo, MA Al-Garadi, WM Book, LC Ivey, FH Rodriguez, CL Raskind-Hood, C Robichaux, A Sarker	07/04/2023
Recruitment and retention in mobile application-based intervention studies: a critical synopsis of challenges and opportunities. Informatics for health & social care	W Bremer, A Sarker	04/03/2023
An analysis of cannabinoid hyperemesis syndrome Reddit posts and themes. Clinical toxicology (Philadelphia, Pa.)	RS Wightman, J Perrone, AB Collins, S Lakamana, A Sarker	04/01/2023
Self-reported Xylazine Experiences: A Mixed Methods Study of Reddit Subscribers. medRxiv : the preprint server for health sciences	A Spadaro, KO Connor, S Lakamana, A Sarker, R Wightman, JS Love, J Perrone	03/14/2023
Can accurate demographic information about people who use prescription medications nonmedically be derived from Twitter? Proceedings of the National Academy of Sciences of the United States of America	YC Yang, MA Al-Garadi, JS Love, HLF Cooper, J Perrone, A Sarker	02/21/2023
Automatic Detection of Intimate Partner Violence Victims from Social Media for Proactive Delivery of Support. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science	Y Guo, S Kim, E Warren, YC Yang, S Lakamana, A Sarker	01/01/2023
Generalizable Natural Language Processing Framework for Migraine Reporting from Social Media. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science	Y Guo, S Rajwal, S Lakamana, CC Chiang, PC Menell, AH Shahid, YC Pharm D, N Chhabra, WJ Chao, CJ Chao, TJ Schwedt, I Banerjee, A Sarker	01/01/2023
A framework for multi-faceted content analysis of social media chatter regarding non-medical use of prescription medications. BMC digital health	S Raza, B Schwartz, S Lakamana, Y Ge, A Sarker	01/01/2023
Barriers to opioid use disorder treatment: A comparison of self-reported information from social media with barriers found in literature. Frontiers in public health	W Bremer, K Plaisance, D Walker, M Bonn, JS Love, J Perrone, A Sarker	01/01/2023
Can adverse childhood experiences predict chronic health conditions? Development of trauma-informed, explainable machine learning models. Frontiers in public health	HB Afzal, T Jahangir, Y Mei, A Madden, A Sarker, S Kim	01/01/2023
#ChronicPain: Automated Building of a Chronic Pain Cohort from Twitter Using Machine Learning. Health data science	A Sarker, S Lakamana, Y Guo, Y Ge, A Leslie, O Okunromade, E Gonzalez-Polledo, J Perrone, AM McKenzie-Brown	01/01/2023
The Early Detection of Fraudulent COVID-19 Products From Twitter Chatter: Data Set and Baseline Approach Using Anomaly Detection. JMIR infodemiology	A Sarker, S Lakamana, R Liao, A Abbas, YC Yang, M Al-Garadi	01/01/2023
Evidence of the emergence of illicit benzodiazepines from online drug forums. European journal of public health	A Sarker, MA Al-Garadi, Y Ge, N Nataraj, L McGlone, CM Jones, SA Sumner	11/29/2022
The Role of Natural Language Processing during the COVID-19 Pandemic: Health Applications, Opportunities, and Challenges. Healthcare (Basel, Switzerland)	MA Al-Garadi, YC Yang, A Sarker	11/12/2022
Natural language model for automatic identification of Intimate Partner Violence reports from Twitter. Array (New York, N.Y.)	MA Al-Garadi, S Kim, Y Guo, E Warren, YC Yang, S Lakamana, A Sarker	09/01/2022
Comparison of Pretraining Models and Strategies for Health-Related Social Media Text Classification. Healthcare (Basel, Switzerland)	Y Guo, Y Ge, YC Yang, MA Al-Garadi, A Sarker	08/05/2022
Thematic Analysis of Reddit Content About Buprenorphine-naloxone Using Manual Annotation and Natural Language Processing Techniques. Journal of addiction medicine	RL Graves, J Perrone, MA Al-Garadi, YC Yang, J Love, K O'Connor, G Gonzalez-Hernandez, A Sarker	07/01/2022
Reddit discussions about buprenorphine associated precipitated withdrawal in the era of fentanyl. Clinical toxicology (Philadelphia, Pa.)	A Spadaro, A Sarker, W Hogg-Bremer, JS Love, N O'Donnell, LS Nelson, J Perrone	06/01/2022
A comparison of few-shot and traditional named entity recognition models for medical text. Proceedings. IEEE International Conference on Healthcare Informatics	Y Ge, Y Guo, YC Yang, MA Al-Garadi, A Sarker	06/01/2022
Signals of increasing co-use of stimulants and opioids from online drug forum data. Harm reduction journal	A Sarker, MA Al-Garadi, Y Ge, N Nataraj, CM Jones, SA Sumner	05/25/2022
Concerns among people who use opioids during the COVID-19 pandemic: a natural language processing analysis of social media posts. Substance abuse treatment, prevention, and policy	A Sarker, N Nataraj, W Siu, S Li, CM Jones, SA Sumner	03/05/2022
Tracking the COVID-19 outbreak in India through Twitter: Opportunities for social media based global pandemic surveillance. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science	S Lakamana, YC Yang, MA Al-Garadi, A Sarker	01/01/2022
Large-Scale Social Media Analysis Reveals Emotions Associated with Nonmedical Prescription Drug Use. Health data science	MA Al-Garadi, YC Yang, Y Guo, S Kim, JS Love, J Perrone, A Sarker	01/01/2022
A Data-Driven Iterative Approach for Semi-automatically Assessing the Correctness of Medication Value Sets: A Proof of Concept Based on Opioids. Methods of information in medicine	L Li, A Grando, A Sarker	12/01/2021
Methadone and suboxone^® mentions on twitter: thematic and sentiment analysis. Clinical toxicology (Philadelphia, Pa.)	M Chenworth, J Perrone, JS Love, R Graves, W Hogg-Bremer, A Sarker	11/01/2021
Defining Patient-Oriented Natural Language Processing: A New Paradigm for Research and Development to Facilitate Adoption and Use by Medical Experts. JMIR medical informatics	A Sarker, MA Al-Garadi, YC Yang, J Choi, AA Quyyumi, GS Martin	09/28/2021
LexExp: a system for automatically expanding concept lexicons for noisy biomedical texts. Bioinformatics (Oxford, England)	A Sarker	08/25/2021
Mining long-COVID symptoms from Reddit: characterizing post-COVID syndrome from patient reports. JAMIA open	A Sarker, Y Ge	07/01/2021
Developing an Automatic System for Classifying Chatter About Health Services on Twitter: Case Study for Medicaid. Journal of medical Internet research	YC Yang, MA Al-Garadi, W Bremer, JM Zhu, D Grande, A Sarker	05/03/2021
Automatic gender detection in Twitter profiles for health-related cohort studies. JAMIA open	YC Yang, MA Al-Garadi, JS Love, J Perrone, A Sarker	04/01/2021
Utilizing a multi-class classification approach to detect therapeutic and recreational misuse of opioids on Twitter. Computers in biology and medicine	SJ Fodeh, M Al-Garadi, O Elsankary, J Perrone, W Becker, A Sarker	02/01/2021
Text classification models for the automatic detection of nonmedical prescription medication use from social media. BMC medical informatics and decision making	MA Al-Garadi, YC Yang, H Cai, Y Ruan, K O'Connor, GH Graciela, J Perrone, A Sarker	01/26/2021