Publications

Individual publication pages

Graciela Gonzalez (Google Scholar, NIH NCBI)

Abeed Sarker (Google Scholar, NIH NCBI)

Masoud Rouhizadeh (Google Scholar)

Karen O’Connor (Google Scholar)

Group publications

Sarker A, Gonzalez G. A corpus for mining drug-related knowledge from Twitter chatter: language models and their utilities. Data Brief. 2016 Nov 23;10:122-131. eCollection 2017 Feb. PMID: 27981203.

Sarker A, Malone D, Gonzalez G. Authors’ Reply to Jouanjus and Colleagues’ Comment on “Social Media Mining for Toxicovigilance: Automatic Monitoring of Prescription Medication Abuse from Twitter”. Drug Safety. 2017 Feb;40(2):187-188. doi: 10.1007/s40264-016-0498-6. PMID: 28070742

Sarker A, Magge A, Sharma A. Dermatologic concerns communicated through Twitter. International Journal of Dermatology. 2017 Feb 12. doi: 10.1111/ijd.13506. PMID: 28191639.

Korkontzelos I, Nikfarjam A, Shardlow M, Sarker A, Ananidou S, Gonzalez G. Improving extraction of adverse drug rections from tweets and forum posts using sentiment analysis features. Journal of Biomedical Informatics. 2016; Vol. 62. 148—158.

Tahsin T, Weissenbacher D, Rivera R, Firago M, Wallstrom G, Scotch M, Gonzalez G. A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records. Journal of the American Medical Informatics Association. 2016 Sep;23(5):934-41. doi: 10.1093/jamia/ocv172. Epub 2016 Jan 17.

Sarker A, O’Connor K, Ginn R, Scotch M, Smith K, Malone D, Gonzalez G. Social Media Mining for Toxicovigilance: Automatic Monitoring of Prescription Medication Abuse from Twitter. 2015; 39(3):231—240.

Sarker A, Mollá D, Paris C. Automatic evidence quality prediction to support evidence-based decision making. Artificial Intelligence in Medicine. 2015; 64(2). 89—103.

Sarker A, Ginn R, Nikfarjam A, O’Connor K, Smith K, Jayaraman S, Upadhaya T, Gonzalez G. Utilizing social media data for pharmacovigilance: a review. Journal of Biomedical Informatics. 2015; Vol. 54. 202—212.

Nikfarjam A, Sarker A, O’Connor K, Ginn R, Gonzalez G. Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features. Journal of the Amedican Medical Informatics Association. 2015; 22(3):671—681.

Sarker A, Gonzalez G. Portable automatic text classification for adverse drug reaction detection via multi-corpus training. Journal of Biomedical Informatics. 2015; Vol. 53: 196—207.

Emadzadeh E, Nikfarjam A,  Ginn RE,  Gonzalez G; Unsupervised gene function extraction using semantic vectors, Oxford University Press, Database (2014) Sep 10;2014. pii: bau084.

Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJF, Wang S, Gobeill J, Ruch P, Tuan Luu A, Kim J, Chiang J, Chen Y, Yang C, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen J, Dai H, Lu Z; Overview of the gene ontology task at BioCreative IV, Oxford University Press, Database (2014) July 2014 : bau086.

Nikfarjam A, Emadzadeh E, Gonzalez G; Towards generating a patient’s timeline: Extracting temporal relationships from clinical notes, Journal of Biomedical Informatics, 2013.

Jonnalagadda SR, Cohen T, Wu S, Liu H, Gonzalez G; Using empirically constructed Lexical Resources for named entity Recognition, Journal of Biomedical Informatics Insights, 2013:6 (Suppl. 1) 17-27.

Nikfarjam A, Emadzadeh E, Gonzalez G; A Hybrid system for Emotion Extraction from Suicide Notes, Journal of Biomedical Informatics Insights, 2012:5 (Suppl. 1) 165-174.

Jonnalagadda SR, Cohen T, Wu S, Gonzalez G; Enhancing clinical concept extraction with distributional semantics, Journal of Biomedical Informatics, 2012 Feb; 45(1):129-40. Epub 2011 Nov 7 (PMID 22085698; PMC3272090).

Conference and Workshop Publications

Sarker A, Gonzalez G. HLP@UPenn at SemEval-2017 Task 4A: A simple, self-optimizing text classification system combining dense and sparse vectors. SemEval 2017. To appear.

Smith K, Sarker A, Nikfarjam A, Malone D, Gonzalez G. Mining Adverse Events in Twitter: Experiences of Adalimumab Users. ISPOR 22nd Annual International Meeting. 2017. Abstract.

Weissenbacher D, Sarker A, Tahsin T, Scotch M, Gonzalez G. Extracting geographic locations from the literature for virus phylogeography using supervised and distant supervision methods. AMIA TBI Joint Summits. 2017.

Chandrashekar P, Magge A, Sarker A, Gonzalez G. Social media mining for identification and exploration of health-related information from pregnant women. Workshop on Mining Online Health Reports (MOHRS). 2017. Cambridge, U.K. Archived at: arXiv:1702.02261.

Sullivan R, Sarker A, O’Connor K, Goodin A, Karlsrud M, Gonzalez G; Finding potentially unsafe nutritional supplements from user reviews with topic modeling. Pacific Symposium of Biocomputing (PSB). 2016; 528—539.

Sarker A, Nikfarjam A, Gonzalez G. Social Media Mining Shared Task Workshop. Pacific Symposium on Biocoputing (PSB). 2016. 581—592.

Paul MJ, Sarker A, Brownstein JS, Nikfarjam A, Scotch M, Smith K, Gonzalez G. Social Media Mining for Public Health Monitoring and Surveillance. Pacific Symposium on Biocomputing (PSB). 2016.  468—479.

Weissenbacher D, Travis JA, Laura W, Amylou D, Dona L, Richard C, Gonzalez G. Towards Automatic Detection of Abnormal Cognitive Decline and Dementia Through Linguistic Analysis of Writing Samples. Proceedings of NAACL. 1198-1207. 2016.

Weissenbacher D, Tahsin T, Beard R, Figaro M, Rivera R, Scotch M, Gonzalez G;  Knowledge-driven geospatial location resolution for phylogeographic models of virus migration, in 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)/14th European Conference on Computational Biology (ECCB). 2015, Accepted: Dublin, Ireland.

Sarker A, Nikfarjam A, Weissenbacher D, Gonzalez G. DIEGOLab: An Approach for Message-level Sentiment Classification in Twitter. SemEval-2015. 2015; 510—514.

O’Connor K, Nikfarjam A, Ginn R, Pimpalkhute P, Sarker A, Smith K, Gonzalez G, Pharmacovigilance on Twitter? Mining Tweets for Adverse Drug Reactions, Proceedings of the Annual Symposium of the American Medical Informatics Association, Washington DC. November 2014.

Ginn R, Pimpalkhute P, Nikfarjam A, Patki A, O’Connor K, Sarker A, Smith K, Gonzalez G. Mining Twitter for adverse drug reaction mentions: a corpus classification benchmark. LREC-14. 2014.

Sullivan R, Yao R, Jarar R, Buchhalter J; Text Classification towards Detecting Misdiagnosis of an Epilepsy Syndrome in a Pediatric Population, Proceedings of the Annual Symposium of the American Medical Informatics Association, Washington DC, November 2014.

Patki A, Sarker A, Pimpalkhute P, Nikfarjam A, Ginn R, O’Connor K, Smith K, Gonzalez G; Mining Adverse Drug Reaction Signals from Social Media: Going Beyond Extraction, In: Proceedings of Phenotype Day @ ISMB, Joint Bio-Ontologies and  BioLink SIGs Session, July 2014, Boston MA.

Pimpalkhute P, Patki A, Nikfarjam A, Gonzalez G; Phonetic spelling filter for keyword selection in drug mention mining from social media. AMIA Summits Transl Sci Proc. 2014 Apr 7;2014:90-5. eCollection 2014.

Furniss SK, Yao R, Gonzalez G; Automatic Gene Prioritization in Support of the Inflammatory Contribution to Alzheimer’s Disease, AMIA Summits on Translational Science Proceedings, 2014.

Tahsin T, Beard R, Rivera R, Lauder R, Wallstrom G, Scotch M, Gonzalez G; Natural language processing methods for enhancing geographic metadata for phylogeography of zoonotic viruses. AMIA Jt Summits Transl Sci Proc. 2014 Apr 7;2014:102-11. eCollection 2014.

*Papers listed here include those that were published prior to the opening of the HLP lab.