The D.I.E.G.O. lab is focused on advancing knowledge extraction, integration, and analysis methods that empower biomedical discoveries. We are particularly interested in existing knowledge that is embedded in biomedical literature and we are currently working in the areas of:
Research Scholar
Email: abeed.sarker@asu.edu | website
Social Media Mining
Natural Language Processing
Machine Learning
Mining Social Network Postings for Mentions of Potential Adverse Drug Reactions
Research Scholar
Email: davy.weissenbacher@asu.edu
Research Specialist
Email: amol.bhalla@asu.edu
Research Assistant
Email: ehsan.emadzadeh@asu.edu
Research Assistant
Email: neel.mehta@asu.edu
Research Assistant
Email: azadeh.nikfarjam@asu.edu
Research Assistant
Email: ryan.sullivan@asu.edu
Research Assistant
Email: tasnia.tahsin@asu.edu
Research Assistant
Email: laura.wojtulewicz@asu.edu
Research Assistant
Email: robertjames.yao@asu.edu
Research Assistant
Research Assistant
Research Assistant
Research Assistant
Research Assistant
Research Assistant
Research Assistant
Abeed Sarker, Karen O'Connor, Rachel Ginn, Matthew Scotch, Karen Smith, Dan Malone, Graciela Gonzalez. Social Media Mining for Toxicovigilance: Automatic Monitoring of Prescription Medication Abuse from Twitter. Drug Safety. 2016 Mar;39(3):231-40. doi: 10.1007/s40264-015-0379-4
Abeed Sarker, Azadeh Nikfarjam, Graciela Gonzalez. Social Media Mining Shared Task Workshop. Pacific Symposium on Biocomputing. 2016.
Ryan Sullivan, Abeed Sarker, Karen O'Connor, Amanda Gooding, Mark Karlsrud, Graciela Gonzalez. Finding Potentially Unsafe Nutritional Supplements from User Reviews With Topic Modeling. Pacific Symposium on Biocomputing. 2016.
Michael J Paul, Abeed Sarker, John S Brownstein, Azadeh Nikfarjam, Matthew Scotch, Karen L Smith, Graciela Gonzalez. Social Media Mining for Public Health Monitoring and Surveillance. Pacific Symposium on Biocomputing. 2016.
Azadeh Nikfarjam, Abeed Sarker, Karen O'Connor, Rachel Ginn, Pranoti Pimpalkhute, Graciela Gonzalez. Pharmacovigilance from social media: Extraction of adverse drug reaction mentions using sequence labeling with word embedding cluster features. Journal of the American Medical Informatics Association.
Abeed Sarker, Rachel Ginn, Azadeh Nikfarjam, Karen O'Connor, Karen Smith, Swetha Jayaraman, Tejaswi Upadhaya, Graciela Gonzalez. Utilizing social media data for pharmacovigilance: A review. Journal of Biomedical Informatics. 54 (2015) 202-212.
Abeed Sarker, Azadeh Nikfarjam, Davy Weissenbacher, Graciela Gonzalez. DIEGOLab: An Approach for Message-level Sentiment Classification in Twitter. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015), pages 510-514, Denver, Colorado, June 4-5, 2015.
Davy Weissenbacher, Tasnia Tahsin, Rachel Beard, Mari Firago, Robert Rivera, Matthew Scotch, Graciela Gonzalez. Knowledge-driven geospatial location resolution for phylogeographic models of virus migration, Bioinformatics (2015) 31 (12): i348-i356. doi: 10.1093/bioinformatics/btv259.
Tasnia Tahsin, Davy Weissenbacher, Robert Rivera, Rachel Beard, Mari Firago, Garrick Wallstrom, Matthew Scotch, Graciela Gonzales. A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records.DOI: http://dx.doi.org/10.1093/jamia/ocv172 ocv172 First published online: 17 January 2016.
Rachel Ginn, Pranoti Pimpalkhute, Azadeh Nikfarjam, Apurv Patki, Karen O'Connor, Abeed Sarker, Karen Smith and Graciela Gonzalez. Mining Twitter for Adverse Drug Reaction Mentions: A Corpus and Classification Benchmark. In proceedings of the Fourth Workshop on Building and Evaluating Resources for Health and Biomedical Text Processing (BioTxtM2014). May, 2014. Reykjavik, Iceland.
Apurv Patki, Abeed Sarker, Pranoti Pimpalkhute, Azadeh Nikfarjam, Rachel Ginn, Karen O'Connor, Karen Smith, Graciela Gonzalez. Mining adverse drug reaction signals from social media: going beyond extraction. In: Proceedings of BioLinkSig 2014; 2014.
Abeed Sarker and Graciela Gonzalez. Portable automatic text classification for adverse drug reaction detection via multi-corpus training. Journal of Biomedical Informatics. 53 (2015) 196–207.
Karen O'Connor, Azadeh Nikfarjam, Rachel Ginn, Pranoti Pimpalkhute, Abeed Sarker, Karen Smith, Graciela Gonzalez. Pharmacovigilance on Twitter? Mining Tweets for Adverse Drug Reactions. AMIA Annual Symposium 2014.
P Pimpalkhute, A Patki, A Nikfarjam, G Gonzalez. "Phonetic spelling filter for keyword selection in drug mention mining from social media." AMIA TBI Summit (2014).
Siddhartha Jonnalagadda, Trevor Cohen, Stephen Wu, Hongfang Liu, and Graciela Gonzalez. 2013.
Evaluating the Use of Empirically Constructed Lexical Resources for Named Entity Recognition. In Proceedings of CSCT 2013, pages 23-33.
Jonnalagadda S, Cohen T, Wu S, Liu H, Gonzalez G.
Using Empirically Constructed Lexical Resources for Named Entity Recognition. Biomed Inform Insights. 2013.
Authors: G Gonzalez, KB Cohen, CS Greene, MG Kann, R Leaman, N Shah, J Ye.
Azadeh Nikfarjam , Ehsan Emadzadeh , Graciela Gonzalez.
Towards generating a patient's timeline: Extracting temporal relationships from clinical notes, Journal of Biomedical Informatics, 46, p.S40-S47, December, 2013
Azadeh Nikfarjam, Ehsan Emadzadeh, Graciela Gonzalez.
Robert Yao, Jeffrey Buchhalter, Graciela Gonzalez
GRACIELA Gonzalez, KEVIN BRETONNEL Cohen, CASEY S Greene, U Hahn, MARICEL G Kann, ROBERT Leaman, NIGAM Shah, JIEPING Ye.
Nikfarjam, Azadeh, et al.
"Temporal relationship extraction from clinical-notes using SVM and graph reasoning." Proceedings of. 2012.
Jonnalagadda S, Cohen T, Wu S, et al.
Enhancing clinical concept extraction with distributional semantics. J Biomed Inform 2012;45:129–40.
Nate Sutton, Laura Wojtulewicz, Neel Mehta, Graciela Gonzalez.
Lee JH, Gonzalez GH.
Towards integrative gene prioritization in Alzheimer's disease. Pacific Symposium on Biocomputing, Hawaii, USA: World Scientific, 2011:4–13.
Nikfarjam, Azadeh and Graciela H. Gonzalez.
"Pattern Mining for Extraction of mentions of Adverse Drug Reactions from User Comments." AMIA Annual Symposium Proceeding, 2011.
Robert Yao, Graciela Gonzalez.
Biomedical Informatics in Translational Research, Hai Hu, Richard J. Mural, Michael N. Liebman (Eds.). Artech House (2008).
Ehsan Emadzadeh, Azadeh Nikfarjam, Graciela Gonzalez.
Double layered learning for biological event extraction from text, Proceedings of the BioNLP Shared Task 2011 Workshop, p.153-154, June 24-24, 2011, Portland, Oregon
Hakenberg J., et al.
The GNAT library for local and remote gene mention normalization. Bioinformatics 2011;27:2769-2771.
Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sergio Matos, Sun Kim, W Wilbur, Luis Rocha, Hagit Shatkay, Ashish V Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu, Rezarta Dogan, Jean-Fred Fontaine, Miguel A Andrade-Navarro, Alfonso Valencia
Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, et al.
The protein-protein interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics 2011;12 Suppl. 8:S3.
Ehsan Emadzadeh, Siddhartha Jonnalagadda, Graciela Gonzalez.
Ryan Sullivan, Robert Leaman, Graciela Gonzalez.
Scotch M, Sarkar IN, Mei C, Leaman R, Cheung KH, Ortiz P, Singraur A, Gonzalez G.
Enhancing phylogeography by improving geographical information from GenBank. J Biomed Inform 2011, 44(1):S44-47.
Jonnalagadda, Siddhartha, et al.
"A distributional semantics approach to simultaneous recognition of multiple classes of named entities." Computational Linguistics and Intelligent Text Processing. Springer Berlin Heidelberg, 2010. 224-235.
L. Tari et al,, 2009.
Parse Tree Database for Information Extraction, IEEE TRANSACTIONS ON KNOWLEDGE & DATA ENGINEERING
Jonnalagadda, Siddhartha, and Graciela Gonzalez.
"BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction." AMIA Annual Symposium Proceedings. Vol. 2010. American Medical Informatics Association, 2010.
Jonnalagadda, Siddhartha, and Graciela Gonzalez.
"Can distributional statistics aid clinical concept extraction." Proceedings of the 2010 i2b2/VA Workshop on Challenges in Natural Language Processing for Clinical Data. Boston, MA, USA: i2b2. 2010.
Jonnalagadda, Siddhartha, and Graciela Gonzalez.
"Sentence simplification aids protein-protein interaction extraction." arXiv preprint arXiv:1001.4273(2010).
Luis Tari, Phan Huy Tu, Jörg Hakenberg, Yi Chen, Tran Cao Son, Graciela Gonzalez, Chitta Baral.
Hakenberg, Jörg, et al.
"Efficient extraction of protein-protein interactions from full-text articles." IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 7.3 (2010): 481-494.
Leaman, Robert, Laura Wojtulewicz, Ryan Sullivan, Annie Skariah, Jian Yang, and Graciela Gonzalez.
"Towards internet-age pharmacovigilance: extracting adverse drug reactions from user posts to health-related social networks."Proceedings of the 2010 workshop on biomedical natural language processing. Association for Computational Linguistics, 2010.
Emadzadeh, Ehsan, Azadeh Nikfarjam, and Saravanan Muthaiyah.
"A comparative study on Measure of Semantic Relatedness function." Computer and Automation Engineering (ICCAE), 2010 The 2nd International Conference on. Vol. 1. IEEE, 2010.
Leaman R, Sullivan R, Gonzalez G.
Proceedings of the BioCreative III workshop; Bethesda MA, USA. CNIO; 2010. A top-down approach for finding interaction detection methods; pp. 99–103.
Emadzadeh, Ehsan, et al.
"Learning Materials Recommendation Using a Hybrid Recommender System with Automated Keyword Extraction." World Applied Sciences Journal 9.11 (2010): 1260-1271.
Jonnalagadda, Siddhartha, and Philip Topham.
"NEMO: Extraction and normalization of organization names from PubMed affiliation strings." Journal of biomedical discovery and collaboration 5 (2010): 50.
Emadzadeh, Ehsan, Saravanan Muthaiyah, and Azadeh Nikfarjam.
"Quality attributes and classification of schema matchers." Computer Engineering and Applications (ICCEA), 2010 Second International Conference on. Vol. 2. IEEE, 2010.
Nikfarjam, Azadeh, Ehsan Emadzadeh, and Saravanan Muthaiyah.
"Text mining approaches for stock market prediction." Computer and Automation Engineering (ICCAE), 2010 The 2nd International Conference on. Vol. 4. IEEE, 2010.
Tari, L. Tu, P. Hakenberg, J. Chen, Y. Son, T. Gonzalez, G. Baral.
“Incremental Information Extraction Using Relational Databases”. Knowledge and Data Engineering, IEEE Transactions on Issue:99 , pp 25-35, 28 October 2010
Robert Leaman, Christopher Miller, Graciela Gonzalez (2009)
Enabling Recognition of Diseases in Biomedical Text with Machine Learning: Corpus and Benchmark, 82-89. In 2009 Symposium on Languages in Biology and Medicine.
Tari L, Tu PH, Hakenberg J, et al.
Integrating querying and retrieval for biomedical information extraction. ICDE. 2009
Jonnalagadda, Siddhartha, et al.
"Towards effective sentence simplification for automatic processing of biomedical text." Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics, Companion Volume: Short Papers. Association for Computational Linguistics, 2009.
Hakenberg,J. et al. (2009)
Molecular event extraction from link grammar parse trees. In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, Association for Computational Linguistics, pp. 86–94.
Jonnalagadda, Siddhartha, Philip Topham, and Graciela Gonzalez.
"Towards automatic extraction of social networks of organizations in PubMed abstracts."Bioinformatics and Biomedicine Workshop, 2009. BIBMW 2009. IEEE International Conference on. IEEE, 2009.
Jonnalagadda, Siddhartha, Philip Topham, and Graciela Gonzalez.
"ONER: Tool for Organization Named Entity Recognition from Affiliation Strings in PubMed Abstracts." The 3rd International Symposium on Languages in Biology and Medicine, Jeju Island, South Korea. 2009.
Tari L, Hakenberg J, Gonzalez G, Baral C.
Querying parse tree database of MEDLINE text to synthesize user-specific biomolecular networks. In: Pacific symposium on biocomputing; 2009. p. 87–98.
Leaman, Robert, and Graciela Gonzalez.
"BANNER: an executable survey of advances in biomedical named entity recognition." Pacific Symposium on Biocomputing. Vol. 13. 2008.
Phan Huy Tu, Chitta Baral, Yi Chen, and Graciela Gonzalez. 2008.
Generalized text extraction from molecular biology text using parse tree database querying. Technical Report TR-08-004, Arizona State University
Gonzalez, G., Uribe, J.C., Armstrong, B., McDonough, W. & Berens, M.E.
GeneRanker: an online system for predicting gene-disease associations for translational research. Summit on Translat. Bioinforma. 2008, 26–30 (2008).
Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzales G.
Inter-species normalization of gene mentions with GNAT. Bioinformatics 2008, 24(16):i126-i132.
Samli, Kausar N., et al.
"Glycoinformatics: Text Mining Lectin and Glycan Interactions in Bioprocesses." GLYCOBIOLOGY. Vol. 18. No. 11. JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA: OXFORD UNIV PRESS INC, 2008.
Chitta Baral, Graciela Gonzalez, Anthony Gitter, Craig Teegarden, Amanda Zeigler.
CBioC: beyond a prototype for collaborative annotation of molecular interactions from the literature. In: Computational systems bioionformatics conference, 2007.
Gonzalez, Graciela, et al.
"Integrating knowledge extracted from biomedical literature: normalization and evidence statements for interactions." Proceedings of the Second BioCreative Challenge Workshop-Critical Assessment of Information Extraction in Molecular Biology. 2007.
Gonzalez, G., et al.
Mining Gene-Disease relationships from Biomedical Literature: Incorporating Interactions, Connectivity, Confidence, and Context Measures. in Pacific Symposium in Biocomputing. 2007. Maui, Hawaii.
L. Tari, P. H. Tu, B. Lumpkin, R. Leaman, G. Gonzalez, and C. Baral.
“Passage relevancy through semantic relatedness,” in Proceedings of the Sixteenth Text REtrieval Conference, TREC 2007, 2007.
Tari L, Tu P, Lumpkin B, Leaman R, Gonzalez G, Baral C.
Passage relevancy through semantic similarity. In The Sixteenth Text REtrieval Conference (TREC 2007) Proceedings 2007.
Gonzalez G, Uribe JC, Tari L, Brophy C, Baral C.
Mining gene-disease relationships from biomedical literature: weighting protein-protein interactions and connectivity measures. Pac Symp Biocomput 2007, 28-39.
Gonzalez, G.; Balasooriya, J.
"Web Service Orchestration for Bioinformatics Systems: Challenges and Current Workflow Definition Approaches," Web Services, 2007. ICWS 2007. IEEE International Conference on , vol., no., pp.1226,1227, 9-13 July 2007
