My Bibliography

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Wei Q, Chen Y, Salimi M, Denny JC, Mei Q, Lasko TA, Chen Q, Wu S, Franklin A, Cohen T, Xu H. Cost-aware active learning for named entity recognition in clinical text. J Am Med Inform Assoc. 2019 Nov 1;26(11):1314-1322. doi: 10.1093/jamia/ocz102. PubMed PMID: 31294792; PubMed Central PMCID: PMC6798575.

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Ji Z, Wei Q, Franklin A, Cohen T, Xu H. Cost-sensitive Active Learning for Phenotyping of Electronic Health Records. AMIA Jt Summits Transl Sci Proc. 2019;2019:829-838. eCollection 2019. PubMed PMID: 31259040; PubMed Central PMCID: PMC6568101.

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Fathiamini S, Johnson AM, Zeng J, Holla V, Sanchez NS, Meric-Bernstam F, Bernstam EV, Cohen T. Rapamycin - mTOR + BRAF = ? Using relational similarity to find therapeutically relevant drug-gene relationships in unstructured text. J Biomed Inform. 2019 Feb;90:103094. doi: 10.1016/j.jbi.2019.103094. Epub 2019 Jan 4. PubMed PMID: 30615938; PubMed Central PMCID: PMC6386529.

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Wei Q, Franklin A, Cohen T, Xu H. Clinical text annotation - what factors are associated with the cost of time?. AMIA Annu Symp Proc. 2018;2018:1552-1560. eCollection 2018. PubMed PMID: 30815201; PubMed Central PMCID: PMC6371268.

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Mower J, Subramanian D, Cohen T. Learning predictive models of drug side-effect relationships from distributed representations of literature-derived semantic predications. J Am Med Inform Assoc. 2018 Oct 1;25(10):1339-1350. doi: 10.1093/jamia/ocy077. PubMed PMID: 30010902; PubMed Central PMCID: PMC6454491.

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Zhang Y, Li HJ, Wang J, Cohen T, Roberts K, Xu H. Adapting Word Embeddings from Multiple Domains to Symptom Recognition from Psychiatric Notes. AMIA Jt Summits Transl Sci Proc. 2018;2017:281-289. eCollection 2018. PubMed PMID: 29888086; PubMed Central PMCID: PMC5961810.

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Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim HE, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone SA, Fore IM, Ohno-Machado L, Grethe JS, Xu H. DataMed - an open source discovery index for finding biomedical datasets. J Am Med Inform Assoc. 2018 Jan 13;. doi: 10.1093/jamia/ocx121. [Epub ahead of print] PubMed PMID: 29346583.

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Cohen T, Widdows D. Bringing Order to Neural Word Embeddings with Embeddings Augmented by Random Permutations (EARP) . In: Proceedings of the 22nd Conference on Computational Natural Language Learning (CoNLL 2018). aclweb.org: Association of Computational Linguistics; 2018. p.465-475.

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Amith M, Cunningham R, Savas LS, Boom J, Schvaneveldt R, Tao C, Cohen T. Using Pathfinder networks to discover alignment between expert and consumer conceptual knowledge from online vaccine content. J Biomed Inform. 2017 Oct;74:33-45. doi: 10.1016/j.jbi.2017.08.007. Epub 2017 Aug 18. PubMed PMID: 28823922; PubMed Central PMCID: PMC5641252.

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Chen Y, Lask TA, Mei Q, Chen Q, Moon S, Wang J, Nguyen K, Dawodu T, Cohen T, Denny JC, Xu H. An active learning-enabled annotation system for clinical named entity recognition. BMC Med Inform Decis Mak. 2017 Jul 5;17(Suppl 2):82. doi: 10.1186/s12911-017-0466-9. PubMed PMID: 28699546; PubMed Central PMCID: PMC5506567.

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Cohen T, Widdows D. Embedding of semantic predications. J Biomed Inform. 2017 Apr;68:150-166. doi: 10.1016/j.jbi.2017.03.003. Epub 2017 Mar 8. PubMed PMID: 28284761; PubMed Central PMCID: PMC5441848.

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Malec SA, Wei P, Xu H, Bernstam EV, Myneni S, Cohen T. Literature-Based Discovery of Confounding in Observational Clinical Data. AMIA Annu Symp Proc. 2016;2016:1920-1929. eCollection 2016. PubMed PMID: 28269951; PubMed Central PMCID: PMC5333204.

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Sridharan V, Cohen T, Cobb N, Myneni S. Characterization of Temporal Semantic Shifts of Peer-to-Peer Communication in a Health-Related Online Community: Implications for Data-driven Health Promotion. AMIA Annu Symp Proc. 2016;2016:1977-1986. eCollection 2016. PubMed PMID: 28269957; PubMed Central PMCID: PMC5333293.

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Myneni S, Cobb NK, Cohen T. Content-specific network analysis of peer-to-peer communication in an online community for smoking cessation. AMIA Annu Symp Proc. 2016;2016:934-943. eCollection 2016. PubMed PMID: 28269890; PubMed Central PMCID: PMC5333292.

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Mower J, Subramanian D, Shang N, Cohen T. Classification-by-Analogy: Using Vector Representations of Implicit Relationships to Identify Plausibly Causal Drug/Side-effect Relationships. AMIA Annu Symp Proc. 2016;2016:1940-1949. eCollection 2016. PubMed PMID: 28269953; PubMed Central PMCID: PMC5333205.

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Sridharan V, Cohen T, Cobb N, Myneni S. Temporal Trends of Psychosociobehavioral Factors Underlying Tobacco Use: A Semi-Automated Exploratory Analysis of Peer-to-Peer Communication in a Health-Related Online Community. Stud Health Technol Inform. 2017;237:123-129. PubMed PMID: 28479554; PubMed Central PMCID: PMC6020071.

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Yu Z, Wallace BC, Johnson T, Cohen T. Retrofitting Concept Vector Representations of Medical Concepts to Improve Estimates of Semantic Similarity and Relatedness. Stud Health Technol Inform. 2017;245:657-661. PubMed PMID: 29295178; PubMed Central PMCID: PMC6464117.

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Cohen T, Widdows D, Heiden JA, Gupta NT, Kleinstein SH. Graded Vector Representations of Immunoglobulins Produced in Response to West Nile Virus . In: Quantum Interaction. QI 2016. de Barros J, Coecke B, Pothos E, editors. Cham (ZG) Switzerland: Springer International Publishing; 2017. p.135-148.

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Cohen T, Roberts K, Gururaj AE, Chen X, Pournejati S, Alter G, Hersh WR, Demner-Fushman D, Ohno-Machado L, Xu H. A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax061. PubMed PMID: 29220453; PubMed Central PMCID: PMC5737202.

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Abraham J, Kannampallil TG, Srinivasan V, Galanter WL, Tagney G, Cohen T. Measuring content overlap during handoff communication using distributional semantics: An exploratory study. J Biomed Inform. 2017 Jan;65:132-144. doi: 10.1016/j.jbi.2016.11.009. Epub 2016 Nov 29. PubMed PMID: 27913246.

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Fathiamini S, Johnson AM, Zeng J, Araya A, Holla V, Bailey AM, Litzenburger BC, Sanchez NS, Khotskaya Y, Xu H, Meric-Bernstam F, Bernstam EV, Cohen T. Automated identification of molecular effects of drugs (AIMED). J Am Med Inform Assoc. 2016 Jul;23(4):758-65. doi: 10.1093/jamia/ocw030. Epub 2016 Apr 23. PubMed PMID: 27107438; PubMed Central PMCID: PMC4926748.

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Xu J, Lee HJ, Zeng J, Wu Y, Zhang Y, Huang LC, Johnson A, Holla V, Bailey AM, Cohen T, Meric-Bernstam F, Bernstam EV, Xu H. Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov. J Am Med Inform Assoc. 2016 Jul;23(4):750-7. doi: 10.1093/jamia/ocw009. Epub 2016 Mar 24. PubMed PMID: 27013523; PubMed Central PMCID: PMC4926744.

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Yu Z, Bernstam E, Cohen T, Wallace BC, Johnson TR. Improving the utility of MeSH® terms using the TopicalMeSH representation. J Biomed Inform. 2016 Jun;61:77-86. doi: 10.1016/j.jbi.2016.03.013. Epub 2016 Mar 19. PubMed PMID: 27001195; PubMed Central PMCID: PMC4893983.

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Myneni S, Cobb N, Cohen T. In Pursuit of Theoretical Ground in Behavior Change Support Systems: Analysis of Peer-to-Peer Communication in a Health-Related Online Community. J Med Internet Res. 2016 Feb 2;18(2):e28. doi: 10.2196/jmir.4671. PubMed PMID: 26839162; PubMed Central PMCID: PMC4756252.

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Widdows D, Cohen T. Graded Semantic Vectors: An Approach to Representing Graded Quantities in Generalized Quantum Models . In: International Symposium on Quantum Interactions. Berlin Heidelberg: Spring Verlag; 2016. p.135-148.

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Widdows D, Cohen T. Reasoning with Vectors: A Continuous Model for Fast Robust Inference. Log J IGPL. 2015 Oct;23(2):141-173. doi: 10.1093/jigpal/jzu028. Epub 2014 Nov 19. PubMed PMID: 26582967; PubMed Central PMCID: PMC4646228.

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Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J. Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol. 2015 Sep;33(9):933-40. doi: 10.1038/nbt.3299. Epub 2015 Aug 10. PubMed PMID: 26258538; PubMed Central PMCID: PMC4568441.

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Myneni S, Fujimoto K, Cobb N, Cohen T. Content-driven analysis of an online community for smoking cessation: integration of qualitative techniques, automated text analysis, and affiliation networks. Am J Public Health. 2015 Jun;105(6):1206-12. doi: 10.2105/AJPH.2014.302464. Epub 2015 Apr 16. PubMed PMID: 25880942; PubMed Central PMCID: PMC4431114.

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Chen G, Zhao J, Cohen T, Tao C, Sun J, Xu H, Bernstam EV, Lawson A, Zeng J, Johnson AM, Holla V, Bailey AM, Lara-Guerra H, Litzenburger B, Meric-Bernstam F, Jim Zheng W. Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. Database (Oxford). 2015;2015:bav034. doi: 10.1093/database/bav034. Print 2015. PubMed PMID: 25858285; PubMed Central PMCID: PMC4390608.

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Cohen T, Widdows D. Embedding Probabilities in Predication Space with Hermitian Holographic Reduced Representations . In: To appear in: Quantum Interactions. Berlin Heidelberg: Springer Verlag; 2015.

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Cohen T, Widdows D. Expansion-by-Analogy: A Vector Symbolic Approach to Semantic Search . In: Quantum Interaction. Atmanspacher H, Bergomi C, Filk T, Kitto K, editors. Switzerland: Springer International Publishing; 2015. p.pp 54-66.

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Shang N, Xu H, Rindflesch TC, Cohen T. Identifying plausible adverse drug reactions using knowledge extracted from the literature. J Biomed Inform. 2014 Dec;52:293-310. doi: 10.1016/j.jbi.2014.07.011. Epub 2014 Jul 19. PubMed PMID: 25046831; PubMed Central PMCID: PMC4261011.

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Cohen T, Widdows D, Stephan C, Zinner R, Kim J, Rindflesch T, Davies P. Predicting high-throughput screening results with scalable literature-based discovery methods. CPT Pharmacometrics Syst Pharmacol. 2014 Oct 8;3:e140. doi: 10.1038/psp.2014.37. PubMed PMID: 25295575; PubMed Central PMCID: PMC4474167.

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Dalai VV, Khalid S, Gottipati D, Kannampallil T, John V, Blatter B, Patel VL, Cohen T. Evaluating the effects of cognitive support on psychiatric clinical comprehension. Artif Intell Med. 2014 Oct;62(2):91-104. doi: 10.1016/j.artmed.2014.08.002. Epub 2014 Aug 19. PubMed PMID: 25179216; PubMed Central PMCID: PMC4253554.

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Cohen T, Widdow D, Wahle M, Schvaneveldt R. Orthogonality and Orthography: Introducing Measured Distance into Semantic Space . In: Quantum Interaction. Atmanspacher H, Haven E, Kitto K, Raine D, editors. Berlin: Springer Berlin Heidelberg; 2014.

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Shang N. Doctoral Dissertation: Integrating Domain Knowledge to Improve Signal Detection From Electronic Health Records for Pharmacovigilance. Houston, TX: University of Texas School of Biomedical Informatics; 2014.

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Moon S, Berster BT, Xu H, Cohen T. Word Sense Disambiguation of clinical abbreviations with hyperdimensional computing. AMIA Annu Symp Proc. 2013;2013:1007-16. eCollection 2013. PubMed PMID: 24551390; PubMed Central PMCID: PMC3900125.

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Jonnalagadda S, Cohen T, Wu S, Liu H, Gonzalez G. Using empirically constructed lexical resources for named entity recognition. Biomed Inform Insights. 2013;6(Suppl 1):17-27. doi: 10.4137/BII.S11664. Print 2013. PubMed PMID: 23847424; PubMed Central PMCID: PMC3702195.

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Myneni S, Cobb NK, Cohen T. Finding meaning in social media: content-based social network analysis of QuitNet to identify new opportunities for health promotion. Stud Health Technol Inform. 2013;192:807-11. PubMed PMID: 23920669.

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Kannampallil TG, Franklin A, Mishra R, Almoosa KF, Cohen T, Patel VL. Understanding the nature of information seeking behavior in critical care: implications for the design of health information technology. Artif Intell Med. 2013 Jan;57(1):21-9. doi: 10.1016/j.artmed.2012.10.002. Epub 2012 Nov 26. PubMed PMID: 23194923.

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Cohen T, Widdows D, Schvaneveldt RW, Davies P, Rindflesch TC. Discovering discovery patterns with Predication-based Semantic Indexing. J Biomed Inform. 2012 Dec;45(6):1049-65. doi: 10.1016/j.jbi.2012.07.003. Epub 2012 Jul 26. PubMed PMID: 22841748; PubMed Central PMCID: PMC3590916.

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Satter RM, Cohen T, Ortiz P, Kahol K, Mackenzie J, Olson C, Johnson M, Patel VL. Avatar-based simulation in the evaluation of diagnosis and management of mental health disorders in primary care. J Biomed Inform. 2012 Dec;45(6):1137-50. doi: 10.1016/j.jbi.2012.07.009. Epub 2012 Aug 3. PubMed PMID: 22884757.

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Wahle M, Widdows D, Herskovic JR, Bernstam EV, Cohen T. Deterministic binary vectors for efficient automated indexing of MEDLINE/PubMed abstracts. AMIA Annu Symp Proc. 2012;2012:940-9. Epub 2012 Nov 3. PubMed PMID: 23304369; PubMed Central PMCID: PMC3540485.

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Berster BT, Goodwin JC, Cohen T. Hyperdimensional computing approach to word sense disambiguation. AMIA Annu Symp Proc. 2012;2012:1129-38. Epub 2012 Nov 3. PubMed PMID: 23304389; PubMed Central PMCID: PMC3540565.

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Herskovic JR, Subramanian D, Cohen T, Bozzo-Silva PA, Bearden CF, Bernstam EV. Graph-based signal integration for high-throughput phenotyping. BMC Bioinformatics. 2012;13 Suppl 13:S2. doi: 10.1186/1471-2105-13-S13-S2. Epub 2012 Aug 24. PubMed PMID: 23320851; PubMed Central PMCID: PMC3426800.

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Goodwin JC, Johnson TR, Cohen T, Herskovic JR, Bernstam EV. Predicting biomedical document access as a function of past use. J Am Med Inform Assoc. 2012 May-Jun;19(3):473-8. doi: 10.1136/amiajnl-2011-000325. Epub 2011 Sep 13. PubMed PMID: 21917645; PubMed Central PMCID: PMC3341785.

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Jonnalagadda S, Cohen T, Wu S, Gonzalez G. Enhancing clinical concept extraction with distributional semantics. J Biomed Inform. 2012 Feb;45(1):129-40. doi: 10.1016/j.jbi.2011.10.007. Epub 2011 Nov 7. PubMed PMID: 22085698; PubMed Central PMCID: PMC3272090.

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Widdows D, Cohen T. Real, Complex and Binary Semantic Vectors . In: Quantum Interaction. Busemeyer JR, Dubois F, Lambert-Mogiliansky A, Melucci M, editors. Berlin: Springer Berlin Heidelberg; 2012. p.24-35.

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Cohen T, Widdows D, De Vine L, Schvaneveldt R, Widdows D. Many Paths Lead to Discovery: Analogical Retrieval of Cancer Therapies . In: Quantum Interaction. Busemeyer JR, Dubois F, Lambert-Mogiliansky A, Melucci M, editors. Berlin Heidelberg: Springer Berlin Heidelberg; 2012. p.pp 90-101.

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Silverman H, Cohen T, Fridsma D. The evolution of a novel biomedical informatics curriculum for medical students. Acad Med. 2012 Jan;87(1):84-90. doi: 10.1097/ACM.0b013e31823a599e. PubMed PMID: 22104049.