Publications
Peer-Reviewed Original Research (Journal Publications)
2024
- A roadmap to artificial intelligence (AI): Methods for designing and building AI ready data to promote fairness.Kidwai-Khan F, Wang R, Skanderson M, Brandt CA, Fodeh S, Womack JA. J Biomed Inform. 2024 Jun; 2024 May 11. PMID: 38740316.
- Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines.Clark T, Mohan J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle-Pipon JC, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T. bioRxiv. 2024 May 24; 2024 May 24. PMID: 38826258.
- Deploying a national clinical text processing infrastructure.McManus KF, Stringer JM, Corson N, Fodeh S, Steinhardt S, Levin FL, Shotqara AS, D'Auria J, Fielstein EM, Gobbel GT, Scott J, Trafton JA, Taddei TH, Erdos J, Tamang SR. J Am Med Inform Assoc. 2024 Feb 16. PMID: 38146986.
- Spatiotemporal trends in COVID-19 vaccine sentiments on a social media platform and correlations with reported vaccine coverage.Zhou X, Zhang X, Larson HJ, de Figueiredo A, Jit M, Fodeh S, Vermund SH, Zang S, Lin L, Hou Z. Bull World Health Organ. 2024 Jan 1; 2023 Oct 31. PMID: 38164328.
2023
- Complementary and Integrative Health Approaches and Pain Care Quality in the Veterans Health Administration Primary Care Setting: A Quasi-Experimental Analysis.Han L, Luther SL, Finch DK, Dobscha SK, Skanderson M, Bathulapalli H, Fodeh SJ, Hahm B, Bouayad L, Lee A, Goulet JL, Brandt CA, Kerns RD. J Integr Complement Med. 2023 Jun-Jul; 2023 Mar 27. PMID: 36971840.
- Assessing the contributions of modifiable risk factors to serious falls and fragility fractures among older persons living with HIV.Womack JA, Murphy TE, Leo-Summers L, Bates J, Jarad S, Gill TM, Hsieh E, Rodriguez-Barradas MC, Tien PC, Yin MT, Brandt CA, Justice AC. J Am Geriatr Soc. 2023 Jun; 2023 Mar 13. PMID: 36912153.
- A Roadmap to Artificial Intelligence (AI): Methods for Designing and Building AI ready Data for Women's Health Studies.Kidwai-Khan F, Wang R, Skanderson M, Brandt CA, Fodeh S, Womack JA. medRxiv. 2023 May 30; 2023 May 30. PMID: 37398113.
- Mental Health Diagnoses are Not Associated With Indicators of Lower Quality Pain Care in Electronic Health Records of a National Sample of Veterans Treated in Veterans Health Administration Primary Care Settings.Dobscha SK, Luther SL, Kerns RD, Finch DK, Goulet JL, Brandt CA, Skanderson M, Bathulapalli H, Fodeh SJ, Hahm B, Bouayad L, Lee A, Han L. J Pain. 2023 Feb; 2022 Sep 24. PMID: 36167230.
- Understanding headache classification coding within the veterans health administration using ICD-9-CM and ICD-10-CM in fiscal years 2014-2017.Fodeh SJ, Fenton BT, Wang R, Skanderson M, Altalib H, Kuruvilla D, Schindler E, Haskell S, Brandt C, Sico JJ. PLoS One. 2023; 2023 Jan 4. PMID: 36598881.
2022
- Predictive Risk Model for Serious Falls Among Older Persons Living With HIV.Womack JA, Murphy TE, Leo-Summers L, Bates J, Jarad S, Smith AC, Gill TM, Hsieh E, Rodriguez-Barradas MC, Tien PC, Yin MT, Brandt CA, Justice AC. J Acquir Immune Defic Syndr. 2022 Oct 1. PMID: 36094483.
- Measuring pain care quality in the Veterans Health Administration primary care setting.Luther SL, Finch DK, Bouayad L, McCart J, Han L, Dobscha SK, Skanderson M, Fodeh SJ, Hahm B, Lee A, Goulet JL, Brandt CA, Kerns RD. Pain. 2022 Jun 1; 2021 Sep 15. PMID: 34724683.
- New JBI policy emphasizes clinically-meaningful novel machine learning methods.Tucker A, Kannampallil T, Fodeh SJ, Peleg M. J Biomed Inform. 2022 Mar; 2022 Jan 24. PMID: 35085812.
2021
- Brief Report: Are Serious Falls Associated With Subsequent Fragility Fractures Among Veterans Living With HIV?Womack JA, Murphy TE, Ramsey C, Bathulapalli H, Leo-Summers L, Smith AC, Bates J, Jarad S, Gill TM, Hsieh E, Rodriguez-Barradas MC, Tien PC, Yin MT, Brandt C, Justice AC. J Acquir Immune Defic Syndr. 2021 Oct 1. PMID: 34506360.
- Twitter-based analysis reveals differential COVID-19 concerns across areas with socioeconomic disparities.Su Y, Venkat A, Yadav Y, Puglisi LB, Fodeh SJ. Comput Biol Med. 2021 May; 2021 Mar 13. PMID: 33761419.
- Utilizing a multi-class classification approach to detect therapeutic and recreational misuse of opioids on Twitter.Fodeh SJ, Al-Garadi M, Elsankary O, Perrone J, Becker W, Sarker A. Comput Biol Med. 2021 Feb; 2020 Nov 20. PMID: 33290931.
- Emergency care and the patient experience: Using sentiment analysis and topic modeling to understand the impact of the COVID-19 pandemic.Chekijian S, Li H, Fodeh S. Health Technol (Berl). 2021; 2021 Aug 13. PMID: 34414063.
2020
- Identification of Patients with Nontraumatic Intracranial Hemorrhage Using Administrative Claims Data.Sangal RB, Fodeh S, Taylor A, Rothenberg C, Finn EB, Sheth K, Matouk C, Ulrich A, Parwani V, Sather J, Venkatesh A. J Stroke Cerebrovasc Dis. 2020 Dec; 2020 Oct 15. PMID: 33070110.
- Serious Falls in Middle-Aged Veterans: Development and Validation of a Predictive Risk Model.Womack JA, Murphy TE, Bathulapalli H, Smith A, Bates J, Jarad S, Redeker NS, Luther SL, Gill TM, Brandt CA, Justice AC. J Am Geriatr Soc. 2020 Dec; 2020 Aug 28. PMID: 32860222.
- Defining facets of social distancing during the COVID-19 pandemic: Twitter analysis.Kwon J, Grady C, Feliciano JT, Fodeh SJ. J Biomed Inform. 2020 Nov; 2020 Oct 14. PMID: 33065264.
- Exploring supervised machine learning approaches to predicting Veterans Health Administration chiropractic service utilization.Coleman BC, Fodeh S, Lisi AJ, Goulet JL, Corcoran KL, Bathulapalli H, Brandt CA. Chiropr Man Therap. 2020 Jul 17; 2020 Jul 17. PMID: 32680545.
- Reducing Annotation Burden Through Multimodal Learning.Lopez K, Fodeh SJ, Allam A, Brandt CA, Krauthammer M. Front Big Data. 2020; 2020 Jun 2. PMID: 33693393.
- Classification of Patients with Coronary Microvascular Dysfunction.Fodeh SJ, Li T, Jarad H, Safdar B. IEEE/ACM Trans Comput Biol Bioinform. 2020 Mar-Apr; 2019 May 2. PMID: 31056516.
2019
- Polypharmacy, Hazardous Alcohol and Illicit Substance Use, and Serious Falls Among PLWH and Uninfected Comparators.Womack JA, Murphy TE, Rentsch CT, Tate JP, Bathulapalli H, Smith AC, Bates J, Jarad S, Gibert CL, Rodriguez-Barradas MC, Tien PC, Yin MT, Gill TM, Friedlaender G, Brandt CA, Justice AC. J Acquir Immune Defic Syndr. 2019 Nov 1. PMID: 31339866.
2018
- Exploiting MEDLINE for gene molecular function prediction via NMF based multi-label classification.Fodeh SJ, Tiwari A. J Biomed Inform. 2018 Oct; 2018 Aug 18. PMID: 30130573.
- Classifying clinical notes with pain assessment using machine learning.Fodeh SJ, Finch D, Bouayad L, Luther SL, Ling H, Kerns RD, Brandt C. Med Biol Eng Comput. 2018 Jul; 2017 Dec 26. PMID: 29280092.
- Automatic extraction of informal topics from online suicidal ideation.Grant RN, Kucher D, León AM, Gemmell JF, Raicu DS, Fodeh SJ. BMC Bioinformatics. 2018 Jun 13; 2018 Jun 13. PMID: 29897319.
2017
- Ranking Medical Terms to Support Expansion of Lay Language Resources for Patient Comprehension of Electronic Health Record Notes: Adapted Distant Supervision Approach.Chen J, Jagannatha AN, Fodeh SJ, Yu H. JMIR Med Inform. 2017 Oct 31; 2017 Oct 31. PMID: 29089288.
- Unlocking echocardiogram measurements for heart disease research through natural language processing.Patterson OV, Freiberg MS, Skanderson M, J Fodeh S, Brandt CA, DuVall SL. BMC Cardiovasc Disord. 2017 Jun 12; 2017 Jun 12. PMID: 28606104.
- Classifying Clinical Notes with Pain Assessment.Fodeh SJ, Finch D, Bouayad L, Luther S, Kerns RD, Brandt C. Stud Health Technol Inform. 2017. PMID: 29295346.
2016
- Estimating healthcare mobility in the Veterans Affairs Healthcare System.Wang KH, Goulet JL, Carroll CM, Skanderson M, Fodeh S, Erdos J, Womack JA, Abel EA, Bathulapalli H, Justice AC, Nunez-Smith M, Brandt CA. BMC Health Serv Res. 2016 Oct 21; 2016 Oct 21. PMID: 27769221.
- Mining Big Data in biomedicine and health care.Fodeh S, Zeng Q. J Biomed Inform. 2016 Oct; 2016 Sep 23. PMID: 27670091.
- Electronic approaches to making sense of the text in the adverse event reporting system.Benin AL, Fodeh SJ, Lee K, Koss M, Miller P, Brandt C. J Healthc Risk Manag. 2016 Aug. PMID: 27547874.
- Classification of radiology reports for falls in an HIV study cohort.Bates J, Fodeh SJ, Brandt CA, Womack JA. J Am Med Inform Assoc. 2016 Apr; 2015 Nov 13. PMID: 26567329.
2015
- Clinical data mining.Zeng QT, Fodeh S. Comput Biol Med. 2015 Jul. PMID: 26067752.
- Baseline cluster membership demonstrates positive associations with first occurrence of multiple gerontologic outcomes over 10 years.Fodeh SJ, Trentalange M, Allore HG, Gill TM, Brandt CA, Murphy TE. Exp Aging Res. 2015. PMID: 25724015.
2013
- Functional impairments as symptoms in the symptom cluster analysis of patients newly diagnosed with advanced cancer.Fodeh SJ, Lazenby M, Bai M, Ercolano E, Murphy T, McCorkle R. J Pain Symptom Manage. 2013 Oct; 2013 Feb 4. PMID: 23380336.
- Complementary ensemble clustering of biomedical data.Fodeh SJ, Brandt C, Luong TB, Haddad A, Schultz M, Murphy T, Krauthammer M. J Biomed Inform. 2013 Jun; 2013 Feb 27. PMID: 23454721.
2012
- Enhancing Clustering by Exploiting Complementary Data Modalities in the Medical Domain.Fodeh SJ, Haddad A, Brandt C, Schultz M, Krauthammer M. IFIP Adv Inf Commun Technol. 2012 Sep. PMID: 29479376.
Invited Editorials and Commentaries
- Zeng QT, Fodeh S. Clinical data mining. Computers in biology and medicine. 2015 Jul 1;62(C):293.
- Fodeh S, Zeng Q. Mining Big Data in Biomedicine and Health Care. Journal of biomedical informatics. J Biomed Inform. 2016 Oct; 63:400-403. doi: 10.1016/j.jbi.2016.09.014.
- Samah Fodeh, Mining Big Biomedical Data, International Journal of Knowledge Discovery in Bioinformatics (IJKDB) 6(1), 2016.
- Samah Fodeh, Knowledge discovery in biomedicine, International Journal of Knowledge Discovery in Bioinformatics (IJKDB), 2018.
- Da Yan, Xin Gao, Samah J. Fodeh, and Jake Y. Chen. Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2019.
Peer-Reviewed Original Research (Conference Publications)
- Kapila Moonesinghe, Samah Fodeh, and Pang-Ning Tan, Frequent Closed Itemset Mining using Prefix Graphs with an Efficient Flow-Based Pruning Strategy, Proc of IEEE Int'l Conf in Data Mining (ICDM-06), Hong Kong (2006)
- Kapila Moonesinghe, Hamed Valizadegan, Samah Fodeh, and Pang-Ning Tan. A Probabilistic Substructure-Based Approach for Graph Classification, to appear in Proc of IEEE Int'l Conf on Tools with Artificial Intelligence (ICTAI-07), Patras, Greece, October 29-31 (2007)
- Samah Fodeh and Pang-Ning Tan. Incorporating Background Knowledge from the World Wide Web Using the Minimum Discriminative Information Principle, Proc of KDD 2007 Workshop on Mining Multiple Information Sources, August 12-15 (2007).
- Samah Fodeh and Pang-Ning Tan. Incorporating Background Knowledge for Subjective Rule Evaluation, in Proc of IEEE Int'l Conf on Tools with Artificial Intelligence (ICTAI-07), Patras, Greece, October 29-31 (2007).
- Samah Fodeh, Bill Punch and Pang-Ning Tan. Combining Statistics and Semantics via Ensemble Model for Document Clustering. In Proc. Of 24th annual ACM Symposiums on Applied Computing. (2009).
- Samah J. Fodeh , Qing T. Zeng, Doug F Redd, Guy Divita, Brandt CA, Clinical Note Type Analysis, AMIA 2011.
- Samah Fodeh, Ali Haddad, Cynthia Brandt, Martin Schultz, Micheal Karauthaumer, Enhancing Clustering by Exploiting Complementary Data Modalities in the Medical Domain, Artificial Intelligence Applications and Innovations AIAI 2012.
- Samah J. Fodeh , Sharmila Chatterjee MD , Brandt CA. Categorizing VA Telephone notes Content using Topic Modeling. The 2013 Electronic Data Methods EDM Forum Stakeholder Symposium, Baltimore.
- Samah J. Fodeh , Sharmila Chatterjee MD , Brandt CA, Analysis of VA Telephone Call Notes using Topic Modeling AMIA 2012.
- H Hamid, S J Fodeh, A G Lizama, R Czlapinski, M J Pugh, W C Lafrance, C A Brandt. Validating a natural language processing tool to exclude psychogenic nonepileptic seizures in electronic medical record-based epilepsy research.
- Samah Fodeh, Maryan Zirkle, Ruth Reeves, Finch Dezon, Joseph Erdos, and Cynthia Brandt. MedCat: A Framework for High Level Conceptualization of Medical Notes. Proc of IEEE Int'l Conf. in Data Mining (ICDM-13), in the Data Mining in Biomedical Informatics and Healthcare Workshop. Best Paper Award.
- Jonathan Bates, Samah Fodeh, Cynthia Brandt, Julie Womack. Detecting Patient Falls from the EHR using NLP and Text Mining. NLM Informatics Training Conference 2014.
- Samah Jamal Fodeh, Bryan Travis Gamble, and Kei-Hoi Cheung. Post-Traumatic Stress Disorder (PTSD) Ontology and Use Case. In proceedings of the 2014 Bio-Ontologies SIG.
- Samah Jamal Fodeh, Cynthia Brandt, Perry Miller, Kyle Lee, Michele Koss, Andrea Benin, Laplacian SVM based Feature Selection Improves Medical Event Reports Classification. DMBIH workshop at ICDM 2015.
- Samah J. Fodeh; Cynthia Brandt; Perry Miller ; Michele Koss ; Andrea L. Benin. Feature Selection Based LapSVM to Classify Medical Event Reports and Enhance Patient Safety. AMIA 2015.
- Andrea Benin, Samah J. Fodeh; Michele Koss; Kyle Lee; Perry Miller; Cynthia Brandt. Using the Adverse Event Reporting System: Can Analysis be Streamlined by Text Processing? AMIA 2015.
- Karen H. Wang ;Constance Carroll ; Brenda Fenton ; Samah J. Fodeh ; Joseph Erdos ; Marcella Nunez-Smith; Amy C. Justice; Cynthia Brandt. Exploring Healthcare Mobility in the US to Improve Quality of Care: Preliminary Results. AMIA 2015.
- Samah Fodeh, Aditya Tiwari, Hong Yu, “Protein Molecular Function Prediction using PubMed via Multi-Label Classification”, Fifth International Workshop on Data Mining in Biomedicine and Healthcare (DMBIH) held with the International conference on Data Mining. 2017
- Samah Fodeh, Joseph Goulet, Cynthia Brandt, Hamada Al-Talib. “Leveraging Twitter to better identify suicide risk”. In Proceedings of Machine Learning Research (PMLR) form the First International Workshop on Medical Informatics and Healthcare (MIH) held with the International conference on Knowledge Discovery and Data Mining, V:69, pp:1-7, 2017. Best Paper Award.
- Reilly Grant, David Kucher, Ana León, Jonathan Gemmell, Daniela Raicu, Samah Fodeh. “Automatic Extraction of Informal Topics from Online Suicidal Ideation”. Proceedings of the 11th International Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO) in conjunction with ACM 26th Conference on Information and Knowledge Management (CIKM), 2017.
- Fodeh, Samah, Aditya Tiwari, and Hong Yu. "Exploiting PubMed for Protein Molecular Function Prediction via NMF Based Multi-label Classification." In Data Mining Workshops (ICDMW), 2017 IEEE International Conference on, pp. 446-451. IEEE, 2017.
- Aditya Tiwari, Samah Fodeh, Steven Baccie, Max Rosen. “Automatic Classification of Critical Findings in Radiology Reports”. Proceedings of The First Workshop Medical Informatics and Healthcare held with the 23rd SIGKDD Conference on Knowledge Discovery and Data Mining, PMLR 69:35-39, 2017.
- Samah Fodeh, Taihua Li, Haya Jarad, Basmah Safdar. Identifying Patients with Coronary Microvascular Dysfunction using Machine Learning. 7th International Workshop on Data Mining in Biomedicine and Healthcare (DMBIH) held with the International conference on Data Mining (ICDM). 2018
- S Fodeh, T Li, K Menczynski, T Burgette, A Harris, G Ilita, S Rao, Using Machine Learning Algorithms to Detect Suicide Risk Factors on Twitter. 2019 International Conference on Data Mining Workshops (ICDMW), 941-948
- Samah J. Fodeh ; Edelman Jennifer ; William Becker ; Cynthia Brandt ; Sally Haskell. Prescription opioid tapering: Mining structured and unstructured data. AMIA,2020
- Samah J. Fodeh ; Brenda Fenton ; Hamada Al-Talib ; Jason Sico. Exploring the Lag in Migraine Diagnoses using Unstructured Clinical Notes. AMIA 2020.
- Jason Sico, Samah J. Fodeh ; Brenda Fenton; Headache Not Otherwise Specified: Impact of the Transition from ICD-9 to ICD-10 Diagnostic Classification within the Veterans Health Administration. AHS 62nd Annual Scientific Meeting.2020.
- Samah Fodeh, Huan Li, Khaled Jarad, Stephen Holt. Integrating Social Media data with Electronic Health Records to better Understand Opioid Use Disorder. AMIA 2020.
- Brian C. Coleman, Samah Fodeh, Anthony J. Lisi, Alicia A. Heapy, Cynthia A. Brandt. Pain Assessment in Veterans Health Administration Chiropractic Clinic Documentation. AMIA 2020.
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