Ontology Research Group

Muhammad "Tuan" Amith

Predoctoral Fellow

Tuan is a PhD Candidate under the supervision of Cui Tao, PhD. He currently holds a B.S. and M.S. in Computer Science and Software Engineering from the University of Houston. His research involves modeling the knowledge space of vaccine information for patient retrieval and learning, using Web Ontology Language (OWL) and mobile devices. He is currently a pre-doctoral fellow through the UTHealth Innovation for Cancer Prevention Research. In addition, he has nearly 10 years of extensive experience working as application developer in a variety of web-, server-based, and mobile software.

Peer-Reviewed Paper Publications (*co-first author)

  1. Muhammad Amith*, Zhe He*, Jiang Bian, Juan Antonio Lossio-Ventura, and Cui Tao. “Assessing the Gaps of the Evaluation for Biomedical Ontologies in BioPortal”. Journal of Biomedical Informatics. (Submitted).

  2. Qiang Wei, Yaoyun Zhang, Muhamamad Amith, Rebecca Lin, Jenay Lapeyrolerie, Cui Tao, and Hua Xu. Recognizing Software Names in Biomedical Literature Using Machine Learning. Health Informatics Journal. (Submitted)

  3. Muhammad Amith, and Cui Tao. “Representing Vaccine Misinformation using Ontologies.” International Workshop on Vaccine and Drug Ontologies (VDOS), International Conference on Biomedical Ontology (ICBO) 2017.(Accpeted)

  4. Muhammad Amith, Rachel Cunningham, Julie Boom, Lara Savas, Roger Schvaneveldt, Cui Tao, and Trevor Cohen. “Finding Alignment Between Expert and Consumer’s Conceptual Knowledge From Online Vaccine Content Using Pathfinder Networks.” Journal of Biomedical Informatics, 2017

  5. Muhammad Amith*, Frank Manion*, Marcelline Harris*, Yaoyun Zhang, Hua Xu, and Cui Tao. “Hootation: Expressing Biomedical Ontologies in Natural Language.” Medinfo 2017 in Xiamen, China, August 21–25, 2017.

  6. Muhammad Amith*, Hsing-Yi Song*, Yaoyun Zhang, Hua Xu, and Cui Tao. “Lightweight Predication Extraction For Patient-Level Cancer Information and Ontology Development.” BMC Medical Informatics and Decision Making 17(Suppl 2):73, 2017.

  7. Muhammad Amith, Yaoyun Zhang, Hua Xu, and Cui Tao. “Knowledge-Based Approach for Named Entity Recognition in Biomedical Literature, a Use Case in Software Identification.” Advances in Artificial Intelligence: From Theory to Practice.

  8. Muhammad Amith and Cui Tao. “Modulated Evaluation Metrics For Drug-Based Ontologies.” Journal of Biomedical Semantics 8. pp. 17, 2017.

  9. Muhammad Amith. “Ontology-based Dialogue Systems for Improved Patient HPV Vaccine Knowledge and Perception.” Doctoral Consortium at International Semantic Web Conference, in: Proceedings of the Doctoral Consortium at the 15th International Semantic Web Conference (ISWC 2016), 2016.

  10. Dennis Wang, Rachel Cunningham, Julie Boom, Muhammad Amith, and Cui Tao. “Towards a HPV Vaccine Knowledgebase for Patient Education Content.” Studies in health technology and informatics 225: pp. 432–436., 2016.

  11. Muhammad Amith, Cui Tao. A Web Application Towards Semiotic-based Evaluation of Biomedical Ontologies. International Workshop on Biomedical Data Mining, Modeling, and Semantic Integration: A Promising Approach to Solving Unmet Medical Needs (BDM2I 2015), October 2015.

  12. Sahiti Myneni, Muhammad Amith, Yimin Geng, Cui Tao. Towards an Ontology-driven Framework to Enable Development of Personalized mHealth Solutions for Cancer Survivors Engagement in Healthy Living. MEDINFO 2015 Conference. (MedInfo Best Paper Finalist)

  13. Muhammad Amith, Yang Gong, Rachel Cunningham, Julie Boom, Cui Tao. Developing VISO: Vaccine Information Statement Ontology for Patient Education. Journal of Biomedical Semantics, 2015.

  14. Muhammad Amith, Cui Tao: Towards the design of a vaccine information ontology for patient education. Vaccine and Drug Ontology Studies (VDOS) Workshop, ICBO 2014.

  15. Muhammad Amith, Cui Tao: A Prototype Mobile Virtual Assistant for Semantic-Based Vaccine Information Retrieval. International Conference for Smart Health 2014: 200-205.

  16. Muhammad Amith, Paul Loubser, John Chapman, Fred Ferreira, Kaafoe Zoker: Optimization of an EHR Mobile Application Using the UFuRT Conceptual Framework. AMIA 2012. (Best of mHealth)

  17. Sharon White, Muhammad Amith: Software Design, a 2011 Primer. ACET Journal Vol 7 2011-2012.

Abstracts and posters

  1. Frank Manion, Marcelline Harris, Hsing-Yi Song, Oliver He, Muhammad Amith, Hua Xu, and Cui Tao. “From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories.” American Medical Informatics Association 2017 Annual Symposium, Washington, DC., November 2017

  2. Hua Xu, Jeffery S. Grethe, [et al, including Muhammad Amith.]. 2016. “Development of DataMed, a Data Discovery Index Prototype by bioCADDIE: Laying the Ground- work for Biomedical Data Discovery.” American Medical Informatics Association 2016 Annual Symposium, Chicago, IL., November 2016.

  3. Jeffery S. Grethe, Burak Ozyurt, [et al, including Muhammad Amith.]. 2016. “A Scal- able Dataset Indexing Infrastructure for the bioCADDIE Data Discovery System.” American Medical Informatics Association 2016 Annual Symposium, Chicago, IL., November 2016.

  4. Dennis Wang, Muhammad Amith and Cui Tao. 2015. “HPV VISO: Encoding HPV Vaccine Education Content For Patient Knowledge-based Systems.” 2015 CPRIT Conference, Austin, TX, November 2015.

  5. Mary Mays, Muhammad Amith, Enid Garcia, Princess Pacheco and Craig Johnson. 2014. “Predictors of Perceived Health Status Among Low Income Community Residents in Puerto Rico.” Seventh Health Disparities Conference, New Orleans, LA, March 2014.

  6. Sharon White and Muhammad Amith. 2010. “Software Design - 2010 Primer.” ACET 46th Annual Conference in League City, TX, October 2010.