LLM Projects

Master's Thesis

Thanh Son Do (Masters in Computer Science, graduated Spring 2025): “A Retrieval Augmented Approach to Improving Accuracy of Biomedical Term Normalization by Large Language Models".

Selected Publications

Journals

  1. Pericharla S*, Hier DB, Obafemi-Ajayi T. From Memorization to Generalization: Fine-Tuning Large Language Models for Biomedical Term-to-Identifier Normalization. in Frontiers in Digital Health 2026.

  2. Hier DB, Carrithers MD, Platt SK, Nguyen A, Giannopoulos I, Obafemi-Ajayi T. Analyzing Biomedical Datasets with Symbolic Tree Adaptive Resonance Theory. Preprocessing of Physician Notes by LLMs Improves Clinical Concept Extraction Without Information Loss. Information. 2025 May 27;16(6):446.

  3. Do TS*, Hier DB, Obafemi-Ajayi T. A Simplified Retriever to Improve Accuracy of Phenotype Normalizations by Large Language Models. Frontiers in Digital Health 2025 Mar 4;7:1495040.

Conferences

  1. Hier DB, Platt SK, Obafemi-Ajayi T. Predicting Failures of LLMs to Link Biomedical Ontology Terms to Identifiers: Evidence Across Models and Ontologies. in Proc. 2025 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) November 2025.

  2. Do TS*, Hier DB, Obafemi-Ajayi T. Balanced Benchmarking of Zero-Shot and RAG Approaches for Biomedical Term Normalization. in Proc. 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) August 2025.

  3. Hier DB, Carrithers MD, Do TS*, Obafemi-Ajayi T. REMOTE: A Framework to Create Fast Healthcare Interoperability Resources (FHIR) from Unstructured Clinical Data. in Proc. 47th International Conference of the IEEE Engineering in Medicine and Biology Society. July 2025.

  4. Do TS*, Hier DB, Obafemi-Ajayi T. Mapping Biomedical Ontology Terms to IDs: Effect of Domain Prevalence on Prediction Accuracy. in Proc. 2025 IEEE Conference on Artificial Intelligence (IEEE-CAI) May 2025.

  5. Hier DB, Munzir SI, Stahlfeld A, Obafemi-Ajayi T, Carrithers MD. High-Throughput Phenotyping of Clinical Text Using Large Language Models. in Proc. 2024 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) 2024.