High-dimensional flow cytometry is a cornerstone of single-cell phenotypic analysis in immunology and oncology. However, the downstream analysis and specifically the manual gating and biological annotation of complex cell populations remains a significant bottleneck. It is time-consuming, susceptible to inter-operator variability, and heavily reliant on domain expertise. While Large Language Models (LLMs) have demonstrated strong zero-shot reasoning capabilities across various biomedical domains, their utility in translating raw immunophenotypic marker profiles into accurate biological cell classifications remains underexplored. To evaluate and compare the accuracy, consistency, and efficiency of three state-of-the-art LLMs in annotating multi-parameter flow cytometry data, we used manual annotations by a panel of domain expert immunologists as the gold standard for both labels and variance. Preliminary results of this comparison will be presented.
Dr. Wes Wilson is a Canadian Tumor Immunologist & Cancer Researcher. In 2021 they received a Young Investigators award for their work on treating solid tumors with immunotherapy. They are currently a Marylou Imgram Scholar through ISAC for their research achievements and contributions to the field. They currently sit on Education and Training committees for various international standards groups. Wilson trained in Tumor Immunology at UWA and did their postdoctoral fellowship in CAR T cell therapy for both hematological malignancies and solid tumors at Penn Medicine. Their current work is focused on neuro-immunotherapy to help develop cellular therapy strategies for treating brain tumors (GBM, DMG/DIPG) in complex tumor microenvironment