Shashidhar Ravishankar

My research sits at the intersection of machine learning and biology: I build the models, the data infrastructure they train on, and the evaluations that say whether they work. Right now that is agentic AI for drug discovery. I am currently the Director of AI/ML at Athos Therapeutics, a clinical-stage biotech company, where I lead the engineering team on two fronts at once: optimizing the agent system we run, and building an evaluation suite that measures how agents perform across every phase of the discovery process, with LLM judges grading their output. Earlier it meant protein language models for T-cell antigen specificity, pipelines that turn billions of immune receptor sequences into training-ready datasets, and frameworks that test whether a model generalizes beyond its training distribution. My work spans immunology, virology, oncology, and infectious disease.

Before Athos, I spent more than six years at the Fred Hutchinson Cancer Center. As a Staff Scientist in the Warren Lab, I led QUEST, a project that uses protein language models to predict which targets T-cells recognize. I built the data and training pipeline for 2.6 billion T-cell and target sequences and trained the models on multi-GPU cloud servers. This work was funded by a Yosemite-American Cancer Society Award, where I was Co-PI. I also combined single-cell, bulk RNA-seq, and immune repertoire data to study the immune response to Kaposi sarcoma, and mapped genetic variation across about 1,500 Epstein-Barr virus genomes. Earlier at Fred Hutch, I built LymphoSeq2, an open-source R package for immune repertoire analysis.

I earned my Ph.D. in Bioinformatics from the Georgia Institute of Technology, where I worked with Dr. Fredrik Vannberg and Dr. Eldin Talundzic. During my Ph.D., I worked with the Malaria Branch at the Centers for Disease Control and Prevention. There I built NeST, a toolkit for tracking malaria drug resistance that became a standard protocol across six CDC laboratories. I also helped assemble a complete genome of the malaria parasite Plasmodium brasilianum.