graph-transformers jobs in San Diego

Lead the scientific vision and execution of a generative AI platform for protein foundation models, starting with antibody and VHH design. You will build and manage a team of AI researchers and ML infrastructure engineers, define pretraining and post-training strategies across self-supervised learning, reinforcement learning, and transfer learning, and design confidence heads with out-of-distribution detection.…See more This is a founding role requiring deep expertise in structure-based generative modeling, multi-node GPU training, and the ability to shape cutting-edge computational approaches for therapeutic molecule discovery.

As an AI/ML advisor for biotherapeutics at Eli Lilly, you will lead training and fine-tuning experiments on proprietary infrastructure (LillyPod), curate and process biological data (sequences, structures, assays), and build evaluations that connect model outputs to experimental results. You will diagnose model failures, collaborate cross-functionally with protein scientists and wet-lab teams, and communicate findings to both computational and experimental audiences.…See more The role requires a Ph.D. in a quantitative field (or M.S. with 3+ years experience) and strong hands-on expertise in Python, PyTorch, and deep learning on GPUs, with preference for experience in geometric deep learning, protein language models, diffusion/flow-matching, and published ML applications to molecular data.