AI/ML Scientist – Protein Foundation Models

Manifold Bio is a company focused on building AI models for protein therapeutic design using proprietary experimental data. They are seeking an AI/ML Scientist to advance their foundation model training efforts, working on pre-training, fine-tuning, and evaluation of models to improve drug design capabilities.

Responsibilities:

• Advance the team's ongoing foundation model training efforts—pretraining, fine-tuning, and evaluating folding, docking, language, and generative design models on Manifold's proprietary experimental data
• Bring depth in training methodology, architecture selection, and optimization to complement the existing team's expertise
• Develop and scale training pipelines for distributed, multi-GPU and multi-node training runs
• Integrate foundation model outputs into mBER to improve binder design success rates and enable new design capabilities
• Design and execute ML experiments with clear hypotheses, rigorous evaluation frameworks, and systematic analysis
• Establish best practices for mixed-precision training, gradient checkpointing, and computational efficiency at scale
• Produce clear documentation and analysis supporting architecture and training decisions