Principal Machine Learning Engineer

Principal Machine Learning Engineer - Foundation Models for Antibody Discovery London, UK (Hybrid) | Up to £140,000 + Equity Stealth AI Biotech Startup | Full-time We're working with a stealth-mode AI biotech company building foundation models purpose-built for antibody discovery and engineering. Their mission is to develop biological foundation models capable of understanding the language of antibodies, antigens, immune systems, and protein interactions at unprecedented scale. By combining large-scale biological datasets with state-of-the-art machine learning, we're creating AI systems that can design, optimise, and predict therapeutic antibodies with significantly greater speed and accuracy than traditional approaches. Their vision is to build the foundational intelligence layer for the next generation of antibody therapeutics. We're hiring a Principal Machine Learning Engineer to lead the development of our core antibody foundation model platform. You'll work at the intersection of large-scale machine learning, protein modelling, and therapeutic discovery, helping define the architecture, infrastructure, and technical direction behind models trained on billions of biological sequences and experimental observations. This is a hands-on leadership role where you'll influence both research strategy and engineering execution while working alongside computational biologists, protein engineers, and ML researchers. The ideal candidate combines deep expertise in foundation models with a genuine interest in solving complex problems in antibody design and immunology. Designing and scaling foundation models trained on large-scale antibody, protein, and biological sequence datasets Building generative AI systems for antibody design, optimisation, and affinity maturation Training multimodal models across sequence, structural, functional, and experimental datasets Scaling distributed training infrastructure for large biological foundation models Applying modern generative modelling techniques to antibody generation and protein engineering workflows Building evaluation frameworks that measure biological plausibility, manufacturability, and therapeutic relevance Driving best practices across experimentation, MLOps, model deployment, and platform engineering Mentoring senior engineers and helping shape the long-term ML strategy of the company 5+ years of experience building advanced machine learning systems in production environments ~ Strong expertise in foundation models, transformers, representation learning, and generative AI ~ Proven experience training large-scale models on distributed GPU infrastructure ~ Strong software engineering and systems design capabilities ~ Experience leading complex technical initiatives and mentoring engineering teams ~ Experience applying machine learning to protein engineering, antibody discovery, or computational biology Familiarity with antibody sequence datasets, immune repertoire modelling, or protein language models Experience with structural biology data including AlphaFold, protein embeddings, or molecular simulation outputs Experience with diffusion models, graph neural networks, or generative protein design approaches Publications in machine learning, protein modelling, computational biology, or AI for Science Build frontier AI systems focused on one of the most impactful areas in modern biotechnology Help create foundation models that could transform antibody discovery and therapeutic development Competitive compensation package with substantial equity participation Collaborate with world-class experts across machine learning, immunology, and protein engineering Flexible hybrid working environment and generous learning budget