Director of Machine Learning - AI Powered Biological Design

About the Role

We are seeking a Director of Machine Learning to join the Allen Institute, where you will lead the charge in applying advanced machine learning techniques to biological design. This is a unique opportunity to work in an AI-powered lab that merges academic creativity with startup execution. As the Director of Machine Learning - AI Powered Biological Design, you will oversee the development of innovative solutions that enhance our understanding of biological systems.

What You'll Do

• Define and own the ML strategy for the enhancer flywheel and additional synthetic biology projects, establishing success metrics and roadmaps.
• Build and manage a central ML team, including ML/data scientists embedded in project teams.
• Architect and implement sequence-to-function and generative models for regulatory elements and other biological designs.
• Collaborate with project teams to design and optimize DBTL loops, supporting assay design and active learning tactics.
• Supervise quantitative analysis and quality control of high-throughput assays, integrating external datasets for transfer learning.
• Establish best practices for ML across projects, focusing on code quality, experiment tracking, and reproducibility.
• Partner with data/engineering teams to maintain the computational infrastructure for large-scale sequence modeling.
• Communicate ML strategies and results to project leads and external collaborators, contributing to publications and presentations.

Requirements

• Ph.D. in Computer Science, Computational Biology, Statistics, or a related field.
• 5+ years of post-Ph.D. experience in building, training, and deploying ML models.
• Deep expertise in ML applied to biological sequences or structured biological data.
• Strong proficiency in Python and at least one modern ML framework (e.g., PyTorch, JAX, TensorFlow).
• Proven track record of technical leadership and mentoring scientists/engineers.
• Excellent communication skills and ability to collaborate with computational and experimental scientists.

Nice to Have

• Experience integrating diverse datasets into predictive or generative models.
• Research experience in regulatory genomics or transcription factor binding.
• Hands-on work with DBTL loops in synthetic biology.
• Experience with generative models for biological sequences.
• Strong publication or open-source record in ML for biology.

What We Offer

• Annualized salary range of $224,200 - $294,250.
• Relocation assistance and work visa sponsorship available.
• Comprehensive health insurance, including medical, dental, and vision.
• 401k plan with employer contributions.
• Paid time off and flexible working arrangements.
• A supportive and inclusive work environment.
• Opportunities for professional development and growth.

Join us in our mission to unlock the complexities of bioscience and improve human health through innovative AI applications. Apply today for the Director of Machine Learning - AI Powered Biological Design position!