Senior Scientist, Machine Learning

About the role

We are seeking a motivated and highly collaborative Senior Scientist to join FL129’s growing team of experimental and computational scientists to build a novel platform technology. The successful candidate will have a strong track record of scientific and technical innovation in machine learning for molecular modeling (proteins and/or small molecule ligands). Additional experience with computational docking methods is preferred. The ideal teammate will be highly adaptable, have strong organizational and communication skills, and will thrive in a highly collaborative and multidisciplinary environment.

This is a unique opportunity to be one of the first employees of a biotech startup that combines an innovative mindset with the resources and know-how of Flagship Pioneering.

Responsibilities

• Technology development, aligned with FL129’s core strategic goals. This role is among the first hires, and we’re looking for someone who thinks critically and will influence the company’s scientific direction.
• Development, training, validation, and application of novel generative chemistry and molecular models.
• Curate training and benchmark datasets, and design and implement rigorous benchmarks to assess model performance.
• Optimize existing workflows and establish best experimental and documentation practices to enable platform excellence.
• Close collaboration with wet lab scientific team to drive achievement of key project goals.
• Translate experimental data into meaningful insights and present results at team meetings.

Qualifications

• Ph.D. in machine learning, computational biology, or a similar field with 5+ years of industry or postdoctoral experience.
• Familiarity with SOTA models such as Boltz-2, ESM-2, Chai-2 and related.
• Experience training and fine-tuning molecular models for tasks such as: protein language modeling, protein structure prediction, binder prediction, protein design, protein engineering, small molecule pose prediction, and related.
• Experience curating publicly available datasets, including mutational scanning data.
• Expertise with a high-level programming language such as Python and modern HPC and cloud compute workflows.

Skills

• Deep structural understanding of proteins (nice to have).
• Motivated team-player and independent force-of-nature with strong organizational and written/verbal communication skills.

Benefits

• Opportunity to lay the scientific foundation of a transformative platform company as an early employee.
• Custom-tailored role to maximize impactful contributions, professional growth, and scientific interests.
• Weekly lunches, monthly social events, and community lunchroom with free snacks, coffee, all embedded in a vibrant community of scientists and entrepreneurs across multiple Flagship Pioneering portfolio companies.
• Healthcare coverage, annual incentive program, retirement benefits, and a broad range of other benefits.

Pay

The salary range for this role is $168,000 - $258,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience.