Senior Scientist, Machine Learning

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 168,000 - 259,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Pioneering, Inc. is seeking a Senior Scientist to join FL129 and build a novel platform for generative chemistry. You will work with experimental and computational scientists to advance molecular modeling for proteins and ligands, contributing to an early-stage biotech platform.

The role emphasizes collaboration, data curation, model development, and rigorous benchmarking to influence the company’s scientific direction and impact in drug discovery.

Qualifications

• PhD in machine learning, computational biology, or a related field.
• 5+ years of industry or postdoctoral experience.
• Experience training and applying molecular models (proteins and ligands).
• Proficiency with Python and HPC/cloud compute workflows.

Responsibilities

• Technology development aligned with core strategic goals at FL129.
• Develop, train, validate and apply generative chemistry and molecular models.
• Curate training datasets and design benchmarks to assess model performance.
• Optimize workflows and establish best practices for platform excellence.
• Collaborate with wet lab teams to drive project goals.
• Translate experimental data into actionable insights and present results.

Skills

Machine learning

Python

Collaboration

Education

PhD in machine learning or computational biology

Tools

Python

HPC/Cloud workflows

Job description

What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

Flagship Labs 129 (FL129) is an early-stage biotechnology startup with an ambitious and exciting mission: to develop a technology to facilitate the data generation necessary for training the next generation of generative chemistry models to unlock the future of small molecule drug discovery. FL129 is developing a revolutionary approach to this challenge and is recruiting a team of top-tier scientists to build this powerful and first-in-category platform. 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.

Position Summary

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 strong track record of scientific and technical innovation in machine learning for molecular modeling (proteins and/ 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.

Key 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.

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

What we can offer you

• 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.

We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidates.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

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. FL129 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL129’s good faith estimate as of the date of publication and may be modified in the future.