Flagship Pioneering

Senior Scientist, Machine Learning

Flagship Pioneering$168K — $258K *
Pharmaceuticals & Biotech
5 - 7 years of experience
Job Overview by Ladders

Qualifications

  • Ph.D. in machine learning, computational biology, or related field with 5+ years of experience.
  • Familiarity with state-of-the-art models such as Boltz-2, ESM-2, and Chai-2.
  • Experience in training and fine-tuning molecular models for tasks like protein language modeling and structure prediction.
  • Skilled in curating datasets, including mutational scanning data.
  • Expertise in a high-level programming language like Python and HPC/cloud workflows.
  • Possesses deep structural understanding of proteins (preferred).
  • Strong organizational and communication skills as a team player.

Responsibilities

  • Drive technology development in alignment with FL129's strategic goals as an early team member.
  • Develop, train, validate, and apply novel generative chemistry and molecular models.
  • Curate training datasets and design benchmarks to assess model performance.
  • Optimize workflows and establish best practices for experiments and documentation.
  • Collaborate closely with wet lab teams to achieve project objectives.
  • Translate experimental data into insights and present findings at team meetings.

Benefits

  • Opportunity to establish the scientific foundation of a transformative platform as an early employee.
  • Custom role designed for impactful contributions and professional growth.
  • Engaging community with weekly lunches, monthly events, and access to snacks and coffee.
Full Job Description
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.

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.

About Flagship Pioneering

Flagship Pioneering is a life sciences innovation enterprise that conceives, creates, resources, and develops first-in-category life sciences companies. The firm operates through its Flagship Labs unit, which is a dedicated innovation foundry that invents and launches transformative companies. Flagship Pioneering has created over 100 scientific ventures, resulting in over $34 billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents. The firm's portfolio includes companies in the fields of therapeutics, health technologies, and sustainability. Flagship Pioneering was founded in 2000 and is headquartered in Cambridge, Massachusetts.
Learn more about Flagship Pioneering
Size
500 employees
Industry

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