Senior Scientist, Machine Learning

Flagship Pioneering; Cambridge (MA); On-site; USD 168,000 - 258,500; Full time

Benefits offered by this job

Weekly lunches

Monthly social events

Coffee, snacks, and community lunches

Job summary

Flagship Labs 129 (FL129) is an early-stage biotech startup within Flagship Pioneering, building a platform to accelerate small molecule drug discovery using generative chemistry models. We seek a Senior Scientist to join a multidisciplinary team of experimental and computational scientists and shape the scientific direction of the platform.

The ideal candidate combines a Ph.D. in ML/comp biology with 5+ years of experience, strong programming in Python, and expertise in molecular modeling,

Qualifications

• Ph.D. in machine learning, computational biology, or a related field; 5+ years of industry or postdoctoral experience.
• Proficiency in Python and modern HPC/cloud compute workflows.
• Experience training and fine‑tuning molecular models for tasks like protein language modeling, structure prediction, and small molecule pose prediction.

Responsibilities

• Develop, train, validate, and apply novel generative chemistry and molecular models.
• Curate training/benchmark datasets and design rigorous benchmarks.
• Collaborate with wet lab teams to drive project goals and translate data into insights.

Skills

Scientific communication

Collaboration

Adaptability

Critical thinking

Education

Ph.D. in ML/Computational Biology

Tools

Python

HPC

Cloud compute workflows

Job description

What if…

you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologiesin order totransform health care and sustainability?

Flagship Labs 129 (FL129) is an early-stage biotechnology startup with an ambitious and exciting mission:to develop a technology tofacilitatethe 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 andknow-howof 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 molecular 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, andwe’relooking for someone who thinks critically and will influence the company’s scientific direction.
• Development, training, validation, and application of novel generative chemistry andmolecular models
• Curate training and benchmark datasets, and design and implement rigorous benchmarks to assess model performance.
• Optimizeexisting workflows andestablishbest 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 andrelated.
• Experience training and fine-tuning molecular models for taskssuch 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.
• Expertisewitha 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 communicationskills, and comfort in working in and contributing to a dynamic and cross-functional team environment. The level of the role will becommensuratewith 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, genderidentityor Veteran status.

Recruitment & Staffing Agencies

: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto

Privacy Notice for Applicants:

When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].

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.

Privacy Notice for Applicants:

When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].