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# Senior Scientist, Machine Learning

- **Company:** Flagship Pioneering, Inc.
- **Location:** Cambridge, MA, United States
- **Experience:** Expert
- **Salary:** $168,000.0 - $258,500.0
- **Contract:** Permanent contract
- **Skills:** Cloud Computing, Computational Biology, Experimental Data, Python (Programming Language), Machine Learning, Language Modeling, Molecular Modeling, Programming Languages
- **Published:** July 27, 2026
- **Apply:** https://www.indeed.com/viewjob?jk=1b6a81563558a86f

## 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 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., * 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., 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.

## Description

* 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., * 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.


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