Senior Scientist, Machine Learning at Flagship Pioneering, Inc.

About the role

Join Flagship Labs 129 (FL129), an innovative biotechnology startup dedicated to advancing technologies that enhance drug discovery. We are looking for a highly skilled Senior Scientist with expertise in machine learning to contribute to the development of a cutting‑edge platform focused on generating data for generative chemistry models. This role offers a unique opportunity to be part of a pioneering team within a well‑resourced organization committed to scientific innovation and transformative breakthroughs. As a key member of the team, you will drive the development of novel models and workflows that will impact drug discovery pipelines, working closely with multidisciplinary teams to translate scientific insights into practical applications.

Key facts

- Location: Cambridge, MA USA
- Engagement: Full-time
- Team: FL129

What you’ll do

- Lead the design, development, and implementation of advanced machine learning models tailored for molecular and chemical data, ensuring alignment with FL129’s strategic goals.
- Develop, train, and validate generative chemistry models, including those focused on small molecules and proteins, to facilitate novel drug discovery efforts.
- Assemble, curate, and preprocess large datasets necessary for training models, ensuring data quality and relevance, and establish rigorous benchmarks to evaluate model performance.
- Improve existing workflows, pipelines, and experimental procedures to enhance reproducibility, efficiency, and robustness of model training and deployment.
- Collaborate with wet lab scientists to integrate computational models with experimental data, ensuring that model predictions are validated and translated into tangible outcomes.
- Analyze complex experimental and computational data to extract meaningful insights, identify patterns, and inform subsequent research directions.
- Present findings, progress reports, and technical insights to internal teams and external partners, fostering effective communication of complex scientific concepts.
- Stay current with the latest developments in machine learning, computational chemistry, and related fields, and incorporate innovative techniques into ongoing projects.
- Contribute to the development of intellectual property, including publications,



patents, and technical documentation, to support the company’s scientific reputation and strategic interests.
- Participate in cross‑functional team meetings, providing expertise on machine learning methodologies and data analysis to support broader project objectives.
- Support the training and mentorship of junior scientists and researchers, fostering a team-oriented and innovative team environment.

Requirements

- Ph.D. in machine learning, computational biology, cheminformatics, bioinformatics, or a related discipline, with a minimum of 5 years of relevant industry or postdoctoral experience.
- Proven track record of applying machine learning techniques to molecular modeling, drug discovery, or related fields, with demonstrated success in developing and deploying models.
- Experience working with molecular data, including small molecules, proteins, and related datasets, is highly desirable.
- Familiarity with computational docking techniques, molecular simulations, or structure‑based modeling is preferred.
- Strong programming skills in Python, along with experience working in high‑performance computing (HPC) environments and cloud computing platforms.
- Ability to design, implement, and optimize machine learning workflows, including data preprocessing, model training, and evaluation.
- Excellent problem‑solving skills, with the ability to analyze complex datasets and derive actionable insights.
- Robust written and verbal communication skills, capable of conveying technical concepts to multidisciplinary teams and external collaborators.
- Proven ability to work independently and collaboratively in a fast‑paced, innovative environment.
- Experience with version control systems, such as Git, and familiarity with software development best practices.

Nice to have

- Knowledge of state‑of‑the‑art models such as Boltz‑2, ESM‑2, and Chai‑2, and their applications in molecular modeling.




- Experience training and fine‑tuning molecular models for tasks such as protein language modeling, structure prediction, binder prediction, and protein design.
- Background in curating and working with publicly available datasets, including mutational scanning data and other large‑scale biological datasets.
- Deep understanding of protein structures, folding, and interactions, with the ability to incorporate structural insights into modeling efforts.
- Familiarity with cheminformatics tools and software, such as RDKit, for molecular data processing and analysis.
- Experience in patent writing, scientific publishing, or presenting at conferences, demonstrating strong scientific communication skills.

Skills & tools

- Machine learning frameworks such as TensorFlow, PyTorch, or similar.
- Computational docking and molecular modeling tools.
- Data curation, benchmarking, and validation techniques.
- Programming in Python, with experience in scientific computing libraries.
- HPC and cloud computing workflows, including AWS, Google Cloud, or Azure.
- Version control systems like Git.
- Familiarity with cheminformatics and structural biology software.

Practical notes

- We welcome applicants from diverse backgrounds and are committed to fostering an inclusive environment that values different perspectives.
- The role’s level will be determined based on the candidate’s education, experience, and expertise.
- Flagship Pioneering does not accept unsolicited resumes from recruitment agencies.
- The position is on‑site in Cambridge, MA, and requires working at the office location.
- We offer a collaborative, innovative, and dynamic work environment where scientific curiosity and creativity are encouraged.
- Our benefits include competitive compensation, health insurance, and opportunities for professional development.
- We are dedicated to supporting work‑life balance and providing a supportive environment for all team members.
- The successful candidate will have the opportunity to contribute to groundbreaking projects that could transform drug discovery and molecular science.
- Join us in shaping the future of healthcare and sustainability through innovative science and technology at Flagship Pioneering.

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📌 Senior Scientist, Machine Learning (Cambridge)
🏢 Flagship Pioneering
📍 Cambridge