Senior Machine Learning Scientist

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?

FL94 Inc., is a privately held, early-stage biotechnology company pioneering the emerging field of Protein Editing. At FL94 we create small molecules that edit protein structure and function to unlock presently undruggable targets and a broad array of therapeutic modalities. Our platform integrates novel small molecule chemistry and chemoproteomic discovery technologies with Machine Learning (ML) to enable generative design. FL94 is backed by Flagship Pioneering, bringing their courage, vision, and resources to guide FL94 from platform validation to patient impact.

We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!

We are seeking an innovative Machine Learning / Data Scientist passionate about the intersection of machine learning and cheminformatics to join our team. You will be at the forefront of evaluating, applying, and developing chemical artificial intelligence models built on large-scale, proprietary multi-omics data to accelerate our small molecule drug discovery efforts.

• Develop and apply state-of-the-art ML models for drug discovery problems at scale.
• Design and implement rigorous in silico benchmarks to accurately assess and track model performance.
• Optimize model performance by identifying and preparing high-quality (pre-)training data and appropriate inductive biases.
• Develop and maintain cheminformatics infrastructure (benchmarks, toolkits, public/commercial databases).
• Manage, analyze, and interpret complex chemical and biological data.
• Provide cross-functional support to drug discovery programs, enabling data-driven decisions.
• Conduct innovative research to advance our computational capabilities.

• PhD in Computational Chemistry, Computer Science, Data Science, Statistics, or related field; exposure to quantum chemistry is a plus.
• Expertise in cheminformatics fundamentals (molecular property prediction, similarity search, molecular diversity, etc.); experience with ADME data is a bonus.
• Fluent in Python ML development stack (pandas, sklearn, etc.) and ML frameworks (PyTorch, Tensor Flow).
• Hands-on experience with cheminformatics software (RDKit, Deep Chem).
• Experience in biotech or life sciences startup environment working with large data volumes is a plus.
• Experience with cloud infrastructure (AWS, GCP, Azure) and workflow platforms (Flyte, Airflow, Dagster) is a plus.

Location:

Cambridge, MA

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in over $90 billion in value. Many companies founded by Flagship address urgent challenges: vaccinating against COVID-19, curing intractable diseases, improving health, preempting illness, and enhancing agricultural sustainability.

Flagship has been recognized on FORTUNE’s “Change the World” list and Fast Company’s list of the World’s Most Innovative Companies. Learn more at

Flagship and its ecosystem companies are committed to equal employment opportunity, regardless of race, color, religion, sex, national origin, sexual orientation, age, disability, gender identity, or veteran status.

Note: We value diverse backgrounds and experiences. If you meet some but not all qualifications, please apply. Experience is diverse, skills are transferable, and passion is key. We look forward to learning about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering does not accept unsolicited resumes unless contacted directly by our Talent Acquisition team. Resumes submitted without a signed agreement will become the property of FSP, and no fees will be owed.