(Senior) Machine Learning Scientist

What if… 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! 

Position Summary: 

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. 

Key Responsibilities: 

• 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 essential 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. 

Qualifications: 

• PhD degree in Computational Chemistry, Computer Science, Data Science, Statistics, or a related field. Exposure to quantum chemistry is a strong plus. 
• Expertise in cheminformatics fundamentals (molecular property prediction, similarity search, molecular diversity, etc.). Experience with ADME data is a bonus. 
• Fluent in the Python ML development stack (pandas, sklearn, etc.) and ML frameworks (PyTorch, TensorFlow). 
• Hands-on experience with common cheminformatics software (RDkit, DeepChem) 
• Experience in a biotech or life sciences startup environment working with large volumes of data is a strong plus. 
• Experience with cloud computing infrastructure (AWS, GCP, Azure) and workflow orchestration platforms (Flyte, Airflow, Dagster) is a plus. 

Location: Cambridge, MA

About Flagship

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 its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com

 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, gender identity or Veteran status.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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 there to.*