Senior Machine Learning Scientist/Engineer – Biomolecular Design

The Role

Pioneering Intelligence (PI) is a Flagship initiative that develops AI/ML based platforms for applications in life sciences and beyond.  We are seeking a Senior Machine Learning Scientist or Engineer with hands-on experience implementing novel methods in generative biomolecular design, large model scaling, data curation, and data engineering.

Responsibilities:

• Be part of a developer team: Work with the PI team to develop the next generation of biomolecular generative models across proteins, small molecules, nucleic acids, and more.
• Hands-on dev: Code the new ideas you develop with the team. Train, test and scale models, with opportunities to validate in the lab.
• Make an impact: The models you develop will be leveraged by multiple Flagship ventures. Work with biologists and chemists to turn your in-silico work into real world impact.

Qualifications:

• PhD in CS, AI/ML, Physics, Biophysics, Biochemistry, Comp Biology, or related.
• Experience developing, implementing and training deep learning models.
• Experience in curation, processing and data engineering of TB-sized datasets.
• Experience with large scale training over multiple nodes on cloud infra.
• Fluent in Python, familiar with PyTorch and Git.

Preferred Experiences with:

• Implementing generative models such as LLMs, diffusion and flow-matching for proteins or small molecules
• Constructing, annotating, and serving large databases of biomolecular data.
• Biomolecular design models and tools such as RFDiffusion, ProteinMPNN, AlphaFold, ESM, DiffDock etc.
• ML software development and cloud services, e.g. Docker, AWS Batch, Step Functions, EKS, AWS ParallelCluster, etc.
• 3+ years industry experience.

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 thereto.