(Senior) Machine Learning Scientist, Systems Biology

Who We Are

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.

Position summary

Pioneering Intelligence (PI) is a Flagship initiative dedicated to developing AI/ML-powered platforms for transformative applications in life sciences and related fields. We are seeking a talented (Senior) ML Scientist, Systems Biology to join a new effort building state-of-the-art AI-based capabilities for propelling the drug development process into an AI-driven future. In this role, you will leverage your technical and creative thinking and biomedical knowledge for developing AI capabilities of high priority to Flagship and its companies.

Responsibilities

• Develop new methods for leveraging biological data in drug discovery
• Develop robust pipelines to extract, integrate, and analyze complex biological databases
• Design and implement LLM pipelines specialized for the biomedical domain
• Develop and apply state-of-the-art AI/ML approaches to biological applications
• Act as a subject matter expert to the team and cross-functionally
• Collaborate with biotech industry experts and ML engineers to validate and refine models
• Present progress in regular research meetings, prepare reports, and present findings for stakeholders and leadership
• Maintain expertise in emerging computational methodologies

Qualifications

• PhD degree in Computational Biology, Bioinformatics, Systems Biology, Computer Science, or similar computational field with focus on biological applications.
• Strong publication record in computational biology or systems biology research
• Expertise querying and integrating public biological databases (e.g. KEGG, Reactome, BioGRID, TCGA, GEO, OpenTargets, etc.)
• Fluency in Python and standard ML tools and packages and libraries (e.g. PyTorch, TensorFlow, sklearn)
• Experience implementing state-of-the-art deep learning models (e.g. transformer architectures, CNNs, GNNs, etc.) in biological applications
• Experience with version control software (e.g. Git) and AWS cloud computing
• Interest in LLMs and their applications
• Demonstrated ability to collaborate in interdisciplinary teams and communicate complex technical concepts effectively
• Ability to take initiative and work independently
• Excellent analytical and problem-solving skills tailored to innovative computational research

Preferred

• Experience leveraging LLMs in development environments
• Prior industry experience (3+ years)

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 imp