Senior ML Scientist — Generative Chemistry & Molecules

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 168,000 - 259,000; Full time

Benefits offered by this job

Weekly lunches

Monthly social events

Community lunchroom with free snacks

Job summary

Flagship Labs FL129 seeks a Senior Scientist to join a growing team of experimental and computational scientists developing a novel platform for generative chemistry and molecular modeling. You will contribute to technology development, data curation, and benchmark design while collaborating with wet-lab colleagues.

The role emphasizes leadership in a highly collaborative, multi-disciplinary environment with strong organizational and communication skills.

Qualifications

• Ph.D. in ML, computational biology, or a related field with 5+ years of experience.
• Experience with SOTA models such as Boltz-2, ESM-2, Chai-2 and related.
• Experience training and fine-tuning molecular models for proteins and small molecule ligands.
• Expertise in Python and HPC/cloud compute workflows.
• Nice to have: deep structural understanding of proteins.

Responsibilities

• Technology development aligned with FL129’s core strategic goals.
• Develop, train, validate, and apply novel generative chemistry and molecular models.
• Curate training and benchmark datasets and design rigorous benchmarks to assess model performance.
• Optimize existing workflows and establish best practices for platform excellence.
• Collaborate with wet lab scientists to drive key project goals.
• Translate experimental data into meaningful insights and present results at team meetings.

Skills

Python

HPC

Cloud compute

Communication

Education

Ph.D. in ML/Computational biology or related field

Tools

Python

HPC

Cloud compute

Job description

Flagship Labs FL129 seeks a Senior Scientist to join a growing team of experimental and computational scientists developing a novel platform for generative chemistry and molecular modeling. You will contribute to technology development, data curation, and benchmark design while collaborating with wet-lab colleagues.

The role emphasizes leadership in a highly collaborative, multi-disciplinary environment with strong organizational and communication skills.