Senior Scientist, Machine Learning

Flagship Pioneering, Inc.•Cambridge, MA

8d•$168,000 - $258,500

About The Position

Flagship Labs 129 (FL129) is an early-stage biotechnology startup with an ambitious and exciting mission: to develop a technology to facilitate the data generation necessary for training the next generation of generative chemistry models to unlock the future of small molecule drug discovery. FL129 is developing a revolutionary approach to this challenge and is recruiting a team of top-tier scientists to build this powerful and first-in-category platform. This is a unique opportunity to be one of the first employees of a biotech startup that combines an innovative mindset with the resources and know-how of Flagship Pioneering. We are seeking a motivated and highly collaborative Senior Scientist to join FL129’s growing team of experimental and computational scientists to build a novel platform technology. The successful candidate will have strong track record of scientific and technical innovation in machine learning for molecular modeling (proteins and/ small molecule ligands). Additional experience with computational docking methods is preferred. The ideal teammate will be highly adaptable, have strong organizational and communication skills, and will thrive in a highly collaborative and multidisciplinary environment.

Requirements

Ph.D. in machine learning, computational biology, or a similar field with 5+ years of industry or postdoctoral experience.
Familiarity with SOTA models such as Boltz-2, ESM-2, Chai-2 and related.
Experience training and fine-tuning molecular models for tasks such as: protein language modeling, protein structure prediction, binder prediction, protein design, protein engineering, small molecule pose prediction, and related.
Experience curating publicly available datasets, including mutational scanning data.
Expertise with a high-level programming language such as Python and modern HPC and cloud compute workflows.
Motivated team-player and independent force-of-nature with strong organizational and written/verbal communication skills.

Nice To Haves

Deep structural understanding of proteins.
Additional experience with computational docking methods is preferred.

Responsibilities

Technology development, aligned with FL129’s core strategic goals. This role is among the first hires, and we’re looking for someone who thinks critically and will influence the company’s scientific direction.
Development, training, validation, and application of novel generative chemistry and molecular models
Curate training and benchmark datasets, and design and implement rigorous benchmarks to assess model performance.
Optimize existing workflows and establish best experimental and documentation practices to enable platform excellence.
Close collaboration with wet lab scientific team to drive achievement of key project goals.
Translate experimental data into meaningful insights and present results at team meetings.