# Principal Scientist, Machine Learning - Biomolecules

**Company**: Flagship Pioneering
**Location**: Cambridge, MA
**Experience**: senior
**Job type**: full-time
**Salary**: $208,000 - $286,000
**Category**: Data Science
**Industry**: Technology

**Apply**: https://job-boards.greenhouse.io/flagshippioneeringinc/jobs/8584537002?utm_source=yubhub.co&utm_medium=jobs_feed&utm_campaign=apply
**Canonical**: https://yubhub.co/jobs/job_70a1a33d-75c

## Description

We are seeking a Principal Scientist (Embedded ML/Computational) to lead multiple AI/ML or computational projects across early stage ventures, as a part of Flagship’s company origination process.

You will define and deliver pragmatic AI strategies, oversee method and platform development, and ensure rigor in model development, benchmarking, scaling, and reporting. You will manage cross-functional contributors, influence company direction, and represent PI to venture teams and external partners.

The ideal candidate is a self-directed serial deep diver - someone who can move from protein design one week to mass spec or docking pipelines the next and then spin up LLM-based agents that automate scientific workflows.

**Key Responsibilities:**

- Program Leadership: Lead development, implementation, control, and reporting of several AI/ML or computational projects within assigned ventures.

- Technical Ownership: Take a specialized technical role on project teams to oversee method development, pipeline development, and LLM-based agent/workflow design.

- Best Practices: Promote operational excellence in AI projects by educating cross-functional collaborators.

- Team Leadership: Manage and/or coordinate internal and external scientists/engineers and cross-functional project teams.

- Planning & Resourcing: Contribute to project planning, including budgets, resources, and timelines.

- Landscape & Strategy: Independently scout emerging literature and the AI/ML landscape.

- Representation & Community: Represent PI to portfolio companies and external partners.

- Communication & Influence: Influence the course of projects and technical approaches.

**Professional Experience & Qualifications:**

- Master’s, or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences) with 5+ years' experience scientific/engineering/computational in academic, pharmaceutical, or biotechnology settings.

- Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fast-paced, entrepreneurial, and technical environments.

- Clear evidence of sustained independent thought and creativity driving high-impact, cross-disciplinary AI/ML projects.

**Preferred Qualifications:**

- Breadth across domains such as protein modeling/design, proteomics/mass spec, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation.

- MLOps expertise: data contracts and lineage, experiment tracking, secure AWS infrastructure, Docker, IaC, and CI/CD.

**Why Pioneering Intelligence:**

- Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision making across multiple new ventures.

- Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs,ship end-to-end systems that scientists rely on daily.

- Compound impact: Convert one-off wins into shared libraries and templates adopted across the PI portfolio.

**Benefits:**

- Healthcare coverage

- Annual incentive program

- Retirement benefits

- Broad range of other benefits

## Skills

### Required
- Python
- modern ML frameworks (PyTorch or JAX/TensorFlow)
- version control
- databases
- deep learning architectures

### Nice to have
- Breadth across domains such as protein modeling/design, proteomics/mass spec, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation
- MLOps expertise: data contracts and lineage, experiment tracking, secure AWS infrastructure, Docker, IaC, and CI/CD

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Source: [Apply at job-boards.greenhouse.io](https://job-boards.greenhouse.io/flagshippioneeringinc/jobs/8584537002?utm_source=yubhub.co&utm_medium=jobs_feed&utm_campaign=apply)