Senior ML Engineer

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 150,000 - 190,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Broad range of other benefits

Job summary

Flagship Pioneering in Cambridge, MA seeks a Senior Machine Learning Engineer to design, build, and deploy ML systems powering our platform. You’ll focus on LLMs, RAG, agentic orchestration, and production-grade deployment, working across the full ML lifecycle with scientists and engineers in a fast-moving, mission-driven environment.

You will own data pipelines, experiment with models, fine-tune for production, and contribute to ML best practices and architecture decisions.

Qualifications

• Master's degree or equivalent practical experience in CS/ML/AI.
• 5+ years of professional ML experience.
• Strong ML, DL, and NLP foundations.
• Proven production deployment of LLM-powered apps.
• Experience with RAG, orchestration, and multi-agent systems preferred.
• Proficiency in Python and ML tooling; end-to-end ownership.

Responsibilities

• Design, build, and deploy ML systems powering the product.
• Architect scalable RAG-LLM based solutions with multi-modal data.
• Develop agentic orchestration frameworks for end-to-end reasoning.
• Own ML pipeline from data collection to deployment and monitoring.
• Fine-tune and evaluate LLMs for production use with focus on reliability and cost.
• Establish lightweight MLOps, CI/CD, reproducibility, and experiment tracking.
• Balance off-the-shelf APIs with custom fine-tuned solutions.
• Influence ML best practices across the team; collaborate cross-functionally.
• Translate interdisciplinary insights into computational frameworks.
• Clearly communicate tradeoffs to technical and non-technical stakeholders.

Skills

LLMs

RAG

Agentic orchestration

Python

PyTorch

vLLM

LangGraph

Data pipelines

MLOps

CI/CD

Production monitoring

NLP

Communication

Education

Master's degree in CS/ML/AI

Tools

PyTorch

vLLM

LangGraph

Job description

The Role

We are seeking a highly motivated Senior Machine Learning Engineer to join our AI/ML team. This individual will play a central role in designing, building, and deploying the machine learning systems that power our platform, with a focus on large language models (LLMs), retrieval-augmented generation (RAG), agentic orchestration, and production-grade model deployment.

You will work across the full ML lifecycle, from framing problems and experimenting with models, to fine-tuning and deploying them in production and monitoring their performance. Beyond shipping models, you will influence architecture decisions, set ML best practices, and help define how AI shapes our product and scientific workflows. This is an opportunity to work closely with world‑class scientists, engineers, and researchers in a fast‑moving, mission‑driven environment.

Key Responsibilities

• Design, build, and deploy ML systems that power the product, translating scientific and product requirements into concrete ML problems (e.g., retrieval, summarization, classification, agentic reasoning)
• Architect and implement scalable RAG and LLM-based systems that integrate multi‑modal data sources, including structured datasets, documents, and knowledge graphs where relevant
• Build and maintain agentic orchestration frameworks that coordinate LLM‑based agents for end‑to‑end reasoning, data retrieval, and decision support
• Own the ML pipeline end‑to‑end: data collection, cleaning, feature engineering, labeling, training, evaluation, and deployment
• Fine‑tune and evaluate LLMs and other models for production use, with attention to reliability, latency, and cost
• Set up lightweight MLOps practices, including CI/CD for models, reproducibility, and experiment tracking
• Make pragmatic technical decisions, balancing off‑the‑shelf APIs (e.g., OpenAI, Anthropic) against custom‑built or fine‑tuned solutions
• Influence architecture decisions and help define ML best practices across the team
• Collaborate cross‑functionally with data engineering, product, and domain experts to translate interdisciplinary insights into computational frameworks
• Communicate findings and technical tradeoffs clearly to both technical and non‑technical stakeholders

Professional Experience & Qualifications

• Master's degree (or above) in Computer Science, Machine Learning, AI, or a related field; equivalent practical experience considered
• 5+ years of professional experience in applied machine learning
• Strong foundation in machine learning, deep learning, and natural language processing (NLP)
• Proven experience deploying LLM‑powered applications in production environments, including experience with frameworks such as PyTorch, vLLM, or LangGraph
• Hands‑on experience with RAG, agentic orchestration, or multi‑agent systems is strongly preferred
• Proficiency in Python and tools for ML development, large‑scale data pipelines, and standard evaluation protocols
• Experience owning systems end‑to‑end in a production environment, including monitoring and iterating post‑deployment
• Self‑motivated and comfortable working in ambiguous, fast‑moving environments with evolving goals
• Excellent communication and presentation skills; able to work with both technical and non‑technical collaborators
• Experience in a previous startup is a plus
• Publications at top ML / NLP venues such as NeurIPS, ICML, ACL, or EMNLP are a bonus

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, pre‑empting 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 arecommitted to equal employment opportunityregardless 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.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI‑assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].

The salary range for this role is $0 - $0. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience.

• healthcare coverage
• annual incentive program
• retirement benefits
• a broad range of other benefits

Compensation and benefits information is based on Flagship Pioneering's good faith estimate as of the date of publication and may be modified in the future.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI‑assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact [e-mail].