Flagship Pioneering
Senior Machine Learning Engineer / Data Scientist
Boston, Massachusetts, USA · Senior · full-time
Stay score
odds of building a lasting career here
Sponsors, but it's cap-subject — you still face the weighted lottery (~45% per draw at Level III). Good if you win; have a cap-exempt backup on your list.
Lottery odds assume a STEM candidate.
Personalize to your clock →H-1B wage level
the lottery is wage-weighted — each level is one more entry
The bottom of this range ($96,000) is below the Level I prevailing wage of $114,275. An H-1B cannot be filed below the prevailing wage, so an offer at the floor of this band could not be sponsored as posted.
Based on the DOL prevailing wage for this occupation and worksite, a base salary of $138,237 would place this position at wage Level II. That figure is within the posted range, and I'd like to target it. This role classifies under "Software Developers" for prevailing-wage purposes.
DOL prevailing wage, 2026-27 wage year · Software Developers (15-1252) · Boston-Cambridge-Newton, MA-NH. Wage level is derived by USCIS from the offered wage, occupation and worksite; the occupation shown is inferred from the job title.
Employer immigration record
from this employer's Department of Labor filings
Files H-1B transfers
Sourced from Department of Labor LCA, PERM and prevailing-wage disclosure data. Employer matching is by name, so figures may be split across an employer's legal entities. Absence of a filing means none appears in our copy of the data, not that none exists.
Community outcomes
No reports yet — be the first to help the next applicant.
About the role
- We are seeking a highly motivated Senior Machine Learning Engineer / Data Scientist to join our AI/ML team.
- This individual will play a central role in designing and implementing advanced AI/ML systems with a focus on Retrieval-Augmented Generation (RAG), graph-based RAG, large language models (LLMs), agentic orchestration, and conversational AI (chatbot) solutions.
Responsibilities
- Architect and implement scalable RAG and LLM-based systems that integrate multi-modal data sources, including knowledge graphs, documents, and structured biological datasets.
- Design and deploy RAG and graph-based RAG pipelines that leverage LLMs and knowledge graphs to retrieve, reason over, and synthesize complex biological information.
- Build and maintain agentic orchestration frameworks (multi-agent systems) that coordinate LLM-based agents for end-to-end scientific reasoning, data retrieval, and decision support.
- Collaborate with data engineering teams to design data pipelines that harmonize and prepare large-scale omics datasets for model training.
- Develop and optimize conversational AI (chatbot) interfaces that enable scientists and stakeholders to query, explore, and interact with internal data and model outputs using natural language.
- Partner with experimental scientists to ensure model outputs are biologically interpretable and experimentally testable.
- Proven track record in building LLM-based applications, with hands-on expertise in RAG, graph-based RAG, agentic orchestration, and/or chatbot development.
- Demonstrated ability to work in cross-disciplinary teams, communicate complex ideas clearly, and deliver results in fast-moving environments.
Nice to have
- About ProFound Therapeutics ProFound Therapeutics is pioneering the discovery of the expanded human proteome to unlock a new universe of potential therapeutics.
- Stay abreast of advances in LLMs, RAG architectures, agentic AI, and conversational AI
- bring innovative ideas into the team.
- or M.S. in a related field with 4-6 years of industry experience.
- Proficiency in Python and LLM/ML frameworks such as LangChain, Hugging Face Transformers, PyTorch, or similar.
- Experience working with multi-omics or high-dimensional biological data is a plus Familiarity with probabilistic modeling, causal reasoning, or statistical inference is a plus.
- Strong experience with knowledge graph technologies, graph databases, and vector databases.
Compensation
- The salary range for this role is $96,000 - $214,500.
Benefits
- Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond.
- 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.
- We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.
- ProFound Therapeutics, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits.
- Compensation and benefits information is based on ProFound Therapeutics, Inc.'s good faith estimate as of the date of publication and may be modified in the future.
Company info
- The Role We are seeking a highly motivated Senior Machine Learning Engineer / Data Scientist to join our AI/ML team.
- Learn more about Flagship at;br> At Flagship, we accept impossible missions to enable bigger leaps.
Equal opportunity
- We are an equal opportunity employer.
Visa & Work Authorization
- California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information
This listing is sourced directly from Flagship Pioneering's careers page and normalized into a canonical job model.