Profound

Senior Machine Learning Engineer / Data Scientist

Boston, MA · Senior

Sponsorship not specified$96k-$215kDetected 6 days ago
PythonMachine LearningPyTorchData EngineeringData ScienceNLPLLMsRAGAgentic AIAI OrchestrationComplianceRecruitingBioinformatics

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.
  • The insights generated will directly support therapeutic discovery and development.

Requirements

  • Proficiency in Python and LLM/ML frameworks such as LangChain, Hugging Face Transformers, PyTorch, or similar.
  • Strong experience with knowledge graph technologies, graph databases, and vector databases.
  • If you have some of the experience listed above but not all, please apply anyway.
  • Ph.D. in Computer Science, Machine Learning, Applied Mathematics, Computational Biology, or related field with 1-3 years of industry experience (preferred)
  • 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.
  • Why Join Us?
  • This role offers a unique opportunity to shape a next-generation AI/ML platform at the intersection of computation and drug discovery. You will work in a collaborative environment with leaders in biology, computation, and therapeutics - helping to expand the boundaries of the proteome and accelerate the development of new medicines for patients.
  • Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity's most urgent challenges: 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.
  • 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.
  • At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

Nice to have

  • or M.S. in a related field with 4-6 years of industry experience.
  • 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.

Compensation

  • ProFound Therapeutics, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits.

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.
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