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Agent guide: [/agents.md](https://www.wearedevelopers.com/agents.md). --- # Senior Machine Learning Engineer / Data Scientist - **Company:** Flagship Pioneering, Inc. - **Location:** Cambridge, MA, United States - **Experience:** Expert - **Salary:** $96,000.0 - $214,500.0 - **Contract:** Permanent contract - **Skills:** Artificial Intelligence, Bioinformatics, Computational Biology, Information Engineering, Data Retrieval, Decision Support Systems, Graph Database, Python (Programming Language), Machine Learning, Tensorflow, Azure Machine Learning, Chatbots, Pytorch, Large Language Models, Multi-Agent Systems, Generative AI, Information Technology, HuggingFace, Machine Learning Operations, Data Pipelines - **Published:** June 3, 2026 - **Apply:** https://www.indeed.com/viewjob?jk=e6615515e3042171 ## About the Role Do you have experience in Cross-functional communication?, * Ph.D. in Computer Science, Machine Learning, Applied Mathematics, Computational Biology, or related field with 1-3 years of industry experience (preferred); or M.S. in a related field with 4-6 years of industry experience. * Proven track record in building LLM-based applications, with hands-on expertise in RAG, graph-based RAG, agentic orchestration, and/or chatbot development. * 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. * Demonstrated ability to work in cross-disciplinary teams, communicate complex ideas clearly, and deliver results in fast-moving environments. ## Description 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. Working closely with the Head of AI/ML and cross-functional partners, you will build and optimize LLM-powered pipelines and multi-agent systems that integrate knowledge graphs, multi-omics data, and biological context to uncover disease-driving proteins and pathways. The insights generated will directly support therapeutic discovery and development., * 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. * Stay abreast of advances in LLMs, RAG architectures, agentic AI, and conversational AI; bring innovative ideas into the team., 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. ## Related Videos - [Geometric deep learning for drug discovery](https://www.wearedevelopers.com/videos/264-geometric-deep-learning-for-drug-discovery) - [Machine learning in the browser with TensorFlowjs](https://www.wearedevelopers.com/videos/155-machine-learning-in-the-browser-with-tensorflowjs) - [Chatbots are going to destroy infrastructures and your cloud bills](https://www.wearedevelopers.com/videos/1130-chatbots-are-going-to-destroy-infrastructures-and-your-cloud-bills) - [Photonic Computing: Programming a New Class of AI Accelerators (incl. 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