Senior Data Scientist, Agentic AI Systems

About the role

Axle is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations nationally and abroad. We work with some of the top research organizations and facilities in the country including multiple institutes at the National Institutes of Health (NIH).

Responsibilities

• Build agentic AI systems for rare disease research workflows.
• This includes the conversation logic, the rules that decide when enough information has been gathered, and the confirmation steps that catch a misreading before it reaches anything downstream.
• Model outputs in Pydantic and use structured output and tool calling, so that every field a model produces is typed, validated, and traceable back to its source.
• Write, version, and regression test the prompts behind clinical and scientific reasoning tasks. Prompts and output schemas are treated as code here, with tests to match.
• Build evaluation for tasks that have no single right answer. Golden sets, offline regression suites, and model-based graders all have a place, and the results should be good enough to decide what ships.
• Keep multi-step LLM workflows responsive under load. This covers async design, concurrency limits, streaming partial results to the client, and timeout and failure handling that holds up in production.
• Log what the system does and why. Request identifiers, latency, errors, and the reasoning behind each automated choice all need to be captured, so that staff can review an AI-assisted result instead of taking it on faith.
• Work out what researchers, clinicians, and patient communities need, and turn it into data models and system behavior.
• Write the work up. You will contribute to manuscripts, conference abstracts, and posters with NIH investigators, and you will be credited as an author on work you helped produce.

Requirements

• Bachelor’s degree in Data Science, Computer Science, Bioinformatics, Biomedical Informatics, or a related field. An advanced degree is preferred. We will consider equivalent professional experience in place of a degree.
• At least 5 years building and operating production software or data systems. At least 2 of those years should involve shipping LLM-powered applications (agents, retrieval, or evaluation) that people depend on.
• Experience with structured output and tool or function calling, meaning you have constrained a model to a typed schema and validated what came back.
• Experience evaluating systems that have no single right answer, using golden sets, offline regression suites, or model-based graders to decide whether a change was an improvement.
• Ability to own a service end to end, from schema design through deployment and operation.
• Ability to obtain and maintain a Public Trust Security clearance.

Qualifications

• Technical Skills: Python, with FastAPI, Pydantic, and pytest. LLM application engineering: provider APIs and gateways, prompt and context design, structured generation, tool use, and tracing. PostgreSQL, including work with embeddings or vector search alongside relational data. Asynchronous and concurrent Python, plus streaming results to a client. Containers and Kubernetes, enough to ship, debug, and operate a service on infrastructure you do not administer. Git-based collaboration and CI/CD in a shared codebase.
• Preferred Skills: A typed agent framework such as Pydantic AI, LangGraph, or the OpenAI or Anthropic agent SDKs, and MCP for tool integration. LLM tracing and evaluation tooling such as Langfuse, LangSmith, Arize Phoenix, or Braintrust. Serving open-weight models in production with Ollama or vLLM behind a gateway such as LiteLLM. Biomedical ontologies and controlled vocabularies, including MONDO, HPO, UMLS, MeSH, and other OBO Foundry resources, along with comfort working through term hierarchies, synonyms, and cross references.
• Background in rare disease, clinical genetics, or translational research. Experience working alongside clinicians, curators, or patient advocacy organizations, and translating their vocabulary into a data model that holds up. Published or presented work that explains your engineering to people who did not build it. Peer-reviewed papers, conference talks, preprints, technical blog posts, and public open source contributions all count.
• Prior or current NIH experience. We are looking for an engineer first. If you have shipped LLM systems that people depend on and have never opened an ontology file, we want to hear from you.

Skills

• Python
• FastAPI
• Pydantic
• pytest
• LLM application engineering
• Structured output and tool or function calling
• Evaluation for tasks with no single right answer
• Async and concurrent Python
• Containers and Kubernetes
• Git-based collaboration and CI/CD
• Typed agent frameworks
• LLM tracing and evaluation tooling
• Serving open-weight models
• Biomedical ontologies and controlled vocabularies

Benefits

• 100% Medical, Dental & Vision Coverage for Employees
• Paid Time Off and Paid Holidays
• 401K match up to 5%
• Educational Benefits for Career Growth
• Employee Referral Bonus
• Flexible Spending Accounts:Healthcare (FSA)
• Parking Reimbursement Account (PRK)
• Dependent Care Assistant Program (DCAP)
• Transportation Reimbursement Account (TRN)

Pay

$130,000 USD - $150,000 USD

Schedule

Remote position within the United States