Principal Software Engineer - Agentic Platform

The Pioneering Intelligence group at Flagship Pioneering is building intelligent software systems that integrate agentic AI with scientific reasoning to accelerate discovery and decision-making. We seek a Principal Software Engineer to own the underlying agentic platform - the durable orchestration layer where long-running, multi-agent, multi-model scientific workflows run reliably. This hands-on architect role requires a senior engineer who has built and operated distributed systems at scale and wants to take agentic AI from research to production., * Own the agentic platform end-to-end, from research prototype to production, building the durable orchestration layer for long-running, multi-stage scientific workflows.

• Architect workflow orchestration, evaluation frameworks, and event-driven distributed systems that deliver scale, resilience, and reliability.
• Define SDK abstractions and API contracts between model and agent outputs and downstream consumers, decoupling rapid model iteration from product stability and reducing integration friction across teams.
• Deliver infrastructure-as-code reference implementations (AWS CDK, Terraform, containerized services) and transform exploratory AI proof-of-concepts into hardened, reusable patterns adopted across product domains.
• Own platform cost-efficiency and scalability while preserving the performance and accuracy that experiments and end users require.
• Explore and template agent design and deployment patterns, and set technical standards, code quality, and architectural direction for the platform.
• Partner across teams (modeling, agent, and product) to align integration points, dependency timelines, and delivery, and mentor engineers and scientists.

• B.S. or M.S. in Computer Science, Engineering, or a related field, with 10+ years of professional software development experience.
• Demonstrated track record architecting and maintaining large-scale distributed systems in production at technology companies.
• Deep expertise in workflow orchestration and event-driven architecture, including stateful execution, idempotency, durable retries, and replay.
• Strong cloud-native engineering on AWS with infrastructure-as-code, containerization, and autoscaling.
• Proven ability to take systems from prototype to hardened, observable, operationally excellent production.
• Experience designing SDKs, APIs, and data contracts that serve multiple downstream teams.
• Excellent communication skills and the ability to build organizational consensus around platform decisions.
• Collaborative and empathetic working style: listens to understand the needs of scientists, engineers, and downstream teams, and leads through influence.
• Proven track record setting technical strategy and direction for a growing engineering organization, and mentoring engineers in a fast-moving environment., * Hands-on experience with agentic AI and orchestration frameworks (e.g., Pydantic AI, LangGraph, LangChain, CrewAI, AutoGen).
• Experience integrating LLMs and model platforms, including Anthropic, OpenAI, Vertex AI, and Amazon Bedrock, and building evaluation and feedback-loop frameworks for agentic systems.
• Familiarity with sandboxed code execution and agent harness development.
• Experience with LLM observability, monitoring tooling, and cost-governance / FinOps for AI infrastructure.
• Background in scientific domains such as biology, chemistry, or complex systems (a plus, not required).

• Own the platform foundation for a category-defining autonomous scientific reasoning engine.
• Take frontier agentic AI from research to dependable production at scale.
• Collaborate with visionary thinkers and top-tier researchers across Flagship’s ecosystem.
• Set the technical standards that the broader platform and product teams build on.
• Shape the future of AI-powered discovery in a role that combines deep engineering excellence with direct human-health impact., The salary range for this role is $188,000 - $257,500, depending on qualifications, skills, competencies, and experience. Compensation and benefits include healthcare coverage, an annual incentive program, retirement benefits, and additional benefits. Compensation is based on a good faith estimate as of the date of publication and may be modified in the future. #J-18808-Ljbffr