Principal Software Engineer - Autonomous AI Platform Architect

Flagship Pioneering Co-Op Program; Cambridge (MA); On-site; USD 188,000 - 258,000; Full time

Job summary

Flagship Pioneering's Pioneering Intelligence group is building an autonomous research platform that combines agentic AI with scientific reasoning to accelerate discovery and decision-making. This hands-on architect role focuses on the durable orchestration layer that runs multi-agent, multi-stage workflows at scale.

The successful candidate will set technical foundations, collaborate with AI scientists and product teams, and translate frontier agent patterns into dependable infrastructure that

Qualifications

• B.S. or M.S. in Computer Science, Engineering, or a related field.
• 10+ years of professional software development experience.
• Experience architecting and maintaining large-scale distributed systems in production at technology companies.
• Deep expertise in workflow orchestration and event-driven architecture.
• Strong AWS cloud-native engineering with infrastructure-as-code and containerization.
• Proven ability to take systems from prototype to production, with observable, reliable performance.

Responsibilities

• 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 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 our 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 and agent teams, product) to align on integration points, dependency timelines, and delivery, and mentor engineers and scientists.

Skills

Distributed systems

Cloud-native engineering

SDKs/APIs design

Workflow orchestration

Event-driven architecture

AWS: infrastructure-as-code

Terraform

Containerization

Production-grade software

Mentoring engineers

Education

B.S. or M.S. in Computer Science, Engineering, or a related field

10+ years of professional software development experience

Tools

AWS CDK

Terraform

Containerized services

Job description

Flagship Pioneering's Pioneering Intelligence group is building an autonomous research platform that combines agentic AI with scientific reasoning to accelerate discovery and decision-making. This hands-on architect role focuses on the durable orchestration layer that runs multi-agent, multi-stage workflows at scale.

The successful candidate will set technical foundations, collaborate with AI scientists and product teams, and translate frontier agent patterns into dependable infrastructure that