Software Engineer, Agents

Output has built a biological reasoning model that understands biology at the scale and complexity life actually operates. Our model independently learned the principles of molecular interactions, opening up drug treatments that were previously impossible. We’re already generating therapies that traditional approaches cannot reach. The hardest problems in both AI and biology are being solved here, and there is room for you to own one.

Output is currently in stealth, operated by a team of repeat founders and biotech veterans with multiple exits in AI x Bio, and backed by top-tier VCs including Y Combinator.

You will build the agent infrastructure that turns model capabilities into usable tools and workflows. This role owns the orchestration layer, the inference serving, the internal tooling, and the interfaces that researchers and external systems interact with.

• You will design and build the agent orchestration system that composes model capabilities into multi-step workflows, handling sequencing, state management, and error recovery
• You will implement agent skills and tools that expose model capabilities to automated and interactive workflows
• You will build inference infrastructure for serving models efficiently, optimizing for latency, throughput, and reliability
• You will design and build APIs and integrations, including MCP-compatible interfaces, that allow external systems and users to interact with Output’s models
• You will build internal tools that accelerate the research team’s work, from experiment management to evaluation pipelines
• You will establish and maintain software engineering practices across the team: testing, CI/CD, code review, and documentation

• You have a BS in Computer Science or a related field, or equivalent experience
• You have 4+ years of experience building production software systems
• You have experience integrating ML models into products or workflows, including LLM-based systems
• You have strong Python engineering skills with a track record of building maintainable, well-tested production code
• You have experience designing APIs and building systems that other engineers and researchers depend on
• You are comfortable with cloud infrastructure, containerization, and deployment pipelines
• You think in systems: you design for reliability, observability, and graceful failure, not just the happy path

Bonus Points

• You have experience with LLM orchestration frameworks, agent architectures, or tool-use patterns
• You have experience with MCP (Model Context Protocol) or similar model-integration protocols
• You have a background in biology, chemistry, computational biology, or a related natural science
• You have experience building internal tools that accelerate research or data science teams
• You have experience with inference optimization for large models

Pulled from the full job description

• Health insurance
• Vision insurance
• Dental insurance, * We encourage new and different ideas, creativity and contrarian thinking
• Healthy feedback focused environment to help you strive - leadership will have high expectations, regularly share constructive feedback, support you and help you grow, and welcome receiving feedback and ideas from you
• You own your day-to-day management. What we care about is that we all hit our milestones
• Competitive salary and equity in a growing, well-funded startup
• Excellent medical, dental, and vision coverage

Compensation Range: $150K - $300K