Software Engineer, Agents

Output Biosciences; New York (NY); On-site; USD 140,000 - 200,000; Full time

Benefits offered by this job

Competitive salary and equity

Excellent medical, dental, and vision

Ownership culture and flexible startup

Job summary

Output Biosciences is building a biology-focused AI platform that aims to turn model capabilities into usable tools for researchers and systems. The role owns the orchestration layer, inference serving, internal tooling, and interfaces used by researchers and external workflows.

You will establish robust software engineering practices and deliver scalable, reliable production systems that integrate ML models, including LLM-based workflows, with a strong emphasis on reliability and observability.

Qualifications

• 4+ years of production software experience.
• Experience integrating ML models into products or workflows, including LLM-based systems.
• Strong Python engineering with maintainable, well-tested production code.
• Experience designing APIs and building systems that other engineers and researchers depend on.
• Comfort with cloud infrastructure, containerization, and deployment pipelines.
• Systems thinking: reliability, observability, and graceful failure.

Responsibilities

• Design and build the agent orchestration system that composes model capabilities into multi-step workflows, handling sequencing, state management, and error recovery.
• Implement agent skills and tools that expose model capabilities to automated workflows.
• Build inference infrastructure for serving models with optimized latency, throughput, and reliability.
• Design and build APIs and MCP-compatible interfaces for external systems to interact with Output’s models.
• Build internal tools to accelerate research, from experiment management to evaluation pipelines.
• Establish and maintain software engineering practices across the team: testing, CI/CD, code reviews, and documentation.

Skills

Production software systems

ML model integration

Python development

API design

Cloud infrastructure

CI/CD

Reliability & observability

LLM orchestration concepts

Education

Bachelor's degree in Computer Science or related field

Equivalent experience acceptable

Job description

The Role

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

About You

• 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

Our Values

Heart: We foster a culture of ownership. We are assembling a team of individuals who are passionate and take pride in their contributions.

Excellence: We have an unwavering commitment to excellence and continuously challenge ourselves to reach the highest standards.

Practicality: We value practicality and results-oriented thinking. We are committed to making a tangible impact on the lives of patients and the broader community.

Honesty: We place a high value on honesty and directness. We firmly believe in addressing issues as they arise, in an open and transparent manner.

Fun: We believe that life is too short to not have fun. Our goal is to create a workplace that is fun, engaging, rewarding and fulfilling.

What We Offer

• 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