Founding Machine Learning Engineer

Novaflow (YC S25); San Francisco (CA); On-site; Full time

Benefits offered by this job

Competitive salary and equity

401(k) with company match

Unlimited PTO

Monthly health and wellness stipend

Meals covered in-office

Team offsites and company events

Job summary

A pioneering AI technology firm in San Francisco is seeking a Founding Machine Learning Engineer to develop LLM-powered systems for bioinformatics solutions. You will take charge of building pipelines that convert natural language queries into actionable workflows. Strong Python skills and experience with LLMs are essential, along with at least 2 years of ML model deployment experience. This role offers a competitive salary, equity, and an opportunity to work closely with the founding team in a dynamic startup environment.

Qualifications

• Minimum 2 years of experience in building and deploying ML models.
• Strong background with LLMs including fine-tuning and prompt engineering.
• Familiarity with cloud services for model training and deployment.

Responsibilities

• Build and improve LLM-powered pipelines for bioinformatics workflows.
• Design evaluation pipelines and benchmarks for model quality.
• Experiment with different model architectures and monitor performance.

Skills

Python skills

Experience with LLMs

Building data pipelines

Experience with PyTorch or TensorFlow

Docker and CI/CD experience

Education

Bachelor's or Master's in Computer Science, Machine Learning, or related field

Tools

AWS

GCP

Docker

Job description

About Novaflow

Novaflow is the AI data analyst for biology labs. Analytics is the bottleneck for scientific discovery. Biologists have to outsource analysis to expensive bioinformaticians or core services and wait weeks or months for results. We're solving this by putting analysis directly back into the hands of researchers, allowing them to go from raw data to publication-ready insights and visualizations in days instead of months. We're well‑funded, growing extremely fast, and backed by leading investors including Y Combinator and BioRender.

About The Role

We're hiring a Founding Machine Learning Engineer to build the AI systems that power our platform. The core challenge: take a natural language query from a biologist and turn it into a correct, reliable bioinformatics workflow. That means working with LLMs, building evaluation systems to know when outputs are good (and when they're not), and shipping models that real scientists depend on every day.

This is a high‑agency, high‑ownership role. You'll work directly with the founders and have real say in our AI strategy. Biology background is not required. What matters is that you're a strong ML engineer who ships.

This role is in‑person at our San Francisco office. The founding team works side by side every day to make fast decisions and ship.

What You'll Work On

• Build and improve the LLM‑powered pipelines that turn natural language into bioinformatics workflows
• Design evaluation pipelines and benchmarks to measure model quality against real scientific expectations
• Experiment with fine‑tuning, RAG, prompt engineering, and different model architectures
• Deploy and scale models in production on AWS or GCP
• Make build‑vs‑buy decisions on AI tooling and infrastructure
• Work across the team to integrate ML capabilities into the product

Requirements

• Bachelor's or Master's in Computer Science, Machine Learning, AI, or a related field (PhD is a plus)
• 2+ years building and deploying ML models in production
• Strong Python skills and hands‑on experience with PyTorch, TensorFlow, or similar
• Real experience with LLMs: fine‑tuning, RAG, prompt engineering, evals
• Experience working with large datasets and building data pipelines
• Familiar with AWS or GCP for model training and deployment
• Docker and CI/CD experience for ML workflows
• Can spot when an LLM is confidently wrong

Nice to Have

• Experience applying ML to scientific or biological data
• Familiarity with Anthropic, OpenAI, or other LLM APIs and agent frameworks
• Terraform and Kubernetes experience
• Startup background or experience in research‑oriented engineering
• Previous startup experience (prior experience either working for or founding a startup)

Why Join Us?

• Competitive salary and meaningful equity as a founding team member
• 401(k) with company match
• Unlimited PTO + federal holidays
• Monthly health and wellness stipend
• Meals covered when you're in the office (lunch daily, dinner when you're working late)
• Team offsites and company events
• If you're curious about being a founder one day, this is your front‑row seat. You'll work side by side with the founders and have full visibility into product strategy, customer conversations, and fundraising as we scale.