AI Engineering Lead

Substrate is spinning out of Automata, the UK lab automation company that has built the workcell platform our labs run on. Our four co-founders are Mostafa ElSayed (CEO and founder of Automata), Oli Hoy (formerly VP Customer Experience at Automata), Alexey Morgunov (AI Scientist co-founder, leading the intelligence software product), and a founding biology lead joining shortly. We are aiming to have ramped up to 32 people by the end of Q1 2027.

We are funded in parallel by a combination of venture funding and government grants. We are not a cloud lab and we are not a CRO. We are an autonomous lab platform with closed-loop integration available as one operating mode for foundation model partners.

Most AI engineering roles at venture-backed companies are either pure AI applications (chat products, copilots, agents on top of someone else’s data) or thin wrappers around foundation model APIs. This is neither. You will be building AI products on top of the operational data of a wet lab that you can sit next to and influence the design of.

AI Scientist decides which experiments are worth running with Substrate’s reserved R&D capacity, by reading the scientific literature and identifying what has not been done well. AI Assays makes the lab better at its own work every week, from the operational metadata of every run. The closest analogue is the internal tooling team at a frontier model lab, with one important difference: you control the data source.

Some engineers find this energising; some find it distracting. Worth knowing in advance which one you are.

You are an experienced software engineer who has put large language models, foundation models, and agentic systems into real production, not as a prototype or a demo. You know the harness layer well: token economics, retrieval, evaluation pipelines, structured output, the operational realities of running a lot of data through LLMs cheaply and reliably. You enjoy that work.

You have some history with biology, biotech, or scientific literature. That can be a formal background, a previous role at a science-adjacent company, or simply that you have read papers in depth, kept up with the field outside of your day job, and have a feel for what experimental data telemetry actually looks like. You do not need a PhD; you do need to be the kind of engineer who finds the science genuinely interesting.

You are direct. You will talk back when you disagree. You are pragmatic about agentic systems and foundation models; you have used them in anger rather than read about them in posts.

We pay competitively against the London market for senior engineers working on LLMs and agentic systems at venture-backed companies, calibrated to seniority and to the specific scope of this role. We will discuss numbers with serious candidates after first conversations.

Equity is meaningful, with vesting on the standard four-year schedule and a one-year cliff. We can talk through the philosophy and the maths in detail when we meet.

Apply via Ashby with whatever you think shows your work best: a CV, links to GitHub or to systems you have built, a piece of writing you are proud of, an evaluation harness you ran on a model that taught you something.. We read everything that comes in.

Our process is four stages. An initial conversation with Alexey to understand what you want from the role and what we want from it. Two technical sessions with our external technical advisor: an architecture deep-dive on how you would build the intelligence software, and a session on how you would build and grow the intelligence team. Finally, an in-person founder-team session covering scope, terms, and any final questions. We aim to move fast on candidates we are excited about; expect roughly two to three weeks end to end.

If you are not sure whether you are a fit, send a note anyway. The most useful conversations we have had so far have been with people who were not sure.

Substrate is an equal opportunity employer. We make hiring decisions on merit, scope-fit, and the strength of the working relationship we expect to build with each hire. Applications welcome from candidates of any background.

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