Senior ML Research Engineer

Final date to receive applications: 19 October 2026

Department: Machine Learning

Employment Type: Full Time

Location: Boston

Compensation: $145,000 - $170,000 / year

Biological data is noisy, high-dimensional, and shaped by the experimental process as much as by biology itself. We are hiring a Senior ML Research Engineer to develop the models and research infrastructure that turn our multi-omic datasets, including metagenomics, metabolomics and 16S, into reliable scientific insight.

You will own high-impact research questions from hypothesis through publication-quality evaluation, while building reproducible training and inference systems that let the team move quickly and trust its results. This role is central to translating our proprietary data and experimental capabilities into a durable scientific and product advantage.

We're hiring one person for this role, and they can be based in either London or Boston.

Here is our timeline for hiring this role:

• Now until October 19th: Accepting applications
• October 26th: Planned start for interviews

• Design and train novel machine-learning models for messy multi-omic data, including metagenomics, metabolomics and 16S, grounded in a strong understanding of biological systems.
• Own research questions end to end, from hypothesis and dataset design through training, evaluation and write-up.
• Set rigorous evaluation standards, accounting for batch effects, leakage, compositional data and correlated samples, to distinguish real results from artifacts.
• Turn research into reproducible infrastructure through versioned training and inference pipelines, extensible codebases and robust experiment tracking.
• Work closely across data and lab teams to shape experiments, define data handoffs, and communicate findings through publications and presentations in leading journals and ML conferences.

• Proven track record building and shipping ML systems with a research component:
  PhD, publications, or equivalent evidence of independent work, with fluency in PyTorch, Tensor Flow or another deep learning framework.
• Experience with software engineering best practices, preferably in Python. You write code others can read and run.
• Foundation model work: pretraining, transfer learning or fine-tuning.
• A collaborative operator. You can hold a real conversation with a biologist about experimental design, take a bioinformatician's pipeline seriously as a dependency, and explain a modeling decision to people who don't build models. You've worked in a small cross-functional team.
• Comfort in a fast-moving, resource-constrained environment where you define your own problem.
• Nice to have: omics, sequencing or molecular data; representation learning over sequences, graphs or chemical structures; small-n, high-dimensional or noisy real-world data, from biology, health or another domain where the data doesn't behave; generative models for molecules or biological sequences; cloud training infrastructure and GPU orchestration.

• You'll own real equity in what you build. We offer meaningful stock options because we believe the people building this company should share in what it becomes. We want teammates who think like owners, and we structure compensation to reflect that.
• Outstanding benefits. Full medical, dental and vision from day one, with Outpost covering 100% of the employee premium on the base plan and 50% for dependents. 401(k) with a 3% match. Short and long-term disability, employer paid. 50% of your MBTA Perq commuter pass. 25 days PTO plus your birthday off, and a paid winter break between Christmas Eve and New Year.
• An ML Lab-in-the-Loop. Your work feeds directly into Outpost's AI platform, and the platform…