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Substrate Bio

Autonomous AI-driven wet labs for biological experimentation

Member of Technical Staff - Bio ML

Applied Machine LearningConfirmed live in the last 24 hours
Full-timeNo salary listedIn-person

About the Job

Requirements

  • Hands-on experience building and training machine-learning models for biology, and understanding where they fail.
  • Experience with protein language, structure, and affinity models, such as ESM C, Boltz-2, OpenFold3, or AlphaFold 3.
  • Experience fine-tuning or post-training pretrained biological models on experimental data and validating results against wet-lab measurements.
  • Experience building reinforcement-learning environments, agent harnesses, or tool interfaces that let large language model agents use machine-learning models.
  • Experience working with noisy experimental data, including replicates, controls, and batch effects.
  • Experience running experiments on data, such as scaling studies, data-mix ablations, and learning curves on small datasets.
  • Clear writing and communication about modeling choices, results, and limitations for machine-learning and scientific audiences.
  • Strong Python and PyTorch or JAX skills, and daily use of coding agents.

Responsibilities

  • Work on the biological side of reinforcement-learning environments and agents, starting with proteins.
  • Build environments in collaboration with scientists to determine their contents.
  • Build harnesses that enable agents to use biological models by integrating public protein models, exposing them as tools, and testing which models help agents and when their predictions can be trusted.
  • Fine-tune or post-train biological models on the organization’s measurements when existing models fall short.
  • Run scaling and data-mix experiments as new measurements arrive to determine what kinds and amounts of data improve models, and recommend what to measure next.
  • Work closely with Applied Reinforcement Learning researchers, protein bioinformaticians, evaluation and infrastructure engineers, and scientists.

Desired Qualifications

  • Experience post-training large language model agents or protein models with reinforcement learning, for example with ProtRL.
  • Experience with antibody or binder design, including developability, affinity, or stability data.
  • Experience with biological data beyond proteins, such as functional genomics or single-cell data.
  • Publications or open-source work in biological machine learning.

About the Company

Substrate Bio

Autonomous AI-driven wet labs for biological experimentation

Substrate Bio operates AI-native data-production infrastructure for biology, connecting computational models with real-world experimentation. The company runs a network of autonomous, robotics-powered wet labs, starting in London with a second planned for San Francisco, running standardized experiments with full provenance, metadata, and quality control. Researchers access the labs via API, submitting experiment parameters and receiving structured data and metadata, while foundation models help design assay selections, cell systems, and gene panels. What sets Substrate Bio apart is its closed feedback loop, where better data improves its models and better models design better experiments. The goal is to make biological experimentation as programmable and scalable as computation itself.

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