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Senior ML Research Engineer, Virtual Cell

SandboxAQ· AI Simulation
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RemoteCA$148k - CA$222kFull-timePosted 3mo ago

About the role

ML Engineer role focused on AQCell, SandboxAQ's virtual cell platform. Develops and maintains models and data infrastructure for expression-perturbation and functional-endpoint prediction, manages large-scale biology datasets, and translates research ideas into production-ready code within a cross-functional team.

Responsibilities

  • Model Development: Build, train, and maintain machine learning models for expression-perturbation prediction and downstream functional-endpoint prediction (e.g. cell viability, IC50, toxicity dose-response).
  • Large-Scale Dataset Management: Acquire, harmonize, and manage large-scale biological datasets (e.g. LINCS L1000, GDSC, Tahoe-100M, DILImap) with schema harmonization, normalization, and de-duplication across cell, drug, and assay identifiers; manage model training pipelines over these pooled datasets.
  • Evaluation & Baselines: Automate and harden the end-to-end evaluation pipeline, including robust baselines (e.g. cell- and drug-conditioned mean baselines) to benchmark model performance.
  • Research Translation: Translate transformer-based perturbation models, knowledge graph and GNN embeddings into production-ready code within the modeling framework.
  • Cross-Functional Collaboration: Partner with computational biologists, software engineers, and product stakeholders to ground models in biology and usability for drug discovery workflows.
  • Communication: Document methods, assumptions, and results; communicate findings to technical and non-technical stakeholders.

Qualifications

  • Bachelor's degree in a scientific or quantitative field (CS, Physics, Mathematics, Biology, Chemistry, or related); MS or PhD preferred.
  • Applied ML in a scientific/industry setting; experience in life sciences preferred.
  • Experience managing large-scale datasets and training models over them, including data ingestion, cleaning, versioning, and pipeline maintenance at scale.
  • Strong Python programming skills and experience with modern ML frameworks (e.g. PyTorch, JAX) and experiment tracking/data versioning tools (e.g. Weights & Biases).
  • Ability to design sound evaluation methodology (e.g. train/test splits, held-out tests) and interpret model performance against meaningful baselines.

Skills

Required:PythonPyTorch or JAXExperiment tracking / data versioning

Benefits

  • Competitive base salary and equity participation.
  • Comprehensive medical, dental, and vision coverage with generous employer contributions.
  • Retirement savings with company matching.
  • Paid parental leave and inclusive family-building benefits.
  • Flexible paid time off, seasonal company breaks, and support for flexible work arrangements.
  • Opportunities for continuous learning and growth through internal programs.
Last updated Sep 9, 2026. Interested? Apply on the company site.

About SandboxAQ

Transforming the World with AI and Advanced Computing

SandboxAQ leverages the compound effects of AI and advanced computing to address some of the biggest challenges impacting society. SandboxAQ technologies include AI simulation, cryptography management for cybersecurity, and AI sensing for global organizations.

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