Senior Machine Learning Research Engineer – Virtual Cell

About the role

The AI Sim R&D team at SandboxAQ is building AQCell, a virtual‑cell platform that predicts transcriptomic responses to drug perturbations and downstream functional endpoints. As a Senior Machine Learning Research Engineer you will develop and maintain the models and data pipelines that power this capability.

Key responsibilities

• Design, train, and maintain ML models for expression‑perturbation and functional‑endpoint prediction.
• Acquire, harmonize, and manage large‑scale biological datasets such as LINCS L1000, GDSC, Tahoe‑100M, and DILImap.
• Automate and harden the end‑to‑end evaluation pipeline, implementing robust statistical baselines.
• Translate state‑of‑the‑art research (e.g., transformer‑based perturbation models, knowledge‑graph embeddings) into production code.
• Collaborate with computational biologists, software engineers, and product stakeholders to ensure models are biologically sound and usable in drug‑discovery workflows.

Required profile

• Bachelor’s degree in a quantitative field (Computer Science, Physics, Mathematics, Biology, Chemistry); advanced degree preferred.
• Proven experience building and maintaining ML models in a scientific or life‑sciences setting.
• Hands‑on experience managing large‑scale datasets and training pipelines at scale.
• Strong Python programming skills and familiarity with modern ML frameworks (PyTorch, JAX) and experiment‑tracking tools (Weights & Biases).
• Ability to design rigorous evaluation methodologies and interpret model performance against meaningful baselines.

Required skills

• Python
• PyTorch
• JAX
• Weights & Biases
• Knowledge‑graph embeddings
• Graph neural networks
• Cheminformatics representations (SMILES, InChI, PubChem IDs)
• Transcriptomics data harmonization and batch‑correction tools

What we offer

• Competitive base salary, performance‑based incentives and equity participation.
• Comprehensive medical, dental and vision coverage with generous employer contributions.
• Retirement savings plan with company matching.
• Paid parental leave and inclusive family‑building benefits.
• Flexible paid time off, seasonal breaks and support for flexible work arrangements.
• Opportunities for continuous learning, cross‑functional collaboration and career development.