Machine Learning Scientist I - Generative & Agentic AI for Drug Discovery
Frontier Medicines
Summary
Frontier Medicines is looking for a Machine Learning Scientist to join our AI team in South San Francisco. You'll build the AI systems our scientists use every day: LLM-powered agents that work across our research data, generative models that design new covalent molecules, and predictive models trained on one of the largest proprietary covalent chemistry and chemoproteomics datasets in the industry.
Job description
This role suits someone with a research mindset who wants their work to reach real decisions. You'll work in a small team with short communication lines to medicinal chemistry, biology, and computational chemistry. Prior drug discovery experience is not required. If you bring strong AI fundamentals and curiosity, we'll teach you the chemistry.
What you'll do
- Build agentic AI systems for scientific workflows, including multi-agent orchestration, tool calling and MCP integrations, task decomposition, and human-in-the-loop checkpoints. These systems connect to our scientific databases and compound registry.
- Develop and adapt generative models (diffusion, autoregressive transformers, RL-guided generation) to explore new covalent chemical space.
- Build multimodal models and RAG pipelines that reason over molecular structures, assay data, protein structures, slide decks, reports, and images.
- Train and benchmark predictive models for property prediction, virtual screening, and SAR. This includes approaches for low-data settings such as transfer, multi-task, and active learning.
- Deploy models and agents so researchers can use them, and see your work influence active programs.
What we're looking for
- MS or PhD in computer science, machine learning, computational chemistry, physics, or a related field, or a BS with 2-3 years of equivalent industry or research experience.
- A track record of research: publications, preprints, thesis work, or substantial open-source contributions in ML.
- Hands-on experience building with LLMs and agents, generative models, or multimodal models.
- Strong Python and PyTorch skills, and comfort with modern AI coding tools.
- The ability to take an open-ended scientific problem and turn it into a working system, independently and collaboratively.
- Clear written and verbal communication.
- Legal authorization to work in the United States.
Nice to have
- Experience with molecular ML, such as GNNs, equivariant models, or molecular representations, or with RDKit and cheminformatics tooling.
- Experience with large-scale or distributed training (DeepSpeed, FSDP, MoE).
- Exposure to biology, chemistry, or drug discovery data.
Requirements
- MS or PhD in computer science, machine learning, computational chemistry, physics, or a related field, or a BS with 2-3 years of equivalent industry or research experience
- A track record of research: publications, preprints, thesis work, or substantial open-source contributions in ML
- Hands-on experience building with LLMs and agents, generative models, or multimodal models
- Strong Python and PyTorch skills
- Comfort with modern AI coding tools
- Ability to take an open-ended scientific problem and turn it into a working system, independently and collaboratively
- Clear written and verbal communication
- Legal authorization to work in the United States
Benefits
- Medical, Dental & Vision
- 401(k) & IRA
- Life Insurance
- Paid Time Off
- Family Leave
- Short & Long Term Disability
- Training & Development
- Free Food & Snacks
- Wellness Resources
- Stock Option Plan
Company overview
Frontier Medicines is a clinical-stage precision medicine biotechnology company founded in 2018 that specializes in developing breakthrough therapies against previously undruggable disease-causing proteins. The company has pioneered a proprietary discovery and development platform called the Frontier™ Platform, which integrates chemoproteomics, covalent drug discovery, and machine learning technologies to target proteins considered inaccessible to conventional drug discovery approaches. Frontier Medicines focuses on oncology and immunology, with its lead program FMC-376 being a first-in-class dual inhibitor of both active and inactive KRAS G12C mutations, which are prevalent in non-small cell lung, colorectal, and pancreatic cancers. The company maintains offices in South San Francisco, California and Boston, Massachusetts, and has established a strategic global partnership with AbbVie to develop novel therapies against difficult-to-drug targets in oncology and immunology. Frontier Medicines is advancing a diversified pipeline of wholly-owned precision medicines and has raised significant venture capital funding to support its mission of expanding the therapeutic landscape for genetically-defined patient populations.