AI Engineer I

Frontier Medicines; South San Francisco (CA); On-site; USD 100,000 - 159,000; Full time

Benefits offered by this job

Health Care Plan (Medical, Dental &amp

Retirement Plan (401k, IRA)

Life Insurance (Basic, Voluntary &

Paid Time Off (Vacation, Sick & P|

Family Leave (Maternity, Paternity)

Short Term & Long Term Disability

Training & Development

Free Food & Snacks

Wellness Resources

Stock Option Plan

Job summary

Frontier Medicines is seeking a highly motivated Scientist, AI Engineer to join our AI organization in South San Francisco. You will design architectures for domain-specific multimodal AI models, build multi-agent systems for scientific workflows, and deploy models to support covalent small molecule drug discovery.

You will work with medicinal chemistry, biology, and cross-functional teams to translate complex data into actionable insights, leveraging proprietary data to accelerate compound

Qualifications

• Bachelor’s degree in computational or quantitative discipline.
• Strong programming skills in Python.
• Excellent written and verbal communication.
• Authorized to work in the United States.

Responsibilities

• Design architecture and training strategies for multimodal AI models.
• Build multi-agent systems for scientific workflows and tool calling.
• Develop generative molecular design approaches and SAR analysis.
• Deploy models into serving infrastructure for researchers.

Skills

Python

Cross-functional collaboration

Data science

Education

Bachelor’s degree in computational/quantitative field

PhD with 1 year experience

Tools

DeepSpeed

FSDP

GNNs

Job description

Frontier Medicines isseekinga highly motivatedScientist,AIEngineerto join ourAIorganization. This role will play a key scientific and technical role in advancing Frontier’sAIand cheminformatics capabilities in support ofcovalentsmall molecule drug discovery.

The successful candidate will design and deploy machine learning models, agentic AI systems, and multimodal foundationand generativemodels thatleverageFrontier’s large-scale covalent chemistry and chemoproteomics data to accelerate compound design, prioritization, and optimization. This role works closely with medicinal chemistry, biology, and cross-functional drug discovery teams to build AI-powered tools that translate complex, heterogeneous data into actionable scientific insight

This position is ideal for an individual contributor who thrives in scientifically uncharted territory and enjoys building novel solutionsformedicinalchemistry, biology, and computational chemistry teams.

This is an exciting opportunity in our South San Francisco site to deployAIto make a difference for patients suffering from debilitating diseases by working in a highly collaborative and energetic team in a startup environment with short communication lines across functions and departments

What we are looking for:

• Design architecture and training strategies for domain-specific multimodalAImodels that reasonovermolecular structures, assay data, protein structures, and scientific text — trained on Frontier’s proprietary data.Familarwithself-supervised learning, andMixture of experts (MoE)andDistributedtraining (DeepSpeed, FSDP)

• Design and build multi-agent systems for scientific research workflows — supervisor/sub-agent orchestration,MCPs,task decomposition, tool calling, error recovery, and human-in-the-loop checkpointsthat interface with internal systems(scientificdatabases,compoundregistries)

• Develop and adapt generative molecular design approaches — diffusion models, autoregressive transformers, VAEs, reinforcement learning–guided generation — to explore and expand covalent compound libraries and novel chemical space.

• Build multimodal RAG pipelines over structured data, slide decks, experimental reports, and images

• Train, evaluate, and deploy deep learning models for molecular property prediction, virtual screening, ADMET modeling, and SAR analysis on Frontier’s covalent chemistry data.

• Implement and benchmark molecular representations — GNNs, equivariant architectures, learned fingerprints — and build multi-task,transferlearning, and active learningapproaches thatleverageproprietary datafor low-data regime predictions on active programs.

• Deploy models into serving infrastructure that researchers and agents can query — endpoints, batch inference, monitoring — so predictionsreachdecisions.

Traits we believe make a strong candidate:

• B.Scin computational or quantitative discipline such ascomputer science, data science,cheminformatics, computationalchemistryorrelated field with 2-3 years industry experience.

• Strong programming skills inPythonand experience with coding tools.

• Ability to work independently while thriving in a highly collaborative, cross-functional environment.

• Excellent written and verbal communication skills.

• Legally authorized to work in the United States.

Leveling Guidelines

Scientist I

• Education & Experience:

  • Bachelor’s degree with 2–3 years of relevant industry experience, or
  • PhD with at least 1 year of relevant industry experience

• Demonstrated ability to independently or with limited guidance design and execute computational and AI approaches for drug discovery problems

• Proven track record of contributing to complex analytical strategies and influencing discovery programs through data-driven insights

• Ability to effectively collaborate with experts across disciplines and contribute to cross-functional team success

• Health Care Plan (Medical, Dental & Vision)
• Retirement Plan (401k, IRA)
• Life Insurance (Basic, Voluntary & AD&D)
• Paid Time Off (Vacation, Sick & Public Holidays)
• Family Leave (Maternity, Paternity)
• Short Term & Long Term Disability
• Training & Development
• Free Food & Snacks
• Wellness Resources
• Stock Option Plan

At Frontier, we strive to build a diverse and equitable workplace. The salary range for this role is $100,000 - $158,900. Compensation for the role will depend on a number of factors, including candidates’ qualifications, skills, competencies and experience. Frontier offers a competitive total rewards package which includes healthcare coverage, 401k and a broad range of other benefits.

This compensation and benefits information is based on Frontier’s knowledge as of the date of publication, and may be modified in the future.