AI Engineer I

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

Benefits offered by this job

Healthcare plan

401k/IRA

Life insurance

PTO

Family leave

Disability (ST/LT)

Training & development

Free snacks

Wellness resources

Stock options

Job summary

Frontier Medicines in South San Francisco seeks a Scientist, AI Engineer to advance its AI and cheminformatics capabilities for covalent small molecule drug discovery. You will design and deploy ML models, agentic AI systems, and multimodal foundation models trained on proprietary data to accelerate design and optimization.

This role involves collaborating with medicinal chemistry, biology, and cross-functional teams in a startup-like environment to deliver AI-powered tools that translate

Qualifications

• Bachelor’s degree with 2–3 years industry experience or PhD with at least 1 year.
• Strong computational and AI design abilities for drug discovery.
• Proven track record of data-driven insights.
• Ability to collaborate across disciplines.
• Legal authorization to work in the United States.

Responsibilities

• Design architecture and training strategies for multimodal AI models.
• Build multi-agent systems for scientific workflows.
• Develop generative molecular design approaches.
• Create multimodal RAG pipelines over diverse data.
• Train, evaluate, deploy deep learning models for molecular prediction.
• Deploy models into research-friendly serving infrastructure.

Skills

Python

Education

Bachelor's degree in computational or quantitative discipline

PhD in relevant field

Tools

DeepSpeed

FSDP

GNNs

MoE

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 checkpoints that 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 learning approaches 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.