Job Description

What if the work you did every day could impact the lives of people you know? Or all of humanity?At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the world. Our efforts enable life-changing discoveries that are transforming human health through the early detection and diagnosis of diseases and new treatment options for patients.Working at Illumina means being part of something bigger than yourself. Every person, in every role, has the opportunity to make a difference. Surrounded by extraordinary people, inspiring leaders, and world changing projects, you will do more and become more than you ever thought possible.

Location

This role is located at our HQ in San Diego, CA.

The Assoc Principal AI Engineer is the most senior individual contributor on the AI Engineering team, responsible for the design, development, and productionization of the most complex AI systems in the organization. This is a deeply technical, hands-on role for an engineer who has spent years in the trenches building, training, fine-tuning, and shipping AI systems at scale and is now ready to set technical direction across multiple teams.

The role combines applied research with production engineering. The Assoc Principal AI Engineer translates the latest advances in foundation models, agentic systems, and machine learning into robust, observable, and economically viable production systems. They write code, design systems, lead the hardest technical decisions, and shape the engineering culture that determines how AI gets built across the company.

Key Responsibilities

Technical Leadership

• Set the technical direction for AI Engineering across foundation model integration, fine-tuning pipelines, RAG systems, agentic workflows, and evaluation infrastructure.
• Own the most complex and ambiguous AI engineering problems in the company, from initial design through production deployment and ongoing optimization.
• Establish engineering standards for model development, prompt management, evaluation, deployment, and observability that the rest of the AI organization adopts.
• Lead architecture reviews and serve as the senior technical reviewer for high-stakes AI initiatives.

AI Systems Development

• Design and build production-grade Generative AI systems including retrieval-augmented generation, multi-agent orchestration, tool-using agents, and domain-adapted models.
• Develop fine-tuning, distillation, and post-training pipelines using techniques such as SFT, DPO, RLHF, and parameter-efficient methods (LoRA, QLoRA, adapters).
• Architect and implement vector retrieval systems, semantic search, and hybrid retrieval pipelines optimized for accuracy, latency, and cost.
• Build robust evaluation frameworks covering automated metrics, LLM-as-judge, human review, regression testing, and safety evaluations.

Platform and Infrastructure

• Design and build the AI platform that powers internal teams, including model serving infrastructure, prompt and prompt-template management, experiment tracking, and feature stores.
• Optimize inference performance across latency, throughput, and cost, including quantization, batching, caching, speculative decoding, and intelligent routing across model providers.
• Establish LLMOps practices for continuous evaluation, drift detection, prompt versioning, rollback strategies, and incident response.
• Partner with platform and infrastructure teams to ensure AI workloads run reliably on GPU and accelerator hardware across cloud environments.

Research to Production

• Stay current with the rapidly evolving AI research landscape and identify which advances translate into production value for the business.
• Prototype emerging techniques (new model architectures, training methods, agent frameworks) and lead the path from experiment to production system.
• Contribute to internal technical strategy on build versus buy decisions for foundation models, vector databases, agent frameworks, and AI tooling.

Cross-Functional Influence

• Partner with product, data science, research, and business stakeholders to scope AI initiatives and shape solutions that deliver measurable business impact.
• Mentor senior and staff engineers, raising the technical bar across the AI organization.
• Represent AI Engineering in executive forums, customer conversations, vendor evaluations, and industry engagements.
• Author technical documents, design docs, and (where appropriate) external publications that contribute to the broader AI community.

Required Qualifications

• 12+ years of software engineering experience, with 6+ years focused on machine learning or AI systems and 2+ years building production Generative AI applications.
• Demonstrated ownership of large-scale AI systems in production, including responsibility for latency, cost, accuracy, and reliability outcomes.
• Deep hands-on expertise in Python and modern ML frameworks (PyTorch, TensorFlow, JAX, Hugging Face Transformers).
• Strong command of LLM application development, including RAG architectures, prompt engineering, function calling, structured outputs, and agentic patterns.
• Experience with model fine-tuning, evaluation, and deployment lifecycles across at least one major cloud platform (GCP, Azure, or AWS).
• Proven ability to design distributed systems, including familiarity with vector databases, message queues, container orchestration, and observability stacks.
• Bachelor's or Master's degree in Computer Science, Machine Learning, Statistics, or a related quantitative discipline. PhD welcomed but not required.

Preferred Qualifications

• Experience training, fine-tuning, or post-training foundation models using techniques such as SFT, DPO, RLHF, RLAIF, or constitutional methods.
• Familiarity with agentic frameworks (LangChain, LangGraph, AutoGen, CrewAI, custom orchestration) and multi-agent system design patterns.
• Background in Voice AI, speech systems, multimodal models, or computer vision applied at production scale.
• Contributions to open source AI projects, peer-reviewed publications, or notable conference presentations.
• Experience in regulated or high-stakes domains (life sciences, healthcare, financial services) where accuracy, safety, and governance requirements are stringent.
• Familiarity with responsible AI practices including red-teaming, jailbreak resistance, content safety, bias evaluation, and AI governance frameworks.
• Typically requires a minimum of 15 years of related experience with a Bachelor’s degree; or 12 years and a Master’s degree; or a PhD with 8 years experience; or equivalent experience.

Technical Skill Profile

Foundation Models and LLMs: GPT-4 class models, Claude, Gemini, open-weight models (Llama, Mistral, Qwen), fine-tuning techniques, instruction tuning, alignment methods.

AI Frameworks and Tooling: PyTorch, Hugging Face Transformers, LangChain, LangGraph, LlamaIndex, DSPy, Ray, vLLM, TensorRT-LLM, model serving frameworks.

RAG and Retrieval: Vector databases (Pinecone, Weaviate, pgvector, Vertex AI Vector Search), embedding models, reranking, hybrid search, chunking strategies, query understanding.

Evaluation and Observability:  RAGAS, DeepEval, custom eval harnesses, LangSmith, Weights and Biases, Arize, OpenTelemetry for AI workloads.

Programming and Engineering: Python (expert), one additional systems language (Go, Java, or Rust), SQL, distributed systems, microservices, API design.

Cloud and Platform: GCP (Vertex AI, AlloyDB, GKE), Azure (Azure AI Foundry, AKS), AWS (Bedrock, SageMaker, EKS), Docker, Kubernetes, Terraform.

Data: Streaming and batch pipelines, lakehouse architectures, feature stores, data versioning (DVC, LakeFS), high-throughput ETL.

Engineering Competencies

• Technical Depth: Expert-level mastery of AI engineering with the ability to operate from research papers down to production code.
• Systems Thinking: Comfort designing systems that span multiple services, data stores, model providers, and failure modes.
• Pragmatism: Strong instinct for when to build, when to buy, and when to wait, with a track record of avoiding over-engineering.
• Communication: Ability to explain complex AI concepts to executives, write design docs that drive decisions, and influence peers across disciplines.
• Builder's Mindset: Genuine enjoyment of writing code and solving hard technical problems, not just reviewing or directing others.
• Curiosity and Continuous Learning: Active engagement with the AI research landscape and a habit of trying new things.

The estimated base salary range for the Associate Principal, AI Engineer role based in the United States of America is: $187,400 - $281,000. Should the level or location of the role change during the hiring process, the applicable base pay range may be updated accordingly. The range reflects long‑term growth in the role; therefore, most candidates are hired between the minimum and middle of the range. Placement depends on experience, skills, location, and internal equity. Additionally, all employees are eligible for one of our variable cash programs (bonus or commission) and eligible roles may receive equity as part of the compensation package. We offer a wide range of benefits as innovative as our work, including access to genomics sequencing, family planning, health/dental/vision, retirement benefits, and paid time off.
We are a company deeply rooted in belonging, promoting an inclusive environment where employees feel valued and empowered to contribute to our mission. Built on a strong foundation, Illumina has always prioritized openness, collaboration, and seeking alternative perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and offer opportunities to engage in social responsibility. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. Illumina conducts background checks on applicants for whom a conditional offer of employment has been made. Qualified applicants with arrest or conviction records will be considered for employment in accordance with applicable local, state, and federal laws. Background check results may potentially result in the withdrawal of a conditional offer of employment. The background check process and any decisions made as a result shall be made in accordance with all applicable local, state, and federal laws. Illumina prohibits the use of generative artificial intelligence (AI) in the application and interview process. If you require accommodation to complete the application or interview process, please contact accommodations@illumina.com. To learn more, visit: https://www.dol.gov/ofccp/regs/compliance/posters/pdf/eeopost.pdf. The position will be posted until a final candidate is selected or the requisition has a sufficient number of qualified applicants.