Principal Engineer - Scientific Authoring (Frontier AI)

Eli Lilly and Company • San Diego, CA

9d

About The Position

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world. Position Summary As a Principal Engineer in Frontier AI, you will build intelligent systems that transform how scientists create, analyze, and manage scientific documents. You will develop AI-powered tools that assist with manuscript preparation, regulatory submissions, patent applications, and technical documentation, helping researchers focus on science while AI handles the mechanics of scientific communication. You will work at the intersection of large language models, scientific knowledge representation, and document engineering to create systems that understand domain context, maintain scientific rigor, and accelerate the authoring lifecycle. Research & Innovation Design and implement AI agents for scientific document authoring, including literature synthesis, citation management, and figure/table generation Build retrieval-augmented generation (RAG) systems over scientific corpora, ELNs, and internal knowledge bases to ground AI outputs in factual content Develop domain-specific fine-tuning and prompt engineering strategies for chemistry, biology, and pharmacology content Create tools for automated quality checking: scientific accuracy, consistency, formatting compliance, and plagiarism detection Build multi-agent workflows that coordinate literature search, data extraction, drafting, and revision cycles Solution Deployment Build production-grade authoring applications with robust software engineering practices (version control, testing, CI/CD) Deploy scalable services on cloud-native infrastructure (Kubernetes, AWS) with appropriate guardrails for scientific content Partner with scientists, medical writers, and regulatory teams to integrate AI authoring tools into real workflows External Engagement Represent Frontier AI in internal forums and external AI/NLP research communities Evaluate external vendors, open-source tools, and academic collaborations for scientific authoring capabilities What Success Looks Like Measurable reduction in time-to-submission for manuscripts, patents, and regulatory documents AI authoring tools become trusted partners for scientists and medical writers High-quality, scientifically accurate outputs that maintain human oversight and accountability

Requirements

• MS + 1 yrs / BS + 2 yrs equivalent experience in Computer Science, Chemical sciences, Bioinformatics, or related discipline with demonstrated scientific domain exposure
• 1-2 years applying NLP/LLM techniques to text generation, summarization, or information extraction (including industry post-doc)
• Hands-on experience with LLM application development (prompt engineering, RAG architectures, agent frameworks)
• Strong software engineering skills: production-quality Python, version control, testing, CI/CD (GitHub portfolio a plus)
• Deep experience with ML/NLP frameworks (PyTorch, HuggingFace, LangChain, LlamaIndex)
• Qualified applicants must be authorized to work in the United States on a full-time basis. Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1.

Nice To Haves

• Experience with scientific document formats (LaTeX, XML/JATS, regulatory submission standards)
• Familiarity with biomedical NLP (PubMed, chemical NER, ontologies like MeSH or ChEBI)
• Working knowledge of vector databases and semantic search (Pinecone, Weaviate, pgvector)
• Publications in relevant ML/NLP venues (ACL, KDD, NeurIPS)

Responsibilities

• Design and implement AI agents for scientific document authoring, including literature synthesis, citation management, and figure/table generation
• Build retrieval-augmented generation (RAG) systems over scientific corpora, ELNs, and internal knowledge bases to ground AI outputs in factual content
• Develop domain-specific fine-tuning and prompt engineering strategies for chemistry, biology, and pharmacology content
• Create tools for automated quality checking: scientific accuracy, consistency, formatting compliance, and plagiarism detection
• Build multi-agent workflows that coordinate literature search, data extraction, drafting, and revision cycles
• Build production-grade authoring applications with robust software engineering practices (version control, testing, CI/CD)
• Deploy scalable services on cloud-native infrastructure (Kubernetes, AWS) with appropriate guardrails for scientific content
• Partner with scientists, medical writers, and regulatory teams to integrate AI authoring tools into real workflows
• Represent Frontier AI in internal forums and external AI/NLP research communities
• Evaluate external vendors, open-source tools, and academic collaborations for scientific authoring capabilities

Benefits

• Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance).
• In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).

What This Job Offers

• Job Type: Full-time
• Career Level: Principal