Principal Engineer - Scientific Authoring (Frontier AI)

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
   

Basic Qualifications

• 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.

Preferred Qualifications

• 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)

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.

Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women’s Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location.  The anticipated wage for this position is

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).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

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