Scientific Lead - Forward Deployed AI Engineer, Applied Intelligence for Discovery

100 Eli Lilly and Company; South San Francisco (CA); On-site; USD 166,000 - 266,000; Full time

Benefits offered by this job

Company bonus

401(k)

Pension

Vacation benefits

Medical, dental, vision benefits

Flexible benefits

Life insurance

Well-being programs

Job summary

Lilly is building an AI foundation for drug discovery. The Forward Deployed AI Engineer will embed with research teams, translating real-world data and scientific constraints into production systems to shorten the path from question to answer.

You will work with biologists and computational scientists on petabytes of multi-omics data, delivering demos, benchmarks, and reusable platform components to scale across therapeutic areas.

Qualifications

• PhD in computational biology, bioinformatics, data science, CS or related field with 3+ years in software/ML deployment; or equivalent biotech software deployment experience.
• MS in computational biology, bioinformatics, data science, CS or related field with 5+ years in software/ML deployment; or equivalent experience.

Responsibilities

• Embed with biology teams to understand workflows, data, tools, and bottlenecks.
• Translate use-cases into prototypes with clear success criteria.
• Design and ship production systems solving scientific problems with data provenance and reliability.
• Apply LLMs, RAG, text-to-SQL, agentic AI frameworks to drug discovery challenges.
• Run evaluation loops to measure model and system quality against benchmarks.

Skills

Python programming

LLMs

Cloud computing

Git

Education

PhD in computational biology

MS in computer science

Tools

PyTorch

HuggingFace

LangChain/LlamaIndex

Job description

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life‑changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.

The Opportunity

We are building something unprecedented — an AI foundation that will push the frontier on what is possible today across drug discovery research, from target identification and disease biology through translational science. The Applied Intelligence for Discovery (AI4D) team is a newly formed group within Lilly Research Laboratories that operates at the intersection of scientific delivery and core platform development. AI4D’s mission is to connect scientists to petabyte‑scale data through natural language interfaces, automated analysis workflows, and intelligent search — and to convert early deployments into repeatable system standards and evaluation practices that scale across therapeutic areas. The Forward Deployed AI Engineer is the connective tissue between what AI can do and what discovery scientists need it to do. You will embed directly with research teams across therapeutic areas translating real‑world data, infrastructure, and scientific constraints into production systems that collapse the time from question to answer from days or weeks to minutes. You will measure success through production adoption, measurable workflow impact, and eval‑driven feedback loops that inform platform and model roadmaps. This is not a traditional software engineering or data science role. You will sit with biologists, geneticists, and computational scientists working with petabytes of multi‑omics data, leading end‑to‑end deployments from scoping through sustained production use.

Key Responsibilities

• Embed with computational biology and disease biology teams in your assigned therapeutic area to develop deep understanding of their workflows, data, tools, and bottlenecks.
• Translate use‑cases into concrete, testable prototypes with clear success criteria.
• Rapidly turn ideas into a working demo, complete with evaluation benchmarks that tighten acceptance criteria over time.
• Design and ship production systems quickly that solve specific scientific problems; owning integrations, data provenance, reliability, and on‑call readiness.
• Apply LLM, retrieval‑augmented generation (RAG), text‑to‑SQL, agentic AI frameworks, and other emerging approaches to drug discovery challenges including target identification, biomarker prioritization, mechanism of action studies, and extraction of insight from large‑scale multi‑omics datasets.
• Run evaluation loops that measure model and system quality against workflow‑specific scientific benchmarks; use results to drive model selection, product changes, and iterative evidence generation that tightens acceptance criteria over time.
• Distill deployment learnings into hardened primitives, reference architectures, validation templates, and benchmark harnesses that scale across therapeutic areas and accelerate future development.
• Partner closely with AI/LLMOps engineers on the AI4D team to ensure your field‑tested solutions feed back into the platform as reusable components, not one‑off builds.
• Contribute to a culture of experimentation, speed, and evidence‑based impact measurement within the AI4D group and the broader LRL research community.

Basic Qualifications

• PhD in computational biology, bioinformatics, data science, computer science, or a related field, with 3+ years of software/ML engineering or technical deployment experience; or equivalent demonstrated experience building and deploying AI/ML tools for scientific applications in biotech, pharma, or scientific software.
• MS in computational biology, bioinformatics, data science, computer science, or a related field, with 5+ years of software/ML engineering or technical deployment experience; or equivalent demonstrated experience building and deploying AI/ML tools for scientific applications in biotech, pharma, or scientific software.

Additional Skills/Preferences

• Strong programming skills in Python and familiarity with the modern AI/ML ecosystem, including experience with LLMs (API usage, prompt engineering, fine‑tuning), and common frameworks (PyTorch, HuggingFace, LangChain/LlamaIndex, or similar).
• Have owned AI deployments end‑to‑end from scoping through production adoption, and improved them through evaluation design, error analysis, and iterative evidence generation.
• Sufficient biological knowledge to have productive conversations with computational scientists and understand the research context behind their problems; prior experience working with multi‑omics data (RNA‑seq, proteomics, GWAS, spatial transcriptomics, or similar) is strongly preferred.
• Experience building data‑driven applications including interactive dashboards, natural language interfaces, or automated analysis pipelines.
• Communicate clearly across scientific, computational, technical, and executive audiences, translating technical tradeoffs into decision quality and measurable outcomes; you build trust with scientists who have deep domain expertise and make complex technology approachable without being condescending.
• Familiarity with cloud computing environments (AWS preferred) and version control (Git).
• Experience in pharmaceutical, biotech, or life sciences R&D environments.
• Familiarity with agentic AI frameworks and building AI‑powered workflows that chain multiple models or tools together.
• Experience with biological foundation models (e.g., scGPT, Geneformer for single‑cell; ESM for proteins; AlphaFold) or their application to research problems.
• Knowledge of biomedical ontologies, knowledge graphs, or experience integrating heterogeneous biological data sources.
• Track record of driving adoption of technical tools among non‑engineering users.
• Contributions to open‑source projects or a public portfolio of applied AI work.

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions.

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.

• Africa, Middle East, Central Asia (AMECA)
• Black Employees at Lilly (BE@Lilly)
• Chinese Culture Network (CCN)
• EnAble
• Evolve
• Lilly Indian Network (LIN)
• Organization of Latinx at Lilly (OLA)
• Pride (LGBTQ+ Allies)
• Veterans Leadership Network (VLN)
• Women’s Initiative for Leading at Lilly (WILL)

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is $166,500 - $266,200 Full‑time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance).

• 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
• 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.

#WeAreLilly At Lilly we strive to ensure our employees are part of a team that cares about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe!