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About the Role

The Applied Intelligence for Discovery (AI4D) team is building an AI foundation to advance drug discovery research. The Forward Deployed AI Engineer will embed with research teams to translate scientific needs into production AI systems, collapsing the time from question to answer from days or weeks to minutes. This role requires end-to-end deployment ownership, working with multi-omics data and leading the integration of AI solutions into research workflows.

Responsibilities

Embed with computational biology and disease biology teams to understand workflows, data, tools, and bottlenecks.
Translate use-cases into testable prototypes with clear success criteria and rapid demos.
Design and ship production systems to solve specific scientific problems, owning integrations, data provenance, reliability, and on-call readiness.
Apply LLM, RAG, text-to-SQL, and agentic AI frameworks to drug discovery challenges.
Run evaluation loops to measure model and system quality against scientific benchmarks and drive iterative improvements.
Distill deployment learnings into reusable primitives, reference architectures, and validation templates.
Partner with AI/LLMOps engineers to ensure field-tested solutions feed back into the platform.
Contribute to a culture of experimentation, speed, and evidence-based impact measurement.

Requirements

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.
Sufficient biological knowledge to have productive conversations with computational scientists and understand the research context.
Communicate clearly across scientific, computational, technical, and executive audiences, translating technical tradeoffs into decision quality and measurable outcomes.

Skills

Python programming
Modern AI/ML ecosystem familiarity
LLMs (API usage, prompt engineering, fine-tuning)
PyTorch
HuggingFace
LangChain/LlamaIndex
End-to-end AI deployment ownership
Evaluation design
Error analysis
Iterative evidence generation
Experience with multi-omics data (RNA-seq, proteomics, GWAS, spatial transcriptomics, or similar)
Building data-driven applications (dashboards, natural language interfaces, automated analysis pipelines)
Cloud computing environments (AWS preferred)
Version control (Git)
Agentic AI frameworks
Biological foundation models (e.g., scGPT, Geneformer for single-cell; ESM for proteins; AlphaFold)
Biomedical ontologies
Knowledge graphs
Integrating heterogeneous biological data sources
Driving adoption of technical tools among non-engineering users
Contributions to open-source projects or a public portfolio of applied AI work

Location

Indianapolis, Indiana

Work Type

Full-time

Experience Level

3+ years of software/ML engineering or technical deployment experience (with PhD)
5+ years of software/ML engineering or technical deployment experience (with MS)

Education Level

PhD in computational biology, bioinformatics, data science, computer science, or a related field
MS in computational biology, bioinformatics, data science, computer science, or a related field

Salary/Compensations

$166,500 - $266,200

Benefits

Company bonus (depending, in part, on company and individual performance)
Company-sponsored 401(k)
Pension
Vacation benefits
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)

About the Company

Lilly is a global healthcare leader headquartered in Indianapolis, Indiana.
Employees discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to communities through philanthropy and volunteerism.
The company values giving best effort and putting people first.
Lilly is building an AI foundation to push the frontier in drug discovery research.

Equal Opportunity

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.
Employee resource groups (ERGs) offer strong support networks for their members and are open to all employees.