Advisor - Scientific Machine Learning & Agentic Workflows Engineer

100 Eli Lilly and Company; Indianapolis (IN); On-site; USD 131,000 - 211,000; Full time

Benefits offered by this job

Job summary

Eli Lilly and Company in Indianapolis, IN, seeks a scientist-engineer to design and implement SciML models and agentic workflows that accelerate physics-based simulation and data analysis. You will work with real solvers and data, validate against experiments, and embed rigorous provenance and governance.

The role emphasizes Python engineering, PyTorch/JAX, HPC/cloud execution, and cross‑functional collaboration to deliver reproducible, credible insights for drug product and process development.

Qualifications

• PhD in applied mathematics, computer science, machine learning, computational mechanics or physics, chemical, mechanical, or biomedical engineering, or a related field
• Strong Python software engineering, including PyTorch or JAX, and Git-based collaborative development
• Hands-on experience building LLM-enabled workflows including multi-step agent orchestration and tool calling or retrieval-augmented generation (RAG)
• Experience running computational work on HPC clusters or cloud infrastructure
• Peer-reviewed publications or open-source contributions in scientific machine learning
• Ability to design, implement, validate, and support complex workflows with credibility and traceability

Responsibilities

• Design, train, and validate SciML models with physics-informed networks and operator learning
• Build LLM-based agentic workflows to plan, set up, execute, and post-process modeling tasks with real solvers
• Ensure provenance, reproducibility, and defensible credibility of all results
• Write maintainable code with CI/CD and containerization
• Collaborate across product development functions to fit workflows into existing processes

Skills

Python engineering

PyTorch

JAX

Git workflows

LLM workflows

HPC/Cloud

SciML prototyping

Education

PhD in related field

Tools

Abaqus

COMSOL

Ansys

OpenFOAM

LAMMPS

GROMACS

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.

Organization Overview

At Eli Lilly and Company, we unite caring with discovery to make life better for people around the world. Lilly is a leader in global healthcare and has been discovering and developing medicines that help improve lives for more than 140 years. Our 50,000 employees around the world work as a team to bring breakthrough medicines to patients who need them. We are looking for motivated, highly skilled scientists and engineers to help us continue to bring breakthrough medicines to patients.

Position Overview

This role builds hybrid physics-and-data models — and the agentic software layer that puts them in the hands of working scientists. It has two connected halves. The first is scientific machine learning: physics-informed networks, operator learning, multi‑fidelity surrogates, Bayesian calibration, and gray-box system identification that accelerate or extend physics-based simulation. The second is AI engineering: agentic workflows that plan, set up, execute, and post‑process modeling and simulation tasks by calling real solvers and real data, so that a scientist can move from question to credible answer without hand‑assembling every step. The role sits within the Computational Modeling & Simulation team in DDCS and works across the programs that the team supports. This is not a standalone research role: the models and tools are built with and for the drug product, device, and process development functions across Product Research & Development that use them. You will independently design, implement, validate, and support the workflows you build, working closely with the DDCS AI Application Development and Data Sciences functions on architecture, platform choices, and compliance.

Key Responsibilities

Scientific Machine Learning Development

Independently design, train, and validate SciML models — physics-informed neural networks, operator-learning architectures (e.g., DeepONet, Fourier neural operators), and Gaussian‑process or multifidelity surrogates — against high‑fidelity simulation and experimental data. Apply Bayesian calibration and uncertainty quantification to deliver predictions with a defensible confidence statement rather than a point estimate. Apply gray‑box identification and symbolic‑regression methods to infer unknown parameters or missing mechanisms from sparse experimental data.

Agentic Modeling Workflow Engineering

Design and build LLM‑based agentic workflows that plan, set up, execute, monitor, and post‑process modeling tasks by calling real tools — solvers (e.g., Abaqus, COMSOL, Ansys, OpenFOAM, LAMMPS, GROMACS), meshing and geometry utilities, HPC schedulers, and internal data services. Implement the tool interfaces, APIs, and retrieval layers that connect agents to DDCS model libraries, simulation archives, and structured data sources. Define and enforce human‑in‑the‑loop checkpoints at the points where a modeling decision requires expert judgment rather than automation. Package workflows so that a scientist who is not a software developer can use them reliably and unaided.

Credibility, Traceability, and Guardrails

Ensure every agent‑executed run emits a complete provenance record: inputs, geometry and discretization, solver and library versions, convergence evidence, random seeds, and the human approvals applied. Design for deterministic replay — any result that informs a decision must be reproducible from its recorded provenance, within a documented tolerance. Build evaluation harnesses — benchmark problems with known solutions, regression tests, and reliability metrics — that quantify how often a workflow produces the right answer. Define credibility practice: defining defensible practice and credibility frameworks for hybrid physics‑ML models in the spirit of ASME V&V 40 and the FDA's 2023 guidance on assessing computational model credibility.

Software Engineering, Deployment, and Cross‑Functional Delivery

Write maintainable, tested code; treat version control, code review, CI/CD, and containerization as defaults. Deploy and operate workflows on HPCs and approved cloud environments, instrumented for observability, latency, and cost. Deploy in partnership with the functions that will use the output — device engineering, drug product and process development, analytical sciences, manufacturing, quality, and regulatory — so that tools fit existing development workflows, data sources, and decision timelines rather than requiring users to change how they work. Apply business judgment when setting priorities: understand the portfolio, program milestones, and decision gates the modeling supports, and direct effort toward the questions where a faster or better answer changes a development decision. Make and defend practical trade‑offs on build versus buy, model fidelity versus cost and turnaround time, and automation versus expert review, keeping total cost of ownership and the needs of downstream users in view. Apply responsible AI, security, and data‑handling controls across the workflow lifecycle, in partnership with IT, Quality, and Information Security.

Partnership, Enablement, and Communication

Work as an embedded member of cross‑functional development teams, engaging directly with drug product, device, and process development colleagues to frame the problem and agree what a useful answer looks like before choosing a method. Partner with continuum and molecular modeling scientists to identify where surrogates and agentic workflows create real value — and where a direct simulation or an experiment remains the better answer. Collaborate with the DDCS Digital Transformation team on architecture, reusable patterns, and platform choices; contribute to GxP and 21 CFR Part 11 considerations where workflows touch regulated systems. Train and support users, and report adoption quantitatively.

Basic Qualifications

• PhD in applied mathematics, computer science, machine learning, computational mechanics or physics, chemical, mechanical, or biomedical engineering, or a related field
• Doctoral research centered on scientific machine learning — physics-informed learning, operator learning, surrogate modeling, or hybrid mechanistic-ML methods
• Demonstrated experience developing SciML models and validating them against physics‑based simulation or experimental data
• Strong Python software engineering, including PyTorch or JAX, and Git‑based collaborative development
• Hands‑on experience building LLM‑enabled workflows including multi‑step agent orchestration and either tool and function calling or retrieval‑augmented generation (RAG)
• Experience running computational work on HPC clusters or cloud infrastructure
• Peer‑reviewed publications or open‑source contributions in scientific machine learning

Additional Preferences

• A working practice grounded in evaluation, provenance, and reproducibility, and the ability to explain to both technical and business audiences what these methods can and cannot do
• Neural operator methods, multifidelity modeling, Bayesian UQ and calibration, active learning, or Bayesian optimization applied to engineering or biomedical problems
• Gray-box identification, symbolic regression, or discovery of pharmacokinetic, pharmacodynamic, or transport models from sparse data
• Experience with agent frameworks and tool‑interoperability standards (e.g., tool‑calling APIs, graph‑based agent orchestration, Model Context Protocol) and with production deployment practice (containers, CI/CD, observability)
• Familiarity with commercial or open‑source simulation solvers and their scripting interfaces and input/output formats
• Awareness of model credibility practice for regulated products (ASME V&V 40; FDA credibility assessment guidance) and of GxP and 21 CFR Part 11 requirements for computerized systems
• Front‑end or full‑stack experience sufficient to build usable interfaces for scientific tools
• Domain exposure to drug delivery, medical devices, combination products, or biomedical transport problems

Other Information

Travel: 0–10% Location: Indianapolis, IN; Lilly Technology Center – North (LTC‑N)

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 (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) and 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 $130,500 - $211,200 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
• 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! #WeAreLilly