AI PhD Foundation Model for Clinical Imaging Internship

100 Eli Lilly and Company; Indianapolis (IN); On-site; USD 122,000 - 150,000; Full time

Benefits offered by this job

Paid time off

Free parking

LIFE fitness center access

Housing assistance for relocation

Mentoring

Job summary

Eli Lilly and Company is offering a hands‑on research internship focused on foundation models for clinical imaging. The intern will develop and evaluate imaging‑based AI models and work with data across MRI, PET, CT, and other modalities.

The role involves collaborating with investigators and presenting results to senior leaders. Lilly emphasizes rigorous ethics, confidentiality, and the practical impact of AI in drug development.

Qualifications

• Currently enrolled in and pursuing a PhD in Computer Science or related quantitative field.
• At least three years of completed graduate work, with foundational knowledge of machine learning, deep learning, medical imaging, or statistical modeling and hands‑on experience programming in Python.
• Authorized to work in the United States on a full‑time basis; Lilly will not provide sponsorship for work authorization or visas.

Responsibilities

• Develop and evaluate imaging‑based AI models that learn rich, generalizable representations from diverse clinical imaging data across modalities.
• Develop, adapt, or fine‑tune foundation models for clinical imaging and integrate representations with clinical or biomarker data.
• Collaborate with clinical, imaging, and scientific teams; stay current with advances in foundation models and clinical imaging AI; communicate results to stakeholders.

Skills

Machine learning

Deep learning

Medical imaging

Python

Education

PhD in Computer Science

Three years of graduate work

Job description

Organization Overview

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 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.

Functional Overview

You will join the Clinical and Development area within Lilly’s Advanced Intelligence & Research organization, where we build and deliver advanced AI and data science solutions that accelerate clinical development and improve decision‑making across the drug development lifecycle. This internship sits within our work on foundation models for clinical imaging. The intern will help develop and evaluate imaging‑based AI models that learn rich, generalizable representations from diverse clinical imaging and related data. The project may involve multiple imaging modalities, including MRI, PET, CT, ultrasound, digital pathology, retinal imaging, and other clinical imaging data. Applications may span multiple therapeutic areas, including neuroscience, cardiometabolic health (CMH), immunology, oncology, and other areas aligned with Lilly research priorities.

As an intern, you will be assigned a scoped project with real business impact and will work alongside experienced research scientists. Key areas of work may include developing, adapting, or fine‑tuning foundation models for clinical imaging; integrating imaging‑derived representations with clinical, biomarker, longitudinal, or other relevant data; applying models to prediction, characterization, stratification, or risk‑assessment tasks across therapeutic areas; evaluating model performance, robustness, generalizability, and scientific interpretability; partnering with clinical, imaging, and scientific collaborators; and staying current with advances in foundation models and clinical imaging AI.

Lilly internships run for 12 continuous weeks over the summer. Each intern actively contributes to the organization, builds a comprehensive understanding of the pharmaceutical industry, and takes part in professional development and social events throughout the summer. At the conclusion of the internship, each intern presents their project highlights, findings, recommendations, and accomplishments to senior leaders and stakeholders.

As part of Lilly's commitment to innovation, interns will have the opportunity to build fluency with AI tools used across the business. We expect interns to approach these tools with curiosity, apply critical thinking to AI‑assisted work, and always prioritize accuracy, confidentiality, and ethical standards in how they use them.

Basic Qualifications

Currently enrolled in and pursuing a PhD in Computer Science, Computational Biology, Operations Research, Statistics, Biostatistics, Mathematics/Applied Math, or similar quantitative field. At least three years of completed graduate work, with foundational knowledge of machine learning, deep learning, medical imaging, or statistical modeling and hands‑on experience programming in Python. 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.

Additional Functional Job Skills & Preference

• Deep knowledge of machine learning and deep learning methods relevant to medical imaging, including representation learning, self‑supervised learning, multimodal learning, transfer learning, model evaluation, and uncertainty or risk prediction.
• Experience developing, fine‑tuning, or applying foundation models to clinical imaging data, including modalities such as MRI, PET, CT, ultrasound, digital pathology, retinal imaging, or related imaging domains across therapeutic areas.
• Familiarity with clinical, imaging, biomarker, or longitudinal healthcare data and the challenges of missingness, data quality, harmonization across studies, and generalization across patient populations.
• Strong programming skills in Python and/or R, and comfort with modern ML and statistical modeling.
• Ability to translate methodological choices and insights for clinical and business stakeholders, with strong written and verbal communication.
• Prior research or internship experience applying foundation models, clinical imaging AI, multimodal learning, or advanced deep learning methods to biomedical, healthcare, or life sciences problems.
• Prior experience using AI tools (e.g., generative AI platforms, automation tools, or AI‑assisted research/analytics tools) in an academic, project, or work setting.

Additional Information

This is a hands‑on research and applied machine learning internship focused on foundation models for clinical imaging. Projects may support research across neuroscience, CMH, immunology, oncology, and other therapeutic areas.

Lilly arranges various intern activities including sporting events, dinners, lunch and learns, volunteer activities, etc. to provide opportunities for socializing, professional development, and learning more about Lilly.

• Interns will receive 1 week of paid time off during the Lilly summer shut‑down (July 5th – July 9th).
• Interns will receive 1:1 mentoring from an experienced professional in the function.
• Interns will receive a competitive salary and free parking at their work site, as well as access to Lilly’s LIFE fitness center, bike garage, and many other discounts.
• If the intern's job position requires a move from another location, Lilly will provide subsidized housing.
• 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.

Equal Employment Opportunity

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

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).

Compensation

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location.

The anticipated wage for this position is $136,000 (PhD) annually. 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.

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!