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.
Organization Overview
Lilly Small Molecule Discovery is an organization purpose-built to create molecules that make life better for people. We focus on using cutting edge science to unlock new approaches that can treat people suffering from diseases with poor treatment options. We continually challenge ourselves to deliver molecules that can provide breakthrough efficacy with the highest possible safety margins. We are dedicated to optimizing our mindset, technology, and processes for faster, more nimble execution. Our success is built on a culture that empowers innovative problem solving through open collaboration and individual accountability.
Discovery Technology and Platforms is a newly established function within this organization. Its mission is to accelerate molecule discovery by building highly optimized foundational platforms, streamlining lab operations through advanced technologies and data connectivity, and intentionally investing in novel technologies and capabilities.
Frontier AI is a purpose-built team that fuses scientific AI, lab automation, and unified data platforms to autonomously design, run, and refine experiments-accelerating molecule discovery.
Position Summary
We are rebuilding the Design-Make-Test-Analyze (DMTA) cycle from the ground up-infusing scientific automation with foundation models, multi-agent systems, and robotics to make scientific discovery intelligent, autonomous, and fast.
As an Applied Research Scientist , you will push the state of the art in AI (LLMs, graph ML, reinforcement learning) and translate those advances into working systems that accelerate chemistry and biology at scale. You will prototype novel algorithms, productionize successful ideas, and partner closely with scientists, engineers, and automation teams to reshape how we discover medicines.
Research & Innovation
Lead cutting-edge research on LLMs, Transformer architectures, graph/sequence hybrid models, and agentic RL for molecular design, assay automation.
Integrate LLM reasoning with domain tools (e.g., RDKit, molecular graph ML, ELN/LIMS APIs) to build composite agents that plan, simulate, and execute DMTA tasks.
Rapidly explore new techniques, run ablation studies, and benchmark against internal and external baselines.
Solution Development
Design, implement, and deploy robust ML pipelines that handle and analyze multi-omics data
Partner with program and product leads to turn scientific opportunities into well-scoped research bets, MVP prototypes, and production roll-outs.
External Engagement
Represent molecule research in the broader AI@Lilly and external AI research community: publish, give talks, review papers, and scout emerging trends.
Evaluate external vendors, open-source projects, and academic collaborations for strategic fit.
What Success Looks Like
Measurable reduction in DMTA turnaround through autonomous planning and execution
Tools you build become indispensable to chemists, biologists, and automation engineers
Basic Qualifications
PhD in Bioinformatics, Cheminformatics, Computer Science, or a related technical field.
Hands-on experience with LLMs/Transformers, including their theoretical underpinnings and practical application in post-training (e.g., fine-tuning, RLHF, prompting, agent development).
Preferred
Approximately 1-2 years of demonstrated ML/AI techniques to complex scientific problems
Proficiency in Python and deep experience with ML/Deep Learning frameworks (e.g., TensorFlow, PyTorch, JAX, HuggingFace, LangChain).
Proven ability as a strong software engineer, capable of writing production-quality code, with experience in ML systems, and deploying AI models (Personal portfolio or Github to share a plus)
Familiarity with MLOps, including model versioning, and continuous integration/continuous deployment for ML systems.
Industry experience in a startup or fast-paced R&D environment.
Experience with LLM post-training and refinements.
Experience with graph-based machine learning techniques.
Meaningful experience or a strong understanding of applying AI/ML in another scientific discipline such as biology, psychology, neuroscience, or a related field.
Demonstrable research experience, evidenced by contributions to projects, and ideally through publications in relevant ML/NLP venues (e.g., NeurIPS, ICML, ICLR, ACL, EMNLP).
Experience mentoring and guiding junior researchers or engineers.
Additional Information:
Physical Demands/Travel:
· The physical demands of this job are consistent with an office and lab environment *.*
· The physical demands here are representative of those that must be met by an employee to successfully perform the essential functions of this job.
Work Environment:
· This position's work environment is in an office. ?
· The work environment characteristics described here are representative of those an employee encounters while performing the essential functions of this job.
· *To perform this job successfully, an individual must be able to perform the role and responsibilities satisfactorily. The requirements listed above are representative of the knowledge, skill, and/or ability required. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions.
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
$142,500 - $228,800
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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