Director / Sr. Director - Machine Learning - Large Molecule Discovery

Location: San Diego
Posted on: June 23, 2025

Job Description:

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. Lilly’s Biotechnology Discovery Research (BioTDR) organization has a track record for delivering novel biotherapeutic medicines advanced into clinical research in key areas of unmet medical needs, across a variety of therapeutic areas. Integrating biology with innovative scientific capabilities in protein discovery, engineering and computational sciences, we are committed to delivering next wave of biomedicines. We are seeking an exceptional senior-level AI/ML scientist to lead our computational efforts in accelerating therapeutic protein and antibody discovery. This position is based at the Lilly Biotechnology Center in San Diego, situated at the intersection of Computational Science, Protein Bioscience, Automation, Protein Engineering, and Information Technology. The successful candidate will spearhead the development and implementation of advanced AI/ML methodologies to establish protein engineering and de novo antibody discovery pipelines, while providing strategic leadership to a team of skilled ML/AI scientists. In this collaborative environment, with access to state-of-the-art technologies and computing resources, you will have the opportunity to contribute to the discovery of life-changing biotherapeutics. Primary Responsibilities: Lead and mentor AI/ML scientists, driving innovation in computational antibody discovery and protein engineering Develop and implement AI/ML techniques to build pipelines for antibody design and optimization including affinity, selectivity, PK, and drug-like properties Train and fine-tune LLM-based models, diffusion models and SOTA algorithms using internal datasets Lead method development de novo antibody discovery Collaborate with multidisciplinary teams to integrate AI/ML strategies in drug discovery Stay updated with AI/ML advancements and drive accelerated internal innovations Represent the company's AI/ML at conferences, collaborate externally, and contribute to the scientific community through publications or patents Basic Qualifications Ph.D. in Computational Biology, Bioinformatics, Computer Science, or a related field with a focus on AI/ML applications in life sciences Minimum of 5 years of relevant experience beyond education/postdoctoral training, in industry or research organization (10 years desired) Additional Skills and Preferences Strong core proficiency in developing and implementing machine learning algorithms, including deep learning architectures such as CNNs, RNNs, and Transformers Proven track record of leading successful AI/ML projects in the pharmaceutical, biotechnology, or research organization Prior experience with de novo protein design and antibody engineering preferred Expertise with state-of-the-art ML models relevant for protein modeling, such as generative models (diffusion, flow-matching, etc), language models (transformers), multimodal learning, geometric deep learning, graph representation learning Extensive knowledge of protein structure analysis, antibody biology, and therapeutic antibody design principles Experience in managing and developing teams of ML/AI scientists Experience with cloud computing platforms and high-performance computing environments Excellent communication and presentation skills, with the ability to convey complex technical concepts to diverse audiences Ability to work productively and collaboratively in an interdisciplinary team environment Additional Information Location: San Diego, CA 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 $184,500 - $321,200 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; 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. WeAreLilly

Keywords: , Bellflower , Director / Sr. Director - Machine Learning - Large Molecule Discovery, Science, Research & Development , San Diego, California