ML Engineer– Drug Discovery & R&D Operations

Elanco; Indianapolis (IN); On-site; USD 150,000 - 210,000; Full time

Benefits offered by this job

Relocation packages

Two weeklong shutdowns (US)

8-week parental leave

Employee Resource Groups

Annual bonus offering

Flexible work arrangements

Up to 6% 401K matching

Job summary

Elanco, a global leader in animal health, seeks an ML Engineer – Drug Discovery & R&D Operations in Indianapolis to accelerate its R&D portfolio by turning proprietary data into predictive models. You will collaborate with discovery and development scientists to build ML and CV models across molecular, in vitro, ADMET, and imaging data to support target identification and biomarker endpoints.

You will design and deploy models on multi-modal data, drive data collection standards, and lead

Qualifications

• PhD in a quantitative field or Master’s with substantial hands-on ML/CV experience.
• 7+ years of industry experience building and deploying ML and computer-vision models for biomedical, pharmaceutical, or related domains.
• Strong Python skills and proficiency with ML/CV libraries (PyTorch, TensorFlow, scikit-learn, OpenCV).

Responsibilities

• Lead ML/CV work for key R&D programs, turning target identification and molecular data into modeling problems with clear success criteria.
• Design, build, and validate advanced ML and CV models on multi-modal data to deliver reliable predictions and classifications.
• Shape data collection, annotation, and synthetic data usage with experimental teams and quality checks; evaluate synthetic data and augmentation to strengthen sparse datasets.
• Operationalize models in R&D workflows by integrating with Databricks and influencing standards for reproducibility and governance.
• Provide technical leadership and mentorship by guiding junior scientists and leading cross-functional modeling initiatives.

Skills

Python

ML/CV libraries

PyTorch

TensorFlow

scikit-learn

OpenCV

Cross-functional collaboration

Education

PhD in a quantitative field

Master’s with ML/CV experience

Tools

Databricks

MLOps tools

Job description

At Elanco (NYSE: ELAN) – it all starts with animals!

As a global leader in animal health, we are dedicated to innovation and delivering products and services to prevent and treat disease in farm animals and pets. At Elanco, we are driven by our vision of Food and Companionship Enriching Life and our purpose – all to Go Beyond for Animals, Customers, Society and Our People.

At Elanco, we pride ourselves on fostering a diverse and inclusive work environment. We believe that diversity is the driving force behind innovation, creativity, and overall business success. Here, you’ll be part of a company that values and champions new ways of thinking, work with dynamic individuals, and acquire new skills and experiences that will propel your career to new heights.

Making animals’ lives better makes life better – join our team today!

Your Role:
As the ML Engineer– Drug Discovery & R&D Operations, you will accelerate Elanco’s R&D portfolio by turning proprietary scientific data into predictive models that guide drug discovery and development decisions. You will partner with discovery and development scientists to build machine learning and computer‑vision models on molecular, in vitro, ADMET, and imaging data to support target identification, molecular optimization, digital biomarkers, and endpoint prediction for animal health.

Your Responsibilities:

• Lead ML/CV work for key R&D programs, partnering with scientists to turn target identification, molecular optimization, in vitro analysis, ADMET, and biomarker questions into modeling problems with clear success criteria.
• Design, build, and validate advanced ML and computer‑vision models—including CNNs, transformers, graph neural networks, and generative approaches—on multi‑modal data (molecular, assay, imaging, behavioral) to deliver reliable predictions and classifications.
• Shape data collection, annotation, and synthetic data usage by working with experimental teams on capture protocols, labeling standards, and quality checks; evaluate synthetic data and augmentation to strengthen sparse datasets while managing bias and risk.
• Operationalize models in R&D workflows by integrating them with tools used by scientists—including building and deploying models in Databricks—and influencing standards for reproducibility, documentation, monitoring, and model governance.
• Provide technical leadership and mentorship by guiding junior scientists, leading cross‑functional modeling initiatives, and clearly communicating technical concepts and results to diverse stakeholders.

What You Need to Succeed (minimum qualifications):

• Education & baseline experience: PhD in a quantitative field (e.g., Data Science, Engineering, Physics, Mathematics, Statistics, Bioinformatics, Computational Chemistry), or a Master’s degree with substantial hands‑on ML/CV experience.
• Applied ML/CV experience: 7+ years of industry experience building and deploying ML and computer‑vision models for scientific problems in biomedical, pharmaceutical, or related domains, with demonstrated impact and close collaboration with wet‑lab or clinical teams.
• Technical and collaboration skills: Strong Python skills and proficiency with modern ML/CV libraries (e.g., PyTorch, TensorFlow, scikit‑learn, OpenCV), solid understanding of statistics and experimental design, and proven ability to work and communicate effectively in cross‑functional, matrixed environments.

What will give you a competitive edge (preferred qualifications):

• Domain expertise and impact: Experience in animal health, pharmaceutical, or biotech R&D, with a record of impactful ML/CV applications (e.g., chemoinformatics, bioinformatics, digital biomarkers) shown through projects, publications, or patents.
• Advanced technical depth and platforms: Hands‑on expertise with methods such as neural networks and generative models, plus practical experience operationalizing models using Databricks and MLOps tools in production‑like or scaled environments.
• Leadership and influence: Demonstrated success leading cross‑functional teams, mentoring junior scientists, and influencing scientific and technical decisions in complex, global organizations.

Additional Information:

• Travel: Up to 10%
• Location: Indianapolis, IN, USA

Don’t meet every single requirement?Studies have shown underrepresented groups are less likely to apply to jobs unless they meet every single qualification. At Elanco we are dedicated to building a diverse and inclusive work environment. If you think you might be a good fit for a role but don't necessarily meet every requirement, we encourage you to apply. You may be the right candidate for this role or other roles!

Elanco Benefits and Perks:

We offer a comprehensive benefits package focusing on financial, physical, and mental well-being while encouraging our employees to pursue our purpose! Some highlights include:

• Multiple relocation packages
• Two weeklong shutdowns (mid-summer and year-end) in the US (in addition to PTO)
• 8-week parental leave
• 9 Employee Resource Groups
• Annual bonus offering
• Flexible work arrangements
• Up to 6% 401K matching

Elanco is an EEO/Affirmative Action Employer and does not discriminate on the basis of age, race, color, religion, gender, sexual orientation, gender identity, gender expression, national origin, protected veteran status, disability or any other legally protected status

Elanco may use automated tools, including AI, to support parts of our recruitment process, such as reviewing applications against job‑related criteria and/or transferrable skills. These tools help ensure a consistent, structured evaluation, but they do not make hiring decisions. All decisions involve a human reviewer. For more information on how we handle personal data, please see our Elanco Workforce Privacy Notice.

Elanco is an EEO/Affirmative Action Employer and does not discriminate on the basis of age, race, color, religion, gender, sexual orientation, gender identity, gender expression, national origin, protected veteran status, disability or any other legally protected status

Elanco may use automated tools, including AI, to support parts of our recruitment process, such as reviewing applications against job‑related criteria and/or transferrable skills. These tools help ensure a consistent, structured evaluation, but they do not make hiring decisions. All decisions involve a human reviewer. For more information on how we handle personal data, please see our Elanco Workforce Privacy Notice.