Eli Lilly and Company · 2 hours ago
Machine Learning Scientist/Sr Scientist, Federated Benchmarking & Validation Engineering
South San Francisco, CA
Full-time
Onsite
Mid, Senior Level
$152K/yr - $244K/yr
2+ years expEli Lilly and Company is a global healthcare leader dedicated to improving lives through innovative medicines. The Machine Learning Scientist/Sr Scientist will play a crucial role in the TuneLab platform, focusing on developing algorithmic solutions to enhance drug discovery while ensuring data privacy and security for biotech partners.
BiotechnologyHealth CareMedicalPharmaceutical
Responsibilities
Federated Test Set Design: Architect and implement privacy-preserving protocols for constructing representative test sets across distributed partner datasets, ensuring statistical validity while maintaining data isolation
Benchmark Suite Development: Create comprehensive benchmark suites covering small molecules (ADMET, solubility, permeability), antibodies (affinity, stability, immunogenicity), and RNA therapeutics (stability, delivery, off-target effects)
Cross-Domain Validation: Develop validation strategies that assess model generalization across different experimental protocols, cell lines, species, and therapeutic indications while respecting partner data boundaries
Public Dataset Integration: Systematically benchmark federated models against public datasets (ChEMBL, PubChem, PDB, Therapeutic Antibody Database) to establish performance baselines and identify gaps
Validation Frameworks: Implement time-split or proper scaffold-split validation protocols that assess model performance on prospective data, simulating real-world deployment scenarios and detecting concept drift
Reproducibility Infrastructure: Build robust MLOps pipelines ensuring complete reproducibility of federated experiments, including versioning of data snapshots, model checkpoints, and hyperparameter configurations
Statistical Rigor: Design statistically powered validation studies accounting for multiple testing, hierarchical data structures, and non-independent observations common in drug discovery datasets
Performance Profiling: Develop comprehensive performance profiling across diverse molecular scaffolds, target classes, and property ranges, identifying systematic biases and failure modes
Platform Integration: Collaborate with engineering teams to integrate validation frameworks with the TuneLab federated learning platform built on NVIDIA FLARE, ensuring scalable and automated testing across partner networks
Qualification
Required
PhD in Computational Biology, Bioinformatics, Cheminformatics, Computer Science, Statistics, or related field from an accredited college or university
Minimum of 2 years of experience in the biopharmaceutical industry or related fields, with demonstrated expertise in drug discovery and early development
Strong foundation in experimental design, statistical validation, and hypothesis testing
Experience with ML model validation, cross-validation strategies, and performance metrics
Proficiency in data engineering, pipeline development, and automation
Preferred
Experience with federated learning platforms and distributed computing
Knowledge of regulatory requirements for AI/ML in pharmaceutical development
Expertise in ADMET assay development and validation
Understanding of antibody engineering and characterization methods
Familiarity with RNA therapeutic design and delivery systems
Experience with clinical biomarker validation and translational research
Proficiency in workflow orchestration tools (Airflow, Kubeflow, Prefect)
Strong knowledge of containerization and cloud computing (Docker, Kubernetes)
Publications on model validation, benchmarking, or reproducibility
Experience with GxP compliance and quality management systems
Exceptional attention to detail and commitment to scientific rigor
Strong technical writing skills for regulatory documentation
Portfolio mindset balancing rigorous validation with rapid deployment for partner value
Benefits
Company bonus (depending, in part, on company and individual performance)
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)
Company
Eli Lilly and Company
We're a medicine company turning science into healing to make life better for people around the world.
10001+ employees
H1B Sponsorship
Eli Lilly and Company has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
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Trends of Total Sponsorships
2025 (514)
2024 (236)
2023 (167)
2022 (133)
2021 (57)
2020 (52)
Funding
Current Stage
Public CompanyTotal Funding
$6.5M2024-02-12Post Ipo Debt· $6.5M
1978-01-13IPO
Leadership Team
David Ricks
Chair, CEO
Lucas Montarce
Executive Vice President and Chief Financial Officer
Recent News
2025-12-30
2025-12-30
Company data provided by crunchbase