Privacy Preserving Machine Learning Jobs in Indianapolis, IN

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

At Lilly, we serve an extraordinary purpose.We make a difference for peoplearound the globeby discovering,developingand delivering medicines that helpthemlive longer, healthier, more active lives. Not only do we deliver breakthrough medications, but you also can count on us to develop creative solutions to support communities through philanthropy and volunteerism.

Purpose

Lilly TuneLab is an AI-powered drug discovery platform that provides biotech companies with access to machine learning models trained on Lilly's extensive proprietary pharmaceutical research data. Through federated learning, the platform enables Lilly to build models on broad, diverse datasets from across the biotech ecosystem while preserving partner data privacy and competitive advantages. Antibody developability prediction is a core workstream within TuneLab - covering aggregation, self-association, polyspecificity, thermal stability, viscosity, and chemical liabilities - that gates progression from discovery into lead optimization, cell line development, and formulation.

The Advisor/Senior Advisor - Antibody Developability Validation & Benchmarking plays an essential role in establishing whether TuneLab's federated antibody models can be trusted to triage real candidates. The person in this seat must understand, at depth, how antibodies are characterized, what makes a sequence developable or not, and how predictions from a federated model translate into go/no-go decisions in a discovery pipeline.

This is a validation-led role that contributes to model design choices. The person will partner closely with antibody modeling scientists on architecture, feature design, and uncertainty quantification - not just downstream of them.

Key Responsibilities

Antibody Developability Benchmark Suite: Build the canonical benchmark suite covering the full developability portfolio - aggregation propensity (AC-SINS, SMAC, CIC), thermal stability (nanoDSF/DSF), polyspecificity (BVP-ELISA, Heparin RT, PSR), self-interaction, viscosity, chemical liabilities (deamidation, isomerization, oxidation, N-glycosylation in CDRs), and immunogenicity surrogates. Define which endpoints are evaluated jointly versus independently and how multi-endpoint reliability rolls up to a triage decision.

Sequence-Aware Federated Test Set Design: Architect privacy-preserving protocols for constructing representative test sets across distributed partner datasets, with splitting strategies appropriate to antibody data - germline-based, CDR-similarity-based, and clonotype-based splits that genuinely test generalization rather than near-duplicate memorization. Account for the structural asymmetry of antibody data (many sequences with shallow characterization, few sequences with deep characterization) when designing held-out evaluation sets.

Public Benchmark Integration: Systematically benchmark federated antibody models against established external resources - SAbDab, OAS, TAP, the Jain et al. clinical-stage antibody panel, FLAb, and equivalent emerging datasets - to characterize generalization gaps and quantify where federated training delivers measurable lift over public-only baselines.

Cross-Domain Validation: Develop validation strategies that assess model generalization across modalities and formats relevant to antibody developability - IgG vs. bispecific vs. fragment formats, different expression systems, different assay protocols across partners - while respecting partner data boundaries.

Validation Frameworks: Implement temporal-split and sequence-similarity-aware validation protocols that simulate prospective deployment, detect concept drift as partner data accumulates, and surface systematic failure modes across CDR length distributions, germline families, and physicochemical regimes.

Model Design Partnership: Work alongside antibody modeling scientists on architectural and feature choices that have direct validation implications - uncertainty quantification approaches, calibration strategies, structure-aware vs. sequence-only representations, and how predictions from different endpoints should be combined or kept independent.

Statistical Rigor: Design statistically powered validation studies that account for multiple testing across endpoints, hierarchical structure in antibody data (sequences clustered by germline, project, partner), and non-independent observations. Provide honest confidence intervals on reported model performance.

Reproducibility Infrastructure: Build robust MLOps pipelines ensuring complete reproducibility of federated experiments, including versioning of data snapshots, model checkpoints, and hyperparameter configurations.

Performance Profiling: Develop comprehensive performance profiling across germline families, CDR length regimes, framework variants, and property ranges, identifying systematic biases and failure modes that should be communicated to partners.

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 the partner network.

Basic Qualifications

• PhD in Computational Biology, Bioinformatics, Computational Chemistry, Computer Science, Statistics, or related field from an accredited college or university
• Minimum of 4 years of post-PhD experience working with antibody discovery, engineering, or developability data in a biopharmaceutical or related (or we can change to academic)setting
• Demonstrated experience analyzing or modeling data from antibody developability assays (e.g., HIC, AC-SINS, nanoDSF, polyspecificity panels, viscosity, chemical liabilities), evidenced by publications, project work, or thesis
• Hands-on experience with antibody numbering tools (ANARCI or equivalent) and working knowledge of Kabat, Chothia, and IMGT numbering schemes
• Demonstrated experience designing ML validation protocols for biological sequence data, including sequence-similarity-aware splits and held-out test design

Additional Preferences

• Experience fine-tuning protein or antibody language models (e.g., ESM-2, AbLang, IgBERT, AntiBERTa) for property prediction tasks, including self-supervised pretraining on OAS and fine-tuning strategies for low-data developability endpoints
• Working knowledge of sequence liability motifs (Asp isomerization, Met oxidation, deamidation, glycosylation sites in CDRs)
• Strong foundation in experimental design, statistical validation, and hypothesis testing
• Proficiency in data engineering, pipeline development, and automation
• Experience with NVIDIA FLARE or comparable federated learning frameworks (Flower, OpenFL, PySyft)
• Working knowledge of antibody structure prediction tools (AlphaFold-Multimer, IgFold, ABodyBuilder) and how their outputs feed downstream developability models
• Familiarity with public antibody resources - SAbDab, OAS, TAP, Jain panel, FLAb
• Understanding of the manufacturability funnel from discovery through CLD and formulation, and which developability properties gate which stage
• Knowledge of regulatory considerations for AI/ML in pharmaceutical development
• Experience with uncertainty quantification methods (conformal prediction, Bayesian approaches, ensemble disagreement) and calibration assessment
• Proficiency in PyTorch and the modern ML ecosystem (Hugging Face, scikit-learn, RDKit)
• Experience with experiment tracking and model registry tools (MLflow, Weights & Biases)
• Publications on antibody developability prediction, model validation, benchmarking, or reproducibility
• Exceptional attention to detail and commitment to scientific rigor
• Strong technical writing skills for partner-facing model cards and validation reports
• Portfolio mindset balancing rigorous validation with rapid deployment for partner value

This role is based at a Lilly site in Indianapolis, San Francisco, or Boston with up to 10% travel (attendance expected at key industry conferences).

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

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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