Advisor - Antibody Developability Validation & Benchmarking

Initial Therapeutics, Inc.; Boston (MA); On-site; USD 166,500 - 266,200; Full time

Benefits offered by this job

Company-sponsored 401(k)

Comprehensive health benefits

Bonus eligibility

Job summary

Initial Therapeutics, Inc. is seeking an Advisor/Senior Advisor – Antibody Developability Validation & Benchmarking based in Boston. This role involves validating AI-powered drug discovery models to ensure their trustworthiness in candidate triage.

Applicants should hold a PhD and possess strong experience in antibody developability data analysis, collaborating closely with modeling scientists on architecture and validation. Up to 10% travel is required for industry conferences.

Qualifications

• PhD in a relevant field from an accredited institution.
• Minimum 4 years of experience in antibody discovery or engineering.
• Experience with antibody developability assays.

Responsibilities

• Build a canonical benchmark suite for antibody developability.
• Define multi-endpoint reliability for triage decisions.
• Collaborate on model validation and uncertainty quantification.

Skills

Antibody characterization

Machine learning validation protocols

Data engineering

Statistical validation

Technical writing

Education

PhD in Computational Biology, Bioinformatics, or related

Tools

PyTorch

NVIDIA FLARE

Job description

Lilly is a global healthcare leader headquartered in Indianapolis, Indiana. We discover and bring life‑changing medicines to help people around the world.

Organization Overview

We make a difference for people around the world by discovering, developing, and delivering medicines that help individuals live longer, healthier, and more active lives. We also 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 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. This validation‑led role requires deep understanding of antibody characterization, developability determinants, and how predictions from a federated model translate into go/no‑go decisions in the discovery pipeline.

The role 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

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.

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.

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.

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.

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.

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.

Design statistically powered validation studies that account for multiple testing across endpoints, hierarchical structure in antibody data, and non‑independent observations. Provide honest confidence intervals on reported model performance.

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

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.

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 a related field from an accredited institution.
• Minimum of 4 years of post‑PhD experience working with antibody discovery, engineering, or developability data in a biopharmaceutical or 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, including attendance at key industry conferences.

We support individuals with disabilities to actively engage in the workforce. If you require accommodation to submit a resume, please complete the accommodation request form: https://careers.lilly.com/us/en/workplace-accommodation.

We are an EEO employer and do 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.

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is $166,500 – $266,200.

Full‑time equivalent employees 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 such as 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 such as 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.