AI/ML Scientist for Antibody Developability

Ginkgobioworks; California (MO); Hybrid; USD 131,000 - 184,000; Full time

Benefits offered by this job

Stock awards

Comprehensive benefits

401(k) with employer contribution

Unlimited PTO

Job summary

Ginkgo Bioworks in Boston, MA, invites applications for a Scientist, AI/ML — Antibody Developability to build and benchmark machine learning models predicting antibody developability. The role sits between the PROPHET-Ab platform and data generation, leveraging IgG, VHH-Fc, and bispecific datasets to enable design campaigns.

You will work with biophysical data, implement robust evaluation for small datasets, and communicate findings across multidisciplinary teams.

Qualifications

• Ph.D. in Computational Biology, Bioinformatics, ML, Biophysics, or related quantitative field with emphasis on applied ML.
• Proficiency in Python and the scientific computing stack (NumPy, pandas, PyTorch/TensorFlow).
• Demonstrated experience in supervised learning on biological datasets, including expertise in cross-validation and bias mitigation.
• Knowledge of protein representations, including PLM embeddings (e.g., ESM, AbLang) and structural featurization.
• Ability to analyze biophysical data with respect to signal-to-noise ratios and experimental dynamic range.
• Effective communication across multidisciplinary teams and ability to manage concurrent technical objectives.

Responsibilities

• Develop and validate predictive models for developability using PLM embeddings, structural features, and physicochemical descriptors.
• Implement leakage-aware evaluation frameworks for rigorous performance assessment of small-scale datasets.
• Evaluate cross-format transferability (IgG to VHH-Fc, bispecifics) and deploy data-efficient training strategies.
• Perform rigorous QC on biophysical assay data to identify outliers and maintain high data integrity for modeling.
• Maintain and develop automated pipelines to ensure reproducibility and facilitate technical reporting.
• Disseminate findings through technical reviews, peer-reviewed manuscripts, and external scientific presentations.

Skills

Python

ML on biology

Cross-validation

Protein representations

Signal-to-noise analysis

Team communication

Education

Ph.D. in Computational Biology/Bioinformatics/ML/Biophysics

Tools

NumPy

Pandas

PyTorch

TensorFlow

Job description

Ginkgo Bioworks in Boston, MA, invites applications for a Scientist, AI/ML — Antibody Developability to build and benchmark machine learning models predicting antibody developability. The role sits between the PROPHET-Ab platform and data generation, leveraging IgG, VHH-Fc, and bispecific datasets to enable design campaigns.

You will work with biophysical data, implement robust evaluation for small datasets, and communicate findings across multidisciplinary teams.