AI/ML Scientist — Antibody Developability

Socket.dev; California (MO); Hybrid; USD 131,000 - 184,000; Full time

Benefits offered by this job

Company stock awards

Health, dental, vision

401(k) with employer contribution

Paid holidays & PTO

Hybrid work

Job summary

Ginkgo Bioworks in Boston, MA is seeking a Scientist to build and benchmark ML models predicting antibody developability. You will sit between our PROPHET-Ab platform and the models it enables, working with customer datasets and public datasets to drive design campaigns.

The ideal candidate has a PhD, strong applied ML, and interest in protein biophysics, with experience in Python and ML frameworks. Hybrid work arrangement with in-office days.

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 with cross-validation and bias mitigation.
• Knowledge of protein representations, PLM embeddings (ESM, AbLang) and structural featurization.
• Ability to analyze biophysical data with respect to signal-to-noise and dynamic range.
• Excellent communication across multidisciplinary teams and ability to manage concurrent 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 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

PhD holder

Python

ML in biology

PLM embeddings

Cross-validation

Bias mitigation

Education

PhD in Computational Biology

Tools

NumPy

Pandas

PyTorch

TensorFlow

Job description

Ginkgo Bioworks in Boston, MA is seeking a Scientist to build and benchmark ML models predicting antibody developability. You will sit between our PROPHET-Ab platform and the models it enables, working with customer datasets and public datasets to drive design campaigns.

The ideal candidate has a PhD, strong applied ML, and interest in protein biophysics, with experience in Python and ML frameworks. Hybrid work arrangement with in-office days.