Applied ML Scientist II - Protein Engineering (Remote)

A-Alpha Bio; Seattle (WA); Remote; USD 139,000 - 175,000; Full time

Job summary

A-Alpha Bio in Seattle, WA is seeking a Scientist II to join the Applied Machine Learning team, turning large-scale protein interaction data into insights and models for antibody and protein engineering. You will lead computational work, connect measurements with sequence/structure data, and guide future experiments.

Remote-eligible with quarterly travel to Seattle HQ, reporting to the Director of Applied Machine Learning.

Qualifications

• PhD in a relevant field with 2+ years of data analysis on biological sequence or structure data; or a BA/BS with 10+ years of relevant experience (5+ years on large-scale data).
• Proven Python expertise for scientific computing, data analysis, visualization, and ML.
• Experience analyzing large experimental datasets and making defensible data-quality decisions.
• Strong understanding of model evaluation, baselines, data leakage, and benchmarking limitations.
• Ability to translate questions into executable plans and deliver reproducible results with limited supervision.
• Clear communication of methods, findings and limitations to computational and experimental audiences.
• Experience contributing to a shared codebase via version control and documentation.

Responsibilities

• Lead analyses of large-scale protein interaction datasets (often 1M PPIs) including binding affinity and specificity.
• Develop, train and evaluate ML models using experimental measurements, sequences and structural data.
• Collaborate with experimental scientists to shape study designs and interpret results.
• Deliver clear presentations and well-documented datasets for internal and external partners.
• Build reusable analytical tools and workflows; contribute to a maintainable Python codebase.

Skills

Python for scientific computing

Data analysis

ML model development

Communication

Version control

Education

PhD in a relevant field

Bachelor's with 10+ years experience

Tools

PyTorch

TensorFlow

Hugging Face

Git

Job description

A-Alpha Bio in Seattle, WA is seeking a Scientist II to join the Applied Machine Learning team, turning large-scale protein interaction data into insights and models for antibody and protein engineering. You will lead computational work, connect measurements with sequence/structure data, and guide future experiments.

Remote-eligible with quarterly travel to Seattle HQ, reporting to the Director of Applied Machine Learning.