Senior ML Engineer - Protein Design Platform

Profluent Bio; Emeryville (CA); On-site; USD 200,000 - 330,000; Full time

Benefits offered by this job

Health insurance

Dental insurance

Vision insurance

401(k) with employer match

Generous PTO

Professional development

Job summary

Profluent Bio in Emeryville, CA is hiring an experienced Machine Learning Engineer to build and optimize large-scale generative models for protein design. You will own ML stack, pipelines, and infrastructure, enabling scientists to work faster and with confidence.

Ideal candidates have 3+ years of PyTorch experience, strong Python, and cloud/containerization skills, plus a drive to ship reliable, scalable ML systems across multi-cloud environments.

Qualifications

• BS or MS in Computer Science, Machine Learning, or a related field.
• 3+ years of hands-on experience building and training ML models in PyTorch.
• Strong Python and software engineering fundamentals including testing, code quality, and version control.
• Experience profiling, benchmarking, and optimizing ML model training and inference.
• Experience implementing or optimizing transformer-based architectures.
• Familiarity with cloud infrastructure and containerization (GCP, AWS, Azure, Kubernetes, Docker).
• Strong fundamentals in ML, statistics, and/or linear algebra.

Responsibilities

• Build robust, reproducible and user-friendly pipelines for automated model fine-tuning, alignment and evaluation.
• Design and implement modular, easy-to-maintain, multi-model pipelines for protein design.
• Develop highly scalable ETL pipelines to process petabyte-scale protein data for model pretraining.
• Optimize model training and inference code to maximize throughput and resource utilization when deployed at scale.
• Develop software and infrastructure that enable the ML team to work quickly and frictionlessly in distributed and multi-cloud environments.
• Partner with ML and protein design scientists to prototype research ideas and bring them into production.

Skills

PyTorch

Python

Cloud computing

Kubernetes

Docker

Transformer models

Performance profiling

Education

BS/MS in CS/ML

Tools

Git

Job description

Profluent Bio in Emeryville, CA is hiring an experienced Machine Learning Engineer to build and optimize large-scale generative models for protein design. You will own ML stack, pipelines, and infrastructure, enabling scientists to work faster and with confidence.

Ideal candidates have 3+ years of PyTorch experience, strong Python, and cloud/containerization skills, plus a drive to ship reliable, scalable ML systems across multi-cloud environments.