Senior ML Engineer: Production NLP & LLM Pipelines

Peptide Atlas; Washington (Washington County); On-site; USD 95,000 - 141,000; Full time

Benefits offered by this job

Healthy team culture

Job summary

Protagonist is seeking a Senior Machine Learning Engineer to build production-ready NLP systems for mission-critical work. You will own the full ML lifecycle from design to deployment, partnering with product, engineering, and client-facing teams to expand what AI can do at Protagonist.

You will develop scalable pipelines spanning narrative detection, NER, event classification, and knowledge-base linking, using Metaflow, Argo, and Kubernetes, with RAG features on AWS Bedrock within GovCloud

Qualifications

• Bachelor's degree in Computer Science, Machine Learning, or related field with 5+ years experience, or master's with 3+ years.
• Proven track record deploying production ML systems with deep NLP expertise.
• Strong Python skills with PyTorch and Hugging Face.

Responsibilities

• Partner with product, engineering, and data science to identify high-impact NLP use cases.
• Own production NLP pipelines including narrative detection, NER, span classification, stance and analysis.
• Design, build, operate pipelines at scale multi-language noisy real-world text.
• Build ML workflows with Metaflow on Argo and Kubernetes (EKS) with GPU training.
• Develop LLM-powered features on AWS Bedrock: RAG pipelines with vector search on OpenSearch, agents.
• Fine-tune and deploy transformer models for domain-specific content.
• Establish ML evaluation frameworks and success criteria with product managers.
• Integrate ML services into Django/PostgreSQL platform and event-driven infrastructure (Kafka, Redis, OpenSearch).
• Lead technical discussions to align cross-functional teams on ML strategy, architecture, and implementation.
• Mentor others and balance innovation with practical delivery.

Skills

NLP expertise

Python

PyTorch

Hugging Face

AWS GovCloud

Kubernetes

Docker

CI/CD

Communication

Mentoring

Education

Bachelor's degree in CS/ML

Master's degree in CS/ML

Tools

Metaflow

Argo Workflows

OpenSearch

Elasticsearch

MLflow

Terraform

Kafka

Redis

Django

REST APIs

Job description

Protagonist is seeking a Senior Machine Learning Engineer to build production-ready NLP systems for mission-critical work. You will own the full ML lifecycle from design to deployment, partnering with product, engineering, and client-facing teams to expand what AI can do at Protagonist.

You will develop scalable pipelines spanning narrative detection, NER, event classification, and knowledge-base linking, using Metaflow, Argo, and Kubernetes, with RAG features on AWS Bedrock within GovCloud