Senior Machine Learning Engineer

Protagonist Therapeutics; Washington (District of Columbia); On-site; USD 95,000 - 141,000; Full time

Job summary

Protagonist Therapeutics is seeking a Senior Machine Learning Engineer who builds production-ready systems for mission-critical work. You bring strong engineering discipline, systems thinking, and a bias toward scalable, well-architected solutions—owning the full ML lifecycle from design to deployment.

You'll collaborate with product, engineering, and client-facing teams to expand AI at Protagonist, stay current with advances in ML and infra, and ensure compliance with GovCloud/ITAR constraints.

Qualifications

• Must have deep NLP expertise (transformers, LLMs, embeddings) and proven ability to deploy production ML systems.
• Strong Python skills; fluency with PyTorch and the Hugging Face ecosystem.
• Experience with AWS, Kubernetes, Docker, Terraform, and CI/CD pipelines;ML orchestration/experiment tracking.

Responsibilities

• Identify high-impact NLP use cases with product/engineering/data science teams and translate business needs into ML solutions.
• Own production NLP pipelines: narrative detection, NER, span classification, stance and characterization analysis, event extraction, deduplication.

Skills

NLP expertise

Python

ML deployment

Education

Bachelor's degree in Computer Science or related field

Master's degree in Computer Science or related field

Tools

PyTorch

Hugging Face

AWS GovCloud

Kubernetes

Docker

Terraform

CI/CD

Metaflow

Argo Workflows

MLflow

OpenSearch

Django

REST APIs

React

Job description

Join Our Talented Team at Protagonist

We fuse rigorous, methodologically sound analysis with our cutting-edge technology platform, Narrative Analytics®. This powerful combination enables us to quantitatively analyze open-source media, deliver strategic recommendations, and craft executive-level communication strategies for clients with missions that matter.

Why Us?

Our team is a vibrant mix of communication specialists, data scientists, and subject matter experts with extensive experience across U.S. Government agencies, non-profit organizations, and Fortune 500 companies. By joining Protagonist, you'll immerse yourself in a collaborative environment where innovation thrives, and your contributions truly matter.

What We Do

• Innovative Solutions: We co-develop cutting-edge solutions with our clients to address tough communication problems and capitalize on opportunities to make a tangible impact.
• Data-Driven Insights: Our tools and methodologies provide actionable insights that help clients meet their communication objectives and stay ahead of global challenges.
• Applied Expertise: We integrate our solutions within client organizations, leveraging our profound expertise to address critical issues and ensure sustainable success.

Be Part of Something Bigger

At Protagonist, you'll work on compelling projects that make a real difference. We seek talented individuals eager to contribute to our mission and grow alongside us. If you're passionate about communication, data analysis, and making an impact, we invite you to explore a career with Protagonist.

Explore Your Future with Us!

Job Description

Protagonist is looking for a Senior Machine Learning Engineer who builds production-ready systems for mission-critical work. You bring strong engineering discipline, systems thinking, and a bias toward scalable, well-architected solutions-owning the full ML lifecycle from design to deployment.

You're a builder and strategic partner across engineering, product, and client-facing teams, expanding what AI can do at Protagonist. You stay curious and current with advances in ML, infrastructure, and software development.

Responsibilities

• Partner with product, engineering, and data science teams to identify high-impact NLP use cases and turn business needs into ML solutions that deliver measurable value
• Own production NLP pipelines spanning narrative detection, NER, span classification, stance and characterization analysis, event extraction, deduplication, and knowledge-base entity linking over multi-language, noisy real-world text
• Design, build, and operate production NLP pipelines, narrative detection, event classification, entity resolution and linking, deduplication - over multi-language, noisy real-world text at scale
• Build and maintain ML workflows in Metaflow orchestrated on Argo Workflows and Kubernetes (EKS), including GPU-accelerated training and batch inference
• Develop LLM-powered features on AWS Bedrock: RAG pipelines with vector search on OpenSearch, tool-using agents, and document-analysis workflows - within GovCloud/ITAR constraints
• Fine-tune and deploy transformer models (classification, embeddings, entity linking) for domain-specific and foreign-language content
• Establish ML evaluation frameworks regression testing, hallucination detection, quality metrics and define success criteria with product managers
• Integrate ML services into our 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, share knowledge, and help evolve ML practices - balancing innovation with practical delivery

Requirements

• U.S. person eligible to work on government contracts; active or prior SECRET clearance preferred
• Bachelor's and 5 years of experience, or master's degree and 3 years of experience, in Computer Science, Machine Learning, or a related technical field
• Proven track record building and deploying production ML systems, with deep NLP expertise (transformers, LLMs, embedding models)
• Strong Python skills and fluency with PyTorch and the Hugging Face ecosystem
• Hands-on experience with AWS (GovCloud experience a strong plus), Kubernetes, Docker, Terraform, and CI/CD pipelines
• Experience with ML orchestration and experiment tracking (e.g., Metaflow, Argo Workflows, MLflow, or similar)
• Experience with vector search and document indexing (OpenSearch/Elasticsearch or similar)
• Experience building LLM applications, RAG, agents, prompt engineering, and evaluation
• Skilled at scaling ML for multi-modal (text, image, video) and domain-specific applications, and working effectively across engineering, product, and business teams

Ideal Candidates

• Experience integrating ML into full-stack products (Django/REST APIs, React frontends) or decision-support tools
• Experience operating in compliance-constrained environments
• Strong communicator and cross-functional collaborator
• Self-starter who thrives in ambiguity and startup-like environments

Protagonist is an Equal Opportunity Employer.

Salary Range: $95,000-$141,000 based on education and level of relevant experience.

Pursuant to the San Francisco Fair Chance Ordinance, we will consider for employment qualified applicants with arrest and conviction records.