Senior Systems Engineer – Clinical NLP Research Support
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Job Description
Senior Systems Engineer developing NLP and LLM pipelines for VA EHR data. Supporting gene-by-environment suicide-risk research using Million Veteran Program records.
Responsibilities:
- Develop methods and infrastructure and refine NLP and LLM approaches to identify predictor variables for suicidal thoughts and behaviors in VA EHR clinical notes
- Build and maintain custom tokenization and text-processing pipelines operating at population scale across the Million Veteran Program cohort
- Extract and validate phenotypes including suicidal ideation, suicide attempts, and related exposures for gene-by-environment analyses
- Prepare, document, and transfer analysis-ready datasets to the study's statistical genetics team
- Manage code version control, testing, documentation, and reproducibility within the VA research computing environment
- Ensure compliance with VA privacy and information security requirements for PHI and PII
- Troubleshoot pipeline performance, scalability, and data quality issues and implement improvements
- Coordinate with the Principal Investigator and study team and provide progress updates against project milestones
- Prepare technical documentation, workflow documentation, and handoff materials
Requirements:
- Bachelor's degree in computer science, engineering, data science, informatics, or a related technical field
- 8+ years of experience in computer systems engineering, software development, data engineering, or technical implementation
- Experience with AI/SI methods development, including developing LLM models, for EHR text evaluation within a federal research environment
- Experience with the technical lifecycle of this type of research, including custom tokenization and population-scale work
- Experience with programming and data pipeline development
- Experience working with PHI and PII in accordance with VA privacy and security requirements
- Ability to work independently in a part-time, remote role while meeting project deadlines
- Ability to communicate effectively with technical and research stakeholders
- Ability to obtain and maintain a public trust clearance
- Legal authorization to work in the United States
- Significant experience developing NLP or LLM methods for VA
- Experience supporting research studies, particularly in genomics, and familiarity with programs like the Million Veteran Program
- Experience with transformer-based models, model fine-tuning, or custom tokenizer development
- Experience developing or validating computable phenotypes, including chart review or annotation workflows
- Experience with GPU-based or high-performance computing environments
- Familiarity with mental health or suicide prevention research
- Experience with version control, technical documentation, and reproducible workflows
- High degree of professionalism, discretion, and mature judgment in handling sensitive information
- Ability to perform the stated physical requirements, including extended sitting, computer use, verbal and written communication, and occasional standing, walking, bending, or lifting up to 15 pounds
Benefits:
- Part-time schedule of 20 hours per week
- 100% remote position
- Potential contract extension into the next option year based on contract continuation and program needs
- Opportunity to support a Department of Veterans Affairs research study and contribute to suicide prevention research
- Potential to work with population-scale Million Veteran Program data and clinical NLP/LLM methods
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