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Marilyn Hayden

@marilynhayden

Senior software engineer at MTSI building CORA, a grounded graph-RAG system for defense documents and missile capability data.

United States

Message

At MTSI, I architected CORA, a grounded, traceable graph-RAG workflow combining embedding retrieval, ArangoDB graph traversal, evidence assembly, and local LLM inference. I built its Streamlit interface and extended the system to a missile capability domain.

At AFRL, I integrated LLMs with AFSIM, JMP, and STORM workflows for scenario generation and data synthesis, reporting a 34% increase in analytic throughput. I also developed campaign-level simulation and trade-space analysis for mission planning.

My computational genomics work at Cleveland Clinic included the analyses underlying figures in a published PTEN study, as well as RNA-seq pipelines and molecular modeling. I’ve also developed bioinformatics and scientific analysis workflows at AFRL, and currently mentor a summer engineering intern at MTSI.

Experience

Work history, roles, and key accomplishments

Current

Senior Software Engineer

Current

MTSI

Jun 2025 - Present (1 year 5 months)

Architected CORA, a graph-RAG workflow with embedding retrieval, ArangoDB graph traversal, evidence assembly, and local LLM inference. Built a comparative retrieval corpus and benchmark workflow, and extended the system to a missile capability domain.

Graph RAG ArangoDB Streamlit LLM Evaluation Precision@K Recall@5 nDCG@5 MRR Maps PyTorch TensorFlow Onnx RHEL Podman

Operations Research Analyst

AFRL Aerospace Systems Directorate

Sep 2023 - Jun 2025 (1 year 9 months)

Integrated LLMs with AFSIM, JMP, and STORM workflows for scenario generation and data synthesis, reporting a 34% increase in analytic throughput. Developed campaign-level simulation and trade-space analysis, and evaluated LLMs for operations research tasks.

LLM Integrations AFSIM JMP Storm Statistical Analysis Machine Learning Operations Research Data Synthesis

Research Biological Scientist

AFRL Air and Space Biosystems Directorate

Jun 2022 - Sep 2024 (2 years 3 months)

Developed pathway enrichment and network modeling modules with 58.7% faster execution and optimized WGS quality assessment for 40.1% faster execution. Integrated Illumina DRAGEN output with custom transcriptomics and variant-analysis workflows.

Pathway Enrichment Analysis Network Modeling WGS DRAGEN Transcriptomics Variant Analysis Multi omics Pipeline Optimization

Associate Research Biological Scientist

AFRL Air and Space Biosystems Directorate

Jun 2020 - Jun 2022 (2 years)

Optimized transcriptomics quality assessment, reducing execution time 75.1%, and built visualizations to diagnose nonviable sequencing runs. Developed wearable-device and omics-based performance classification workflows and designed a MongoDB schema for COVID-19 study data.

Transcriptomics Quality Assessment Visualization Wearable Devices Omics MongoDB R Shiny Data Cleaning Workflow Development

Bioinformatics Consultant

Cleveland Clinic Genomic Medicine Institute

Jun 2016 - Jun 2020 (4 years)

Developed fault-tolerant 10X-based small RNA, miRNA, and total RNA sequencing pipelines and R tools for Linux and IRB-compliant HPC workflows. Applied machine learning and molecular modeling analyses to published PTEN studies and contributed to multiple peer-reviewed publications.