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David Nicholson
dnicholson329@gmail.com • 412-607-6313 • Lansdowne, PA (Open to Remote)
Summary
Data Scientist experienced in architecting machine learning workflows, fine-tuning LLMs, and managing multi-tenant database systems. Adept at bridging technical data engineering with business decision-making through interactive dashboards, automated metadata pipelines, and production-ready NLP models.
Skills & Proficiency
- Machine Learning & NLP: PyTorch, TensorFlow, Scikit-Learn, Transformers, Large Language Models (Claude, Gemini, Ollama), Clustering (HDBSCAN, K-Means), Dimensionality Reduction (UMAP), Document Embeddings, Knowledge Graphs, Entity Resolution, Text Mining and Extraction, Automatic Metadata Extraction, Weak Supervision (Snorkel)
- Data Engineering & Systems: Google Bigquery, PostgreSQL, ETL/ELT Pipelines, Parallel Processing (Dask), Linux Server Maintenance
- Dashboards & Visualization: Plotly/Dash, Seaborn/Matplotlib, Web Applications (Flask/FastAPI)
- Core Infrastructure: Python, SQL, Git, Docker, CI/CD, AWS/GCP
Professional Experience
Data Scientist
Digital Science & Research Solutions, Ltd.
June 2022 - Present
- LLM & Automated Annotation: Constructed an LLM-backed document metadata and labeling pipeline to automatically fetch, categorize and summarize clusters across multiple document types for United States Federal Research Funding Agencies and Institutes.
- Vector Databases & Scalable Search: Conducted benchmarking across enterprise vector databases to optimize query latency and storage efficiency for 10M+ high-dimensional document vectors.
- ETL & Big Data Engineering: Engineered automated ETL pipelines to extract external unstructured web/literature data alongside secure ingestion and processing of HHS-affiliated client’s data using Python and SQL. Also, maintained and modified other ETL pipelines for processing 100GB+ of unstructured literature data.
- Dashboards & Reporting: Built interactive dashboards (Plotly/Streamlit) for internal use to explore dynamic topic clusters, research trends, and growth metrics in real time.
Graduate Researcher Scientist
University of Pennsylvania
August 2016 - June 2022
- Large-Scale NLP & Computational Modeling: Designed and deployed unsupervised NLP frameworks (Word2Vec, FastText) to analyze over 20,000 temporal semantic shifts across millions of unstructured scientific documents.
- Pipeline Engineering & Big Data: Built automated, parallelized Python pipelines to ingest, clean, and analyze multi-gigabyte genomic and textual datasets, reducing data processing bottlenecks by over 40%.
- Statistical Modeling & Algorithm Optimization: Applied high-dimensional dimensionality reduction (UMAP) and clustering algorithms (K-Means) to extract hidden patterns in complex biological networks.
- Cross-Functional Collaboration & Technical Communication: Collaborated with cross-departmental teams of bioinformaticians, software engineers, and domain experts; presented complex quantitative findings to non-technical stakeholders and external partners.
- Software Development & Maintainability: Maintained open-source codebase repositories on GitHub using strict version control (Git/GitHub), unit testing, and Docker containerization.
Publications
- Unmasking The Language Of Science Through Textual Analyses On Biomedical Preprints And Published PapersOn Biomedical Preprints And Published Papers
Nicholson, D. N. (2022) - Changing Word Meanings in Biomedical Literature Reveal Pandemics and New Technologies
Nicholson, D. N. Alquaddoomi, F., Rubinetti, V., Greene, C. S. (2023) - Characterization of the Genome and Silk-gland Transcriptomes of Darwin’s Bark Spider (Caerostris darwini)
Babb, P. L., Gregorič, M., Lahens, N. F.,Nicholson, D. N., Hayashi, C. Y., Higgins, L., Kuntner, M., Agnarsson, I., Voight, B. F. (2022) - Examining Linguistic Shifts between Preprints and Publications
Nicholson, D. N., Rubinetti, V., Hu, D., Thielk, M., Hunter, L. E., Greene, C. S. (2022) - Expanding a Database-derived Biomedical Knowledge Graph via Multi- Relation Extraction from Biomedical Abstracts
Nicholson, D. N., Himmelstein, D. S., Greene, C. S. (2022) - Ten important roles for academic leaders to promote equity, diversity, and inclusion in data science.
Moore JH, Truong VQ, Robbins AB, Nicholson D. N., Williams-Devane CL. (2021) - Constructing Knowledge Graphs and Their Biomedical Applications
Nicholson, D. N., Greene, C. S. (2020) - The Nephila Clavipes Genome Highlights the Diversity of Spider Silk Genes and their Complex Expression
Babb, P. L., Lahens, N. F., Correa-Garhwal, S. M., Nicholson, D. N., Kim, E.J., Hogenesch, J.B., Kuntner, M., Higgins, L., Hayashi, C. Y., Agnarsson, I., Voight, B.F. (2017)
Education
Doctor of Philosophy (Ph.D.), Genomics and Computational Biology; University of Pennsylvania (Philadelphia, PA)
Postbaccalaureate Program (Penn Prep); University of Pennsylvania (Philadelphia, PA)
Bachelor of Science, Computer Science; University of Maryland Baltimore County (Baltimore, MD)