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lespernater/README.md

Hi ๐Ÿ‘‹

I'm Nate โ€” AI engineer and bioinformatics researcher specializing in machine learning and intelligent systems for ecological and genomic analysis.


Programming Languages:

Python R Bash SQL

Development & Tooling

Git HPC uv Docker

Artificial Intelligence and Machine Learning:

PyTorch TensorFlow HuggingFace scikit-learn OpenAI Anthropic

Scientific Computing and Bioinformatics:

NumPy pandas Biopython Bioconductor Nextflow matplotlib ggplot2

Data Engineering and Web:

FastAPI SQLite Streamlit Flask Quarto


Work I Enjoy

๐Ÿ”ญ Building agentic AI systems and custom MCP servers for scientific data analysis

๐Ÿงฌ Developing deep learning architectures for multi-omics research in medicine and biodiversity

๐ŸŒฑ Exploring the intersection of machine learning, genomics, and biodiversity informatics

๐Ÿ“Š Creating tools that democratize sophisticated data analysis for domain experts


Recent Highlights

MCP Server & Agentic AI Systems Development - Custom Model Context Protocol server connecting LLMs to 40M+ phenology observations; Autonomous agentic data analysis workflows in phenology - Vector Institute & USA National Phenology Network

Deep Learning for Genomics - Novel deep learning architecture achieving improved accuracy for viral detection in metagenomic sequences compared to Kraken2 - CFIA (GigaScience, Aug 2025)

Vision-Language Models + RAG - Taxonomic classification for rare arthropod species pairing image captioning with RAG - MLRG, CBG & ABC (Canadian AI Conference, May 2025)


Past Collaborations

  • University of Guelph's Machine Learning Research Group (MLRG)
  • Vector Institute for Artificial Intelligence
  • USA National Phenology Network (USA-NPN)
  • Canadian Food Inspection Agency (CFIA)
  • Centre for Biodiversity Genomics (CBG)
  • AI and Biodiversity Change Global Centre (ABC)

๐Ÿ“ซ Email ๐Ÿ’ผ LinkedIn

Pinned Loading

  1. uoguelph-mlrg/taxonomic-rag-system uoguelph-mlrg/taxonomic-rag-system Public

    Code for "Taxonomic Reasoning for Rare Arthropods: Combining Dense Image Captioning with RAG for Interpretable Classification" - proceedings of the 38th Canadian Conference on Artificial Intelligence

    Python

  2. VectorInstitute/usa-npn-mcp-server VectorInstitute/usa-npn-mcp-server Public

    Model Context Protocol server for USA-NPN Data Web Service API

    Python 4

  3. VectorInstitute/agent-bootcamp VectorInstitute/agent-bootcamp Public

    Reference Implementations for the Agentic AI bootcamp

    Python 24 105