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| <h1 class="u-custom-font u-font-roboto-slab u-text u-text-color-var u-title u-text-2" spellcheck="false"> 🧬 mtDNA Location Classifier</h1> |
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| <h3>Brief System Pipeline and Usage Guide</h3> |
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| <p>The <strong>mtDNA Tool</strong> is a lightweight pipeline designed to help researchers extract metadata such as geographic origin, sample type (ancient/modern), and optional niche labels (e.g., ethnicity, specific location) from mtDNA GenBank accession numbers. It supports batch input and produces structured Excel summaries.</p> |
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| <h3>System Overview Diagram</h3> |
| <p>The figure below shows the core execution flow—from input accession to final output.</p> |
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| src="https://huggingface.co/spaces/VyLala/mtDNALocation/resolve/main/flowchart.png" |
| alt="mtDNA Pipeline Flowchart"> |
| </div> |
| <h3>Key Steps</h3> |
| <ol> |
| <li><strong>Input</strong>: One or more GenBank accession numbers are submitted (e.g., via UI, CSV, or text).</li> |
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| <li><strong>Metadata Collection</strong>: Using <code>fetch_ncbi_metadata</code>, the pipeline retrieves metadata like country, isolate, collection date, and reference title. If available, supplementary material and full-text articles are parsed using DOI, PubMed, or Google Custom Search.</li> |
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| <li><strong>Text Extraction & Preprocessing</strong>: |
| <ul> |
| <li>All available documents are parsed and cleaned (tables, paragraphs, overlapping sections).</li> |
| <li>Text is merged into two formats: a smaller <code>chunk</code> and a full <code>all_output</code>.</li> |
| </ul> |
| </li> |
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| <li><strong>LLM-based Inference (Gemini + RAG)</strong>: |
| <ul> |
| <li>Chunks are embedded with FAISS and stored for reuse.</li> |
| <li>The Gemini model answers specific queries like predicted country, sample type, and any niche label requested by the user.</li> |
| </ul> |
| </li> |
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| <li><strong>Result Structuring</strong>: |
| <ul> |
| <li>Each output includes predicted fields + explanation text (methods used, quotes, sources).</li> |
| <li>Summarized and saved using <code>save_to_excel</code>.</li> |
| </ul> |
| </li> |
| </ol> |
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| <h3>Output Format</h3> |
| <p>The final output is an Excel file with the following fields:</p> |
| <ul> |
| <li><code>Sample ID</code></li> |
| <li><code>Predicted Country</code> and <code>Country Explanation</code></li> |
| <li><code>Predicted Sample Type</code> and <code>Sample Type Explanation</code></li> |
| <li><code>Sources</code> (links to articles)</li> |
| <li><code>Time Cost</code></li> |
| </ul> |
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| <h3>System Highlights</h3> |
| <ul> |
| <li>RAG + Gemini integration for improved explanation and transparency</li> |
| <li>Excel export for structured research use</li> |
| <li>Optional ethnic/location/language inference using isolate names</li> |
| <li>Quality check (e.g., fallback on short explanations, low token count)</li> |
| <li>Report Button – After results are displayed, users can submit errors or mismatches using the report text box below the output table</li> |
| </ul> |
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| <h3>Citation</h3> |
| <div class="highlight"> |
| Phung, V. (2025). mtDNA Location Classifier. HuggingFace Spaces. https://huggingface.co/spaces/VyLala/mtDNALocation |
| </div> |
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| <h3>Contact</h3> |
| <p>If you are a researcher working with historical mtDNA data or edge-case accessions and need scalable inference or logging, reach out through the HuggingFace space or email provided in the repo README.</p> |
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