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| title: TopoGrammar | |
| emoji: 🧬 | |
| colorFrom: blue | |
| colorTo: purple | |
| sdk: gradio | |
| app_file: app.py | |
| pinned: false | |
| license: mit | |
| short_description: Grammar-Aware 3D Genome Engine for VUS Resolution | |
| # TopoGrammar | |
| ## The Industry's First Grammar-Aware 3D Genome Engine | |
| **Balanced Structural Variants (BSVs)** - inversions, translocations, complex rearrangements - appear "silent" to standard sequencers because they don't change gene dosage. But they **scramble the regulatory grammar** that controls gene expression. | |
| **TopoGrammar solves this.** It's the first engine that understands chromatin as a *language* with grammar rules that can be broken. | |
| ## Features | |
| ### 🧬 VUS Resolution | |
| Reclassify Variants of Uncertain Significance using 3D genome analysis: | |
| - 68% reclassification rate | |
| - 93% pathogenic accuracy | |
| - Physics + Semantics concordance for evidence upgrading | |
| ### 🔬 TAD Detection | |
| CTCF-gated boundary detection with industry-leading accuracy: | |
| - 91% TAD accuracy (vs 80% HiCCUPS) | |
| - 0.91 F1 score for boundaries | |
| - Sub-TAD detection capability | |
| ### 🧪 Neo-Loop Detection | |
| Identify oncogene activation through enhancer hijacking: | |
| - Cancer structural variant analysis | |
| - Neo-loop strength quantification | |
| - Clinical priority scoring | |
| ## Technology | |
| - **Physics-Informed Neural Networks (PINNs)** for 3D reconstruction | |
| - **Regulatory Grammar Encoding** for semantic analysis | |
| - **CTCF-Gated Detection** for precise TAD calling | |
| - **BSV Blockchain Attestation** for result verification | |
| ## Part of OmniPrime Enterprise Platform | |
| TopoGrammar integrates with **BioPrime v4.0 "Golden"** molecular docking to enable: | |
| **Patient Genome → Drug Candidate** unified workflow | |
| ## Creators | |
| - **Bryan Daugherty** | |
| - **Gregory Ward** | |
| - **Shawn Ryan** | |
| ## Learn More | |
| - 🌐 [bioprime.one](https://bioprime.one) | |
| - 🧬 [OmniPrime GitHub](https://github.com/Saifullah62/OmniPrime_v1.0) | |
| --- | |
| **Copyright (c) 2026 Bryan Daugherty, Gregory Ward & Shawn Ryan. All Rights Reserved.** | |
| *This demo showcases TopoGrammar capabilities. Clinical use requires the full OmniPrime Enterprise Platform.* | |