Spaces:
Sleeping
A newer version of the Gradio SDK is available:
6.9.0
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
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.