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+# MutationPredictor-CNN v4
+
+## Overview
+
+MutationPredictor-CNN v4 is a sequence-based convolutional neural network designed to predict pathogenicity of genomic variants with splice-awareness.
+
+The model uses:
+
+- 401 bp genomic window (GRCh38)
+- One-hot encoded forward and reverse complement sequence
+- Positional encoding
+- Canonical splice motif features (GT/AG)
+- Explicit mutation type encoding (12 SNV classes)
+- Auxiliary region and splice feature embeddings
+
+This model is trained on ClinVar-derived labeled splice-impact variants.
+
+---
+
+## Architecture
+
+Input Features:
+- 11-channel sequence encoding
+- 12-dim mutation one-hot encoding
+- 2-dim region embedding
+- 3-dim splice embedding
+
+Model:
+
+Conv1d(11 → 64, kernel=7)  
+Conv1d(64 → 128, kernel=5)  
+Conv1d(128 → 256, kernel=3)  
+AdaptiveAvgPool1d(1)
+
+Fully connected layers:
+- 312 → 128
+- 128 → 64
+- 64 → 1 (logit output)
+
+Activation: ReLU  
+Regularization: Dropout(0.3)  
+Loss: BCEWithLogitsLoss  
+
+---
+
+## Training Details
+
+- Genome build: GRCh38
+- Window size: 401 bp
+- Optimizer: Adam
+- Learning rate: 0.001
+- Epochs: 30
+- Batch size: 256
+
+Best model selected by highest training AUC.
+
+---
+
+## Evaluation
+
+### Internal (ClinVar-derived)
+AUC ≈ 0.97
+
+### External Benchmark – SpliceAI Comparison (1000 variants)
+AUC ≈ 0.91
+
+### Strict Fair Benchmark (134 variants not seen in training context)
+AUC ≈ 0.54
+
+### Fair Benchmark by Consequence
+
+| Variant Type        | Count | AUC  |
+|---------------------|-------|------|
+| Splice Donor        | 37    | 0.53 |
+| Splice Acceptor     | 34    | 0.51 |
+| Other Consequences  | 63    | 0.61 |
+
+---
+
+## Known Limitations
+
+- Trained primarily on ClinVar-labeled variants
+- Limited indel generalization
+- 401 bp receptive field (short-range context)
+- Not validated for clinical decision-making
+- Research-use only
+
+---
+
+## Intended Use
+
+This model is intended as:
+
+- Research tool
+- Variant prioritization support
+- Experimental splice-aware classifier
+
+Not intended for direct clinical decision-making.
+
+---
+
+## Future Directions
+
+- Expand receptive field (>2kb)
+- Dilated convolutions
+- Transformer-based architecture
+- Multi-task pathogenicity + splice scoring
+- Larger independent external validation
+
+---
+
+## License
+
+Research use only.
+
+---
+
+## Author
+
+Nilesh Hanotia