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+# GET (Gene Expression Transformer) Implementation Mindmap
+
+## Implementation Status Overview
+- [x] Basic Setup Complete (Repository & Structure)
+- [ ] Data Pipeline Ready
+- [ ] Model Running
+- [ ] Results Validation
+
+## Data Pipeline
+- Input Processing
+  - [ ] Gene expression data preprocessing
+  - [ ] Normalization techniques
+  - [ ] Feature selection
+  - [ ] Batch effect correction
+
+## Model Architecture
+- Transformer-based
+  - [x] Self-attention layers (code available)
+  - [x] Feed-forward networks (code available)
+  - [x] Layer normalization (code available)
+- Gene Expression Specific
+  - [x] Gene-gene interaction modeling (code available)
+  - [x] Pathway integration (code available)
+  - [x] Expression pattern recognition (code available)
+
+## Training Pipeline
+- Data splitting
+  - [ ] Training set preparation
+  - [ ] Validation set preparation
+  - [ ] Test set preparation
+- Loss functions
+  - [x] Expression prediction loss (code available)
+  - [x] Regulatory network loss (code available)
+- Optimization
+  - [x] Learning rate scheduling (code available)
+  - [x] Gradient clipping (code available)
+  - [x] Early stopping (code available)
+
+## Inference Pipeline
+- [ ] Batch processing
+- [ ] Expression prediction
+- [ ] Feature importance analysis
+- [ ] Uncertainty quantification
+
+## Data Requirements
+- Gene Expression Data
+  - [ ] PBMC data processed
+  - [ ] Peak sorting verified (chr1,chr2,chr3 order)
+  - [ ] Count matrix prepared
+  - [ ] Depth check (>3M recommended)
+- Reference Data
+  - [ ] Gene annotation data
+  - [ ] Pathway databases
+  - [ ] Regulatory network information
+
+## Output Processing
+- Analysis Tools
+  - [ ] Expression profile analysis
+  - [ ] Differential expression
+  - [ ] Pathway enrichment
+- Visualization
+  - [ ] Expression heatmaps
+  - [ ] Network visualization
+  - [ ] PCA/t-SNE plots
+
+## Model Evaluation
+- Performance Metrics
+  - [ ] MSE/MAE for expression prediction
+  - [ ] ROC/PR curves for classification
+- [ ] Cross-validation
+- [ ] Benchmarking against baselines