Update README.md

README.md

@@ -32,3 +32,75 @@ configs:
   - split: test
     path: data/test-*
 ---
+
+
+
+## Background
+
+### What is Protein Contact Prediction?
+
+Protein contact prediction is a fundamental task in computational biology that aims to predict which amino acid residues in a protein sequence are in close spatial proximity (typically within 8Å) in the protein's 3D structure. This information is crucial for:
+
+- **Protein structure prediction**
+- **Understanding protein folding mechanisms**
+- **Drug discovery and design**
+- **Evolutionary analysis**
+
+### Linear Probing for Protein Language Models
+
+Linear probing is a technique used to evaluate the quality of learned representations from pre-trained language models. In the context of protein language models (PLMs):
+
+1. **Freeze** the pre-trained model parameters
+2. **Train** only a simple linear classifier on top of the frozen embeddings
+3. **Evaluate** how well the linear classifier performs on downstream tasks
+
+This approach helps assess the quality of protein representations learned by different PLMs without the confounding effects of fine-tuning the entire model.
+
+
+
+## Task Definition
+
+### Contact Map Generation
+
+| Parameter | Value | Description |
+|-----------|--------|-------------|
+| **Distance Threshold** | 8.0 Å | Distance between Cα atoms |
+| **Sequence Separation** | ≥ 6 residues | Minimum separation (\|i-j\| ≥ 6) |
+| **Valid Contacts** | Required | Only consider residues with valid 3D coordinates |
+
+### Evaluation Metrics
+
+The evaluation follows standard contact prediction protocols with precision at different coverage levels:
+
+#### Range Categories
+
+| Range | Separation | Description |
+|-------|------------|-------------|
+| **Short Range** | 6 ≤ \|i-j\| ≤ 11 | Local contacts |
+| **Medium Range** | 12 ≤ \|i-j\| ≤ 23 | Medium-distance contacts |
+| **Long Range** | \|i-j\| ≥ 24 | Long-distance contacts |
+
+#### Precision Metrics
+
+- **P@L**: Precision at top L contacts (L = sequence length)
+- **P@L/2**: Precision at top L/2 contacts
+- **P@L/5**: Precision at top L/5 contacts
+
+Each metric is calculated separately for each range category, resulting in **9 total metrics** per evaluation.
+
+
+
+### Dataset Format
+
+The system uses HuggingFace datasets with entries containing:
+
+```json
+{
+    "seq": "MKTFFVLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFL",
+    "tertiary": [[x1,y1,z1], [x2,y2,z2], ...],
+    "valid_mask": [true, true, false, ...]
+}
+```
+
+**Default Dataset**: `fredzzp/contact_data` (automatically downloaded from HuggingFace Hub)
+