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README.md

@@ -11,9 +11,9 @@ tags:
 pipeline_tag: feature-extraction
 ---
 
-# DQFormer Encoder (Stage 1)
+# EDT-Former Encoder (Stage 1)
 
-The pretrained **DQ-Former encoder** from EDT-Former, as described in the ICLR 2026 paper:
+The pretrained **EDT-Former encoder** from the ICLR 2026 paper:
 
 > **Entropy-Guided Dynamic Tokens for Graph-LLM Alignment in Molecular Understanding**
 > Zihao Jing, Qiuhao Zeng, Ruiyi Fang, Yan Sun, Boyu Wang, Pingzhao Hu
@@ -21,10 +21,10 @@ The pretrained **DQ-Former encoder** from EDT-Former, as described in the ICLR 2
 
 ## Model Description
 
-The DQ-Former encoder is a Dual Q-Former that bridges molecular graphs and language. It uses:
+The EDT-Former encoder is a Dual Q-Former that bridges molecular graphs and language. It uses:
 - **Entropy-guided dynamic token selection** to focus on informative molecular patches
 - **BRICS fragment IDs** for substructural awareness
-- **Cross-attention over graph node features** to generate a variable-length token sequence aligned with text
+- **Cross-attention over graph node features** to generate a token sequence aligned with text
 
 This Stage 1 checkpoint (~699 MB) is trained on the PubChem pretraining corpus and is used to initialize Stage 2 (full model) training.
 
@@ -41,16 +41,15 @@ Use this checkpoint as the Stage 1 initialization for Stage 2 fine-tuning:
 
 ```yaml
 # configs/stage2_dqw2d/model_config.yaml
-stage1_path: path/to/DQFormer-encoder/model.safetensors
+stage1_path: path/to/EDT-Former-encoder/model.safetensors
 ```
 
-Or load directly:
+Or download and use directly:
 
 ```python
-# First clone the repo and install dependencies (see github.com/selmiss/DQ-Former)
-from models.edt_former import EDTFormerEncoder
+from huggingface_hub import snapshot_download
 
-encoder = EDTFormerEncoder.from_pretrained("zihaojing/DQFormer-encoder")
+snapshot_download("zihaojing/EDT-Former-encoder", local_dir="checkpoints/edt_former_s1_large/final_model")
 ```
 
 To reproduce Stage 1 training from scratch:
@@ -64,9 +63,9 @@ bash scripts/training/pretraining.sh
 
 | Resource | Link |
 |----------|------|
-| Pretrain Data | [zihaojing/DQFormer-pretrain-data](https://huggingface.co/datasets/zihaojing/DQFormer-pretrain-data) |
-| SFT Data | [zihaojing/DQFormer-sft-data](https://huggingface.co/datasets/zihaojing/DQFormer-sft-data) |
-| Full Model (Stage 2) | [zihaojing/DQFormer-model](https://huggingface.co/zihaojing/DQFormer-model) |
+| Pretrain Data | [zihaojing/EDT-Former-pretrain-data](https://huggingface.co/datasets/zihaojing/EDT-Former-pretrain-data) |
+| SFT Data | [zihaojing/EDT-Former-sft-data](https://huggingface.co/datasets/zihaojing/EDT-Former-sft-data) |
+| Full Model (Stage 2) | [zihaojing/EDT-Former-model](https://huggingface.co/zihaojing/EDT-Former-model) |
 | Code | [selmiss/DQ-Former](https://github.com/selmiss/DQ-Former) |
 
 ## Citation