chq1155 Claude Opus 4.8 (1M context) commited on
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Remove data files, update citation, drop external download links

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- Delete data/train.csv and data/test.csv (data not distributed)
- Update citation to LMRL Workshop at ICLR 2026 with full author list
- Remove Google Drive placeholder link; checkpoints ship in repo

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Files changed (3) hide show
  1. README.md +7 -12
  2. data/test.csv +0 -0
  3. data/train.csv +0 -0
README.md CHANGED
@@ -21,9 +21,7 @@ pip install -e .
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  ## Data and Checkpoints
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- Download the pretrained checkpoints and data from [Google Drive (TBA)](placeholder_link).
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-
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- Place the files as follows:
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  ```
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  TD3B/
@@ -31,9 +29,6 @@ TD3B/
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  β”‚ β”œβ”€β”€ pretrained.ckpt # Pre-trained MDLM weights
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  β”‚ β”œβ”€β”€ td3b.ckpt # Fine-tuned TD3B model
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  β”‚ └── direction_oracle.pt # Direction Oracle weights
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- β”œβ”€β”€ data/
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- β”‚ β”œβ”€β”€ train.csv # Training set (target-binder pairs)
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- β”‚ └── test.csv # Test set
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  β”œβ”€β”€ scoring/functions/classifiers/
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  β”‚ β”œβ”€β”€ binding-affinity.pt
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  β”‚ β”œβ”€β”€ hemolysis-xgboost.json
@@ -131,11 +126,11 @@ bash run.sh --baseline tds --device cuda:0
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  ```bibtex
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  @inproceedings{
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- cao2026td3b,
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- title={TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation},
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- author={Anonymous},
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- booktitle={Forty-third International Conference on Machine Learning},
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- year={2026},
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- url={https://openreview.net/forum?id=RNuC8Nj6rD}
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  }
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  ```
 
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  ## Data and Checkpoints
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+ The checkpoints ship with this repository. The expected layout is:
 
 
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  ```
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  TD3B/
 
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  β”‚ β”œβ”€β”€ pretrained.ckpt # Pre-trained MDLM weights
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  β”‚ β”œβ”€β”€ td3b.ckpt # Fine-tuned TD3B model
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  β”‚ └── direction_oracle.pt # Direction Oracle weights
 
 
 
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  β”œβ”€β”€ scoring/functions/classifiers/
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  β”‚ β”œβ”€β”€ binding-affinity.pt
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  β”‚ β”œβ”€β”€ hemolysis-xgboost.json
 
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  ```bibtex
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  @inproceedings{
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+ cao2026tdb,
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+ title={{TD}3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation},
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+ author={Hanqun Cao and Aastha Pal and Sophia Tang and Yinuo Zhang and Jingjie Zhang and Pheng-Ann Heng and Pranam Chatterjee},
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+ booktitle={Learning Meaningful Representations of Life (LMRL) Workshop at ICLR 2026},
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+ year={2026},
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+ url={https://openreview.net/forum?id=uMUicLylVp}
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  }
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  ```
data/test.csv DELETED
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data/train.csv DELETED
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