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PROTAC-Splitter-EncoderDecoder-lr_reduce-rand-smiles-train-0.75
ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-rand-smiles-train-0.75
PROTAC-Splitter-EncoderDecoder-lr_reduce-rand-smiles-train-0.75 is a machine learning model from ailab-bio. Use it for the machine learning task on the model card, and read the license before you ship it in a product. It is set up for transformers. The card lists the license as mit.
should probably proofread and complete it, then remove this comment. --
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At a glance
- Library
- transformers
- License
- mit
- Model type
- encoder-decoder
- Access
- Public
- Created
- Mar 14, 2025
- Updated
- Mar 14, 2025
- SHA
- 891decad
Base models
Model card
From the Hugging Face model README
<!-- This model card has been generated automatically according to the information the Trainer had access to. You
should probably proofread and complete it, then remove this comment. -->
ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-rand-smiles-train-0.75
This model is a fine-tuned version of seyonec/ChemBERTa-zinc-base-v1 on the ailab-bio/PROTAC-Splitter-Dataset dataset. It achieves the following results on the evaluation set:
- Loss: 0.3562
- E3 Heavy Atoms Difference: 0.5450
- Tanimoto Similarity: 0.0
- Linker Heavy Atoms Difference: 0.2341
- Poi Graph Edit Distance: inf
- Poi Heavy Atoms Difference Norm: 0.0500
- Reassembly Nostereo: 0.6352
- Has All Attachment Points: 0.9914
- Num Fragments: 2.9996
- Linker Equal: 0.8443
- Reassembly: 0.6021
- E3 Graph Edit Distance Norm: inf
- Poi Valid: 0.9499
- E3 Graph Edit Distance: inf
- E3 Equal: 0.8238
- Poi Heavy Atoms Difference: 1.5246
- E3 Heavy Atoms Difference Norm: 0.0139
- Has Three Substructures: 0.9996
- Linker Valid: 0.9984
- Linker Has Attachment Point(s): 0.9984
- Poi Graph Edit Distance Norm: inf
- Heavy Atoms Difference Norm: 0.0733
- Valid: 0.9362
- E3 Valid: 0.9859
- Linker Heavy Atoms Difference Norm: 0.0034
- Poi Tanimoto Similarity: 0.0
- Poi Equal: 0.7947
- Linker Tanimoto Similarity: 0.0
- All Ligands Equal: 0.5946
- Linker Graph Edit Distance Norm: inf
- Poi Has Attachment Point(s): 0.9499
- E3 Has Attachment Point(s): 0.9859
- Linker Graph Edit Distance: 15934844192634561100698130285457299401122608004817217891860480.0000
- E3 Tanimoto Similarity: 0.0
- Heavy Atoms Difference: 5.5146
Model description
More information needed
Intended uses & limitations
More information needed
Training and evaluation data
More information needed
Training procedure
Training hyperparameters
The following hyperparameters were used during training:
- learning_rate: 5e-05
- train_batch_size: 128
- eval_batch_size: 64
- seed: 42
- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
- lr_scheduler_type: reduce_lr_on_plateau
- lr_scheduler_warmup_steps: 400
- training_steps: 100000
- mixed_precision_training: Native AMP
Training results
| Training Loss | Epoch | Step | Validation Loss | E3 Heavy Atoms Difference | Tanimoto Similarity | Linker Heavy Atoms Difference | Poi Graph Edit Distance | Poi Heavy Atoms Difference Norm | Reassembly Nostereo | Has All Attachment Points | Num Fragments | Linker Equal | Reassembly | E3 Graph Edit Distance Norm | Poi Valid | E3 Graph Edit Distance | E3 Equal | Poi Heavy Atoms Difference | E3 Heavy Atoms Difference Norm | Has Three Substructures | Linker Valid | Linker Has Attachment Point(s) | Poi Graph Edit Distance Norm | Heavy Atoms Difference Norm | Valid | E3 Valid | Linker Heavy Atoms Difference Norm | Poi Tanimoto Similarity | Poi Equal | Linker Tanimoto Similarity | All Ligands Equal | Linker Graph Edit Distance Norm | Poi Has Attachment Point(s) | E3 Has Attachment Point(s) | Linker Graph Edit Distance | E3 Tanimoto Similarity | Heavy Atoms Difference |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0.0006 | 10.5208 | 80000 | 0.3546 | 0.2397 | 0.0 | 0.2432 | inf | 0.0551 | 0.6277 | 0.9911 | 2.9999 | 0.8418 | 0.5965 | inf | 0.9407 | inf | 0.8234 | 1.7421 | 0.0025 | 0.9999 | 0.9980 | 0.9980 | inf | 0.0768 | 0.9301 | 0.9907 | 0.0018 | 0.0 | 0.7882 | 0.0 | 0.5897 | inf | 0.9407 | 0.9907 | 20361189801699711253012395652022580557179454652619232886390784.0000 | 0.0 | 5.7380 |
| 0.0006 | 13.1510 | 100000 | 0.3562 | 0.5450 | 0.0 | 0.2341 | inf | 0.0500 | 0.6352 | 0.9914 | 2.9996 | 0.8443 | 0.6021 | inf | 0.9499 | inf | 0.8238 | 1.5246 | 0.0139 | 0.9996 | 0.9984 | 0.9984 | inf | 0.0733 | 0.9362 | 0.9859 | 0.0034 | 0.0 | 0.7947 | 0.0 | 0.5946 | inf | 0.9499 | 0.9859 | 15934844192634561100698130285457299401122608004817217891860480.0000 | 0.0 | 5.5146 |
Framework versions
- Transformers 4.44.2
- Pytorch 2.4.1+cu121
- Datasets 3.0.0
- Tokenizers 0.19.1
- Library
- transformers
- Type
- encoder-decoder
- License
- mit
- Created
- Mar 14, 2025
- Updated
- Mar 14, 2025