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PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles

Transformers
TensorBoard
Safetensors
encoder-decoder
text2text-generation
PROTAC
cheminformatics
Generated from Trainer
Model card Files
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Initial version

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  1. README.md +98 -0
  2. generation_config.json +10 -0
README.md ADDED
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+ ---
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+ library_name: transformers
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+ license: mit
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+ base_model: seyonec/ChemBERTa-zinc-base-v1
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+ tags:
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+ - PROTAC
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+ - cheminformatics
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+ - generated_from_trainer
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+ model-index:
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+ - name: ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles
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+ results: []
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+ ---
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+
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+ <!-- This model card has been generated automatically according to the information the Trainer had access to. You
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+ should probably proofread and complete it, then remove this comment. -->
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+
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+ # ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles
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+
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+ This model is a fine-tuned version of [seyonec/ChemBERTa-zinc-base-v1](https://huggingface.co/seyonec/ChemBERTa-zinc-base-v1) on the ailab-bio/PROTAC-Splitter-Dataset dataset.
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+ It achieves the following results on the evaluation set:
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+ - Loss: 0.3251
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+ - All Ligands Equal: 0.5455
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+ - E3 Tanimoto Similarity: 0.0
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+ - E3 Graph Edit Distance Norm: inf
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+ - E3 Heavy Atoms Difference Norm: 0.0123
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+ - Linker Tanimoto Similarity: 0.0
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+ - Tanimoto Similarity: 0.0
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+ - E3 Valid: 0.9866
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+ - Linker Heavy Atoms Difference Norm: -0.0013
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+ - Num Fragments: 2.9997
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+ - Heavy Atoms Difference: 5.7446
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+ - E3 Has Attachment Point(s): 0.9866
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+ - E3 Equal: 0.8076
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+ - Reassembly: 0.5548
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+ - Poi Has Attachment Point(s): 0.9458
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+ - Poi Graph Edit Distance Norm: inf
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+ - Linker Graph Edit Distance: inf
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+ - Poi Heavy Atoms Difference Norm: 0.0510
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+ - Linker Has Attachment Point(s): 0.9952
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+ - Poi Equal: 0.7632
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+ - E3 Heavy Atoms Difference: 0.4690
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+ - Has All Attachment Points: 0.9866
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+ - Linker Graph Edit Distance Norm: inf
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+ - Has Three Substructures: 0.9990
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+ - Linker Equal: 0.7856
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+ - Poi Valid: 0.9458
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+ - Valid: 0.9308
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+ - Poi Tanimoto Similarity: 0.0
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+ - Reassembly Nostereo: 0.5789
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+ - Linker Valid: 0.9952
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+ - Heavy Atoms Difference Norm: 0.0744
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+ - Linker Heavy Atoms Difference: 0.2002
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+ - Poi Heavy Atoms Difference: 1.7548
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+ - Poi Graph Edit Distance: inf
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+ - E3 Graph Edit Distance: inf
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+
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+ ## Model description
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+
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+ More information needed
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+
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+ ## Intended uses & limitations
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+
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+ More information needed
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+
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+ ## Training and evaluation data
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+
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+ More information needed
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+
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+ ## Training procedure
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+
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+ ### Training hyperparameters
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+
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+ The following hyperparameters were used during training:
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+ - learning_rate: 5e-05
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+ - train_batch_size: 128
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+ - eval_batch_size: 64
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+ - seed: 42
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+ - optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
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+ - lr_scheduler_type: reduce_lr_on_plateau
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+ - lr_scheduler_warmup_steps: 800
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+ - training_steps: 10000
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+ - mixed_precision_training: Native AMP
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+
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+ ### Training results
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+
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+ | Training Loss | Epoch | Step | Validation Loss | All Ligands Equal | E3 Tanimoto Similarity | E3 Graph Edit Distance Norm | E3 Heavy Atoms Difference Norm | Linker Tanimoto Similarity | Tanimoto Similarity | E3 Valid | Linker Heavy Atoms Difference Norm | Num Fragments | Heavy Atoms Difference | E3 Has Attachment Point(s) | E3 Equal | Reassembly | Poi Has Attachment Point(s) | Poi Graph Edit Distance Norm | Linker Graph Edit Distance | Poi Heavy Atoms Difference Norm | Linker Has Attachment Point(s) | Poi Equal | E3 Heavy Atoms Difference | Has All Attachment Points | Linker Graph Edit Distance Norm | Has Three Substructures | Linker Equal | Poi Valid | Valid | Poi Tanimoto Similarity | Reassembly Nostereo | Linker Valid | Heavy Atoms Difference Norm | Linker Heavy Atoms Difference | Poi Heavy Atoms Difference | Poi Graph Edit Distance | E3 Graph Edit Distance |
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+ |:-------------:|:------:|:-----:|:---------------:|:-----------------:|:----------------------:|:---------------------------:|:------------------------------:|:--------------------------:|:-------------------:|:--------:|:----------------------------------:|:-------------:|:----------------------:|:--------------------------:|:--------:|:----------:|:---------------------------:|:----------------------------:|:-------------------------------------------------------------------:|:-------------------------------:|:------------------------------:|:---------:|:-------------------------:|:-------------------------:|:-------------------------------:|:-----------------------:|:------------:|:---------:|:------:|:-----------------------:|:-------------------:|:------------:|:---------------------------:|:-----------------------------:|:--------------------------:|:-----------------------:|:----------------------:|
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+ | 0.0107 | 0.4932 | 5000 | 0.3008 | 0.5011 | 0.0 | inf | 0.0105 | 0.0 | 0.0 | 0.9859 | 0.0173 | 3.0002 | 4.6779 | 0.9859 | 0.7894 | 0.5097 | 0.9624 | inf | inf | 0.0317 | 0.9978 | 0.7466 | 0.4474 | 0.9880 | inf | 0.9993 | 0.7242 | 0.9624 | 0.9481 | 0.0 | 0.5343 | 0.9978 | 0.0617 | 0.5834 | 1.1262 | inf | inf |
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+ | 0.0058 | 0.7398 | 7500 | 0.3187 | 0.5325 | 0.0 | inf | 0.0172 | 0.0 | 0.0 | 0.9835 | 0.0039 | 2.9999 | 4.7889 | 0.9835 | 0.8015 | 0.5402 | 0.9616 | inf | 59313031161473085686992099539504630098717768674496038276431872.0000 | 0.0264 | 0.9941 | 0.7586 | 0.6172 | 0.9898 | inf | 0.9992 | 0.7643 | 0.9616 | 0.9417 | 0.0 | 0.5643 | 0.9941 | 0.0626 | 0.2995 | 0.9886 | inf | inf |
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+ | 0.0049 | 0.9864 | 10000 | 0.3251 | 0.5455 | 0.0 | inf | 0.0123 | 0.0 | 0.0 | 0.9866 | -0.0013 | 2.9997 | 5.7446 | 0.9866 | 0.8076 | 0.5548 | 0.9458 | inf | inf | 0.0510 | 0.9952 | 0.7632 | 0.4690 | 0.9866 | inf | 0.9990 | 0.7856 | 0.9458 | 0.9308 | 0.0 | 0.5789 | 0.9952 | 0.0744 | 0.2002 | 1.7548 | inf | inf |
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+
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+
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+ ### Framework versions
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+
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+ - Transformers 4.44.2
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+ - Pytorch 2.4.1+cu121
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+ - Datasets 3.0.0
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+ - Tokenizers 0.19.1
generation_config.json ADDED
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+ {
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+ "bos_token_id": 0,
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+ "do_sample": true,
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+ "eos_token_id": 2,
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+ "max_length": 512,
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+ "num_beams": 5,
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+ "pad_token_id": 1,
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+ "top_k": 20,
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+ "transformers_version": "4.44.2"
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+ }