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PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25

Transformers
TensorBoard
Safetensors
encoder-decoder
text2text-generation
PROTAC
cheminformatics
Generated from Trainer
Model card Files
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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_cosine-opt25
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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_cosine-opt25
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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: 0.3124
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+ - E3 Graph Edit Distance Norm: inf
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+ - Poi Has Attachment Point(s): 0.9294
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+ - Linker Heavy Atoms Difference: 0.3252
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+ - Reassembly Nostereo: 0.5845
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+ - E3 Valid: 0.9942
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+ - Poi Heavy Atoms Difference Norm: 0.0668
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+ - Linker Graph Edit Distance: inf
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+ - All Ligands Equal: 0.5477
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+ - Has All Attachment Points: 0.9857
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+ - Linker Valid: 0.9951
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+ - E3 Tanimoto Similarity: 0.0
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+ - Heavy Atoms Difference: 6.4929
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+ - Tanimoto Similarity: 0.0
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+ - Reassembly: 0.5549
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+ - E3 Heavy Atoms Difference: 0.3628
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+ - Poi Graph Edit Distance Norm: inf
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+ - Valid: 0.9232
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+ - Linker Tanimoto Similarity: 0.0
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+ - Linker Heavy Atoms Difference Norm: 0.0050
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+ - Poi Valid: 0.9294
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+ - Linker Graph Edit Distance Norm: inf
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+ - Poi Equal: 0.7673
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+ - Linker Equal: 0.7726
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+ - E3 Graph Edit Distance: inf
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+ - Poi Graph Edit Distance: inf
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+ - Has Three Substructures: 0.9983
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+ - Poi Heavy Atoms Difference: 2.0849
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+ - Num Fragments: 3.0008
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+ - Poi Tanimoto Similarity: 0.0
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+ - E3 Heavy Atoms Difference Norm: 0.0044
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+ - E3 Has Attachment Point(s): 0.9942
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+ - E3 Equal: 0.8035
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+ - Linker Has Attachment Point(s): 0.9951
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+ - Heavy Atoms Difference Norm: 0.0854
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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: cosine
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+ - lr_scheduler_warmup_steps: 699
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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 | E3 Graph Edit Distance Norm | Poi Has Attachment Point(s) | Linker Heavy Atoms Difference | Reassembly Nostereo | E3 Valid | Poi Heavy Atoms Difference Norm | Linker Graph Edit Distance | All Ligands Equal | Has All Attachment Points | Linker Valid | E3 Tanimoto Similarity | Heavy Atoms Difference | Tanimoto Similarity | Reassembly | E3 Heavy Atoms Difference | Poi Graph Edit Distance Norm | Valid | Linker Tanimoto Similarity | Linker Heavy Atoms Difference Norm | Poi Valid | Linker Graph Edit Distance Norm | Poi Equal | Linker Equal | E3 Graph Edit Distance | Poi Graph Edit Distance | Has Three Substructures | Poi Heavy Atoms Difference | Num Fragments | Poi Tanimoto Similarity | E3 Heavy Atoms Difference Norm | E3 Has Attachment Point(s) | E3 Equal | Linker Has Attachment Point(s) | Heavy Atoms Difference Norm |
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+ |:-------------:|:------:|:-----:|:---------------:|:---------------------------:|:---------------------------:|:-----------------------------:|:-------------------:|:--------:|:-------------------------------:|:-------------------------------------------------------------------:|:-----------------:|:-------------------------:|:------------:|:----------------------:|:----------------------:|:-------------------:|:----------:|:-------------------------:|:----------------------------:|:------:|:--------------------------:|:----------------------------------:|:---------:|:-------------------------------:|:---------:|:------------:|:----------------------:|:-----------------------:|:-----------------------:|:--------------------------:|:-------------:|:-----------------------:|:------------------------------:|:--------------------------:|:--------:|:------------------------------:|:---------------------------:|
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+ | 0.0086 | 0.4932 | 5000 | 0.2931 | inf | 0.9248 | 0.6527 | 0.5238 | 0.9949 | 0.0785 | 46033994334277620957572376380209976047687534236138629465374720.0000 | 0.4899 | 0.9820 | 0.9954 | 0.0 | 7.4350 | 0.0 | 0.4972 | 0.3592 | inf | 0.9182 | 0.0 | 0.0200 | 0.9248 | 0.0544 | 0.7416 | 0.7092 | inf | inf | 0.9988 | 2.4199 | 3.0004 | 0.0 | 0.0041 | 0.9949 | 0.7832 | 0.9954 | 0.0974 |
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+ | 0.004 | 0.7398 | 7500 | 0.3098 | inf | 0.9225 | 0.2498 | 0.5729 | 0.9924 | 0.0709 | 59313031161473097104973641187183678565005524270457129338404864.0000 | 0.5381 | 0.9818 | 0.9941 | 0.0 | 6.9868 | 0.0 | 0.5451 | 0.4005 | inf | 0.9147 | 0.0 | -0.0010 | 0.9225 | inf | 0.7603 | 0.7604 | inf | inf | 0.9978 | 2.2024 | 3.0006 | 0.0 | 0.0081 | 0.9924 | 0.8044 | 0.9941 | 0.0924 |
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+ | 0.003 | 0.9864 | 10000 | 0.3124 | inf | 0.9294 | 0.3252 | 0.5845 | 0.9942 | 0.0668 | inf | 0.5477 | 0.9857 | 0.9951 | 0.0 | 6.4929 | 0.0 | 0.5549 | 0.3628 | inf | 0.9232 | 0.0 | 0.0050 | 0.9294 | inf | 0.7673 | 0.7726 | inf | inf | 0.9983 | 2.0849 | 3.0008 | 0.0 | 0.0044 | 0.9942 | 0.8035 | 0.9951 | 0.0854 |
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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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+ }