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PROTAC-Splitter-EncoderDecoder-lr_cosine_restarts-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_cosine_restarts-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_cosine_restarts-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: 0.3093
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+ - Linker Heavy Atoms Difference: 0.3372
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+ - Has Three Substructures: 0.9991
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+ - Poi Valid: 0.9534
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+ - Linker Graph Edit Distance Norm: inf
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+ - Reassembly: 0.5402
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+ - Valid: 0.9458
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+ - Poi Heavy Atoms Difference: 1.3755
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+ - E3 Has Attachment Point(s): 0.9922
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+ - Poi Heavy Atoms Difference Norm: 0.0422
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+ - Heavy Atoms Difference: 4.5184
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+ - Has All Attachment Points: 0.9900
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+ - Poi Tanimoto Similarity: 0.0
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+ - Heavy Atoms Difference Norm: 0.0596
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+ - E3 Heavy Atoms Difference: 0.2046
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+ - All Ligands Equal: 0.5318
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+ - E3 Heavy Atoms Difference Norm: -0.0014
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+ - Linker Heavy Atoms Difference Norm: 0.0044
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+ - Tanimoto Similarity: 0.0
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+ - E3 Graph Edit Distance Norm: inf
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+ - Poi Equal: 0.7580
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+ - Poi Has Attachment Point(s): 0.9534
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+ - Poi Graph Edit Distance Norm: inf
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+ - Num Fragments: 2.9998
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+ - Linker Graph Edit Distance: inf
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+ - Linker Valid: 0.9980
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+ - Linker Tanimoto Similarity: 0.0
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+ - Poi Graph Edit Distance: inf
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+ - E3 Equal: 0.8017
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+ - Linker Has Attachment Point(s): 0.9980
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+ - Linker Equal: 0.7645
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+ - E3 Tanimoto Similarity: 0.0
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+ - Reassembly Nostereo: 0.5728
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+ - E3 Valid: 0.9922
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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: cosine_with_restarts
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+ - lr_scheduler_warmup_steps: 100
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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 | Linker Heavy Atoms Difference | Has Three Substructures | Poi Valid | Linker Graph Edit Distance Norm | Reassembly | Valid | Poi Heavy Atoms Difference | E3 Has Attachment Point(s) | Poi Heavy Atoms Difference Norm | Heavy Atoms Difference | Has All Attachment Points | Poi Tanimoto Similarity | Heavy Atoms Difference Norm | E3 Heavy Atoms Difference | All Ligands Equal | E3 Heavy Atoms Difference Norm | Linker Heavy Atoms Difference Norm | Tanimoto Similarity | E3 Graph Edit Distance Norm | Poi Equal | Poi Has Attachment Point(s) | Poi Graph Edit Distance Norm | Num Fragments | Linker Graph Edit Distance | Linker Valid | Linker Tanimoto Similarity | Poi Graph Edit Distance | E3 Equal | Linker Has Attachment Point(s) | Linker Equal | E3 Tanimoto Similarity | Reassembly Nostereo | E3 Valid | E3 Graph Edit Distance |
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+ |:-------------:|:------:|:-----:|:---------------:|:-----------------------------:|:-----------------------:|:---------:|:-------------------------------:|:----------:|:------:|:--------------------------:|:--------------------------:|:-------------------------------:|:----------------------:|:-------------------------:|:-----------------------:|:---------------------------:|:-------------------------:|:-----------------:|:------------------------------:|:----------------------------------:|:-------------------:|:---------------------------:|:---------:|:---------------------------:|:----------------------------:|:-------------:|:-------------------------------------------------------------------:|:------------:|:--------------------------:|:-----------------------:|:--------:|:------------------------------:|:------------:|:----------------------:|:-------------------:|:--------:|:----------------------:|
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+ | 0.0212 | 0.4932 | 5000 | 0.2852 | 0.5099 | 0.9994 | 0.9528 | inf | 0.4464 | 0.9500 | 1.4706 | 0.9979 | 0.0414 | 4.6065 | 0.9903 | 0.0 | 0.0591 | 0.1237 | 0.4396 | -0.0043 | 0.0050 | 0.0 | inf | 0.7208 | 0.9528 | inf | 3.0001 | 24787535410764872823308202666266910179524056896382338942894080.0000 | 0.9975 | 0.0 | inf | 0.7734 | 0.9975 | 0.6416 | 0.0 | 0.4783 | 0.9979 | inf |
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+ | 0.011 | 0.7398 | 7500 | 0.3022 | 0.3255 | 0.9990 | 0.9389 | 0.0511 | 0.4896 | 0.9294 | 2.2561 | 0.9905 | 0.0673 | 6.6114 | 0.9858 | 0.0 | 0.0846 | 0.5439 | 0.4827 | 0.0117 | -0.0008 | 0.0 | inf | 0.7332 | 0.9389 | inf | 3.0001 | 27443342776203963485595838968590031296472552664861602492710912.0000 | 0.9973 | 0.0 | inf | 0.7827 | 0.9973 | 0.7075 | 0.0 | 0.5176 | 0.9905 | inf |
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+ | 0.007 | 0.9864 | 10000 | 0.3093 | 0.3372 | 0.9991 | 0.9534 | inf | 0.5402 | 0.9458 | 1.3755 | 0.9922 | 0.0422 | 4.5184 | 0.9900 | 0.0 | 0.0596 | 0.2046 | 0.5318 | -0.0014 | 0.0044 | 0.0 | inf | 0.7580 | 0.9534 | inf | 2.9998 | inf | 0.9980 | 0.0 | inf | 0.8017 | 0.9980 | 0.7645 | 0.0 | 0.5728 | 0.9922 | 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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+ }