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--- |
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base_model: seyonec/ChemBERTa-zinc-base-v1 |
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library_name: transformers |
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license: mit |
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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 |
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results: [] |
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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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# ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25 |
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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: 0.3420 |
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- Num Fragments: 3.0002 |
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- Linker Heavy Atoms Difference: 0.1689 |
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- Linker Graph Edit Distance: 37181303116147309234962303999400365269286085344573508414341120.0000 |
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- Tanimoto Similarity: 0.0 |
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- Linker Tanimoto Similarity: 0.0 |
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- E3 Valid: 0.9732 |
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- Linker Has Attachment Point(s): 0.9963 |
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- Poi Equal: 0.7897 |
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- Heavy Atoms Difference: 8.0244 |
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- Poi Has Attachment Point(s): 0.9305 |
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- E3 Equal: 0.8302 |
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- Linker Graph Edit Distance Norm: inf |
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- E3 Has Attachment Point(s): 0.9732 |
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- Has Three Substructures: 0.9995 |
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- Poi Heavy Atoms Difference Norm: 0.0690 |
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- Linker Equal: 0.8419 |
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- Heavy Atoms Difference Norm: 0.1076 |
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- E3 Heavy Atoms Difference: 1.0454 |
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- Poi Valid: 0.9305 |
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- Valid: 0.9027 |
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- Linker Heavy Atoms Difference Norm: -0.0046 |
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- Has All Attachment Points: 0.9796 |
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- E3 Graph Edit Distance: inf |
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- Linker Valid: 0.9963 |
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- Poi Tanimoto Similarity: 0.0 |
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- Poi Graph Edit Distance Norm: inf |
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- Poi Heavy Atoms Difference: 2.0482 |
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- Poi Graph Edit Distance: inf |
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- Reassembly Nostereo: 0.6261 |
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- E3 Graph Edit Distance Norm: inf |
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- E3 Heavy Atoms Difference Norm: 0.0335 |
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- Reassembly: 0.6073 |
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- All Ligands Equal: 0.5992 |
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- E3 Tanimoto Similarity: 0.0 |
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## Model description |
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More information needed |
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## Intended uses & limitations |
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More information needed |
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## Training and evaluation data |
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More information needed |
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## Training procedure |
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### Training hyperparameters |
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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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- training_steps: 100000 |
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- mixed_precision_training: Native AMP |
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### Training results |
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| Training Loss | Epoch | Step | Validation Loss | Num Fragments | Linker Heavy Atoms Difference | Linker Graph Edit Distance | Tanimoto Similarity | Linker Tanimoto Similarity | E3 Valid | Linker Has Attachment Point(s) | Poi Equal | Heavy Atoms Difference | Poi Has Attachment Point(s) | E3 Equal | Linker Graph Edit Distance Norm | E3 Has Attachment Point(s) | Has Three Substructures | Poi Heavy Atoms Difference Norm | Linker Equal | Heavy Atoms Difference Norm | E3 Heavy Atoms Difference | Poi Valid | Valid | Linker Heavy Atoms Difference Norm | Has All Attachment Points | E3 Graph Edit Distance | Linker Valid | Poi Tanimoto Similarity | Poi Graph Edit Distance Norm | Poi Heavy Atoms Difference | Poi Graph Edit Distance | Reassembly Nostereo | E3 Graph Edit Distance Norm | E3 Heavy Atoms Difference Norm | Reassembly | All Ligands Equal | E3 Tanimoto Similarity | |
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|:-------------:|:------:|:------:|:---------------:|:-------------:|:-----------------------------:|:-------------------------------------------------------------------:|:-------------------:|:--------------------------:|:--------:|:------------------------------:|:---------:|:----------------------:|:---------------------------:|:--------:|:-------------------------------:|:--------------------------:|:-----------------------:|:-------------------------------:|:------------:|:---------------------------:|:-------------------------:|:---------:|:------:|:----------------------------------:|:-------------------------:|:----------------------:|:------------:|:-----------------------:|:----------------------------:|:--------------------------:|:--------------------------------------------------------------------:|:-------------------:|:---------------------------:|:------------------------------:|:----------:|:-----------------:|:----------------------:| |
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| 0.0005 | 7.8911 | 80000 | 0.3375 | 2.9994 | 0.2223 | inf | 0.0 | 0.0 | 0.9717 | 0.9961 | 0.7867 | 9.0605 | 0.9179 | 0.8268 | inf | 0.9717 | 0.9994 | 0.0813 | 0.8393 | 0.1211 | 0.9062 | 0.9179 | 0.8893 | 0.0019 | 0.9788 | inf | 0.9961 | 0.0 | inf | 2.4517 | 820644475920679939503384490879847350906393395732940812913213440.0000 | 0.6211 | inf | 0.0334 | 0.6011 | 0.5936 | 0.0 | |
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| 0.0005 | 9.8639 | 100000 | 0.3420 | 3.0002 | 0.1689 | 37181303116147309234962303999400365269286085344573508414341120.0000 | 0.0 | 0.0 | 0.9732 | 0.9963 | 0.7897 | 8.0244 | 0.9305 | 0.8302 | inf | 0.9732 | 0.9995 | 0.0690 | 0.8419 | 0.1076 | 1.0454 | 0.9305 | 0.9027 | -0.0046 | 0.9796 | inf | 0.9963 | 0.0 | inf | 2.0482 | inf | 0.6261 | inf | 0.0335 | 0.6073 | 0.5992 | 0.0 | |
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### Framework versions |
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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 |
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