| --- |
| base_model: seyonec/ChemBERTa-zinc-base-v1 |
| library_name: transformers |
| license: mit |
| tags: |
| - PROTAC |
| - cheminformatics |
| - generated_from_trainer |
| model-index: |
| - name: ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25 |
| results: [] |
| --- |
| |
| <!-- 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-opt25 |
| |
| 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. |
| It achieves the following results on the evaluation set: |
| - Loss: 0.3420 |
| - Num Fragments: 3.0002 |
| - Linker Heavy Atoms Difference: 0.1689 |
| - Linker Graph Edit Distance: 37181303116147309234962303999400365269286085344573508414341120.0000 |
| - Tanimoto Similarity: 0.0 |
| - Linker Tanimoto Similarity: 0.0 |
| - E3 Valid: 0.9732 |
| - Linker Has Attachment Point(s): 0.9963 |
| - Poi Equal: 0.7897 |
| - Heavy Atoms Difference: 8.0244 |
| - Poi Has Attachment Point(s): 0.9305 |
| - E3 Equal: 0.8302 |
| - Linker Graph Edit Distance Norm: inf |
| - E3 Has Attachment Point(s): 0.9732 |
| - Has Three Substructures: 0.9995 |
| - Poi Heavy Atoms Difference Norm: 0.0690 |
| - Linker Equal: 0.8419 |
| - Heavy Atoms Difference Norm: 0.1076 |
| - E3 Heavy Atoms Difference: 1.0454 |
| - Poi Valid: 0.9305 |
| - Valid: 0.9027 |
| - Linker Heavy Atoms Difference Norm: -0.0046 |
| - Has All Attachment Points: 0.9796 |
| - E3 Graph Edit Distance: inf |
| - Linker Valid: 0.9963 |
| - Poi Tanimoto Similarity: 0.0 |
| - Poi Graph Edit Distance Norm: inf |
| - Poi Heavy Atoms Difference: 2.0482 |
| - Poi Graph Edit Distance: inf |
| - Reassembly Nostereo: 0.6261 |
| - E3 Graph Edit Distance Norm: inf |
| - E3 Heavy Atoms Difference Norm: 0.0335 |
| - Reassembly: 0.6073 |
| - All Ligands Equal: 0.5992 |
| - E3 Tanimoto Similarity: 0.0 |
| |
| ## 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 |
| - training_steps: 100000 |
| - mixed_precision_training: Native AMP |
|
|
| ### Training results |
|
|
| | 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 | |
| |:-------------:|:------:|:------:|:---------------:|:-------------:|:-----------------------------:|:-------------------------------------------------------------------:|:-------------------:|:--------------------------:|:--------:|:------------------------------:|:---------:|:----------------------:|:---------------------------:|:--------:|:-------------------------------:|:--------------------------:|:-----------------------:|:-------------------------------:|:------------:|:---------------------------:|:-------------------------:|:---------:|:------:|:----------------------------------:|:-------------------------:|:----------------------:|:------------:|:-----------------------:|:----------------------------:|:--------------------------:|:--------------------------------------------------------------------:|:-------------------:|:---------------------------:|:------------------------------:|:----------:|:-----------------:|:----------------------:| |
| | 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 | |
| | 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 |
|
|
| - Transformers 4.44.2 |
| - Pytorch 2.4.1+cu121 |
| - Datasets 3.0.0 |
| - Tokenizers 0.19.1 |
|
|
