--- 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-rand-smiles results: [] --- # ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25-rand-smiles 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: 0.3251 - All Ligands Equal: 0.5455 - E3 Tanimoto Similarity: 0.0 - E3 Graph Edit Distance Norm: inf - E3 Heavy Atoms Difference Norm: 0.0123 - Linker Tanimoto Similarity: 0.0 - Tanimoto Similarity: 0.0 - E3 Valid: 0.9866 - Linker Heavy Atoms Difference Norm: -0.0013 - Num Fragments: 2.9997 - Heavy Atoms Difference: 5.7446 - E3 Has Attachment Point(s): 0.9866 - E3 Equal: 0.8076 - Reassembly: 0.5548 - Poi Has Attachment Point(s): 0.9458 - Poi Graph Edit Distance Norm: inf - Linker Graph Edit Distance: inf - Poi Heavy Atoms Difference Norm: 0.0510 - Linker Has Attachment Point(s): 0.9952 - Poi Equal: 0.7632 - E3 Heavy Atoms Difference: 0.4690 - Has All Attachment Points: 0.9866 - Linker Graph Edit Distance Norm: inf - Has Three Substructures: 0.9990 - Linker Equal: 0.7856 - Poi Valid: 0.9458 - Valid: 0.9308 - Poi Tanimoto Similarity: 0.0 - Reassembly Nostereo: 0.5789 - Linker Valid: 0.9952 - Heavy Atoms Difference Norm: 0.0744 - Linker Heavy Atoms Difference: 0.2002 - Poi Heavy Atoms Difference: 1.7548 - Poi Graph Edit Distance: inf - E3 Graph Edit Distance: inf ## 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 - lr_scheduler_warmup_steps: 800 - training_steps: 10000 - mixed_precision_training: Native AMP ### Training results | 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 | |:-------------:|:------:|:-----:|:---------------:|:-----------------:|:----------------------:|:---------------------------:|:------------------------------:|:--------------------------:|:-------------------:|:--------:|:----------------------------------:|:-------------:|:----------------------:|:--------------------------:|:--------:|:----------:|:---------------------------:|:----------------------------:|:-------------------------------------------------------------------:|:-------------------------------:|:------------------------------:|:---------:|:-------------------------:|:-------------------------:|:-------------------------------:|:-----------------------:|:------------:|:---------:|:------:|:-----------------------:|:-------------------:|:------------:|:---------------------------:|:-----------------------------:|:--------------------------:|:-----------------------:|:----------------------:| | 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 | | 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 | | 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 | ### Framework versions - Transformers 4.44.2 - Pytorch 2.4.1+cu121 - Datasets 3.0.0 - Tokenizers 0.19.1