--- 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_cosine-opt25-rand-smiles results: [] --- # ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_cosine-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: 0.3184 - E3 Tanimoto Similarity: 0.0 - Poi Equal: 0.7620 - E3 Equal: 0.8036 - Poi Tanimoto Similarity: 0.0 - Poi Valid: 0.9589 - Reassembly: 0.5459 - All Ligands Equal: 0.5390 - Poi Graph Edit Distance: inf - Linker Graph Edit Distance: 28328611898016997512352231618590754490884636453008387363307520.0000 - Poi Graph Edit Distance Norm: inf - Linker Tanimoto Similarity: 0.0 - Valid: 0.9547 - E3 Graph Edit Distance Norm: inf - Poi Has Attachment Point(s): 0.9589 - Linker Equal: 0.7668 - Linker Heavy Atoms Difference Norm: 0.0034 - Has All Attachment Points: 0.9905 - Heavy Atoms Difference: 4.1049 - Has Three Substructures: 0.9992 - Tanimoto Similarity: 0.0 - Heavy Atoms Difference Norm: 0.0536 - Poi Heavy Atoms Difference Norm: 0.0352 - Linker Has Attachment Point(s): 0.9972 - E3 Heavy Atoms Difference: 0.2976 - E3 Graph Edit Distance: inf - Linker Valid: 0.9972 - E3 Heavy Atoms Difference Norm: 0.0033 - E3 Has Attachment Point(s): 0.9966 - E3 Valid: 0.9966 - Reassembly Nostereo: 0.5799 - Linker Heavy Atoms Difference: 0.3031 - Num Fragments: 3.0003 - Linker Graph Edit Distance Norm: inf - Poi Heavy Atoms Difference: 1.1856 ## 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: cosine - lr_scheduler_warmup_steps: 699 - training_steps: 10000 - mixed_precision_training: Native AMP ### Training results | Training Loss | Epoch | Step | Validation Loss | E3 Tanimoto Similarity | Poi Equal | E3 Equal | Poi Tanimoto Similarity | Poi Valid | Reassembly | All Ligands Equal | Poi Graph Edit Distance | Linker Graph Edit Distance | Poi Graph Edit Distance Norm | Linker Tanimoto Similarity | Valid | E3 Graph Edit Distance Norm | Poi Has Attachment Point(s) | Linker Equal | Linker Heavy Atoms Difference Norm | Has All Attachment Points | Heavy Atoms Difference | Has Three Substructures | Tanimoto Similarity | Heavy Atoms Difference Norm | Poi Heavy Atoms Difference Norm | Linker Has Attachment Point(s) | E3 Heavy Atoms Difference | E3 Graph Edit Distance | Linker Valid | E3 Heavy Atoms Difference Norm | E3 Has Attachment Point(s) | E3 Valid | Reassembly Nostereo | Linker Heavy Atoms Difference | Num Fragments | Linker Graph Edit Distance Norm | Poi Heavy Atoms Difference | |:-------------:|:------:|:-----:|:---------------:|:----------------------:|:---------:|:--------:|:-----------------------:|:---------:|:----------:|:-----------------:|:-----------------------:|:-------------------------------------------------------------------:|:----------------------------:|:--------------------------:|:------:|:---------------------------:|:---------------------------:|:------------:|:----------------------------------:|:-------------------------:|:----------------------:|:-----------------------:|:-------------------:|:---------------------------:|:-------------------------------:|:------------------------------:|:-------------------------:|:----------------------:|:------------:|:------------------------------:|:--------------------------:|:--------:|:-------------------:|:-----------------------------:|:-------------:|:-------------------------------:|:--------------------------:| | 0.012 | 0.4932 | 5000 | 0.3055 | 0.0 | 0.7354 | 0.7897 | 0.0 | 0.9479 | 0.4899 | 0.4824 | inf | 25672804532577903995569209904347871257364201785538851047997440.0000 | inf | 0.0 | 0.9441 | inf | 0.9479 | 0.6946 | 0.0103 | 0.9873 | 4.9586 | 0.9995 | 0.0 | 0.0650 | 0.0421 | 0.9974 | 0.1648 | inf | 0.9974 | -0.0036 | 0.9972 | 0.9972 | 0.5198 | 0.5344 | 3.0005 | inf | 1.4326 | | 0.0064 | 0.7398 | 7500 | 0.3156 | 0.0 | 0.7551 | 0.8017 | 0.0 | 0.9532 | 0.5359 | 0.5282 | inf | 40722379603399433924006332951724209580646664901199556834754560.0000 | inf | 0.0 | 0.9477 | inf | 0.9532 | 0.7533 | -0.0000 | 0.9873 | 4.5195 | 0.9985 | 0.0 | 0.0593 | 0.0396 | 0.9959 | 0.3429 | inf | 0.9959 | 0.0053 | 0.9944 | 0.9944 | 0.5689 | 0.2564 | 3.0003 | 0.0452 | 1.3395 | | 0.0051 | 0.9864 | 10000 | 0.3184 | 0.0 | 0.7620 | 0.8036 | 0.0 | 0.9589 | 0.5459 | 0.5390 | inf | 28328611898016997512352231618590754490884636453008387363307520.0000 | inf | 0.0 | 0.9547 | inf | 0.9589 | 0.7668 | 0.0034 | 0.9905 | 4.1049 | 0.9992 | 0.0 | 0.0536 | 0.0352 | 0.9972 | 0.2976 | inf | 0.9972 | 0.0033 | 0.9966 | 0.9966 | 0.5799 | 0.3031 | 3.0003 | inf | 1.1856 | ### Framework versions - Transformers 4.44.2 - Pytorch 2.4.1+cu121 - Datasets 3.0.0 - Tokenizers 0.19.1