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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-rand-smiles-train-0.5 |
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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-rand-smiles-train-0.5 |
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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: 0.3751 |
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- Reassembly: 0.5970 |
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- E3 Graph Edit Distance Norm: inf |
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- Linker Graph Edit Distance Norm: inf |
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- All Ligands Equal: 0.5899 |
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- Poi Heavy Atoms Difference Norm: 0.0419 |
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- Poi Graph Edit Distance Norm: inf |
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- Linker Heavy Atoms Difference: 0.2883 |
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- Linker Equal: 0.8472 |
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- Poi Has Attachment Point(s): 0.9510 |
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- E3 Tanimoto Similarity: 0.0 |
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- Reassembly Nostereo: 0.6329 |
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- E3 Graph Edit Distance: inf |
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- Linker Has Attachment Point(s): 0.9977 |
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- E3 Heavy Atoms Difference Norm: 0.0037 |
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- Linker Valid: 0.9977 |
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- Poi Equal: 0.7890 |
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- Linker Graph Edit Distance: 23016997167138810478786188190104988023843767118069314732687360.0000 |
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- E3 Equal: 0.8240 |
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- Num Fragments: 3.0003 |
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- E3 Heavy Atoms Difference: 0.2737 |
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- Poi Graph Edit Distance: inf |
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- Has Three Substructures: 0.9996 |
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- Heavy Atoms Difference: 4.7685 |
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- Linker Tanimoto Similarity: 0.0 |
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- Poi Heavy Atoms Difference: 1.3950 |
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- E3 Valid: 0.9944 |
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- Poi Tanimoto Similarity: 0.0 |
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- Valid: 0.9450 |
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- Heavy Atoms Difference Norm: 0.0634 |
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- Tanimoto Similarity: 0.0 |
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- E3 Has Attachment Point(s): 0.9944 |
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- Has All Attachment Points: 0.9938 |
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- Poi Valid: 0.9510 |
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- Linker Heavy Atoms Difference Norm: 0.0067 |
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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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- lr_scheduler_warmup_steps: 400 |
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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 | Reassembly | E3 Graph Edit Distance Norm | Linker Graph Edit Distance Norm | All Ligands Equal | Poi Heavy Atoms Difference Norm | Poi Graph Edit Distance Norm | Linker Heavy Atoms Difference | Linker Equal | Poi Has Attachment Point(s) | E3 Tanimoto Similarity | Reassembly Nostereo | E3 Graph Edit Distance | Linker Has Attachment Point(s) | E3 Heavy Atoms Difference Norm | Linker Valid | Poi Equal | Linker Graph Edit Distance | E3 Equal | Num Fragments | E3 Heavy Atoms Difference | Poi Graph Edit Distance | Has Three Substructures | Heavy Atoms Difference | Linker Tanimoto Similarity | Poi Heavy Atoms Difference | E3 Valid | Poi Tanimoto Similarity | Valid | Heavy Atoms Difference Norm | Tanimoto Similarity | E3 Has Attachment Point(s) | Has All Attachment Points | Poi Valid | Linker Heavy Atoms Difference Norm | |
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|:-------------:|:-------:|:------:|:---------------:|:----------:|:---------------------------:|:-------------------------------:|:-----------------:|:-------------------------------:|:----------------------------:|:-----------------------------:|:------------:|:---------------------------:|:----------------------:|:-------------------:|:----------------------:|:------------------------------:|:------------------------------:|:------------:|:---------:|:-------------------------------------------------------------------:|:--------:|:-------------:|:-------------------------:|:-----------------------:|:-----------------------:|:----------------------:|:--------------------------:|:--------------------------:|:--------:|:-----------------------:|:------:|:---------------------------:|:-------------------:|:--------------------------:|:-------------------------:|:---------:|:----------------------------------:| |
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| 0.0006 | 15.7822 | 80000 | 0.3655 | 0.5977 | inf | inf | 0.5904 | 0.0477 | inf | 0.1988 | 0.8371 | 0.9528 | 0.0 | 0.6278 | inf | 0.9952 | 0.0221 | 0.9952 | 0.7851 | inf | 0.8250 | 2.9996 | 0.7440 | inf | 0.9994 | 5.9070 | 0.0 | 1.4796 | 0.9796 | 0.0 | 0.9315 | 0.0782 | 0.0 | 0.9796 | 0.9879 | 0.9528 | -0.0014 | |
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| 0.0006 | 19.7278 | 100000 | 0.3751 | 0.5970 | inf | inf | 0.5899 | 0.0419 | inf | 0.2883 | 0.8472 | 0.9510 | 0.0 | 0.6329 | inf | 0.9977 | 0.0037 | 0.9977 | 0.7890 | 23016997167138810478786188190104988023843767118069314732687360.0000 | 0.8240 | 3.0003 | 0.2737 | inf | 0.9996 | 4.7685 | 0.0 | 1.3950 | 0.9944 | 0.0 | 0.9450 | 0.0634 | 0.0 | 0.9944 | 0.9938 | 0.9510 | 0.0067 | |
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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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