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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-0.25 |
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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-0.25 |
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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: 0.3624 |
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- Linker Equal: 0.8351 |
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- E3 Graph Edit Distance Norm: inf |
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- Poi Heavy Atoms Difference Norm: 0.0311 |
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- Poi Has Attachment Point(s): 0.9593 |
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- Poi Graph Edit Distance Norm: inf |
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- Valid: 0.9367 |
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- Poi Valid: 0.9593 |
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- Poi Graph Edit Distance: inf |
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- Reassembly Nostereo: 0.6220 |
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- Linker Has Attachment Point(s): 0.9970 |
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- Poi Heavy Atoms Difference: 1.1101 |
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- Has Three Substructures: 1.0 |
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- E3 Heavy Atoms Difference Norm: 0.0153 |
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- Linker Valid: 0.9970 |
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- Linker Tanimoto Similarity: 0.0 |
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- E3 Has Attachment Point(s): 0.9798 |
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- Poi Equal: 0.7936 |
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- All Ligands Equal: 0.5870 |
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- Heavy Atoms Difference Norm: 0.0731 |
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- Linker Heavy Atoms Difference Norm: 0.0030 |
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- Heavy Atoms Difference: 5.4708 |
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- Tanimoto Similarity: 0.0 |
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- Num Fragments: 3.0 |
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- E3 Graph Edit Distance: inf |
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- Linker Graph Edit Distance: inf |
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- Linker Heavy Atoms Difference: 0.2800 |
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- Poi Tanimoto Similarity: 0.0 |
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- Linker Graph Edit Distance Norm: inf |
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- Has All Attachment Points: 0.9888 |
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- E3 Tanimoto Similarity: 0.0 |
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- Reassembly: 0.5944 |
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- E3 Heavy Atoms Difference: 0.4994 |
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- E3 Equal: 0.8276 |
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- E3 Valid: 0.9798 |
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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 | Linker Equal | E3 Graph Edit Distance Norm | Poi Heavy Atoms Difference Norm | Poi Has Attachment Point(s) | Poi Graph Edit Distance Norm | Valid | Poi Valid | Poi Graph Edit Distance | Reassembly Nostereo | Linker Has Attachment Point(s) | Poi Heavy Atoms Difference | Has Three Substructures | E3 Heavy Atoms Difference Norm | Linker Valid | Linker Tanimoto Similarity | E3 Has Attachment Point(s) | Poi Equal | All Ligands Equal | Heavy Atoms Difference Norm | Linker Heavy Atoms Difference Norm | Heavy Atoms Difference | Tanimoto Similarity | Num Fragments | E3 Graph Edit Distance | Linker Graph Edit Distance | Linker Heavy Atoms Difference | Poi Tanimoto Similarity | Linker Graph Edit Distance Norm | Has All Attachment Points | E3 Tanimoto Similarity | Reassembly | E3 Heavy Atoms Difference | E3 Equal | E3 Valid | |
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|:-------------:|:-------:|:------:|:---------------:|:------------:|:---------------------------:|:-------------------------------:|:---------------------------:|:----------------------------:|:------:|:---------:|:-----------------------:|:-------------------:|:------------------------------:|:--------------------------:|:-----------------------:|:------------------------------:|:------------:|:--------------------------:|:--------------------------:|:---------:|:-----------------:|:---------------------------:|:----------------------------------:|:----------------------:|:-------------------:|:-------------:|:----------------------:|:--------------------------:|:-----------------------------:|:-----------------------:|:-------------------------------:|:-------------------------:|:----------------------:|:----------:|:-------------------------:|:--------:|:--------:| |
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| 0.0006 | 31.5582 | 80000 | 0.3577 | 0.8324 | inf | 0.0305 | 0.9579 | inf | 0.9328 | 0.9579 | inf | 0.6230 | 0.9967 | 1.0626 | 0.9999 | 0.0251 | 0.9967 | 0.0 | 0.9771 | 0.7863 | 0.5856 | 0.0758 | 0.0051 | 5.7523 | 0.0 | 3.0001 | inf | inf | 0.2647 | 0.0 | inf | 0.9890 | 0.0 | 0.5934 | 0.8042 | 0.8272 | 0.9771 | |
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| 0.0005 | 39.4477 | 100000 | 0.3624 | 0.8351 | inf | 0.0311 | 0.9593 | inf | 0.9367 | 0.9593 | inf | 0.6220 | 0.9970 | 1.1101 | 1.0 | 0.0153 | 0.9970 | 0.0 | 0.9798 | 0.7936 | 0.5870 | 0.0731 | 0.0030 | 5.4708 | 0.0 | 3.0 | inf | inf | 0.2800 | 0.0 | inf | 0.9888 | 0.0 | 0.5944 | 0.4994 | 0.8276 | 0.9798 | |
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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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