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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-0.75 |
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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-0.75 |
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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: 0.3562 |
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- E3 Heavy Atoms Difference: 0.5450 |
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- Tanimoto Similarity: 0.0 |
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- Linker Heavy Atoms Difference: 0.2341 |
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- Poi Graph Edit Distance: inf |
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- Poi Heavy Atoms Difference Norm: 0.0500 |
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- Reassembly Nostereo: 0.6352 |
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- Has All Attachment Points: 0.9914 |
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- Num Fragments: 2.9996 |
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- Linker Equal: 0.8443 |
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- Reassembly: 0.6021 |
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- E3 Graph Edit Distance Norm: inf |
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- Poi Valid: 0.9499 |
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- E3 Graph Edit Distance: inf |
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- E3 Equal: 0.8238 |
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- Poi Heavy Atoms Difference: 1.5246 |
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- E3 Heavy Atoms Difference Norm: 0.0139 |
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- Has Three Substructures: 0.9996 |
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- Linker Valid: 0.9984 |
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- Linker Has Attachment Point(s): 0.9984 |
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- Poi Graph Edit Distance Norm: inf |
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- Heavy Atoms Difference Norm: 0.0733 |
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- Valid: 0.9362 |
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- E3 Valid: 0.9859 |
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- Linker Heavy Atoms Difference Norm: 0.0034 |
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- Poi Tanimoto Similarity: 0.0 |
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- Poi Equal: 0.7947 |
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- Linker Tanimoto Similarity: 0.0 |
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- All Ligands Equal: 0.5946 |
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- Linker Graph Edit Distance Norm: inf |
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- Poi Has Attachment Point(s): 0.9499 |
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- E3 Has Attachment Point(s): 0.9859 |
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- Linker Graph Edit Distance: 15934844192634561100698130285457299401122608004817217891860480.0000 |
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- E3 Tanimoto Similarity: 0.0 |
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- Heavy Atoms Difference: 5.5146 |
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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 | E3 Heavy Atoms Difference | Tanimoto Similarity | Linker Heavy Atoms Difference | Poi Graph Edit Distance | Poi Heavy Atoms Difference Norm | Reassembly Nostereo | Has All Attachment Points | Num Fragments | Linker Equal | Reassembly | E3 Graph Edit Distance Norm | Poi Valid | E3 Graph Edit Distance | E3 Equal | Poi Heavy Atoms Difference | E3 Heavy Atoms Difference Norm | Has Three Substructures | Linker Valid | Linker Has Attachment Point(s) | Poi Graph Edit Distance Norm | Heavy Atoms Difference Norm | Valid | E3 Valid | Linker Heavy Atoms Difference Norm | Poi Tanimoto Similarity | Poi Equal | Linker Tanimoto Similarity | All Ligands Equal | Linker Graph Edit Distance Norm | Poi Has Attachment Point(s) | E3 Has Attachment Point(s) | Linker Graph Edit Distance | E3 Tanimoto Similarity | Heavy Atoms Difference | |
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|:-------------:|:-------:|:------:|:---------------:|:-------------------------:|:-------------------:|:-----------------------------:|:-----------------------:|:-------------------------------:|:-------------------:|:-------------------------:|:-------------:|:------------:|:----------:|:---------------------------:|:---------:|:----------------------:|:--------:|:--------------------------:|:------------------------------:|:-----------------------:|:------------:|:------------------------------:|:----------------------------:|:---------------------------:|:------:|:--------:|:----------------------------------:|:-----------------------:|:---------:|:--------------------------:|:-----------------:|:-------------------------------:|:---------------------------:|:--------------------------:|:-------------------------------------------------------------------:|:----------------------:|:----------------------:| |
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| 0.0006 | 10.5208 | 80000 | 0.3546 | 0.2397 | 0.0 | 0.2432 | inf | 0.0551 | 0.6277 | 0.9911 | 2.9999 | 0.8418 | 0.5965 | inf | 0.9407 | inf | 0.8234 | 1.7421 | 0.0025 | 0.9999 | 0.9980 | 0.9980 | inf | 0.0768 | 0.9301 | 0.9907 | 0.0018 | 0.0 | 0.7882 | 0.0 | 0.5897 | inf | 0.9407 | 0.9907 | 20361189801699711253012395652022580557179454652619232886390784.0000 | 0.0 | 5.7380 | |
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| 0.0006 | 13.1510 | 100000 | 0.3562 | 0.5450 | 0.0 | 0.2341 | inf | 0.0500 | 0.6352 | 0.9914 | 2.9996 | 0.8443 | 0.6021 | inf | 0.9499 | inf | 0.8238 | 1.5246 | 0.0139 | 0.9996 | 0.9984 | 0.9984 | inf | 0.0733 | 0.9362 | 0.9859 | 0.0034 | 0.0 | 0.7947 | 0.0 | 0.5946 | inf | 0.9499 | 0.9859 | 15934844192634561100698130285457299401122608004817217891860480.0000 | 0.0 | 5.5146 | |
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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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