|
|
--- |
|
|
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: [] |
|
|
--- |
|
|
|
|
|
<!-- This model card has been generated automatically according to the information the Trainer had access to. You |
|
|
should probably proofread and complete it, then remove this comment. --> |
|
|
|
|
|
# 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 |
|
|
|
