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---
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_reduce-rand-smiles-train-0.5
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_reduce-rand-smiles-train-0.5
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: 0.3751
- Reassembly: 0.5970
- E3 Graph Edit Distance Norm: inf
- Linker Graph Edit Distance Norm: inf
- All Ligands Equal: 0.5899
- Poi Heavy Atoms Difference Norm: 0.0419
- Poi Graph Edit Distance Norm: inf
- Linker Heavy Atoms Difference: 0.2883
- Linker Equal: 0.8472
- Poi Has Attachment Point(s): 0.9510
- E3 Tanimoto Similarity: 0.0
- Reassembly Nostereo: 0.6329
- E3 Graph Edit Distance: inf
- Linker Has Attachment Point(s): 0.9977
- E3 Heavy Atoms Difference Norm: 0.0037
- Linker Valid: 0.9977
- Poi Equal: 0.7890
- Linker Graph Edit Distance: 23016997167138810478786188190104988023843767118069314732687360.0000
- E3 Equal: 0.8240
- Num Fragments: 3.0003
- E3 Heavy Atoms Difference: 0.2737
- Poi Graph Edit Distance: inf
- Has Three Substructures: 0.9996
- Heavy Atoms Difference: 4.7685
- Linker Tanimoto Similarity: 0.0
- Poi Heavy Atoms Difference: 1.3950
- E3 Valid: 0.9944
- Poi Tanimoto Similarity: 0.0
- Valid: 0.9450
- Heavy Atoms Difference Norm: 0.0634
- Tanimoto Similarity: 0.0
- E3 Has Attachment Point(s): 0.9944
- Has All Attachment Points: 0.9938
- Poi Valid: 0.9510
- Linker Heavy Atoms Difference Norm: 0.0067
## 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: reduce_lr_on_plateau
- lr_scheduler_warmup_steps: 400
- training_steps: 100000
- mixed_precision_training: Native AMP
### Training results
| 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 |
|:-------------:|:-------:|:------:|:---------------:|:----------:|:---------------------------:|:-------------------------------:|:-----------------:|:-------------------------------:|:----------------------------:|:-----------------------------:|:------------:|:---------------------------:|:----------------------:|:-------------------:|:----------------------:|:------------------------------:|:------------------------------:|:------------:|:---------:|:-------------------------------------------------------------------:|:--------:|:-------------:|:-------------------------:|:-----------------------:|:-----------------------:|:----------------------:|:--------------------------:|:--------------------------:|:--------:|:-----------------------:|:------:|:---------------------------:|:-------------------:|:--------------------------:|:-------------------------:|:---------:|:----------------------------------:|
| 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 |
| 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 |
### Framework versions
- Transformers 4.44.2
- Pytorch 2.4.1+cu121
- Datasets 3.0.0
- Tokenizers 0.19.1
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