---
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-0.25
  results: []
---

<!-- This model card has been generated automatically according to the information the Trainer had access to. You
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# ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-rand-smiles-train-0.25

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: 0.3624
- Linker Equal: 0.8351
- E3 Graph Edit Distance Norm: inf
- Poi Heavy Atoms Difference Norm: 0.0311
- Poi Has Attachment Point(s): 0.9593
- Poi Graph Edit Distance Norm: inf
- Valid: 0.9367
- Poi Valid: 0.9593
- Poi Graph Edit Distance: inf
- Reassembly Nostereo: 0.6220
- Linker Has Attachment Point(s): 0.9970
- Poi Heavy Atoms Difference: 1.1101
- Has Three Substructures: 1.0
- E3 Heavy Atoms Difference Norm: 0.0153
- Linker Valid: 0.9970
- Linker Tanimoto Similarity: 0.0
- E3 Has Attachment Point(s): 0.9798
- Poi Equal: 0.7936
- All Ligands Equal: 0.5870
- Heavy Atoms Difference Norm: 0.0731
- Linker Heavy Atoms Difference Norm: 0.0030
- Heavy Atoms Difference: 5.4708
- Tanimoto Similarity: 0.0
- Num Fragments: 3.0
- E3 Graph Edit Distance: inf
- Linker Graph Edit Distance: inf
- Linker Heavy Atoms Difference: 0.2800
- Poi Tanimoto Similarity: 0.0
- Linker Graph Edit Distance Norm: inf
- Has All Attachment Points: 0.9888
- E3 Tanimoto Similarity: 0.0
- Reassembly: 0.5944
- E3 Heavy Atoms Difference: 0.4994
- E3 Equal: 0.8276
- E3 Valid: 0.9798

## 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 | 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 |
|:-------------:|:-------:|:------:|:---------------:|:------------:|:---------------------------:|:-------------------------------:|:---------------------------:|:----------------------------:|:------:|:---------:|:-----------------------:|:-------------------:|:------------------------------:|:--------------------------:|:-----------------------:|:------------------------------:|:------------:|:--------------------------:|:--------------------------:|:---------:|:-----------------:|:---------------------------:|:----------------------------------:|:----------------------:|:-------------------:|:-------------:|:----------------------:|:--------------------------:|:-----------------------------:|:-----------------------:|:-------------------------------:|:-------------------------:|:----------------------:|:----------:|:-------------------------:|:--------:|:--------:|
| 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   |
| 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   |


### Framework versions

- Transformers 4.44.2
- Pytorch 2.4.1+cu121
- Datasets 3.0.0
- Tokenizers 0.19.1