---
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
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# 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