---
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-opt25
  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-opt25

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: 0.3420
- Num Fragments: 3.0002
- Linker Heavy Atoms Difference: 0.1689
- Linker Graph Edit Distance: 37181303116147309234962303999400365269286085344573508414341120.0000
- Tanimoto Similarity: 0.0
- Linker Tanimoto Similarity: 0.0
- E3 Valid: 0.9732
- Linker Has Attachment Point(s): 0.9963
- Poi Equal: 0.7897
- Heavy Atoms Difference: 8.0244
- Poi Has Attachment Point(s): 0.9305
- E3 Equal: 0.8302
- Linker Graph Edit Distance Norm: inf
- E3 Has Attachment Point(s): 0.9732
- Has Three Substructures: 0.9995
- Poi Heavy Atoms Difference Norm: 0.0690
- Linker Equal: 0.8419
- Heavy Atoms Difference Norm: 0.1076
- E3 Heavy Atoms Difference: 1.0454
- Poi Valid: 0.9305
- Valid: 0.9027
- Linker Heavy Atoms Difference Norm: -0.0046
- Has All Attachment Points: 0.9796
- E3 Graph Edit Distance: inf
- Linker Valid: 0.9963
- Poi Tanimoto Similarity: 0.0
- Poi Graph Edit Distance Norm: inf
- Poi Heavy Atoms Difference: 2.0482
- Poi Graph Edit Distance: inf
- Reassembly Nostereo: 0.6261
- E3 Graph Edit Distance Norm: inf
- E3 Heavy Atoms Difference Norm: 0.0335
- Reassembly: 0.6073
- All Ligands Equal: 0.5992
- E3 Tanimoto Similarity: 0.0

## 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
- training_steps: 100000
- mixed_precision_training: Native AMP

### Training results

| Training Loss | Epoch  | Step   | Validation Loss | Num Fragments | Linker Heavy Atoms Difference | Linker Graph Edit Distance                                          | Tanimoto Similarity | Linker Tanimoto Similarity | E3 Valid | Linker Has Attachment Point(s) | Poi Equal | Heavy Atoms Difference | Poi Has Attachment Point(s) | E3 Equal | Linker Graph Edit Distance Norm | E3 Has Attachment Point(s) | Has Three Substructures | Poi Heavy Atoms Difference Norm | Linker Equal | Heavy Atoms Difference Norm | E3 Heavy Atoms Difference | Poi Valid | Valid  | Linker Heavy Atoms Difference Norm | Has All Attachment Points | E3 Graph Edit Distance | Linker Valid | Poi Tanimoto Similarity | Poi Graph Edit Distance Norm | Poi Heavy Atoms Difference | Poi Graph Edit Distance                                              | Reassembly Nostereo | E3 Graph Edit Distance Norm | E3 Heavy Atoms Difference Norm | Reassembly | All Ligands Equal | E3 Tanimoto Similarity |
|:-------------:|:------:|:------:|:---------------:|:-------------:|:-----------------------------:|:-------------------------------------------------------------------:|:-------------------:|:--------------------------:|:--------:|:------------------------------:|:---------:|:----------------------:|:---------------------------:|:--------:|:-------------------------------:|:--------------------------:|:-----------------------:|:-------------------------------:|:------------:|:---------------------------:|:-------------------------:|:---------:|:------:|:----------------------------------:|:-------------------------:|:----------------------:|:------------:|:-----------------------:|:----------------------------:|:--------------------------:|:--------------------------------------------------------------------:|:-------------------:|:---------------------------:|:------------------------------:|:----------:|:-----------------:|:----------------------:|
| 0.0005        | 7.8911 | 80000  | 0.3375          | 2.9994        | 0.2223                        | inf                                                                 | 0.0                 | 0.0                        | 0.9717   | 0.9961                         | 0.7867    | 9.0605                 | 0.9179                      | 0.8268   | inf                             | 0.9717                     | 0.9994                  | 0.0813                          | 0.8393       | 0.1211                      | 0.9062                    | 0.9179    | 0.8893 | 0.0019                             | 0.9788                    | inf                    | 0.9961       | 0.0                     | inf                          | 2.4517                     | 820644475920679939503384490879847350906393395732940812913213440.0000 | 0.6211              | inf                         | 0.0334                         | 0.6011     | 0.5936            | 0.0                    |
| 0.0005        | 9.8639 | 100000 | 0.3420          | 3.0002        | 0.1689                        | 37181303116147309234962303999400365269286085344573508414341120.0000 | 0.0                 | 0.0                        | 0.9732   | 0.9963                         | 0.7897    | 8.0244                 | 0.9305                      | 0.8302   | inf                             | 0.9732                     | 0.9995                  | 0.0690                          | 0.8419       | 0.1076                      | 1.0454                    | 0.9305    | 0.9027 | -0.0046                            | 0.9796                    | inf                    | 0.9963       | 0.0                     | inf                          | 2.0482                     | inf                                                                  | 0.6261              | inf                         | 0.0335                         | 0.6073     | 0.5992            | 0.0                    |


### Framework versions

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