This model is a fine-tuned version of seyonec/ChemBERTa-zinc-base-v1 on the ailab-bio/PROTAC-Splitter-Dataset dataset. It achieves the following results on the evaluation set:

Loss: 0.3124
E3 Graph Edit Distance Norm: inf
Poi Has Attachment Point(s): 0.9294
Linker Heavy Atoms Difference: 0.3252
Reassembly Nostereo: 0.5845
E3 Valid: 0.9942
Poi Heavy Atoms Difference Norm: 0.0668
Linker Graph Edit Distance: inf
All Ligands Equal: 0.5477
Has All Attachment Points: 0.9857
Linker Valid: 0.9951
E3 Tanimoto Similarity: 0.0
Heavy Atoms Difference: 6.4929
Tanimoto Similarity: 0.0
Reassembly: 0.5549
E3 Heavy Atoms Difference: 0.3628
Poi Graph Edit Distance Norm: inf
Valid: 0.9232
Linker Tanimoto Similarity: 0.0
Linker Heavy Atoms Difference Norm: 0.0050
Poi Valid: 0.9294
Linker Graph Edit Distance Norm: inf
Poi Equal: 0.7673
Linker Equal: 0.7726
E3 Graph Edit Distance: inf
Poi Graph Edit Distance: inf
Has Three Substructures: 0.9983
Poi Heavy Atoms Difference: 2.0849
Num Fragments: 3.0008
Poi Tanimoto Similarity: 0.0
E3 Heavy Atoms Difference Norm: 0.0044
E3 Has Attachment Point(s): 0.9942
E3 Equal: 0.8035
Linker Has Attachment Point(s): 0.9951
Heavy Atoms Difference Norm: 0.0854

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 Graph Edit Distance Norm	Poi Has Attachment Point(s)	Linker Heavy Atoms Difference	Reassembly Nostereo	E3 Valid	Poi Heavy Atoms Difference Norm	Linker Graph Edit Distance	All Ligands Equal	Has All Attachment Points	Linker Valid	Heavy Atoms Difference	Reassembly	E3 Heavy Atoms Difference	Poi Graph Edit Distance Norm	Valid	Linker Heavy Atoms Difference Norm	Poi Valid	Linker Graph Edit Distance Norm	Poi Equal	Linker Equal	E3 Graph Edit Distance	Poi Graph Edit Distance	Has Three Substructures	Poi Heavy Atoms Difference	Num Fragments	E3 Heavy Atoms Difference Norm	E3 Has Attachment Point(s)	E3 Equal	Linker Has Attachment Point(s)	Heavy Atoms Difference Norm
0.0086	0.4932	5000	0.2931	inf	0.9248	0.6527	0.5238	0.9949	0.0785	46033994334277620957572376380209976047687534236138629465374720.0000	0.4899	0.9820	0.9954	7.4350	0.4972	0.3592	inf	0.9182	0.0200	0.9248	0.0544	0.7416	0.7092	inf	inf	0.9988	2.4199	3.0004	0.0041	0.9949	0.7832	0.9954	0.0974
0.004	0.7398	7500	0.3098	inf	0.9225	0.2498	0.5729	0.9924	0.0709	59313031161473097104973641187183678565005524270457129338404864.0000	0.5381	0.9818	0.9941	6.9868	0.5451	0.4005	inf	0.9147	-0.0010	0.9225	inf	0.7603	0.7604	inf	inf	0.9978	2.2024	3.0006	0.0081	0.9924	0.8044	0.9941	0.0924
0.003	0.9864	10000	0.3124	inf	0.9294	0.3252	0.5845	0.9942	0.0668	inf	0.5477	0.9857	0.9951	6.4929	0.5549	0.3628	inf	0.9232	0.0050	0.9294	inf	0.7673	0.7726	inf	inf	0.9983	2.0849	3.0008	0.0044	0.9942	0.8035	0.9951	0.0854

Framework versions

Transformers 4.44.2
Pytorch 2.4.1+cu121
Datasets 3.0.0
Tokenizers 0.19.1