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: 0.3562
E3 Heavy Atoms Difference: 0.5450
Tanimoto Similarity: 0.0
Linker Heavy Atoms Difference: 0.2341
Poi Graph Edit Distance: inf
Poi Heavy Atoms Difference Norm: 0.0500
Reassembly Nostereo: 0.6352
Has All Attachment Points: 0.9914
Num Fragments: 2.9996
Linker Equal: 0.8443
Reassembly: 0.6021
E3 Graph Edit Distance Norm: inf
Poi Valid: 0.9499
E3 Graph Edit Distance: inf
E3 Equal: 0.8238
Poi Heavy Atoms Difference: 1.5246
E3 Heavy Atoms Difference Norm: 0.0139
Has Three Substructures: 0.9996
Linker Valid: 0.9984
Linker Has Attachment Point(s): 0.9984
Poi Graph Edit Distance Norm: inf
Heavy Atoms Difference Norm: 0.0733
Valid: 0.9362
E3 Valid: 0.9859
Linker Heavy Atoms Difference Norm: 0.0034
Poi Tanimoto Similarity: 0.0
Poi Equal: 0.7947
Linker Tanimoto Similarity: 0.0
All Ligands Equal: 0.5946
Linker Graph Edit Distance Norm: inf
Poi Has Attachment Point(s): 0.9499
E3 Has Attachment Point(s): 0.9859
Linker Graph Edit Distance: 15934844192634561100698130285457299401122608004817217891860480.0000
E3 Tanimoto Similarity: 0.0
Heavy Atoms Difference: 5.5146

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	E3 Heavy Atoms Difference	Tanimoto Similarity	Linker Heavy Atoms Difference	Poi Graph Edit Distance	Poi Heavy Atoms Difference Norm	Reassembly Nostereo	Has All Attachment Points	Num Fragments	Linker Equal	Reassembly	E3 Graph Edit Distance Norm	Poi Valid	E3 Graph Edit Distance	E3 Equal	Poi Heavy Atoms Difference	E3 Heavy Atoms Difference Norm	Has Three Substructures	Linker Valid	Linker Has Attachment Point(s)	Poi Graph Edit Distance Norm	Heavy Atoms Difference Norm	Valid	E3 Valid	Linker Heavy Atoms Difference Norm	Poi Tanimoto Similarity	Poi Equal	Linker Tanimoto Similarity	All Ligands Equal	Linker Graph Edit Distance Norm	Poi Has Attachment Point(s)	E3 Has Attachment Point(s)	Linker Graph Edit Distance	E3 Tanimoto Similarity	Heavy Atoms Difference
0.0006	10.5208	80000	0.3546	0.2397	0.0	0.2432	inf	0.0551	0.6277	0.9911	2.9999	0.8418	0.5965	inf	0.9407	inf	0.8234	1.7421	0.0025	0.9999	0.9980	0.9980	inf	0.0768	0.9301	0.9907	0.0018	0.0	0.7882	0.0	0.5897	inf	0.9407	0.9907	20361189801699711253012395652022580557179454652619232886390784.0000	0.0	5.7380
0.0006	13.1510	100000	0.3562	0.5450	0.0	0.2341	inf	0.0500	0.6352	0.9914	2.9996	0.8443	0.6021	inf	0.9499	inf	0.8238	1.5246	0.0139	0.9996	0.9984	0.9984	inf	0.0733	0.9362	0.9859	0.0034	0.0	0.7947	0.0	0.5946	inf	0.9499	0.9859	15934844192634561100698130285457299401122608004817217891860480.0000	0.0	5.5146

Framework versions

Transformers 4.44.2
Pytorch 2.4.1+cu121
Datasets 3.0.0
Tokenizers 0.19.1