ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-rand-smiles-train-0.75

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