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 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