ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25-rand-smiles

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: 0.3184
• E3 Tanimoto Similarity: 0.0
• Poi Equal: 0.7620
• E3 Equal: 0.8036
• Poi Tanimoto Similarity: 0.0
• Poi Valid: 0.9589
• Reassembly: 0.5459
• All Ligands Equal: 0.5390
• Poi Graph Edit Distance: inf
• Linker Graph Edit Distance: 28328611898016997512352231618590754490884636453008387363307520.0000
• Poi Graph Edit Distance Norm: inf
• Linker Tanimoto Similarity: 0.0
• Valid: 0.9547
• E3 Graph Edit Distance Norm: inf
• Poi Has Attachment Point(s): 0.9589
• Linker Equal: 0.7668
• Linker Heavy Atoms Difference Norm: 0.0034
• Has All Attachment Points: 0.9905
• Heavy Atoms Difference: 4.1049
• Has Three Substructures: 0.9992
• Tanimoto Similarity: 0.0
• Heavy Atoms Difference Norm: 0.0536
• Poi Heavy Atoms Difference Norm: 0.0352
• Linker Has Attachment Point(s): 0.9972
• E3 Heavy Atoms Difference: 0.2976
• E3 Graph Edit Distance: inf
• Linker Valid: 0.9972
• E3 Heavy Atoms Difference Norm: 0.0033
• E3 Has Attachment Point(s): 0.9966
• E3 Valid: 0.9966
• Reassembly Nostereo: 0.5799
• Linker Heavy Atoms Difference: 0.3031
• Num Fragments: 3.0003
• Linker Graph Edit Distance Norm: inf
• Poi Heavy Atoms Difference: 1.1856

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 Tanimoto Similarity	Poi Equal	E3 Equal	Poi Tanimoto Similarity	Poi Valid	Reassembly	All Ligands Equal	Poi Graph Edit Distance	Linker Graph Edit Distance	Poi Graph Edit Distance Norm	Linker Tanimoto Similarity	Valid	E3 Graph Edit Distance Norm	Poi Has Attachment Point(s)	Linker Equal	Linker Heavy Atoms Difference Norm	Has All Attachment Points	Heavy Atoms Difference	Has Three Substructures	Tanimoto Similarity	Heavy Atoms Difference Norm	Poi Heavy Atoms Difference Norm	Linker Has Attachment Point(s)	E3 Heavy Atoms Difference	E3 Graph Edit Distance	Linker Valid	E3 Heavy Atoms Difference Norm	E3 Has Attachment Point(s)	E3 Valid	Reassembly Nostereo	Linker Heavy Atoms Difference	Num Fragments	Linker Graph Edit Distance Norm	Poi Heavy Atoms Difference
0.012	0.4932	5000	0.3055	0.0	0.7354	0.7897	0.0	0.9479	0.4899	0.4824	inf	25672804532577903995569209904347871257364201785538851047997440.0000	inf	0.0	0.9441	inf	0.9479	0.6946	0.0103	0.9873	4.9586	0.9995	0.0	0.0650	0.0421	0.9974	0.1648	inf	0.9974	-0.0036	0.9972	0.9972	0.5198	0.5344	3.0005	inf	1.4326
0.0064	0.7398	7500	0.3156	0.0	0.7551	0.8017	0.0	0.9532	0.5359	0.5282	inf	40722379603399433924006332951724209580646664901199556834754560.0000	inf	0.0	0.9477	inf	0.9532	0.7533	-0.0000	0.9873	4.5195	0.9985	0.0	0.0593	0.0396	0.9959	0.3429	inf	0.9959	0.0053	0.9944	0.9944	0.5689	0.2564	3.0003	0.0452	1.3395
0.0051	0.9864	10000	0.3184	0.0	0.7620	0.8036	0.0	0.9589	0.5459	0.5390	inf	28328611898016997512352231618590754490884636453008387363307520.0000	inf	0.0	0.9547	inf	0.9589	0.7668	0.0034	0.9905	4.1049	0.9992	0.0	0.0536	0.0352	0.9972	0.2976	inf	0.9972	0.0033	0.9966	0.9966	0.5799	0.3031	3.0003	inf	1.1856

Framework versions

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