ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_cosine_restarts-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: 0.3093
• Linker Heavy Atoms Difference: 0.3372
• Has Three Substructures: 0.9991
• Poi Valid: 0.9534
• Linker Graph Edit Distance Norm: inf
• Reassembly: 0.5402
• Valid: 0.9458
• Poi Heavy Atoms Difference: 1.3755
• E3 Has Attachment Point(s): 0.9922
• Poi Heavy Atoms Difference Norm: 0.0422
• Heavy Atoms Difference: 4.5184
• Has All Attachment Points: 0.9900
• Poi Tanimoto Similarity: 0.0
• Heavy Atoms Difference Norm: 0.0596
• E3 Heavy Atoms Difference: 0.2046
• All Ligands Equal: 0.5318
• E3 Heavy Atoms Difference Norm: -0.0014
• Linker Heavy Atoms Difference Norm: 0.0044
• Tanimoto Similarity: 0.0
• E3 Graph Edit Distance Norm: inf
• Poi Equal: 0.7580
• Poi Has Attachment Point(s): 0.9534
• Poi Graph Edit Distance Norm: inf
• Num Fragments: 2.9998
• Linker Graph Edit Distance: inf
• Linker Valid: 0.9980
• Linker Tanimoto Similarity: 0.0
• Poi Graph Edit Distance: inf
• E3 Equal: 0.8017
• Linker Has Attachment Point(s): 0.9980
• Linker Equal: 0.7645
• E3 Tanimoto Similarity: 0.0
• Reassembly Nostereo: 0.5728
• E3 Valid: 0.9922
• E3 Graph Edit Distance: inf

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_with_restarts
• lr_scheduler_warmup_steps: 100
• training_steps: 10000
• mixed_precision_training: Native AMP

Training results

Training Loss	Epoch	Step	Validation Loss	Linker Heavy Atoms Difference	Has Three Substructures	Poi Valid	Linker Graph Edit Distance Norm	Reassembly	Valid	Poi Heavy Atoms Difference	E3 Has Attachment Point(s)	Poi Heavy Atoms Difference Norm	Heavy Atoms Difference	Has All Attachment Points	Poi Tanimoto Similarity	Heavy Atoms Difference Norm	E3 Heavy Atoms Difference	All Ligands Equal	E3 Heavy Atoms Difference Norm	Linker Heavy Atoms Difference Norm	Tanimoto Similarity	E3 Graph Edit Distance Norm	Poi Equal	Poi Has Attachment Point(s)	Poi Graph Edit Distance Norm	Num Fragments	Linker Graph Edit Distance	Linker Valid	Linker Tanimoto Similarity	Poi Graph Edit Distance	E3 Equal	Linker Has Attachment Point(s)	Linker Equal	E3 Tanimoto Similarity	Reassembly Nostereo	E3 Valid	E3 Graph Edit Distance
0.0212	0.4932	5000	0.2852	0.5099	0.9994	0.9528	inf	0.4464	0.9500	1.4706	0.9979	0.0414	4.6065	0.9903	0.0	0.0591	0.1237	0.4396	-0.0043	0.0050	0.0	inf	0.7208	0.9528	inf	3.0001	24787535410764872823308202666266910179524056896382338942894080.0000	0.9975	0.0	inf	0.7734	0.9975	0.6416	0.0	0.4783	0.9979	inf
0.011	0.7398	7500	0.3022	0.3255	0.9990	0.9389	0.0511	0.4896	0.9294	2.2561	0.9905	0.0673	6.6114	0.9858	0.0	0.0846	0.5439	0.4827	0.0117	-0.0008	0.0	inf	0.7332	0.9389	inf	3.0001	27443342776203963485595838968590031296472552664861602492710912.0000	0.9973	0.0	inf	0.7827	0.9973	0.7075	0.0	0.5176	0.9905	inf
0.007	0.9864	10000	0.3093	0.3372	0.9991	0.9534	inf	0.5402	0.9458	1.3755	0.9922	0.0422	4.5184	0.9900	0.0	0.0596	0.2046	0.5318	-0.0014	0.0044	0.0	inf	0.7580	0.9534	inf	2.9998	inf	0.9980	0.0	inf	0.8017	0.9980	0.7645	0.0	0.5728	0.9922	inf

Framework versions

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