ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-rand-smiles-train-0.25

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: 0.3624
• Linker Equal: 0.8351
• E3 Graph Edit Distance Norm: inf
• Poi Heavy Atoms Difference Norm: 0.0311
• Poi Has Attachment Point(s): 0.9593
• Poi Graph Edit Distance Norm: inf
• Valid: 0.9367
• Poi Valid: 0.9593
• Poi Graph Edit Distance: inf
• Reassembly Nostereo: 0.6220
• Linker Has Attachment Point(s): 0.9970
• Poi Heavy Atoms Difference: 1.1101
• Has Three Substructures: 1.0
• E3 Heavy Atoms Difference Norm: 0.0153
• Linker Valid: 0.9970
• Linker Tanimoto Similarity: 0.0
• E3 Has Attachment Point(s): 0.9798
• Poi Equal: 0.7936
• All Ligands Equal: 0.5870
• Heavy Atoms Difference Norm: 0.0731
• Linker Heavy Atoms Difference Norm: 0.0030
• Heavy Atoms Difference: 5.4708
• Tanimoto Similarity: 0.0
• Num Fragments: 3.0
• E3 Graph Edit Distance: inf
• Linker Graph Edit Distance: inf
• Linker Heavy Atoms Difference: 0.2800
• Poi Tanimoto Similarity: 0.0
• Linker Graph Edit Distance Norm: inf
• Has All Attachment Points: 0.9888
• E3 Tanimoto Similarity: 0.0
• Reassembly: 0.5944
• E3 Heavy Atoms Difference: 0.4994
• E3 Equal: 0.8276
• E3 Valid: 0.9798

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	Linker Equal	E3 Graph Edit Distance Norm	Poi Heavy Atoms Difference Norm	Poi Has Attachment Point(s)	Poi Graph Edit Distance Norm	Valid	Poi Valid	Poi Graph Edit Distance	Reassembly Nostereo	Linker Has Attachment Point(s)	Poi Heavy Atoms Difference	Has Three Substructures	E3 Heavy Atoms Difference Norm	Linker Valid	Linker Tanimoto Similarity	E3 Has Attachment Point(s)	Poi Equal	All Ligands Equal	Heavy Atoms Difference Norm	Linker Heavy Atoms Difference Norm	Heavy Atoms Difference	Tanimoto Similarity	Num Fragments	E3 Graph Edit Distance	Linker Graph Edit Distance	Linker Heavy Atoms Difference	Poi Tanimoto Similarity	Linker Graph Edit Distance Norm	Has All Attachment Points	E3 Tanimoto Similarity	Reassembly	E3 Heavy Atoms Difference	E3 Equal	E3 Valid
0.0006	31.5582	80000	0.3577	0.8324	inf	0.0305	0.9579	inf	0.9328	0.9579	inf	0.6230	0.9967	1.0626	0.9999	0.0251	0.9967	0.0	0.9771	0.7863	0.5856	0.0758	0.0051	5.7523	0.0	3.0001	inf	inf	0.2647	0.0	inf	0.9890	0.0	0.5934	0.8042	0.8272	0.9771
0.0005	39.4477	100000	0.3624	0.8351	inf	0.0311	0.9593	inf	0.9367	0.9593	inf	0.6220	0.9970	1.1101	1.0	0.0153	0.9970	0.0	0.9798	0.7936	0.5870	0.0731	0.0030	5.4708	0.0	3.0	inf	inf	0.2800	0.0	inf	0.9888	0.0	0.5944	0.4994	0.8276	0.9798

Framework versions

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