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ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25

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ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_reduce-opt25

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: 0.3420
—Num Fragments: 3.0002
—Linker Heavy Atoms Difference: 0.1689
—Linker Graph Edit Distance: 37181303116147309234962303999400365269286085344573508414341120.0000
—Tanimoto Similarity: 0.0
—Linker Tanimoto Similarity: 0.0
—E3 Valid: 0.9732
—Linker Has Attachment Point(s): 0.9963
—Poi Equal: 0.7897
—Heavy Atoms Difference: 8.0244
—Poi Has Attachment Point(s): 0.9305
—E3 Equal: 0.8302
—Linker Graph Edit Distance Norm: inf
—E3 Has Attachment Point(s): 0.9732
—Has Three Substructures: 0.9995
—Poi Heavy Atoms Difference Norm: 0.0690
—Linker Equal: 0.8419
—Heavy Atoms Difference Norm: 0.1076
—E3 Heavy Atoms Difference: 1.0454
—Poi Valid: 0.9305
—Valid: 0.9027
—Linker Heavy Atoms Difference Norm: -0.0046
—Has All Attachment Points: 0.9796
—E3 Graph Edit Distance: inf
—Linker Valid: 0.9963
—Poi Tanimoto Similarity: 0.0
—Poi Graph Edit Distance Norm: inf
—Poi Heavy Atoms Difference: 2.0482
—Poi Graph Edit Distance: inf
—Reassembly Nostereo: 0.6261
—E3 Graph Edit Distance Norm: inf
—E3 Heavy Atoms Difference Norm: 0.0335
—Reassembly: 0.6073
—All Ligands Equal: 0.5992
—E3 Tanimoto Similarity: 0.0

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
—trainbatchsize: 128
—evalbatchsize: 64
—seed: 42
—optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
—lrschedulertype: reducelron_plateau
—training_steps: 100000
—mixedprecisiontraining: Native AMP

Training results

Training Loss	Epoch	Step	Validation Loss	Num Fragments	Linker Heavy Atoms Difference	Linker Graph Edit Distance	Tanimoto Similarity	Linker Tanimoto Similarity	E3 Valid	Linker Has Attachment Point(s)	Poi Equal	Heavy Atoms Difference	Poi Has Attachment Point(s)	E3 Equal	Linker Graph Edit Distance Norm	E3 Has Attachment Point(s)	Has Three Substructures	Poi Heavy Atoms Difference Norm	Linker Equal	Heavy Atoms Difference Norm	E3 Heavy Atoms Difference	Poi Valid	Valid	Linker Heavy Atoms Difference Norm	Has All Attachment Points	E3 Graph Edit Distance	Linker Valid	Poi Tanimoto Similarity	Poi Graph Edit Distance Norm	Poi Heavy Atoms Difference	Poi Graph Edit Distance	Reassembly Nostereo	E3 Graph Edit Distance Norm	E3 Heavy Atoms Difference Norm	Reassembly	All Ligands Equal	E3 Tanimoto Similarity
0.0005	7.8911	80000	0.3375	2.9994	0.2223	inf	0.0	0.0	0.9717	0.9961	0.7867	9.0605	0.9179	0.8268	inf	0.9717	0.9994	0.0813	0.8393	0.1211	0.9062	0.9179	0.8893	0.0019	0.9788	inf	0.9961	0.0	inf	2.4517	820644475920679939503384490879847350906393395732940812913213440.0000	0.6211	inf	0.0334	0.6011	0.5936	0.0
0.0005	9.8639	100000	0.3420	3.0002	0.1689	37181303116147309234962303999400365269286085344573508414341120.0000	0.0	0.0	0.9732	0.9963	0.7897	8.0244	0.9305	0.8302	inf	0.9732	0.9995	0.0690	0.8419	0.1076	1.0454	0.9305	0.9027	-0.0046	0.9796	inf	0.9963	0.0	inf	2.0482	inf	0.6261	inf	0.0335	0.6073	0.5992	0.0

Framework versions

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