ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_cosine_restarts-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: 0.3584
• Linker Has Attachment Point(s): 0.9983
• E3 Valid: 0.9934
• E3 Graph Edit Distance Norm: inf
• E3 Has Attachment Point(s): 0.9934
• E3 Heavy Atoms Difference: 0.1883
• Poi Valid: 0.9567
• Poi Tanimoto Similarity: 0.0
• Has All Attachment Points: 0.9939
• Num Fragments: 2.9997
• Reassembly: 0.6015
• Poi Equal: 0.7927
• Poi Graph Edit Distance: inf
• Linker Graph Edit Distance Norm: inf
• Linker Valid: 0.9983
• Linker Heavy Atoms Difference Norm: 0.0036
• Poi Has Attachment Point(s): 0.9567
• Valid: 0.9493
• Poi Heavy Atoms Difference Norm: 0.0441
• Tanimoto Similarity: 0.0
• Linker Tanimoto Similarity: 0.0
• Linker Graph Edit Distance: inf
• Linker Equal: 0.8512
• Heavy Atoms Difference Norm: 0.0570
• E3 Heavy Atoms Difference Norm: 0.0026
• Heavy Atoms Difference: 4.2382
• Poi Graph Edit Distance Norm: inf
• Linker Heavy Atoms Difference: 0.2012
• Reassembly Nostereo: 0.6357
• E3 Graph Edit Distance: inf
• E3 Tanimoto Similarity: 0.0
• Has Three Substructures: 0.9997
• E3 Equal: 0.8282
• Poi Heavy Atoms Difference: 1.3882
• All Ligands Equal: 0.5946

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: 800
• training_steps: 100000
• mixed_precision_training: Native AMP

Training results

Training Loss	Epoch	Step	All Ligands Equal	E3 Equal	E3 Graph Edit Distance	E3 Graph Edit Distance Norm	E3 Has Attachment Point(s)	E3 Heavy Atoms Difference	E3 Heavy Atoms Difference Norm	E3 Tanimoto Similarity	E3 Valid	Has All Attachment Points	Has Three Substructures	Heavy Atoms Difference	Heavy Atoms Difference Norm	Linker Equal	Linker Graph Edit Distance	Linker Graph Edit Distance Norm	Linker Has Attachment Point(s)	Linker Heavy Atoms Difference	Linker Heavy Atoms Difference Norm	Linker Tanimoto Similarity	Linker Valid	Validation Loss	Num Fragments	Poi Equal	Poi Graph Edit Distance	Poi Graph Edit Distance Norm	Poi Has Attachment Point(s)	Poi Heavy Atoms Difference	Poi Heavy Atoms Difference Norm	Poi Tanimoto Similarity	Poi Valid	Reassembly	Reassembly Nostereo	Tanimoto Similarity	Valid
0.0212	0.4932	5000	0.4396	0.7734	inf	inf	0.9979	0.1237	-0.0043	0.0	0.9979	0.9903	0.9994	4.6065	0.0591	0.6416	24787535410764872823308202666266910179524056896382338942894080.0000	inf	0.9975	0.5099	0.0050	0.0	0.9975	0.2852	3.0001	0.7208	inf	inf	0.9528	1.4706	0.0414	0.0	0.9528	0.4464	0.4783	0.0	0.9500
0.011	0.7398	7500	0.4827	0.7827	inf	inf	0.9905	0.5439	0.0117	0.0	0.9905	0.9858	0.9990	6.6114	0.0846	0.7075	27443342776203963485595838968590031296472552664861602492710912.0000	0.0511	0.9973	0.3255	-0.0008	0.0	0.9973	0.3022	3.0001	0.7332	inf	inf	0.9389	2.2561	0.0673	0.0	0.9389	0.4896	0.5176	0.0	0.9294
0.007	0.9864	10000	0.5318	0.8017	inf	inf	0.9922	0.2046	-0.0014	0.0	0.9922	0.9900	0.9991	4.5184	0.0596	0.7645	inf	inf	0.9980	0.3372	0.0044	0.0	0.9980	0.3093	2.9998	0.7580	inf	inf	0.9534	1.3755	0.0422	0.0	0.9534	0.5402	0.5728	0.0	0.9458
0.0005	6.9047	70000	0.3363	0.9977	0.9890	inf	0.9890	0.3207	0.9573	0.0	0.9891	2.9997	0.5983	0.7900	inf	inf	0.9977	0.0009	0.9573	0.9452	0.0404	0.0	0.0	23016997167138810478786188190104988023843767118069314732687360.0000	0.8439	0.0615	0.0015	4.7337	inf	0.2010	0.6325	inf	0.0	0.9996	0.8273	1.3261	0.5905
0.0005	7.1513	72500	0.3347	0.9974	0.9887	inf	0.9887	0.3786	0.9609	0.0	0.9926	3.0003	0.5987	0.7891	inf	inf	0.9974	0.0033	0.9609	0.9487	0.0401	0.0	0.0	25672804532577903995569209904347871257364201785538851047997440.0000	0.8407	0.0588	0.0044	4.5035	inf	0.2400	0.6343	inf	0.0	0.9994	0.8260	1.3144	0.5911
0.0008	7.3979	75000	0.3530	0.9965	0.9897	inf	0.9897	0.2380	0.9452	0.0	0.9885	2.9999	0.5951	0.7843	inf	inf	0.9965	0.0028	0.9452	0.9335	0.0534	0.0	0.0	inf	0.8362	0.0716	-0.0004	5.4047	inf	0.2346	0.6308	inf	0.0	0.9992	0.8239	1.6527	0.5876
0.0016	7.6445	77500	0.3554	0.9958	0.9887	inf	0.9887	0.4638	0.9404	0.0	0.9874	3.0001	0.5911	0.7801	inf	inf	0.9958	0.0081	0.9404	0.9281	0.0595	0.0	0.0	41607648725212467950762725601724932775058748689346341705351168.0000	0.8252	0.0795	0.0085	5.9789	inf	0.3348	0.6265	inf	0.0	0.9988	0.8217	1.7751	0.5832
0.0004	7.8911	80000	0.3551	0.9988	0.9888	inf	0.9888	0.4881	0.9533	0.0	0.9912	2.9999	0.6013	0.7877	inf	inf	0.9988	-0.0009	0.9533	0.9417	0.0421	0.0	0.0	inf	0.8503	0.0657	0.0099	5.0296	inf	0.1533	0.6381	inf	0.0	0.9997	0.8263	1.4026	0.5946
0.0005	8.1377	82500	0.3597	0.9981	0.9889	inf	0.9889	0.1790	0.9525	0.0	0.9868	3.0002	0.6001	0.7882	inf	inf	0.9981	0.0018	0.9525	0.9414	0.0426	0.0	0.0	19475920679886688644237544649700905829055126460433539077767168.0000	0.8470	0.0655	0.0028	4.8411	inf	0.1896	0.6345	inf	0.0	0.9995	0.8283	1.3738	0.5931
0.0006	8.3843	85000	0.3532	0.9969	0.9912	inf	0.9912	0.1049	0.9551	0.0	0.9896	2.9999	0.5975	0.7880	inf	inf	0.9969	0.0045	0.9551	0.9444	0.0424	0.0	0.0	inf	0.8409	0.0589	-0.0023	4.4111	inf	0.2537	0.6296	inf	0.0	0.9997	0.8255	1.3678	0.5902
0.0015	8.6309	87500	0.3422	0.9975	0.9941	inf	0.9941	0.1578	0.9388	0.0	0.9927	2.9999	0.5950	0.7813	inf	inf	0.9975	0.0093	0.9388	0.9317	0.0561	0.0	0.0	24787535410764872823308202666266910179524056896382338942894080.0000	0.8415	0.0740	-0.0025	5.6405	inf	0.3237	0.6294	inf	0.0	0.9999	0.8237	1.7777	0.5883
0.0004	8.8775	90000	0.3554	0.9982	0.9916	inf	0.9916	0.1501	0.9603	0.0	0.9942	2.9996	0.6016	0.7898	inf	inf	0.9982	0.0017	0.9603	0.9511	0.0345	0.0	0.0	17705382436260626299715530173538983673374836682120514867560448.0000	0.8493	0.0532	-0.0026	4.1205	inf	0.1871	0.6375	inf	0.0	0.9996	0.8269	1.1763	0.5943
0.0004	9.1241	92500	0.3515	0.9974	0.9851	inf	0.9851	0.4341	0.9510	0.0	0.9898	2.9996	0.6034	0.7930	inf	inf	0.9974	0.0031	0.9510	0.9348	0.0433	0.0	0.0	inf	0.8492	0.0691	0.0076	5.2700	inf	0.2049	0.6379	inf	0.0	0.9996	0.8267	1.4062	0.5962
0.0006	9.3707	95000	0.3472	0.9978	0.9886	inf	0.9886	0.3374	0.9533	0.0	0.9892	2.9997	0.5980	0.7876	inf	inf	0.9978	0.0030	0.9533	0.9408	0.0424	0.0	0.0	inf	0.8475	0.0656	0.0104	4.8067	inf	0.2247	0.6291	inf	0.0	0.9997	0.8252	1.2974	0.5910
0.0009	9.6173	97500	0.3462	0.9970	0.9955	inf	0.9955	0.2014	0.9459	0.0	0.9920	2.9999	0.5945	0.7863	inf	inf	0.9970	-0.0004	0.9459	0.9390	0.0480	0.0	0.0	30099150141643059856874246094752676646564926231321411573514240.0000	0.8381	0.0651	0.0015	4.9979	inf	0.1987	0.6289	inf	0.0	0.9999	0.8247	1.5948	0.5873
0.0004	9.8639	100000	0.3584	0.9983	0.9934	inf	0.9934	0.1883	0.9567	0.0	0.9939	2.9997	0.6015	0.7927	inf	inf	0.9983	0.0036	0.9567	0.9493	0.0441	0.0	0.0	inf	0.8512	0.0570	0.0026	4.2382	inf	0.2012	0.6357	inf	0.0	0.9997	0.8282	1.3882	0.5946

Framework versions

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