ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_cosine

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: 0.3829
• E3 Graph Edit Distance: inf
• Poi Valid: 0.9394
• Tanimoto Similarity: 0.0
• Has All Attachment Points: 0.9847
• Linker Graph Edit Distance: inf
• Poi Heavy Atoms Difference: 1.8056
• E3 Graph Edit Distance Norm: inf
• Poi Has Attachment Point(s): 0.9394
• Reassembly Nostereo: 0.6318
• Linker Heavy Atoms Difference: 0.1547
• Reassembly: 0.6055
• Poi Equal: 0.7955
• Linker Valid: 0.9978
• Linker Tanimoto Similarity: 0.0
• Heavy Atoms Difference: 6.1064
• Num Fragments: 3.0001
• Has Three Substructures: 0.9992
• E3 Has Attachment Point(s): 0.9871
• Linker Heavy Atoms Difference Norm: -0.0018
• Poi Graph Edit Distance Norm: inf
• Heavy Atoms Difference Norm: 0.0815
• E3 Tanimoto Similarity: 0.0
• E3 Heavy Atoms Difference Norm: 0.0085
• Valid: 0.9267
• E3 Equal: 0.8283
• Linker Equal: 0.8496
• Linker Has Attachment Point(s): 0.9978
• Poi Heavy Atoms Difference Norm: 0.0577
• E3 Valid: 0.9871
• Poi Tanimoto Similarity: 0.0
• All Ligands Equal: 0.5981
• Poi Graph Edit Distance: inf
• Linker Graph Edit Distance Norm: inf
• E3 Heavy Atoms Difference: 0.4042

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: 100
• 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
0.0086	0.4932	5000	0.4899	0.7832	inf	inf	0.9949	0.3592	0.0041	0.0	0.9949	0.9820	0.9988	7.4350	0.0974	0.7092	46033994334277620957572376380209976047687534236138629465374720.0000	0.0544	0.9954	0.6527	0.0200	0.0	0.9954	0.2931	3.0004	0.7416	inf	inf	0.9248	2.4199	0.0785	0.0	0.9248	0.4972	0.5238	0.0	0.9182
0.004	0.7398	7500	0.5381	0.8044	inf	inf	0.9924	0.4005	0.0081	0.0	0.9924	0.9818	0.9978	6.9868	0.0924	0.7604	59313031161473097104973641187183678565005524270457129338404864.0000	inf	0.9941	0.2498	-0.0010	0.0	0.9941	0.3098	3.0006	0.7603	inf	inf	0.9225	2.2024	0.0709	0.0	0.9225	0.5451	0.5729	0.0	0.9147
0.003	0.9864	10000	0.5477	0.8035	inf	inf	0.9942	0.3628	0.0044	0.0	0.9942	0.9857	0.9983	6.4929	0.0854	0.7726	inf	inf	0.9951	0.3252	0.0050	0.0	0.9951	0.3124	3.0008	0.7673	inf	inf	0.9294	2.0849	0.0668	0.0	0.9294	0.5549	0.5845	0.0	0.9232
0.0003	6.9047	70000	0.3754	inf	0.9355	0.0	0.9836	inf	1.9803	inf	0.9355	0.6316	0.2073	0.6043	0.7957	0.9971	0.0	6.5326	3.0	0.9996	0.9876	-0.0003	inf	0.0869	0.0	0.0041	0.9217	0.8272	0.8437	0.9971	0.0637	0.9876	0.0	0.5963	inf	inf	0.3279
0.0003	7.1513	72500	0.3778	inf	0.9374	0.0	0.9861	28328611898016997512352231618590754490884636453008387363307520.0000	1.8700	inf	0.9374	0.6300	0.2291	0.6030	0.7948	0.9972	0.0	6.2126	2.9996	0.9995	0.9891	0.0029	inf	0.0832	0.0	0.0052	0.9257	0.8270	0.8452	0.9972	0.0606	0.9891	0.0	0.5959	inf	inf	0.3385
0.0002	7.3979	75000	0.3793	inf	0.9372	0.0	0.9868	26558073654390935167830217142428832335204346674695363153100800.0000	1.8756	inf	0.9372	0.6299	0.2073	0.6038	0.7967	0.9973	0.0	6.3769	3.0004	0.9996	0.9872	0.0021	inf	0.0854	0.0	0.0091	0.9240	0.8280	0.8485	0.9973	0.0608	0.9872	0.0	0.5968	inf	inf	0.4008
0.0002	7.6445	77500	0.3748	inf	0.9388	0.0	0.9822	29213881019830025830117853444751953452152842443174626702917632.0000	1.7786	inf	0.9388	0.6312	0.1710	0.6030	0.7936	0.9971	0.0	6.2552	3.0004	0.9993	0.9864	-0.0014	inf	0.0838	0.0	0.0097	0.9256	0.8279	0.8461	0.9971	0.0583	0.9864	0.0	0.5958	inf	inf	0.4591
0.0002	7.8911	80000	0.3756	inf	0.9376	0.0	0.9819	29213881019830031539108624268591477685296720241155172233904128.0000	1.8252	inf	0.9376	0.6275	0.1621	0.6034	0.7962	0.9971	0.0	6.2378	3.0003	0.9990	0.9868	-0.0021	inf	0.0836	0.0	0.0076	0.9251	0.8282	0.8482	0.9971	0.0589	0.9868	0.0	0.5972	inf	inf	0.3862
0.0002	8.1377	82500	0.3801	inf	0.9384	0.0	0.9845	inf	1.8311	inf	0.9384	0.6323	0.1549	0.6044	0.7944	0.9973	0.0	6.1100	3.0003	0.9994	0.9884	-0.0015	inf	0.0817	0.0	0.0055	0.9263	0.8283	0.8495	0.9973	0.0602	0.9884	0.0	0.5973	inf	inf	0.3154
0.0002	8.3843	85000	0.3848	inf	0.9398	0.0	0.9845	inf	1.7613	inf	0.9398	0.6299	0.1742	0.6047	0.7948	0.9974	0.0	6.0281	2.9998	0.9995	0.9881	-0.0006	inf	0.0807	0.0	0.0073	0.9275	0.8276	0.8492	0.9974	0.0565	0.9881	0.0	0.5976	inf	inf	0.3526
0.0002	8.6309	87500	0.3832	inf	0.9403	0.0	0.9849	inf	1.7714	inf	0.9403	0.6306	0.1990	0.6055	0.7955	0.9968	0.0	6.1018	3.0005	0.9991	0.9884	0.0010	inf	0.0814	0.0	0.0073	0.9280	0.8282	0.8494	0.9968	0.0564	0.9884	0.0	0.5987	inf	inf	0.3752
0.0002	8.8775	90000	0.3839	inf	0.9399	0.0	0.9855	inf	1.7940	inf	0.9399	0.6316	0.1469	0.6054	0.7959	0.9980	0.0	5.8978	3.0	0.9995	0.9896	-0.0024	inf	0.0787	0.0	0.0045	0.9292	0.8275	0.8491	0.9980	0.0573	0.9896	0.0	0.5978	inf	inf	0.3037
0.0002	9.1241	92500	0.3835	inf	0.9397	0.0	0.9851	24787535410764875677803588078186672296095995795372611708387328.0000	1.7906	inf	0.9397	0.6319	0.1631	0.6053	0.7953	0.9975	0.0	6.0297	3.0003	0.9992	0.9880	-0.0023	inf	0.0803	0.0	0.0067	0.9277	0.8277	0.8500	0.9975	0.0573	0.9880	0.0	0.5980	inf	0.0280	0.3639
0.0002	9.3707	95000	0.3829	inf	0.9406	0.0	0.9850	21246458923512745279768788302023303751591538440766017756987392.0000	1.7691	inf	0.9406	0.6318	0.1466	0.6056	0.7951	0.9979	0.0	5.9969	3.0002	0.9993	0.9872	-0.0028	inf	0.0802	0.0	0.0080	0.9279	0.8282	0.8501	0.9979	0.0564	0.9872	0.0	0.5981	inf	inf	0.3920
0.0002	9.6173	97500	0.3829	inf	0.9394	0.0	0.9849	22131728045325776452029795540104264829431683329922529862090752.0000	1.8058	inf	0.9394	0.6317	0.1543	0.6054	0.7955	0.9978	0.0	6.1170	3.0002	0.9993	0.9869	-0.0018	inf	0.0817	0.0	0.0085	0.9265	0.8282	0.8499	0.9978	0.0576	0.9869	0.0	0.5980	inf	inf	0.4062
0.0002	9.8639	100000	0.3829	inf	0.9394	0.0	0.9847	inf	1.8056	inf	0.9394	0.6318	0.1547	0.6055	0.7955	0.9978	0.0	6.1064	3.0001	0.9992	0.9871	-0.0018	inf	0.0815	0.0	0.0085	0.9267	0.8283	0.8496	0.9978	0.0577	0.9871	0.0	0.5981	inf	inf	0.4042

Framework versions

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