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PROTAC-Splitter-Trial-15

Transformers
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Safetensors
encoder-decoder
text2text-generation
PROTAC
cheminformatics
Generated from Trainer
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README.md CHANGED
@@ -18,41 +18,41 @@ should probably proofread and complete it, then remove this comment. -->
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  This model is a fine-tuned version of [seyonec/ChemBERTa-zinc-base-v1](https://huggingface.co/seyonec/ChemBERTa-zinc-base-v1) on the ailab-bio/PROTAC-Splitter-Dataset dataset.
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  It achieves the following results on the evaluation set:
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- - Loss: 0.0003
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- - Reassembly: 0.9991
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- - Tanimoto Similarity: 0.0
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- - Poi Valid: 1.0
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- - E3 Tanimoto Similarity: 0.0
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- - Reassembly Nostereo: 0.9991
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- - Linker Has Attachment Point(s): 1.0
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- - Heavy Atoms Difference Norm: -0.0000
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- - Linker Valid: 1.0
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- - E3 Heavy Atoms Difference: 0.0068
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- - Linker Heavy Atoms Difference Norm: -0.0023
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- - Num Fragments: 3.0
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  - Valid: 1.0
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- - Has Three Substructures: 1.0
 
 
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  - E3 Graph Edit Distance Norm: inf
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  - Poi Graph Edit Distance: inf
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- - Poi Tanimoto Similarity: 0.0
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- - Poi Graph Edit Distance Norm: inf
 
 
 
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  - Linker Graph Edit Distance Norm: inf
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- - All Ligands Equal: 0.9874
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  - E3 Valid: 1.0
 
 
 
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  - Poi Has Attachment Point(s): 1.0
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- - Linker Tanimoto Similarity: 0.0
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- - Linker Equal: 0.9878
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- - Poi Equal: 0.9928
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- - Poi Heavy Atoms Difference Norm: 0.0003
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- - Heavy Atoms Difference: 0.0
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- - Poi Heavy Atoms Difference: 0.0118
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- - E3 Graph Edit Distance: inf
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- - E3 Has Attachment Point(s): 1.0
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- - Linker Graph Edit Distance: 0.1165
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- - E3 Equal: 0.9944
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- - E3 Heavy Atoms Difference Norm: 0.0003
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- - Linker Heavy Atoms Difference: -0.0186
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- - Has All Attachment Points: 1.0
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  ## Model description
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@@ -78,17 +78,33 @@ The following hyperparameters were used during training:
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  - optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
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  - lr_scheduler_type: cosine_with_restarts
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  - lr_scheduler_warmup_steps: 699
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- - training_steps: 100000
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  - mixed_precision_training: Native AMP
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  ### Training results
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- | Training Loss | Epoch | Step | Validation Loss | Reassembly | Tanimoto Similarity | Poi Valid | E3 Tanimoto Similarity | Reassembly Nostereo | Linker Has Attachment Point(s) | Heavy Atoms Difference Norm | Linker Valid | E3 Heavy Atoms Difference | Linker Heavy Atoms Difference Norm | Num Fragments | Valid | Has Three Substructures | E3 Graph Edit Distance Norm | Poi Graph Edit Distance | Poi Tanimoto Similarity | Poi Graph Edit Distance Norm | Linker Graph Edit Distance Norm | All Ligands Equal | E3 Valid | Poi Has Attachment Point(s) | Linker Tanimoto Similarity | Linker Equal | Poi Equal | Poi Heavy Atoms Difference Norm | Heavy Atoms Difference | Poi Heavy Atoms Difference | E3 Graph Edit Distance | E3 Has Attachment Point(s) | Linker Graph Edit Distance | E3 Equal | E3 Heavy Atoms Difference Norm | Linker Heavy Atoms Difference | Has All Attachment Points |
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- |:-------------:|:------:|:------:|:---------------:|:----------:|:-------------------:|:---------:|:----------------------:|:-------------------:|:------------------------------:|:---------------------------:|:------------:|:-------------------------:|:----------------------------------:|:-------------:|:------:|:-----------------------:|:---------------------------:|:-----------------------:|:-----------------------:|:----------------------------:|:-------------------------------:|:-----------------:|:--------:|:---------------------------:|:--------------------------:|:------------:|:---------:|:-------------------------------:|:----------------------:|:--------------------------:|:----------------------:|:--------------------------:|:--------------------------:|:--------:|:------------------------------:|:-----------------------------:|:-------------------------:|
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- | 0.0008 | 6.5543 | 70000 | 0.0003 | 0.9976 | 0.0 | 1.0 | 0.0 | 0.9978 | 1.0 | -0.0000 | 1.0 | 0.0063 | -0.0030 | 3.0 | 1.0 | 1.0 | inf | inf | 0.0 | inf | inf | 0.9846 | 1.0 | 1.0 | 0.0 | 0.9859 | 0.9915 | 0.0002 | -0.0009 | 0.0118 | inf | 1.0 | 0.1331 | 0.9935 | 0.0003 | -0.0189 | 1.0 |
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- | 0.0011 | 7.4906 | 80000 | 0.0004 | 0.9968 | 0.0 | 0.9998 | 0.0 | 0.9968 | 1.0 | 0.0003 | 1.0 | 0.0048 | -0.0026 | 3.0 | 0.9998 | 1.0 | inf | inf | 0.0 | inf | inf | 0.9849 | 1.0 | 0.9998 | 0.0 | 0.9869 | 0.9916 | 0.0005 | 0.0326 | 0.0318 | inf | 1.0 | inf | 0.9937 | 0.0002 | -0.0146 | 1.0 |
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- | 0.0006 | 8.4270 | 90000 | 0.0003 | 0.9990 | 0.0 | 1.0 | 0.0 | 0.9990 | 1.0 | 0.0000 | 1.0 | 0.0047 | -0.0018 | 3.0 | 1.0 | 1.0 | inf | inf | 0.0 | inf | inf | 0.9864 | 1.0 | 1.0 | 0.0 | 0.9867 | 0.9925 | -0.0005 | 0.0009 | -0.0036 | inf | 1.0 | inf | 0.9938 | 0.0002 | -0.0003 | 1.0 |
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- | 0.0005 | 9.3633 | 100000 | 0.0003 | 0.9991 | 0.0 | 1.0 | 0.0 | 0.9991 | 1.0 | -0.0000 | 1.0 | 0.0068 | -0.0023 | 3.0 | 1.0 | 1.0 | inf | inf | 0.0 | inf | inf | 0.9874 | 1.0 | 1.0 | 0.0 | 0.9878 | 0.9928 | 0.0003 | 0.0 | 0.0118 | inf | 1.0 | 0.1165 | 0.9944 | 0.0003 | -0.0186 | 1.0 |
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  ### Framework versions
 
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  This model is a fine-tuned version of [seyonec/ChemBERTa-zinc-base-v1](https://huggingface.co/seyonec/ChemBERTa-zinc-base-v1) on the ailab-bio/PROTAC-Splitter-Dataset dataset.
20
  It achieves the following results on the evaluation set:
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+ - Loss: 0.0002
 
 
 
 
 
 
 
 
 
 
 
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  - Valid: 1.0
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+ - Linker Equal: 0.9882
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+ - Linker Graph Edit Distance: 0.1158
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+ - Linker Tanimoto Similarity: 0.0
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  - E3 Graph Edit Distance Norm: inf
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  - Poi Graph Edit Distance: inf
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+ - E3 Has Attachment Point(s): 1.0
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+ - Has Three Substructures: 1.0
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+ - Reassembly: 0.9997
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+ - E3 Heavy Atoms Difference Norm: 0.0002
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+ - Linker Heavy Atoms Difference Norm: -0.0027
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  - Linker Graph Edit Distance Norm: inf
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+ - E3 Tanimoto Similarity: 0.0
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+ - Poi Heavy Atoms Difference: 0.0124
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+ - Linker Valid: 1.0
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+ - Heavy Atoms Difference: -0.0001
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+ - Num Fragments: 3.0
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+ - All Ligands Equal: 0.9880
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+ - Has All Attachment Points: 1.0
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+ - E3 Graph Edit Distance: inf
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+ - Linker Has Attachment Point(s): 1.0
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+ - Poi Heavy Atoms Difference Norm: 0.0003
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+ - Heavy Atoms Difference Norm: -0.0000
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+ - Linker Heavy Atoms Difference: -0.0166
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+ - Tanimoto Similarity: 0.0
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+ - E3 Equal: 0.9951
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+ - Poi Valid: 1.0
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  - E3 Valid: 1.0
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+ - Poi Tanimoto Similarity: 0.0
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+ - Poi Graph Edit Distance Norm: inf
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+ - Poi Equal: 0.9930
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  - Poi Has Attachment Point(s): 1.0
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+ - E3 Heavy Atoms Difference: 0.0041
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+ - Reassembly Nostereo: 0.9997
 
 
 
 
 
 
 
 
 
 
 
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  ## Model description
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  - optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
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  - lr_scheduler_type: cosine_with_restarts
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  - lr_scheduler_warmup_steps: 699
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+ - training_steps: 500000
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  - mixed_precision_training: Native AMP
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  ### Training results
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+ | 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 |
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+ |:-------------:|:-------:|:------:|:-----------------:|:--------:|:----------------------:|:---------------------------:|:--------------------------:|:-------------------------:|:------------------------------:|:----------------------:|:--------:|:-------------------------:|:-----------------------:|:----------------------:|:---------------------------:|:------------:|:--------------------------:|:-------------------------------:|:------------------------------:|:-----------------------------:|:----------------------------------:|:--------------------------:|:------------:|:---------------:|:-------------:|:---------:|:-----------------------:|:----------------------------:|:---------------------------:|:--------------------------:|:-------------------------------:|:-----------------------:|:---------:|:----------:|:-------------------:|:-------------------:|:------:|
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+ | 0.0008 | 6.5543 | 70000 | 0.9846 | 0.9935 | inf | inf | 1.0 | 0.0063 | 0.0003 | 0.0 | 1.0 | 1.0 | 1.0 | -0.0009 | -0.0000 | 0.9859 | 0.1331 | inf | 1.0 | -0.0189 | -0.0030 | 0.0 | 1.0 | 0.0003 | 3.0 | 0.9915 | inf | inf | 1.0 | 0.0118 | 0.0002 | 0.0 | 1.0 | 0.9976 | 0.9978 | 0.0 | 1.0 |
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+ | 0.0011 | 7.4906 | 80000 | 0.9849 | 0.9937 | inf | inf | 1.0 | 0.0048 | 0.0002 | 0.0 | 1.0 | 1.0 | 1.0 | 0.0326 | 0.0003 | 0.9869 | inf | inf | 1.0 | -0.0146 | -0.0026 | 0.0 | 1.0 | 0.0004 | 3.0 | 0.9916 | inf | inf | 0.9998 | 0.0318 | 0.0005 | 0.0 | 0.9998 | 0.9968 | 0.9968 | 0.0 | 0.9998 |
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+ | 0.0006 | 8.4270 | 90000 | 0.9864 | 0.9938 | inf | inf | 1.0 | 0.0047 | 0.0002 | 0.0 | 1.0 | 1.0 | 1.0 | 0.0009 | 0.0000 | 0.9867 | inf | inf | 1.0 | -0.0003 | -0.0018 | 0.0 | 1.0 | 0.0003 | 3.0 | 0.9925 | inf | inf | 1.0 | -0.0036 | -0.0005 | 0.0 | 1.0 | 0.9990 | 0.9990 | 0.0 | 1.0 |
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+ | 0.0005 | 9.3633 | 100000 | 0.9874 | 0.9944 | inf | inf | 1.0 | 0.0068 | 0.0003 | 0.0 | 1.0 | 1.0 | 1.0 | 0.0 | -0.0000 | 0.9878 | 0.1165 | inf | 1.0 | -0.0186 | -0.0023 | 0.0 | 1.0 | 0.0003 | 3.0 | 0.9928 | inf | inf | 1.0 | 0.0118 | 0.0003 | 0.0 | 1.0 | 0.9991 | 0.9991 | 0.0 | 1.0 |
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+ | 0.0004 | 32.7715 | 350000 | 0.0002 | 1.0 | 0.9888 | 0.1068 | 0.0 | inf | inf | 1.0 | 1.0 | 0.9996 | 0.0003 | -0.0037 | inf | 0.0 | 0.0260 | 1.0 | 0.0004 | 3.0 | 0.9886 | 1.0 | inf | 1.0 | 0.0009 | 0.0000 | -0.0323 | 0.0 | 0.9949 | 1.0 | 1.0 | 0.0 | inf | 0.9937 | 1.0 | 0.0066 | 0.9996 |
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+ | 0.0003 | 33.7079 | 360000 | 0.0002 | 1.0 | 0.9880 | 0.1166 | 0.0 | inf | inf | 1.0 | 1.0 | 0.9994 | 0.0002 | -0.0030 | inf | 0.0 | 0.0190 | 1.0 | 0.0021 | 3.0 | 0.9877 | 1.0 | inf | 1.0 | 0.0005 | 0.0000 | -0.0203 | 0.0 | 0.9948 | 1.0 | 1.0 | 0.0 | inf | 0.9930 | 1.0 | 0.0034 | 0.9994 |
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+ | 0.0003 | 34.6442 | 370000 | 0.0002 | 1.0 | 0.9880 | inf | 0.0 | inf | inf | 1.0 | 1.0 | 0.9995 | 0.0002 | -0.0026 | inf | 0.0 | 0.0116 | 1.0 | -0.0012 | 3.0 | 0.9879 | 1.0 | inf | 1.0 | 0.0003 | -0.0000 | -0.0175 | 0.0 | 0.9953 | 1.0 | 1.0 | 0.0 | inf | 0.9927 | 1.0 | 0.0047 | 0.9995 |
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+ | 0.0003 | 35.5805 | 380000 | 0.0002 | 1.0 | 0.9884 | inf | 0.0 | inf | inf | 1.0 | 1.0 | 0.9997 | 0.0002 | -0.0032 | inf | 0.0 | 0.0189 | 1.0 | -0.0005 | 3.0 | 0.9883 | 1.0 | inf | 1.0 | 0.0005 | -0.0000 | -0.0239 | 0.0 | 0.9951 | 1.0 | 1.0 | 0.0 | inf | 0.9933 | 1.0 | 0.0045 | 0.9997 |
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+ | 0.0003 | 36.5169 | 390000 | 0.0002 | 1.0 | 0.9890 | 0.1027 | 0.0 | inf | inf | 1.0 | 1.0 | 0.9996 | 0.0002 | -0.0030 | inf | 0.0 | 0.0237 | 1.0 | -0.0002 | 3.0 | 0.9887 | 1.0 | inf | 1.0 | 0.0008 | -0.0000 | -0.0285 | 0.0 | 0.9950 | 1.0 | 1.0 | 0.0 | inf | 0.9936 | 1.0 | 0.0046 | 0.9996 |
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+ | 0.0003 | 37.4532 | 400000 | 0.0002 | 1.0 | 0.9890 | 0.1059 | 0.0 | inf | inf | 1.0 | 1.0 | 0.9995 | 0.0002 | -0.0025 | inf | 0.0 | 0.0115 | 1.0 | -0.0002 | 3.0 | 0.9887 | 1.0 | inf | 1.0 | 0.0002 | -0.0000 | -0.0148 | 0.0 | 0.9949 | 1.0 | 1.0 | 0.0 | inf | 0.9938 | 1.0 | 0.0031 | 0.9995 |
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+ | 0.0003 | 38.3895 | 410000 | 0.0002 | 1.0 | 0.9885 | 0.1101 | 0.0 | inf | inf | 1.0 | 1.0 | 0.9995 | 0.0002 | -0.0033 | inf | 0.0 | 0.0214 | 1.0 | -0.0002 | 3.0 | 0.9882 | 1.0 | inf | 1.0 | 0.0006 | -0.0000 | -0.0250 | 0.0 | 0.9950 | 1.0 | 1.0 | 0.0 | inf | 0.9930 | 1.0 | 0.0034 | 0.9995 |
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+ | 0.0003 | 39.3258 | 420000 | 0.0002 | 0.9999 | 0.9887 | inf | 0.0 | inf | inf | 1.0 | 1.0 | 0.9993 | 0.0002 | -0.0026 | inf | 0.0 | 0.0184 | 1.0 | 0.0064 | 3.0 | 0.9881 | 1.0 | inf | 1.0 | 0.0005 | 0.0001 | -0.0207 | 0.0 | 0.9950 | 0.9999 | 1.0 | 0.0 | inf | 0.9930 | 0.9999 | 0.0047 | 0.9993 |
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+ | 0.0003 | 40.2622 | 430000 | 0.0002 | 1.0 | 0.9884 | 0.1125 | 0.0 | inf | inf | 1.0 | 1.0 | 0.9999 | 0.0002 | -0.0034 | inf | 0.0 | 0.0236 | 1.0 | 0.0 | 3.0 | 0.9883 | 1.0 | 0.0333 | 1.0 | 0.0007 | 0.0 | -0.0272 | 0.0 | 0.9949 | 1.0 | 1.0 | 0.0 | inf | 0.9933 | 1.0 | 0.0036 | 0.9999 |
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+ | 0.0003 | 41.1985 | 440000 | 0.0002 | 1.0 | 0.9882 | 0.1105 | 0.0 | inf | inf | 1.0 | 1.0 | 0.9993 | 0.0002 | -0.0032 | 0.0022 | 0.0 | 0.0229 | 1.0 | -0.0008 | 3.0 | 0.9877 | 1.0 | inf | 1.0 | 0.0007 | -0.0000 | -0.0275 | 0.0 | 0.9943 | 1.0 | 1.0 | 0.0 | inf | 0.9930 | 1.0 | 0.0038 | 0.9994 |
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+ | 0.0003 | 42.1348 | 450000 | 0.0002 | 1.0 | 0.9880 | inf | 0.0 | inf | inf | 1.0 | 1.0 | 0.9994 | 0.0002 | -0.0027 | inf | 0.0 | 0.0171 | 1.0 | 0.0009 | 3.0 | 0.9877 | 1.0 | inf | 1.0 | 0.0005 | 0.0000 | -0.0201 | 0.0 | 0.9949 | 1.0 | 1.0 | 0.0 | inf | 0.9929 | 1.0 | 0.0039 | 0.9995 |
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+ | 0.0003 | 43.0712 | 460000 | 0.0002 | 1.0 | 0.9883 | 0.1074 | 0.0 | inf | inf | 1.0 | 1.0 | 0.9997 | 0.0002 | -0.0033 | inf | 0.0 | 0.0244 | 1.0 | 0.0009 | 3.0 | 0.9882 | 1.0 | inf | 1.0 | 0.0008 | 0.0000 | -0.0282 | 0.0 | 0.9950 | 1.0 | 1.0 | 0.0 | inf | 0.9930 | 1.0 | 0.0047 | 0.9997 |
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+ | 0.0003 | 44.0075 | 470000 | 0.0002 | 1.0 | 0.9887 | inf | 0.0 | inf | inf | 1.0 | 1.0 | 0.9994 | 0.0002 | -0.0032 | inf | 0.0 | 0.0232 | 1.0 | 0.0009 | 3.0 | 0.9885 | 1.0 | inf | 1.0 | 0.0007 | 0.0000 | -0.0272 | 0.0 | 0.9950 | 1.0 | 1.0 | 0.0 | inf | 0.9936 | 1.0 | 0.0049 | 0.9994 |
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+ | 0.0003 | 44.9438 | 480000 | 0.0002 | 1.0 | 0.9892 | inf | 0.0 | inf | inf | 1.0 | 1.0 | 0.9997 | 0.0002 | -0.0037 | inf | 0.0 | 0.0295 | 1.0 | -0.0001 | 3.0 | 0.9890 | 1.0 | inf | 1.0 | 0.0010 | -0.0000 | -0.0341 | 0.0 | 0.9951 | 1.0 | 1.0 | 0.0 | inf | 0.9938 | 1.0 | 0.0044 | 0.9997 |
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+ | 0.0003 | 45.8801 | 490000 | 0.0002 | 1.0 | 0.9884 | inf | 0.0 | inf | inf | 1.0 | 1.0 | 0.9997 | 0.0002 | -0.0027 | inf | 0.0 | 0.0108 | 1.0 | -0.0001 | 3.0 | 0.9882 | 1.0 | inf | 1.0 | 0.0002 | -0.0000 | -0.0148 | 0.0 | 0.9951 | 1.0 | 1.0 | 0.0 | inf | 0.9930 | 1.0 | 0.0040 | 0.9997 |
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+ | 0.0003 | 46.8165 | 500000 | 0.0002 | 1.0 | 0.9882 | 0.1158 | 0.0 | inf | inf | 1.0 | 1.0 | 0.9997 | 0.0002 | -0.0027 | inf | 0.0 | 0.0124 | 1.0 | -0.0001 | 3.0 | 0.9880 | 1.0 | inf | 1.0 | 0.0003 | -0.0000 | -0.0166 | 0.0 | 0.9951 | 1.0 | 1.0 | 0.0 | inf | 0.9930 | 1.0 | 0.0041 | 0.9997 |
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  ### Framework versions
model.safetensors CHANGED
@@ -1,3 +1,3 @@
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