Initial version

README.md

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+---
+library_name: transformers
+license: mit
+base_model: seyonec/ChemBERTa-zinc-base-v1
+tags:
+- PROTAC
+- cheminformatics
+- generated_from_trainer
+model-index:
+- name: ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25-rand-smiles
+  results: []
+---
+
+<!-- This model card has been generated automatically according to the information the Trainer had access to. You
+should probably proofread and complete it, then remove this comment. -->
+
+# ailab-bio/PROTAC-Splitter-EncoderDecoder-lr_cosine-opt25-rand-smiles
+
+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.
+It achieves the following results on the evaluation set:
+- Loss: 0.3184
+- E3 Tanimoto Similarity: 0.0
+- Poi Equal: 0.7620
+- E3 Equal: 0.8036
+- Poi Tanimoto Similarity: 0.0
+- Poi Valid: 0.9589
+- Reassembly: 0.5459
+- All Ligands Equal: 0.5390
+- Poi Graph Edit Distance: inf
+- Linker Graph Edit Distance: 28328611898016997512352231618590754490884636453008387363307520.0000
+- Poi Graph Edit Distance Norm: inf
+- Linker Tanimoto Similarity: 0.0
+- Valid: 0.9547
+- E3 Graph Edit Distance Norm: inf
+- Poi Has Attachment Point(s): 0.9589
+- Linker Equal: 0.7668
+- Linker Heavy Atoms Difference Norm: 0.0034
+- Has All Attachment Points: 0.9905
+- Heavy Atoms Difference: 4.1049
+- Has Three Substructures: 0.9992
+- Tanimoto Similarity: 0.0
+- Heavy Atoms Difference Norm: 0.0536
+- Poi Heavy Atoms Difference Norm: 0.0352
+- Linker Has Attachment Point(s): 0.9972
+- E3 Heavy Atoms Difference: 0.2976
+- E3 Graph Edit Distance: inf
+- Linker Valid: 0.9972
+- E3 Heavy Atoms Difference Norm: 0.0033
+- E3 Has Attachment Point(s): 0.9966
+- E3 Valid: 0.9966
+- Reassembly Nostereo: 0.5799
+- Linker Heavy Atoms Difference: 0.3031
+- Num Fragments: 3.0003
+- Linker Graph Edit Distance Norm: inf
+- Poi Heavy Atoms Difference: 1.1856
+
+## 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: 699
+- training_steps: 10000
+- mixed_precision_training: Native AMP
+
+### Training results
+
+| Training Loss | Epoch  | Step  | Validation Loss | E3 Tanimoto Similarity | Poi Equal | E3 Equal | Poi Tanimoto Similarity | Poi Valid | Reassembly | All Ligands Equal | Poi Graph Edit Distance | Linker Graph Edit Distance                                          | Poi Graph Edit Distance Norm | Linker Tanimoto Similarity | Valid  | E3 Graph Edit Distance Norm | Poi Has Attachment Point(s) | Linker Equal | Linker Heavy Atoms Difference Norm | Has All Attachment Points | Heavy Atoms Difference | Has Three Substructures | Tanimoto Similarity | Heavy Atoms Difference Norm | Poi Heavy Atoms Difference Norm | Linker Has Attachment Point(s) | E3 Heavy Atoms Difference | E3 Graph Edit Distance | Linker Valid | E3 Heavy Atoms Difference Norm | E3 Has Attachment Point(s) | E3 Valid | Reassembly Nostereo | Linker Heavy Atoms Difference | Num Fragments | Linker Graph Edit Distance Norm | Poi Heavy Atoms Difference |
+|:-------------:|:------:|:-----:|:---------------:|:----------------------:|:---------:|:--------:|:-----------------------:|:---------:|:----------:|:-----------------:|:-----------------------:|:-------------------------------------------------------------------:|:----------------------------:|:--------------------------:|:------:|:---------------------------:|:---------------------------:|:------------:|:----------------------------------:|:-------------------------:|:----------------------:|:-----------------------:|:-------------------:|:---------------------------:|:-------------------------------:|:------------------------------:|:-------------------------:|:----------------------:|:------------:|:------------------------------:|:--------------------------:|:--------:|:-------------------:|:-----------------------------:|:-------------:|:-------------------------------:|:--------------------------:|
+| 0.012         | 0.4932 | 5000  | 0.3055          | 0.0                    | 0.7354    | 0.7897   | 0.0                     | 0.9479    | 0.4899     | 0.4824            | inf                     | 25672804532577903995569209904347871257364201785538851047997440.0000 | inf                          | 0.0                        | 0.9441 | inf                         | 0.9479                      | 0.6946       | 0.0103                             | 0.9873                    | 4.9586                 | 0.9995                  | 0.0                 | 0.0650                      | 0.0421                          | 0.9974                         | 0.1648                    | inf                    | 0.9974       | -0.0036                        | 0.9972                     | 0.9972   | 0.5198              | 0.5344                        | 3.0005        | inf                             | 1.4326                     |
+| 0.0064        | 0.7398 | 7500  | 0.3156          | 0.0                    | 0.7551    | 0.8017   | 0.0                     | 0.9532    | 0.5359     | 0.5282            | inf                     | 40722379603399433924006332951724209580646664901199556834754560.0000 | inf                          | 0.0                        | 0.9477 | inf                         | 0.9532                      | 0.7533       | -0.0000                            | 0.9873                    | 4.5195                 | 0.9985                  | 0.0                 | 0.0593                      | 0.0396                          | 0.9959                         | 0.3429                    | inf                    | 0.9959       | 0.0053                         | 0.9944                     | 0.9944   | 0.5689              | 0.2564                        | 3.0003        | 0.0452                          | 1.3395                     |
+| 0.0051        | 0.9864 | 10000 | 0.3184          | 0.0                    | 0.7620    | 0.8036   | 0.0                     | 0.9589    | 0.5459     | 0.5390            | inf                     | 28328611898016997512352231618590754490884636453008387363307520.0000 | inf                          | 0.0                        | 0.9547 | inf                         | 0.9589                      | 0.7668       | 0.0034                             | 0.9905                    | 4.1049                 | 0.9992                  | 0.0                 | 0.0536                      | 0.0352                          | 0.9972                         | 0.2976                    | inf                    | 0.9972       | 0.0033                         | 0.9966                     | 0.9966   | 0.5799              | 0.3031                        | 3.0003        | inf                             | 1.1856                     |
+
+
+### Framework versions
+
+- Transformers 4.44.2
+- Pytorch 2.4.1+cu121
+- Datasets 3.0.0
+- Tokenizers 0.19.1

generation_config.json

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+{
+  "bos_token_id": 0,
+  "do_sample": true,
+  "eos_token_id": 2,
+  "max_length": 512,
+  "num_beams": 5,
+  "pad_token_id": 1,
+  "top_k": 20,
+  "transformers_version": "4.44.2"
+}

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training_args.bin

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