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_reduce-rand-smiles-train-0.75
+  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_reduce-rand-smiles-train-0.75
+
+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: 0.3562
+- E3 Heavy Atoms Difference: 0.5450
+- Tanimoto Similarity: 0.0
+- Linker Heavy Atoms Difference: 0.2341
+- Poi Graph Edit Distance: inf
+- Poi Heavy Atoms Difference Norm: 0.0500
+- Reassembly Nostereo: 0.6352
+- Has All Attachment Points: 0.9914
+- Num Fragments: 2.9996
+- Linker Equal: 0.8443
+- Reassembly: 0.6021
+- E3 Graph Edit Distance Norm: inf
+- Poi Valid: 0.9499
+- E3 Graph Edit Distance: inf
+- E3 Equal: 0.8238
+- Poi Heavy Atoms Difference: 1.5246
+- E3 Heavy Atoms Difference Norm: 0.0139
+- Has Three Substructures: 0.9996
+- Linker Valid: 0.9984
+- Linker Has Attachment Point(s): 0.9984
+- Poi Graph Edit Distance Norm: inf
+- Heavy Atoms Difference Norm: 0.0733
+- Valid: 0.9362
+- E3 Valid: 0.9859
+- Linker Heavy Atoms Difference Norm: 0.0034
+- Poi Tanimoto Similarity: 0.0
+- Poi Equal: 0.7947
+- Linker Tanimoto Similarity: 0.0
+- All Ligands Equal: 0.5946
+- Linker Graph Edit Distance Norm: inf
+- Poi Has Attachment Point(s): 0.9499
+- E3 Has Attachment Point(s): 0.9859
+- Linker Graph Edit Distance: 15934844192634561100698130285457299401122608004817217891860480.0000
+- E3 Tanimoto Similarity: 0.0
+- Heavy Atoms Difference: 5.5146
+
+## 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: reduce_lr_on_plateau
+- lr_scheduler_warmup_steps: 400
+- training_steps: 100000
+- mixed_precision_training: Native AMP
+
+### Training results
+
+| Training Loss | Epoch   | Step   | Validation Loss | E3 Heavy Atoms Difference | Tanimoto Similarity | Linker Heavy Atoms Difference | Poi Graph Edit Distance | Poi Heavy Atoms Difference Norm | Reassembly Nostereo | Has All Attachment Points | Num Fragments | Linker Equal | Reassembly | E3 Graph Edit Distance Norm | Poi Valid | E3 Graph Edit Distance | E3 Equal | Poi Heavy Atoms Difference | E3 Heavy Atoms Difference Norm | Has Three Substructures | Linker Valid | Linker Has Attachment Point(s) | Poi Graph Edit Distance Norm | Heavy Atoms Difference Norm | Valid  | E3 Valid | Linker Heavy Atoms Difference Norm | Poi Tanimoto Similarity | Poi Equal | Linker Tanimoto Similarity | All Ligands Equal | Linker Graph Edit Distance Norm | Poi Has Attachment Point(s) | E3 Has Attachment Point(s) | Linker Graph Edit Distance                                          | E3 Tanimoto Similarity | Heavy Atoms Difference |
+|:-------------:|:-------:|:------:|:---------------:|:-------------------------:|:-------------------:|:-----------------------------:|:-----------------------:|:-------------------------------:|:-------------------:|:-------------------------:|:-------------:|:------------:|:----------:|:---------------------------:|:---------:|:----------------------:|:--------:|:--------------------------:|:------------------------------:|:-----------------------:|:------------:|:------------------------------:|:----------------------------:|:---------------------------:|:------:|:--------:|:----------------------------------:|:-----------------------:|:---------:|:--------------------------:|:-----------------:|:-------------------------------:|:---------------------------:|:--------------------------:|:-------------------------------------------------------------------:|:----------------------:|:----------------------:|
+| 0.0006        | 10.5208 | 80000  | 0.3546          | 0.2397                    | 0.0                 | 0.2432                        | inf                     | 0.0551                          | 0.6277              | 0.9911                    | 2.9999        | 0.8418       | 0.5965     | inf                         | 0.9407    | inf                    | 0.8234   | 1.7421                     | 0.0025                         | 0.9999                  | 0.9980       | 0.9980                         | inf                          | 0.0768                      | 0.9301 | 0.9907   | 0.0018                             | 0.0                     | 0.7882    | 0.0                        | 0.5897            | inf                             | 0.9407                      | 0.9907                     | 20361189801699711253012395652022580557179454652619232886390784.0000 | 0.0                    | 5.7380                 |
+| 0.0006        | 13.1510 | 100000 | 0.3562          | 0.5450                    | 0.0                 | 0.2341                        | inf                     | 0.0500                          | 0.6352              | 0.9914                    | 2.9996        | 0.8443       | 0.6021     | inf                         | 0.9499    | inf                    | 0.8238   | 1.5246                     | 0.0139                         | 0.9996                  | 0.9984       | 0.9984                         | inf                          | 0.0733                      | 0.9362 | 0.9859   | 0.0034                             | 0.0                     | 0.7947    | 0.0                        | 0.5946            | inf                             | 0.9499                      | 0.9859                     | 15934844192634561100698130285457299401122608004817217891860480.0000 | 0.0                    | 5.5146                 |
+
+
+### 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"
+}