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-0.25
+  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-0.25
+
+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: 0.3624
+- Linker Equal: 0.8351
+- E3 Graph Edit Distance Norm: inf
+- Poi Heavy Atoms Difference Norm: 0.0311
+- Poi Has Attachment Point(s): 0.9593
+- Poi Graph Edit Distance Norm: inf
+- Valid: 0.9367
+- Poi Valid: 0.9593
+- Poi Graph Edit Distance: inf
+- Reassembly Nostereo: 0.6220
+- Linker Has Attachment Point(s): 0.9970
+- Poi Heavy Atoms Difference: 1.1101
+- Has Three Substructures: 1.0
+- E3 Heavy Atoms Difference Norm: 0.0153
+- Linker Valid: 0.9970
+- Linker Tanimoto Similarity: 0.0
+- E3 Has Attachment Point(s): 0.9798
+- Poi Equal: 0.7936
+- All Ligands Equal: 0.5870
+- Heavy Atoms Difference Norm: 0.0731
+- Linker Heavy Atoms Difference Norm: 0.0030
+- Heavy Atoms Difference: 5.4708
+- Tanimoto Similarity: 0.0
+- Num Fragments: 3.0
+- E3 Graph Edit Distance: inf
+- Linker Graph Edit Distance: inf
+- Linker Heavy Atoms Difference: 0.2800
+- Poi Tanimoto Similarity: 0.0
+- Linker Graph Edit Distance Norm: inf
+- Has All Attachment Points: 0.9888
+- E3 Tanimoto Similarity: 0.0
+- Reassembly: 0.5944
+- E3 Heavy Atoms Difference: 0.4994
+- E3 Equal: 0.8276
+- E3 Valid: 0.9798
+
+## 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 | Linker Equal | E3 Graph Edit Distance Norm | Poi Heavy Atoms Difference Norm | Poi Has Attachment Point(s) | Poi Graph Edit Distance Norm | Valid  | Poi Valid | Poi Graph Edit Distance | Reassembly Nostereo | Linker Has Attachment Point(s) | Poi Heavy Atoms Difference | Has Three Substructures | E3 Heavy Atoms Difference Norm | Linker Valid | Linker Tanimoto Similarity | E3 Has Attachment Point(s) | Poi Equal | All Ligands Equal | Heavy Atoms Difference Norm | Linker Heavy Atoms Difference Norm | Heavy Atoms Difference | Tanimoto Similarity | Num Fragments | E3 Graph Edit Distance | Linker Graph Edit Distance | Linker Heavy Atoms Difference | Poi Tanimoto Similarity | Linker Graph Edit Distance Norm | Has All Attachment Points | E3 Tanimoto Similarity | Reassembly | E3 Heavy Atoms Difference | E3 Equal | E3 Valid |
+|:-------------:|:-------:|:------:|:---------------:|:------------:|:---------------------------:|:-------------------------------:|:---------------------------:|:----------------------------:|:------:|:---------:|:-----------------------:|:-------------------:|:------------------------------:|:--------------------------:|:-----------------------:|:------------------------------:|:------------:|:--------------------------:|:--------------------------:|:---------:|:-----------------:|:---------------------------:|:----------------------------------:|:----------------------:|:-------------------:|:-------------:|:----------------------:|:--------------------------:|:-----------------------------:|:-----------------------:|:-------------------------------:|:-------------------------:|:----------------------:|:----------:|:-------------------------:|:--------:|:--------:|
+| 0.0006        | 31.5582 | 80000  | 0.3577          | 0.8324       | inf                         | 0.0305                          | 0.9579                      | inf                          | 0.9328 | 0.9579    | inf                     | 0.6230              | 0.9967                         | 1.0626                     | 0.9999                  | 0.0251                         | 0.9967       | 0.0                        | 0.9771                     | 0.7863    | 0.5856            | 0.0758                      | 0.0051                             | 5.7523                 | 0.0                 | 3.0001        | inf                    | inf                        | 0.2647                        | 0.0                     | inf                             | 0.9890                    | 0.0                    | 0.5934     | 0.8042                    | 0.8272   | 0.9771   |
+| 0.0005        | 39.4477 | 100000 | 0.3624          | 0.8351       | inf                         | 0.0311                          | 0.9593                      | inf                          | 0.9367 | 0.9593    | inf                     | 0.6220              | 0.9970                         | 1.1101                     | 1.0                     | 0.0153                         | 0.9970       | 0.0                        | 0.9798                     | 0.7936    | 0.5870            | 0.0731                      | 0.0030                             | 5.4708                 | 0.0                 | 3.0           | inf                    | inf                        | 0.2800                        | 0.0                     | inf                             | 0.9888                    | 0.0                    | 0.5944     | 0.4994                    | 0.8276   | 0.9798   |
+
+
+### 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"
+}