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-opt25
+  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-opt25
+
+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: 0.3420
+- Num Fragments: 3.0002
+- Linker Heavy Atoms Difference: 0.1689
+- Linker Graph Edit Distance: 37181303116147309234962303999400365269286085344573508414341120.0000
+- Tanimoto Similarity: 0.0
+- Linker Tanimoto Similarity: 0.0
+- E3 Valid: 0.9732
+- Linker Has Attachment Point(s): 0.9963
+- Poi Equal: 0.7897
+- Heavy Atoms Difference: 8.0244
+- Poi Has Attachment Point(s): 0.9305
+- E3 Equal: 0.8302
+- Linker Graph Edit Distance Norm: inf
+- E3 Has Attachment Point(s): 0.9732
+- Has Three Substructures: 0.9995
+- Poi Heavy Atoms Difference Norm: 0.0690
+- Linker Equal: 0.8419
+- Heavy Atoms Difference Norm: 0.1076
+- E3 Heavy Atoms Difference: 1.0454
+- Poi Valid: 0.9305
+- Valid: 0.9027
+- Linker Heavy Atoms Difference Norm: -0.0046
+- Has All Attachment Points: 0.9796
+- E3 Graph Edit Distance: inf
+- Linker Valid: 0.9963
+- Poi Tanimoto Similarity: 0.0
+- Poi Graph Edit Distance Norm: inf
+- Poi Heavy Atoms Difference: 2.0482
+- Poi Graph Edit Distance: inf
+- Reassembly Nostereo: 0.6261
+- E3 Graph Edit Distance Norm: inf
+- E3 Heavy Atoms Difference Norm: 0.0335
+- Reassembly: 0.6073
+- All Ligands Equal: 0.5992
+- E3 Tanimoto Similarity: 0.0
+
+## 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
+- training_steps: 100000
+- mixed_precision_training: Native AMP
+
+### Training results
+
+| Training Loss | Epoch  | Step   | Validation Loss | Num Fragments | Linker Heavy Atoms Difference | Linker Graph Edit Distance                                          | Tanimoto Similarity | Linker Tanimoto Similarity | E3 Valid | Linker Has Attachment Point(s) | Poi Equal | Heavy Atoms Difference | Poi Has Attachment Point(s) | E3 Equal | Linker Graph Edit Distance Norm | E3 Has Attachment Point(s) | Has Three Substructures | Poi Heavy Atoms Difference Norm | Linker Equal | Heavy Atoms Difference Norm | E3 Heavy Atoms Difference | Poi Valid | Valid  | Linker Heavy Atoms Difference Norm | Has All Attachment Points | E3 Graph Edit Distance | Linker Valid | Poi Tanimoto Similarity | Poi Graph Edit Distance Norm | Poi Heavy Atoms Difference | Poi Graph Edit Distance                                              | Reassembly Nostereo | E3 Graph Edit Distance Norm | E3 Heavy Atoms Difference Norm | Reassembly | All Ligands Equal | E3 Tanimoto Similarity |
+|:-------------:|:------:|:------:|:---------------:|:-------------:|:-----------------------------:|:-------------------------------------------------------------------:|:-------------------:|:--------------------------:|:--------:|:------------------------------:|:---------:|:----------------------:|:---------------------------:|:--------:|:-------------------------------:|:--------------------------:|:-----------------------:|:-------------------------------:|:------------:|:---------------------------:|:-------------------------:|:---------:|:------:|:----------------------------------:|:-------------------------:|:----------------------:|:------------:|:-----------------------:|:----------------------------:|:--------------------------:|:--------------------------------------------------------------------:|:-------------------:|:---------------------------:|:------------------------------:|:----------:|:-----------------:|:----------------------:|
+| 0.0005        | 7.8911 | 80000  | 0.3375          | 2.9994        | 0.2223                        | inf                                                                 | 0.0                 | 0.0                        | 0.9717   | 0.9961                         | 0.7867    | 9.0605                 | 0.9179                      | 0.8268   | inf                             | 0.9717                     | 0.9994                  | 0.0813                          | 0.8393       | 0.1211                      | 0.9062                    | 0.9179    | 0.8893 | 0.0019                             | 0.9788                    | inf                    | 0.9961       | 0.0                     | inf                          | 2.4517                     | 820644475920679939503384490879847350906393395732940812913213440.0000 | 0.6211              | inf                         | 0.0334                         | 0.6011     | 0.5936            | 0.0                    |
+| 0.0005        | 9.8639 | 100000 | 0.3420          | 3.0002        | 0.1689                        | 37181303116147309234962303999400365269286085344573508414341120.0000 | 0.0                 | 0.0                        | 0.9732   | 0.9963                         | 0.7897    | 8.0244                 | 0.9305                      | 0.8302   | inf                             | 0.9732                     | 0.9995                  | 0.0690                          | 0.8419       | 0.1076                      | 1.0454                    | 0.9305    | 0.9027 | -0.0046                            | 0.9796                    | inf                    | 0.9963       | 0.0                     | inf                          | 2.0482                     | inf                                                                  | 0.6261              | inf                         | 0.0335                         | 0.6073     | 0.5992            | 0.0                    |
+
+
+### 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"
+}

model.safetensors

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+oid sha256:7ed9dafb4f89466da90f482fa9ea939c2143dddfc45be8d62b4d4118c45672b1
 size 409608164

runs/Mar19_09-12-04_alvis3-24/events.out.tfevents.1742371928.alvis3-24.2626959.25

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+size 21049