Initial version

README.md

@@ -0,0 +1,97 @@
+---
+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-0.5
+  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-0.5
+
+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: 0.3751
+- Reassembly: 0.5970
+- E3 Graph Edit Distance Norm: inf
+- Linker Graph Edit Distance Norm: inf
+- All Ligands Equal: 0.5899
+- Poi Heavy Atoms Difference Norm: 0.0419
+- Poi Graph Edit Distance Norm: inf
+- Linker Heavy Atoms Difference: 0.2883
+- Linker Equal: 0.8472
+- Poi Has Attachment Point(s): 0.9510
+- E3 Tanimoto Similarity: 0.0
+- Reassembly Nostereo: 0.6329
+- E3 Graph Edit Distance: inf
+- Linker Has Attachment Point(s): 0.9977
+- E3 Heavy Atoms Difference Norm: 0.0037
+- Linker Valid: 0.9977
+- Poi Equal: 0.7890
+- Linker Graph Edit Distance: 23016997167138810478786188190104988023843767118069314732687360.0000
+- E3 Equal: 0.8240
+- Num Fragments: 3.0003
+- E3 Heavy Atoms Difference: 0.2737
+- Poi Graph Edit Distance: inf
+- Has Three Substructures: 0.9996
+- Heavy Atoms Difference: 4.7685
+- Linker Tanimoto Similarity: 0.0
+- Poi Heavy Atoms Difference: 1.3950
+- E3 Valid: 0.9944
+- Poi Tanimoto Similarity: 0.0
+- Valid: 0.9450
+- Heavy Atoms Difference Norm: 0.0634
+- Tanimoto Similarity: 0.0
+- E3 Has Attachment Point(s): 0.9944
+- Has All Attachment Points: 0.9938
+- Poi Valid: 0.9510
+- Linker Heavy Atoms Difference Norm: 0.0067
+
+## 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 | Reassembly | E3 Graph Edit Distance Norm | Linker Graph Edit Distance Norm | All Ligands Equal | Poi Heavy Atoms Difference Norm | Poi Graph Edit Distance Norm | Linker Heavy Atoms Difference | Linker Equal | Poi Has Attachment Point(s) | E3 Tanimoto Similarity | Reassembly Nostereo | E3 Graph Edit Distance | Linker Has Attachment Point(s) | E3 Heavy Atoms Difference Norm | Linker Valid | Poi Equal | Linker Graph Edit Distance                                          | E3 Equal | Num Fragments | E3 Heavy Atoms Difference | Poi Graph Edit Distance | Has Three Substructures | Heavy Atoms Difference | Linker Tanimoto Similarity | Poi Heavy Atoms Difference | E3 Valid | Poi Tanimoto Similarity | Valid  | Heavy Atoms Difference Norm | Tanimoto Similarity | E3 Has Attachment Point(s) | Has All Attachment Points | Poi Valid | Linker Heavy Atoms Difference Norm |
+|:-------------:|:-------:|:------:|:---------------:|:----------:|:---------------------------:|:-------------------------------:|:-----------------:|:-------------------------------:|:----------------------------:|:-----------------------------:|:------------:|:---------------------------:|:----------------------:|:-------------------:|:----------------------:|:------------------------------:|:------------------------------:|:------------:|:---------:|:-------------------------------------------------------------------:|:--------:|:-------------:|:-------------------------:|:-----------------------:|:-----------------------:|:----------------------:|:--------------------------:|:--------------------------:|:--------:|:-----------------------:|:------:|:---------------------------:|:-------------------:|:--------------------------:|:-------------------------:|:---------:|:----------------------------------:|
+| 0.0006        | 15.7822 | 80000  | 0.3655          | 0.5977     | inf                         | inf                             | 0.5904            | 0.0477                          | inf                          | 0.1988                        | 0.8371       | 0.9528                      | 0.0                    | 0.6278              | inf                    | 0.9952                         | 0.0221                         | 0.9952       | 0.7851    | inf                                                                 | 0.8250   | 2.9996        | 0.7440                    | inf                     | 0.9994                  | 5.9070                 | 0.0                        | 1.4796                     | 0.9796   | 0.0                     | 0.9315 | 0.0782                      | 0.0                 | 0.9796                     | 0.9879                    | 0.9528    | -0.0014                            |
+| 0.0006        | 19.7278 | 100000 | 0.3751          | 0.5970     | inf                         | inf                             | 0.5899            | 0.0419                          | inf                          | 0.2883                        | 0.8472       | 0.9510                      | 0.0                    | 0.6329              | inf                    | 0.9977                         | 0.0037                         | 0.9977       | 0.7890    | 23016997167138810478786188190104988023843767118069314732687360.0000 | 0.8240   | 3.0003        | 0.2737                    | inf                     | 0.9996                  | 4.7685                 | 0.0                        | 1.3950                     | 0.9944   | 0.0                     | 0.9450 | 0.0634                      | 0.0                 | 0.9944                     | 0.9938                    | 0.9510    | 0.0067                             |
+
+
+### Framework versions
+
+- Transformers 4.44.2
+- Pytorch 2.4.1+cu121
+- Datasets 3.0.0
+- Tokenizers 0.19.1

generation_config.json

@@ -0,0 +1,10 @@
+{
+  "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

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:0f18ce4cbd95e0db674acdf88a65d7216d8955eab9350b232d8b41db01b75645
+oid sha256:2790709e38d495ed69451e2e98588967f60dac42ae76070227ad36e62492bafe
 size 409608164