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--- |
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datasets: [COCONUTDB] |
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language: [code] |
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library_name: sentence-transformers |
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metrics: |
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- pearson_cosine |
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- spearman_cosine |
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- pearson_manhattan |
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- spearman_manhattan |
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- pearson_euclidean |
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- spearman_euclidean |
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- pearson_dot |
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- spearman_dot |
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- pearson_max |
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- spearman_max |
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pipeline_tag: sentence-similarity |
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tags: |
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- sentence-transformers |
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- sentence-similarity |
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- feature-extraction |
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- generated_from_trainer |
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- dataset_size:1,183,174 |
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- loss:CosineSimilarityLoss |
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widget: |
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- source_sentence: '[O][=C][Branch2][Branch2][Ring1][O][C][C][Branch2][Ring1][=Branch1][O][C][=Branch1][C][=O][C][C][C][C][C][C][=C][C][C][C][C][C][C][C][C][C][C][O][P][=Branch1][C][=O][Branch1][C][O][O][C][C][Branch2][Ring1][Branch1][O][C][O][C][Branch1][Ring1][C][O][C][Branch1][C][O][C][Branch1][C][O][C][Ring1][#Branch2][O][C][Branch1][C][O][C][Branch1][C][O][C][Branch1][C][O][C][Ring2][Ring1][Branch1][O][C][O][C][Branch1][Ring1][C][O][C][Branch1][C][O][C][Branch1][C][O][C][Ring1][#Branch2][O][C][C][C][C][C][C][C][C][C][C][C][C][C][C]' |
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sentences: |
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- '[O][=C][Branch2][Ring1][N][N][N][=C][Branch1][N][C][=C][C][=C][Branch1][C][Cl][C][=C][Ring1][#Branch1][C][=C][C][=C][Branch1][C][Cl][C][=C][Ring1][#Branch1][C][=C][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=C][Ring1][#Branch2][O]' |
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- '[O][=C][Branch1][C][O][C][=C][Branch1][C][C][C][C][=Branch1][C][=O][O][C]' |
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- '[O][=C][Branch1][C][O][C][C][C][C][C][C][C][C][Branch1][C][O][C][Branch1][C][O][C][Branch1][C][O][C][#C][C][Branch1][C][O][C][C][C][C]' |
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- source_sentence: '[O][=C][Branch1][#Branch1][O][C][Branch1][C][C][C][C][C][C][C][C][C][C][C]' |
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sentences: |
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- '[O][=C][O][C][C][Branch1][C][O][C][C][Ring1][#Branch1][=C][C][C][C][C][C][C][C][C][C][C][C][C][C]' |
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- '[O][=C][C][=C][C][O][C][O][C][=Ring1][Branch1][C][=C][Ring1][=Branch2][Br]' |
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- '[O][=C][Branch2][#Branch1][=C][O][C][C][=Branch1][C][=C][C][C][Branch1][#Branch1][O][C][=Branch1][C][=O][C][C][C][C][=Branch1][C][=O][C][Branch2][=Branch1][Ring1][O][C][C][Ring1][Branch2][Branch1][C][C][C][Ring1][=Branch1][Branch1][C][O][C][Branch1][#Branch1][O][C][=Branch1][C][=O][C][C][Branch1][#Branch1][O][C][=Branch1][C][=O][C][C][Ring2][Ring1][N][Branch1][#C][C][O][C][=Branch1][C][=O][C][=C][C][=C][C][=C][Ring1][=Branch1][C][Branch1][Branch2][C][O][C][=Branch1][C][=O][C][C][Ring2][Ring2][S][C][C][=C][C][=C][C][=C][C][=C][Ring1][=Branch1]' |
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- source_sentence: '[O][=C][O][C][=C][Branch2][Ring1][#C][C][=C][C][O][C][N][Branch1][S][C][=C][C][=C][Branch1][=Branch1][O][C][C][C][C][C][=C][Ring1][O][C][C][Ring2][Ring1][Branch1][=Ring1][P][C][=Branch1][=C][=C][Ring2][Ring1][=Branch2][C][C][=C][C][=C][C][=C][Ring1][=Branch1][C]' |
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sentences: |
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- '[O][=C][N][C][Branch1][S][C][=Branch1][C][=O][N][C][=C][C][=C][C][=C][Ring1][N][Ring1][=Branch1][C][C][=Branch1][C][=O][N][C][C][C][=N][C][=Branch1][Branch1][=C][S][Ring1][Branch1][C]' |
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- '[O][=C][C][=C][Branch2][Branch2][O][O][C][=C][C][Branch2][Ring2][#C][O][C][C][Branch1][Ring1][C][O][C][C][C][=C][C][NH1][C][=C][C][=Ring1][Branch1][C][=C][Ring1][=Branch2][C][C][=Branch1][C][=O][C][Branch1][Ring1][C][O][C][C][=Branch1][Branch2][=C][Ring2][Ring1][#C][Ring2][Ring1][O][C][Ring1][#Branch2][=C][C][Branch2][Ring2][O][O][C][Branch1][Ring2][C][Ring1][Branch1][C][Branch1][C][O][C][Branch2][Ring1][Branch2][C][=C][C][C][Branch1][S][N][Branch1][=Branch1][C][C][C][O][C][C][C][C][Ring1][S][Ring1][O][C][C][C][C][C][O][=C][Ring2][Branch1][=Branch2][C][O][C][=Branch1][C][=O][O][C][C]' |
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- '[O][C][C][O][C][Branch2][Branch2][#Branch2][O][C][C][Branch1][C][O][C][Branch1][C][O][C][Branch2][#Branch1][#Branch2][O][C][Ring1][Branch2][O][C][C][C][C][Branch2][=Branch1][=N][C][=Branch2][Branch1][P][=C][C][Branch1][C][O][C][Branch1][C][C][C][Ring1][Branch2][C][C][Branch1][C][O][C][C][Branch1][=Branch2][C][C][C][Ring1][O][Ring1][Branch1][C][C][Branch2][Ring1][Branch1][O][C][O][C][Branch1][Ring1][C][O][C][Branch1][C][O][C][Branch1][C][O][C][Ring1][#Branch2][O][Branch1][C][C][C][C][=C][C][Branch1][C][C][C][C][Ring2][Ring2][=Branch2][Branch1][C][C][C][C][C][O][C][Branch1][C][O][C][Branch1][C][O][C][Ring2][Branch1][S][O]' |
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- source_sentence: '[O][=C][O][C][=C][C][=C][Branch1][O][O][C][=Branch1][C][=O][N][Branch1][C][C][C][C][=C][Ring1][N][C][=Branch1][Ring2][=C][Ring1][S][C][O][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=Ring1][=Branch2]' |
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sentences: |
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- '[O][=C][C][=Branch2][#Branch1][=N][=C][C][Branch2][Ring2][N][C][NH1+1][C][=Branch2][Ring2][Ring1][=C][Branch1][#Branch2][C][=N][C][=C][C][Ring1][Branch2][Ring1][Branch1][C][C][=C][C][=Branch1][S][=C][C][=Branch1][Ring2][=C][Ring1][=Branch1][C][C][C][O][C][C][Ring1][=Branch1][C][C][C][O][C][Branch1][C][O][C][C][Branch1][C][C][C][C][C][=Branch1][C][=O][C][Branch1][C][C][Branch1][C][C][C][Ring1][#Branch2][C][C][C][Ring1][=C][Branch1][C][C][C][Ring2][Ring2][=C][Branch1][C][C][C][Ring2][Branch1][C][C][Branch1][C][C][C][C][Branch1][C][O][C][O][C][Ring1][Ring1][Branch1][C][C][C]' |
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- '[O][=C][Branch1][C][O][C][Branch2][O][P][O][C][C][=Branch1][C][=O][N][C][C][Branch1][C][O][C][C][Branch2][=Branch2][=Branch2][O][C][C][=Branch1][C][=O][N][C][C][Branch1][C][O][C][C][Branch2][=Branch1][P][O][C][C][Branch1][C][O][C][Branch1][C][O][C][Branch1][C][O][C][Branch2][Branch1][#Branch2][O][P][=Branch1][C][=O][Branch1][C][O][O][C][C][Branch2][Ring1][O][N][C][=Branch1][C][=O][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][Branch1][C][O][C][=C][C][C][C][C][C][C][C][C][C][C][C][C][Ring2][Branch1][#Branch1][O][Branch1][P][O][C][Ring2][Branch1][S][C][Branch1][C][O][C][Branch1][C][O][C][O][C][C][=Branch1][C][=O][O][Branch1][P][O][C][Ring2][#Branch1][=Branch1][C][Branch1][C][O][C][Branch1][C][O][C][O][C][C][=Branch1][C][=O][O][O][C][Branch1][N][C][Branch1][C][O][C][Branch1][C][O][C][O][C][C][Branch1][Branch2][N][C][=Branch1][C][=O][C][O][C][Branch1][C][O][C][Ring2][=Branch2][Branch2]' |
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- '[O][=C][Branch1][C][N][C][=N][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=Branch1][C][=O][N][Ring1][O][C][C][O][C]' |
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- source_sentence: '[O][=C][Branch1][#Branch1][C][=C][C][C][C][=C][C]' |
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sentences: |
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- '[O][=C][Branch1][C][O][C][C][C][C][C][C][C][C][Branch1][C][O][C][=C][C][#C][C][=C][C][C][C]' |
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- '[O][C][C][O][C][Branch2][=Branch2][Ring1][O][C][Branch1][C][C][C][C][C][Branch1][C][O][O][C][C][C][C][C][C][C][C][C][Branch2][Branch1][N][O][C][O][C][Branch1][Ring1][C][O][C][Branch2][Ring2][#Branch1][O][C][O][C][Branch1][Ring1][C][O][C][Branch1][C][O][C][Branch1][C][O][C][Ring1][#Branch2][O][C][O][C][Branch1][C][C][C][Branch1][C][O][C][Branch1][C][O][C][Ring1][=Branch2][O][C][Branch1][C][O][C][Ring2][Ring1][#C][O][C][C][C][Ring2][Ring2][#Branch1][Branch1][C][C][C][Ring2][Ring2][N][C][C][C][Ring2][Ring2][S][Branch1][C][C][C][Ring2][Branch1][Ring2][C][Ring2][Branch1][Branch2][C][C][Branch1][C][O][C][Branch1][C][O][C][Ring2][=Branch1][=Branch1][O]' |
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- '[O][=C][Branch1][#Branch2][C][=C][C][#C][C][#C][C][#C][C][N][C][C][C][=C][C][=C][C][=C][Ring1][=Branch1]' |
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model-index: |
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- name: SentenceTransformer |
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results: |
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- task: |
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type: semantic-similarity |
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name: Semantic Similarity |
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dataset: |
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name: NP isotest |
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type: NP-isotest |
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metrics: |
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- type: pearson_cosine |
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value: 0.936731178796972 |
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name: Pearson Cosine |
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- type: spearman_cosine |
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value: 0.93027366634068 |
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name: Spearman Cosine |
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- type: pearson_manhattan |
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value: 0.826340669261792 |
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name: Pearson Manhattan |
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- type: spearman_manhattan |
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value: 0.845192256146849 |
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name: Spearman Manhattan |
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- type: pearson_euclidean |
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value: 0.842726066770598 |
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name: Pearson Euclidean |
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- type: spearman_euclidean |
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value: 0.865381289346298 |
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name: Spearman Euclidean |
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- type: pearson_dot |
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value: 0.924283770507162 |
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name: Pearson Dot |
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- type: spearman_dot |
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value: 0.923230424410894 |
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name: Spearman Dot |
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- type: pearson_max |
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value: 0.936731178796972 |
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name: Pearson Max |
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- type: spearman_max |
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value: 0.93027366634068 |
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name: Spearman Max |
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--- |
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# ChEmbed v0.1 - Chemical Embeddings |
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This prototype is a [sentence-transformers](https://www.SBERT.net) based on [MiniLM-L6-H384-uncased](https://huggingface.co/nreimers/MiniLM-L6-H384-uncased) fine-tuned on around 1 million pairs of valid natural compounds' SELFIES [(Krenn et al. 2020)](https://github.com/aspuru-guzik-group/selfies) taken from COCONUTDB [(Sorokina et al. 2021)](https://coconut.naturalproducts.net/). It maps compounds' *Self-Referencing Embedded Strings* (SELFIES) into a 768-dimensional dense vector space, potentially can be used for chemical similarity, similarity search, classification, clustering, and more. |
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I am planning to train this model with more epochs on current dataset, before moving on to a larger dataset with 6 million pairs generated from ChemBL34. However, this will take some time due to computational and financial constraints. A future project of mine is to develop a custom model specifically for cheminformatics to address any biases and optimization issues in repurposing an embedding model designed for NLP tasks. |
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|
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### Disclaimer: For Academic Purposes Only |
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The information and model provided is for academic purposes only. It is intended for educational and research use, and should not be used for any commercial or legal purposes. The author do not guarantee the accuracy, completeness, or reliability of the information. |
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|
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## Model Details |
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### Model Description |
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- **Model Type:** Sentence Transformer |
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- **Base model:** [MiniLM-L6-H384-uncased](https://huggingface.co/nreimers/MiniLM-L6-H384-uncased) |
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- **Maximum Sequence Length:** 512 tokens |
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- **Output Dimensionality:** 768 tokens |
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- **Similarity Function:** Cosine Similarity |
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- **Training Dataset:** SELFIES pairs generated from COCONUTDB |
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- **Language:** SELFIES |
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- **License:** CC BY-NC 4.0 |
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### Full Model Architecture |
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|
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``` |
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SentenceTransformer( |
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(0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: BertModel |
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(1): Pooling({'word_embedding_dimension': 384, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': True, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': False}) |
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) |
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``` |
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## Usage |
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### Direct Usage (Sentence Transformers) |
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First install the Sentence Transformers library: |
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```bash |
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pip install -U sentence-transformers |
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``` |
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Then you can load this model and run inference. |
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```python |
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from sentence_transformers import SentenceTransformer |
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# Download from the 🤗 Hub |
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model = SentenceTransformer("gbyuvd/ChEmbed-v01") |
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# Run inference |
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sentences = [ |
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'[O][=C][Branch1][#Branch1][C][=C][C][C][C][=C][C]', |
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'[O][=C][Branch1][C][O][C][C][C][C][C][C][C][C][Branch1][C][O][C][=C][C][#C][C][=C][C][C][C]', |
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'[O][C][C][O][C][Branch2][=Branch2][Ring1][O][C][Branch1][C][C][C][C][C][Branch1][C][O][O][C][C][C][C][C][C][C][C][C][Branch2][Branch1][N][O][C][O][C][Branch1][Ring1][C][O][C][Branch2][Ring2][#Branch1][O][C][O][C][Branch1][Ring1][C][O][C][Branch1][C][O][C][Branch1][C][O][C][Ring1][#Branch2][O][C][O][C][Branch1][C][C][C][Branch1][C][O][C][Branch1][C][O][C][Ring1][=Branch2][O][C][Branch1][C][O][C][Ring2][Ring1][#C][O][C][C][C][Ring2][Ring2][#Branch1][Branch1][C][C][C][Ring2][Ring2][N][C][C][C][Ring2][Ring2][S][Branch1][C][C][C][Ring2][Branch1][Ring2][C][Ring2][Branch1][Branch2][C][C][Branch1][C][O][C][Branch1][C][O][C][Ring2][=Branch1][=Branch1][O]', |
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] |
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embeddings = model.encode(sentences) |
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print(embeddings.shape) |
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# [3, 768] |
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# Get the similarity scores for the embeddings |
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similarities = model.similarity(embeddings, embeddings) |
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print(similarities.shape) |
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# [3, 3] |
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``` |
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## Dataset |
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| Dataset | Reference | Number of Pairs | |
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|:---------------------------|:-----------|:-----------| |
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| COCONUTDB (0.8:0.1:0.1 split) | [(Sorokina et al. 2021)](https://coconut.naturalproducts.net/) | 1,183,174 | |
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## Evaluation |
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### Metrics |
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#### Semantic Similarity |
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* Dataset: `NP-isotest` |
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* Number of test pairs: 118,318 |
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* Evaluated with [<code>EmbeddingSimilarityEvaluator</code>](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.EmbeddingSimilarityEvaluator) |
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| Metric | Value | |
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|:--------------------|:-----------| |
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| pearson_cosine | 0.9367 | |
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| **spearman_cosine** | **0.9303** | |
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| pearson_manhattan | 0.8263 | |
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| spearman_manhattan | 0.8452 | |
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| pearson_euclidean | 0.8654 | |
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| spearman_euclidean | 0.9243 | |
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| pearson_dot | 0.9232 | |
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| spearman_dot | 0.9367 | |
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| pearson_max | 0.9303 | |
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| spearman_max | 0.8961 | |
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## Limitations |
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For now, the model might be ineffective in embedding synthetic drugs, since it is still trained on just natural products. Also, the tokenizer used is still uncustomized one. |
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## Testing Generated Embeddings' Clusters |
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The plot below shows how the model's embeddings (at this stage) cluster different classes of compounds, compared to using MACCS fingerprints. |
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 |
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 |
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### Framework Versions |
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- Python: 3.9.13 |
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- Sentence Transformers: 3.0.1 |
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- Transformers: 4.41.2 |
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- PyTorch: 2.3.1+cu121 |
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- Accelerate: 0.31.0 |
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- Datasets: 2.20.0 |
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- Tokenizers: 0.19.1 |
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## Contact |
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|
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G Bayu ([email protected]) |
