pankajrajdeo commited on
Commit
f8ff613
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1 Parent(s): f0e700f

Add FP16 version of the model

Browse files
1_Pooling/config.json ADDED
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+ {
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+ "word_embedding_dimension": 384,
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+ "pooling_mode_cls_token": false,
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+ "pooling_mode_mean_tokens": true,
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+ "pooling_mode_max_tokens": false,
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+ "pooling_mode_mean_sqrt_len_tokens": false,
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+ "pooling_mode_weightedmean_tokens": false,
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+ "pooling_mode_lasttoken": false,
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+ "include_prompt": true
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+ }
README.md ADDED
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+ ---
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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:1441905
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+ - loss:CachedMultipleNegativesRankingLoss
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+ widget:
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+ - source_sentence: Treponema caused disease or disorder
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+ sentences:
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+ - bejel
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+ - tumor of ureter
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+ - debrisoquine, ultrarapid metabolism of
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+ - source_sentence: B cell (antibody) deficiencies
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+ sentences:
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+ - distal phalanx of digit IV
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+ - well-differentiated fetal adenocarcinoma of the lung
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+ - deficiency of humoral immunity
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+ - source_sentence: Elevated AdoHcy concentration
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+ sentences:
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+ - gepulste Abgabe
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+ - Elevated circulating S-adenosyl-L-homocysteine concentration
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+ - Frequently cries for no reason
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+ - source_sentence: Isoelectric focusing of serum transferrin consistent with CDG type
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+ II
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+ sentences:
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+ - Amblyomma aureolatum
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+ - squamous cell carcinoma of the bile duct
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+ - Abnormal isoelectric focusing of serum transferrin, type 2 pattern
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+ - source_sentence: Light-chain amyloidosis
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+ sentences:
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+ - partial deletion of the long arm of chromosome X
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+ - Teneria teneriensis
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+ - amyloidosis primary systemic
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+ pipeline_tag: sentence-similarity
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+ library_name: sentence-transformers
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+ metrics:
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+ - cosine_accuracy@1
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+ - cosine_accuracy@3
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+ - cosine_accuracy@5
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+ - cosine_accuracy@10
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+ - cosine_precision@1
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+ - cosine_precision@3
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+ - cosine_precision@5
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+ - cosine_precision@10
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+ - cosine_recall@1
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+ - cosine_recall@3
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+ - cosine_recall@5
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+ - cosine_recall@10
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+ - cosine_ndcg@10
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+ - cosine_mrr@10
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+ - cosine_map@100
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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: information-retrieval
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+ name: Information Retrieval
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+ dataset:
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+ name: owl ontology eval
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+ type: owl_ontology_eval
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+ metrics:
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+ - type: cosine_accuracy@1
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+ value: 0.6302799165287473
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+ name: Cosine Accuracy@1
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+ - type: cosine_accuracy@3
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+ value: 0.8147801683816651
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+ name: Cosine Accuracy@3
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+ - type: cosine_accuracy@5
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+ value: 0.8775275239260272
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+ name: Cosine Accuracy@5
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+ - type: cosine_accuracy@10
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+ value: 0.9268187378570915
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+ name: Cosine Accuracy@10
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+ - type: cosine_precision@1
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+ value: 0.6302799165287473
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+ name: Cosine Precision@1
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+ - type: cosine_precision@3
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+ value: 0.27634261591230724
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+ name: Cosine Precision@3
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+ - type: cosine_precision@5
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+ value: 0.17979420018709072
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+ name: Cosine Precision@5
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+ - type: cosine_precision@10
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+ value: 0.09566812981218968
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+ name: Cosine Precision@10
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+ - type: cosine_recall@1
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+ value: 0.6216929313281044
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+ name: Cosine Recall@1
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+ - type: cosine_recall@3
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+ value: 0.8081120625554675
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+ name: Cosine Recall@3
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+ - type: cosine_recall@5
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+ value: 0.8723585426111152
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+ name: Cosine Recall@5
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+ - type: cosine_recall@10
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+ value: 0.9241442997289582
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+ name: Cosine Recall@10
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+ - type: cosine_ndcg@10
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+ value: 0.7796907170635903
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+ name: Cosine Ndcg@10
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+ - type: cosine_mrr@10
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+ value: 0.7342337217921898
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+ name: Cosine Mrr@10
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+ - type: cosine_map@100
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+ value: 0.734065731352359
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+ name: Cosine Map@100
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+ ---
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+
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+ # SentenceTransformer
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+
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+ This is a [sentence-transformers](https://www.SBERT.net) model trained on the json dataset. It maps sentences & paragraphs to a 384-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, text classification, clustering, and more.
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+
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+ ## Model Details
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+
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+ ### Model Description
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+ - **Model Type:** Sentence Transformer
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+ <!-- - **Base model:** [Unknown](https://huggingface.co/unknown) -->
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+ - **Maximum Sequence Length:** 1024 tokens
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+ - **Output Dimensionality:** 384 dimensions
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+ - **Similarity Function:** Cosine Similarity
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+ - **Training Dataset:**
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+ - json
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+ <!-- - **Language:** Unknown -->
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+ <!-- - **License:** Unknown -->
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+
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+ ### Model Sources
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+
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+ - **Documentation:** [Sentence Transformers Documentation](https://sbert.net)
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+ - **Repository:** [Sentence Transformers on GitHub](https://github.com/UKPLab/sentence-transformers)
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+ - **Hugging Face:** [Sentence Transformers on Hugging Face](https://huggingface.co/models?library=sentence-transformers)
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+
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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': 1024, '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': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
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+ )
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+ ```
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+
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+ ## Usage
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+
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+ ### Direct Usage (Sentence Transformers)
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+
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+ First install the Sentence Transformers library:
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+
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+ ```bash
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+ pip install -U sentence-transformers
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+ ```
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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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+
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+ # Download from the 🤗 Hub
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+ model = SentenceTransformer("pankajrajdeo/bond-embed-16L")
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+ # Run inference
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+ sentences = [
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+ 'Light-chain amyloidosis',
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+ 'amyloidosis primary systemic',
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+ 'partial deletion of the long arm of chromosome X',
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+ ]
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+ embeddings = model.encode(sentences)
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+ print(embeddings.shape)
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+ # [3, 384]
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+
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+ # Get the similarity scores for the embeddings
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+ similarities = model.similarity(embeddings, embeddings)
171
+ print(similarities.shape)
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+ # [3, 3]
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+ ```
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+
175
+ <!--
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+ ### Direct Usage (Transformers)
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+
178
+ <details><summary>Click to see the direct usage in Transformers</summary>
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+
180
+ </details>
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+ -->
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+
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+ <!--
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+ ### Downstream Usage (Sentence Transformers)
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+
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+ You can finetune this model on your own dataset.
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+
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+ <details><summary>Click to expand</summary>
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+
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+ </details>
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+ -->
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+
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+ <!--
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+ ### Out-of-Scope Use
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+
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+ *List how the model may foreseeably be misused and address what users ought not to do with the model.*
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+ -->
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+
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+ ## Evaluation
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+
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+ ### Metrics
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+
203
+ #### Information Retrieval
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+
205
+ * Dataset: `owl_ontology_eval`
206
+ * Evaluated with [<code>InformationRetrievalEvaluator</code>](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.InformationRetrievalEvaluator)
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+
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+ | Metric | Value |
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+ |:--------------------|:-----------|
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+ | cosine_accuracy@1 | 0.6303 |
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+ | cosine_accuracy@3 | 0.8148 |
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+ | cosine_accuracy@5 | 0.8775 |
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+ | cosine_accuracy@10 | 0.9268 |
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+ | cosine_precision@1 | 0.6303 |
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+ | cosine_precision@3 | 0.2763 |
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+ | cosine_precision@5 | 0.1798 |
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+ | cosine_precision@10 | 0.0957 |
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+ | cosine_recall@1 | 0.6217 |
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+ | cosine_recall@3 | 0.8081 |
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+ | cosine_recall@5 | 0.8724 |
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+ | cosine_recall@10 | 0.9241 |
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+ | **cosine_ndcg@10** | **0.7797** |
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+ | cosine_mrr@10 | 0.7342 |
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+ | cosine_map@100 | 0.7341 |
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+
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+ <!--
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+ ## Bias, Risks and Limitations
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+
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+ *What are the known or foreseeable issues stemming from this model? You could also flag here known failure cases or weaknesses of the model.*
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+ -->
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+
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+ <!--
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+ ### Recommendations
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+
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+ *What are recommendations with respect to the foreseeable issues? For example, filtering explicit content.*
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+ -->
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+
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+ ## Training Details
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+
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+ ### Training Dataset
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+
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+ #### json
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+
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+ * Dataset: json
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+ * Size: 1,441,905 training samples
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+ * Columns: <code>anchor</code> and <code>positive</code>
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+ * Approximate statistics based on the first 1000 samples:
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+ | | anchor | positive |
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+ |:--------|:---------------------------------------------------------------------------------|:---------------------------------------------------------------------------------|
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+ | type | string | string |
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+ | details | <ul><li>min: 3 tokens</li><li>mean: 9.48 tokens</li><li>max: 47 tokens</li></ul> | <ul><li>min: 3 tokens</li><li>mean: 8.68 tokens</li><li>max: 30 tokens</li></ul> |
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+ * Samples:
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+ | anchor | positive |
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+ |:-------------------------------------|:-------------------------------------|
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+ | <code>Mangshan horned toad</code> | <code>Mangshan spadefoot toad</code> |
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+ | <code>Leuconotopicos borealis</code> | <code>Picoides borealis</code> |
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+ | <code>Cylindrella teneriensis</code> | <code>Teneria teneriensis</code> |
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+ * Loss: [<code>CachedMultipleNegativesRankingLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#cachedmultiplenegativesrankingloss) with these parameters:
259
+ ```json
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+ {
261
+ "scale": 20.0,
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+ "similarity_fct": "cos_sim"
263
+ }
264
+ ```
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+
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+ ### Training Hyperparameters
267
+ #### Non-Default Hyperparameters
268
+
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+ - `eval_strategy`: steps
270
+ - `per_device_train_batch_size`: 1024
271
+ - `learning_rate`: 1.5e-05
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+ - `num_train_epochs`: 5
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+ - `lr_scheduler_type`: cosine
274
+ - `warmup_ratio`: 0.05
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+ - `bf16`: True
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+ - `dataloader_num_workers`: 32
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+ - `load_best_model_at_end`: True
278
+ - `gradient_checkpointing`: True
279
+
280
+ #### All Hyperparameters
281
+ <details><summary>Click to expand</summary>
282
+
283
+ - `overwrite_output_dir`: False
284
+ - `do_predict`: False
285
+ - `eval_strategy`: steps
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+ - `prediction_loss_only`: True
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+ - `per_device_train_batch_size`: 1024
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+ - `per_device_eval_batch_size`: 8
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+ - `per_gpu_train_batch_size`: None
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+ - `per_gpu_eval_batch_size`: None
291
+ - `gradient_accumulation_steps`: 1
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+ - `eval_accumulation_steps`: None
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+ - `torch_empty_cache_steps`: None
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+ - `learning_rate`: 1.5e-05
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+ - `weight_decay`: 0.0
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+ - `adam_beta1`: 0.9
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+ - `adam_beta2`: 0.999
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+ - `adam_epsilon`: 1e-08
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+ - `max_grad_norm`: 1.0
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+ - `num_train_epochs`: 5
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+ - `max_steps`: -1
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+ - `lr_scheduler_type`: cosine
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+ - `lr_scheduler_kwargs`: {}
304
+ - `warmup_ratio`: 0.05
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+ - `warmup_steps`: 0
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+ - `log_level`: passive
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+ - `log_level_replica`: warning
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+ - `log_on_each_node`: True
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+ - `logging_nan_inf_filter`: True
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+ - `save_safetensors`: True
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+ - `save_on_each_node`: False
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+ - `save_only_model`: False
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+ - `restore_callback_states_from_checkpoint`: False
314
+ - `no_cuda`: False
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+ - `use_cpu`: False
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+ - `use_mps_device`: False
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+ - `seed`: 42
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+ - `data_seed`: None
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+ - `jit_mode_eval`: False
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+ - `use_ipex`: False
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+ - `bf16`: True
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+ - `fp16`: False
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+ - `fp16_opt_level`: O1
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+ - `half_precision_backend`: auto
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+ - `bf16_full_eval`: False
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+ - `fp16_full_eval`: False
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+ - `tf32`: None
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+ - `local_rank`: 0
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+ - `ddp_backend`: None
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+ - `tpu_num_cores`: None
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+ - `tpu_metrics_debug`: False
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+ - `debug`: []
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+ - `dataloader_drop_last`: False
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+ - `dataloader_num_workers`: 32
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+ - `dataloader_prefetch_factor`: None
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+ - `past_index`: -1
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+ - `disable_tqdm`: False
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+ - `remove_unused_columns`: True
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+ - `label_names`: None
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+ - `load_best_model_at_end`: True
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+ - `ignore_data_skip`: False
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+ - `fsdp`: []
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+ - `fsdp_min_num_params`: 0
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+ - `fsdp_config`: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}
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+ - `fsdp_transformer_layer_cls_to_wrap`: None
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+ - `accelerator_config`: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}
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+ - `deepspeed`: None
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+ - `label_smoothing_factor`: 0.0
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+ - `optim`: adamw_torch
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+ - `optim_args`: None
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+ - `adafactor`: False
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+ - `group_by_length`: False
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+ - `length_column_name`: length
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+ - `ddp_find_unused_parameters`: None
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+ - `ddp_bucket_cap_mb`: None
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+ - `ddp_broadcast_buffers`: False
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+ - `dataloader_pin_memory`: True
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+ - `dataloader_persistent_workers`: False
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+ - `skip_memory_metrics`: True
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+ - `use_legacy_prediction_loop`: False
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+ - `push_to_hub`: False
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+ - `resume_from_checkpoint`: None
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+ - `hub_model_id`: None
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+ - `hub_strategy`: every_save
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+ - `hub_private_repo`: None
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+ - `hub_always_push`: False
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+ - `hub_revision`: None
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+ - `gradient_checkpointing`: True
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+ - `gradient_checkpointing_kwargs`: None
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+ - `include_inputs_for_metrics`: False
371
+ - `include_for_metrics`: []
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+ - `eval_do_concat_batches`: True
373
+ - `fp16_backend`: auto
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+ - `push_to_hub_model_id`: None
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+ - `push_to_hub_organization`: None
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+ - `mp_parameters`:
377
+ - `auto_find_batch_size`: False
378
+ - `full_determinism`: False
379
+ - `torchdynamo`: None
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+ - `ray_scope`: last
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+ - `ddp_timeout`: 1800
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+ - `torch_compile`: False
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+ - `torch_compile_backend`: None
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+ - `torch_compile_mode`: None
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+ - `include_tokens_per_second`: False
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+ - `include_num_input_tokens_seen`: False
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+ - `neftune_noise_alpha`: None
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+ - `optim_target_modules`: None
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+ - `batch_eval_metrics`: False
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+ - `eval_on_start`: False
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+ - `use_liger_kernel`: False
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+ - `liger_kernel_config`: None
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+ - `eval_use_gather_object`: False
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+ - `average_tokens_across_devices`: False
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+ - `prompts`: None
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+ - `batch_sampler`: batch_sampler
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+ - `multi_dataset_batch_sampler`: proportional
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+
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+ </details>
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+
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+ ### Training Logs
402
+ | Epoch | Step | Training Loss | owl_ontology_eval_cosine_ndcg@10 |
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+ |:------:|:----:|:-------------:|:--------------------------------:|
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+ | 0.0717 | 100 | 1.3232 | - |
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+ | 0.1434 | 200 | 1.021 | - |
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+ | 0.2151 | 300 | 0.9633 | - |
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+ | 0.2867 | 400 | 0.9068 | - |
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+ | 0.3297 | 460 | - | 0.7207 |
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+ | 0.3584 | 500 | 0.8723 | - |
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+ | 0.4301 | 600 | 0.852 | - |
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+ | 0.5018 | 700 | 0.8161 | - |
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+ | 0.5735 | 800 | 0.7939 | - |
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+ | 0.6452 | 900 | 0.7935 | - |
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+ | 0.6595 | 920 | - | 0.7364 |
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+ | 0.7168 | 1000 | 0.7646 | - |
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+ | 0.7885 | 1100 | 0.7464 | - |
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+ | 0.8602 | 1200 | 0.7376 | - |
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+ | 0.9319 | 1300 | 0.7313 | - |
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+ | 0.9892 | 1380 | - | 0.7468 |
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+ | 1.0036 | 1400 | 0.7099 | - |
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+ | 1.0753 | 1500 | 0.6884 | - |
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+ | 1.1470 | 1600 | 0.6776 | - |
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+ | 1.2186 | 1700 | 0.6694 | - |
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+ | 1.2903 | 1800 | 0.6641 | - |
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+ | 1.3190 | 1840 | - | 0.7561 |
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+ | 1.3620 | 1900 | 0.6526 | - |
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+ | 1.4337 | 2000 | 0.6524 | - |
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+ | 1.5054 | 2100 | 0.6364 | - |
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+ | 1.5771 | 2200 | 0.6339 | - |
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+ | 1.6487 | 2300 | 0.626 | 0.7614 |
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+ | 1.7204 | 2400 | 0.6197 | - |
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+ | 1.7921 | 2500 | 0.6193 | - |
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+ | 1.8638 | 2600 | 0.6155 | - |
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+ | 1.9355 | 2700 | 0.6142 | - |
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+ | 1.9785 | 2760 | - | 0.7662 |
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+ | 2.0072 | 2800 | 0.5853 | - |
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+ | 2.0789 | 2900 | 0.5824 | - |
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+ | 2.1505 | 3000 | 0.5769 | - |
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+ | 2.2222 | 3100 | 0.5765 | - |
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+ | 2.2939 | 3200 | 0.5608 | - |
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+ | 2.3082 | 3220 | - | 0.7698 |
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+ | 2.3656 | 3300 | 0.5695 | - |
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+ | 2.4373 | 3400 | 0.5641 | - |
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+ | 2.5090 | 3500 | 0.5638 | - |
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+ | 2.5806 | 3600 | 0.554 | - |
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+ | 2.6380 | 3680 | - | 0.7735 |
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+ | 2.6523 | 3700 | 0.5539 | - |
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+ | 2.7240 | 3800 | 0.5495 | - |
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+ | 2.7957 | 3900 | 0.5556 | - |
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+ | 2.8674 | 4000 | 0.5397 | - |
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+ | 2.9391 | 4100 | 0.5447 | - |
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+ | 2.9677 | 4140 | - | 0.7757 |
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+ | 3.0108 | 4200 | 0.5331 | - |
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+ | 3.0824 | 4300 | 0.5336 | - |
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+ | 3.1541 | 4400 | 0.5346 | - |
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+ | 3.2258 | 4500 | 0.5247 | - |
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+ | 3.2975 | 4600 | 0.5241 | 0.7775 |
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+ | 3.3692 | 4700 | 0.5257 | - |
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+ | 3.4409 | 4800 | 0.5241 | - |
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+ | 3.5125 | 4900 | 0.5171 | - |
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+ | 3.5842 | 5000 | 0.5215 | - |
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+ | 3.6272 | 5060 | - | 0.7787 |
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+ | 3.6559 | 5100 | 0.5203 | - |
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+ | 3.7276 | 5200 | 0.5214 | - |
465
+ | 3.7993 | 5300 | 0.5266 | - |
466
+ | 3.8710 | 5400 | 0.5127 | - |
467
+ | 3.9427 | 5500 | 0.5062 | - |
468
+ | 3.9570 | 5520 | - | 0.7790 |
469
+ | 4.0143 | 5600 | 0.5104 | - |
470
+ | 4.0860 | 5700 | 0.5155 | - |
471
+ | 4.1577 | 5800 | 0.5042 | - |
472
+ | 4.2294 | 5900 | 0.5174 | - |
473
+ | 4.2867 | 5980 | - | 0.7797 |
474
+ | 4.3011 | 6000 | 0.509 | - |
475
+ | 4.3728 | 6100 | 0.5106 | - |
476
+ | 4.4444 | 6200 | 0.5076 | - |
477
+ | 4.5161 | 6300 | 0.5046 | - |
478
+ | 4.5878 | 6400 | 0.5077 | - |
479
+ | 4.6165 | 6440 | - | 0.7795 |
480
+ | 4.6595 | 6500 | 0.5114 | - |
481
+ | 4.7312 | 6600 | 0.5103 | - |
482
+ | 4.8029 | 6700 | 0.5106 | - |
483
+ | 4.8746 | 6800 | 0.5102 | - |
484
+ | 4.9462 | 6900 | 0.5076 | 0.7797 |
485
+
486
+
487
+ ### Framework Versions
488
+ - Python: 3.11.11
489
+ - Sentence Transformers: 3.4.1
490
+ - Transformers: 4.53.2
491
+ - PyTorch: 2.6.0+cu124
492
+ - Accelerate: 1.5.2
493
+ - Datasets: 3.2.0
494
+ - Tokenizers: 0.21.0
495
+
496
+ ## Citation
497
+
498
+ ### BibTeX
499
+
500
+ #### Sentence Transformers
501
+ ```bibtex
502
+ @inproceedings{reimers-2019-sentence-bert,
503
+ title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
504
+ author = "Reimers, Nils and Gurevych, Iryna",
505
+ booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
506
+ month = "11",
507
+ year = "2019",
508
+ publisher = "Association for Computational Linguistics",
509
+ url = "https://arxiv.org/abs/1908.10084",
510
+ }
511
+ ```
512
+
513
+ #### CachedMultipleNegativesRankingLoss
514
+ ```bibtex
515
+ @misc{gao2021scaling,
516
+ title={Scaling Deep Contrastive Learning Batch Size under Memory Limited Setup},
517
+ author={Luyu Gao and Yunyi Zhang and Jiawei Han and Jamie Callan},
518
+ year={2021},
519
+ eprint={2101.06983},
520
+ archivePrefix={arXiv},
521
+ primaryClass={cs.LG}
522
+ }
523
+ ```
524
+
525
+ <!--
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+ ## Glossary
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+
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+ *Clearly define terms in order to be accessible across audiences.*
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+ -->
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+
531
+ <!--
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+ ## Model Card Authors
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+
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+ *Lists the people who create the model card, providing recognition and accountability for the detailed work that goes into its construction.*
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+ -->
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+
537
+ <!--
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+ ## Model Card Contact
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+
540
+ *Provides a way for people who have updates to the Model Card, suggestions, or questions, to contact the Model Card authors.*
541
+ -->
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