pankajrajdeo commited on
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1 Parent(s): c8337e3

Add new SentenceTransformer 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:3997120
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+ - loss:MultipleNegativesSymmetricMarginLoss
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+ widget:
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+ - source_sentence: Orciprenaline 20 mg oral tablet
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+ sentences:
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+ - Metaproterenol 20 mg oral tablet
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+ - SNOMED_CT
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+ - synonym
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+ - source_sentence: Borreliella burgdorferi ZS7
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+ sentences:
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+ - NCBITAXON
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+ - Borrelia burgdorferi str. ZS7
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+ - synonym
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+ - source_sentence: Mos (mouse)
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+ sentences:
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+ - A protein coding gene Mos in mouse.
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+ - PR
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+ - definition
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+ - source_sentence: On examination - respiratory examination NOS
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+ sentences:
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+ - synonym
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+ - On examination - respiratory examination NOS (finding)
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+ - SNOMED_CT
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+ - source_sentence: pisiform joint
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+ sentences:
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+ - definition
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+ - UBERON
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+ - It is a joint between the pisiform and triquetrum.
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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: foundational eval
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+ type: foundational_eval
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+ metrics:
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+ - type: cosine_accuracy@1
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+ value: 0.8786757730980839
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+ name: Cosine Accuracy@1
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+ - type: cosine_accuracy@3
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+ value: 0.9251090874596851
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+ name: Cosine Accuracy@3
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+ - type: cosine_accuracy@5
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+ value: 0.9369664200341491
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+ name: Cosine Accuracy@5
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+ - type: cosine_accuracy@10
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+ value: 0.9473534433693797
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+ name: Cosine Accuracy@10
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+ - type: cosine_precision@1
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+ value: 0.8786757730980839
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+ name: Cosine Precision@1
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+ - type: cosine_precision@3
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+ value: 0.45155884398912294
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+ name: Cosine Precision@3
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+ - type: cosine_precision@5
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+ value: 0.29832100170745596
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+ name: Cosine Precision@5
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+ - type: cosine_precision@10
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+ value: 0.16140675393663445
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+ name: Cosine Precision@10
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+ - type: cosine_recall@1
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+ value: 0.6510243437934023
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+ name: Cosine Recall@1
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+ - type: cosine_recall@3
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+ value: 0.8341248818490324
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+ name: Cosine Recall@3
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+ - type: cosine_recall@5
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+ value: 0.871880844859248
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+ name: Cosine Recall@5
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+ - type: cosine_recall@10
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+ value: 0.9021978114122614
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+ name: Cosine Recall@10
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+ - type: cosine_ndcg@10
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+ value: 0.8777720626935165
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+ name: Cosine Ndcg@10
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+ - type: cosine_mrr@10
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+ value: 0.9037414965986426
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+ name: Cosine Mrr@10
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+ - type: cosine_map@100
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+ value: 0.8544223899209221
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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:** 256 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': 256, '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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+
146
+ First install the Sentence Transformers library:
147
+
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+ ```bash
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+ pip install -U sentence-transformers
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+ ```
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+
152
+ Then you can load this model and run inference.
153
+ ```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/BioForge-bioformer-16L-foundational")
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+ # Run inference
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+ sentences = [
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+ 'pisiform joint',
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+ 'It is a joint between the pisiform and triquetrum.',
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+ 'UBERON',
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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)
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+ print(similarities.shape)
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+ # [3, 3]
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+ ```
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+
174
+ <!--
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+ ### Direct Usage (Transformers)
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+
177
+ <details><summary>Click to see the direct usage in Transformers</summary>
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+
179
+ </details>
180
+ -->
181
+
182
+ <!--
183
+ ### Downstream Usage (Sentence Transformers)
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+
185
+ You can finetune this model on your own dataset.
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+
187
+ <details><summary>Click to expand</summary>
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+
189
+ </details>
190
+ -->
191
+
192
+ <!--
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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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+
200
+ ### Metrics
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+
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+ #### Information Retrieval
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+
204
+ * Dataset: `foundational_eval`
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+ * 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 | 0.8787 |
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+ | cosine_accuracy@3 | 0.9251 |
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+ | cosine_accuracy@5 | 0.937 |
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+ | cosine_accuracy@10 | 0.9474 |
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+ | cosine_precision@1 | 0.8787 |
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+ | cosine_precision@3 | 0.4516 |
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+ | cosine_precision@5 | 0.2983 |
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+ | cosine_precision@10 | 0.1614 |
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+ | cosine_recall@1 | 0.651 |
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+ | cosine_recall@3 | 0.8341 |
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+ | cosine_recall@5 | 0.8719 |
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+ | cosine_recall@10 | 0.9022 |
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+ | **cosine_ndcg@10** | **0.8778** |
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+ | cosine_mrr@10 | 0.9037 |
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+ | cosine_map@100 | 0.8544 |
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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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+
237
+ ## Training Details
238
+
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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: 3,997,120 training samples
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+ * Columns: <code>anchor</code>, <code>positive</code>, <code>source</code>, and <code>pair_type</code>
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+ * Approximate statistics based on the first 1000 samples:
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+ | | anchor | positive | source | pair_type |
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+ |:--------|:-----------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------|:--------------------------------------------------------------------------------|:--------------------------------------------------------------------------------|
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+ | type | string | string | string | string |
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+ | details | <ul><li>min: 3 tokens</li><li>mean: 12.57 tokens</li><li>max: 256 tokens</li></ul> | <ul><li>min: 3 tokens</li><li>mean: 15.69 tokens</li><li>max: 256 tokens</li></ul> | <ul><li>min: 3 tokens</li><li>mean: 5.12 tokens</li><li>max: 7 tokens</li></ul> | <ul><li>min: 3 tokens</li><li>mean: 3.06 tokens</li><li>max: 9 tokens</li></ul> |
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+ * Samples:
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+ | anchor | positive | source | pair_type |
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+ |:-------------------------------------------|:---------------------------------------------------------|:-----------------------|:-----------------------|
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+ | <code>IM - Intramuscular sedation</code> | <code>Intramuscular sedation</code> | <code>SNOMED_CT</code> | <code>synonym</code> |
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+ | <code>Metergoline</code> | <code>Sodium channel protein type 2 subunit alpha</code> | <code>DrugBank</code> | <code>target</code> |
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+ | <code>Trichomycterus sp. MBML6210_4</code> | <code>unclassified Trichomycterus</code> | <code>NCBITAXON</code> | <code>hierarchy</code> |
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+ * Loss: <code>__main__.MultipleNegativesSymmetricMarginLoss</code> with these parameters:
258
+ ```json
259
+ {
260
+ "scale": 20.0,
261
+ "similarity_fct": "cos_sim"
262
+ }
263
+ ```
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+
265
+ ### Training Hyperparameters
266
+ #### Non-Default Hyperparameters
267
+
268
+ - `eval_strategy`: steps
269
+ - `per_device_train_batch_size`: 512
270
+ - `gradient_accumulation_steps`: 4
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+ - `learning_rate`: 1.2e-05
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+ - `lr_scheduler_type`: cosine
273
+ - `warmup_ratio`: 0.05
274
+ - `bf16`: True
275
+ - `dataloader_num_workers`: 16
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+ - `load_best_model_at_end`: True
277
+ - `gradient_checkpointing`: True
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+
279
+ #### All Hyperparameters
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+ <details><summary>Click to expand</summary>
281
+
282
+ - `overwrite_output_dir`: False
283
+ - `do_predict`: False
284
+ - `eval_strategy`: steps
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+ - `prediction_loss_only`: True
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+ - `per_device_train_batch_size`: 512
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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
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+ - `gradient_accumulation_steps`: 4
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+ - `eval_accumulation_steps`: None
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+ - `torch_empty_cache_steps`: None
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+ - `learning_rate`: 1.2e-05
294
+ - `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`: 3
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+ - `max_steps`: -1
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+ - `lr_scheduler_type`: cosine
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+ - `lr_scheduler_kwargs`: {}
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+ - `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
309
+ - `save_safetensors`: True
310
+ - `save_on_each_node`: False
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+ - `save_only_model`: False
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+ - `restore_callback_states_from_checkpoint`: False
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+ - `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
325
+ - `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`: 16
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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
362
+ - `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
366
+ - `hub_revision`: None
367
+ - `gradient_checkpointing`: True
368
+ - `gradient_checkpointing_kwargs`: None
369
+ - `include_inputs_for_metrics`: False
370
+ - `include_for_metrics`: []
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+ - `eval_do_concat_batches`: True
372
+ - `fp16_backend`: auto
373
+ - `push_to_hub_model_id`: None
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+ - `push_to_hub_organization`: None
375
+ - `mp_parameters`:
376
+ - `auto_find_batch_size`: False
377
+ - `full_determinism`: False
378
+ - `torchdynamo`: None
379
+ - `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
383
+ - `torch_compile_mode`: None
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+ - `include_tokens_per_second`: False
385
+ - `include_num_input_tokens_seen`: False
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+ - `neftune_noise_alpha`: None
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+ - `optim_target_modules`: None
388
+ - `batch_eval_metrics`: False
389
+ - `eval_on_start`: False
390
+ - `use_liger_kernel`: False
391
+ - `liger_kernel_config`: None
392
+ - `eval_use_gather_object`: False
393
+ - `average_tokens_across_devices`: False
394
+ - `prompts`: None
395
+ - `batch_sampler`: batch_sampler
396
+ - `multi_dataset_batch_sampler`: proportional
397
+
398
+ </details>
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+
400
+ ### Training Logs
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+ | Epoch | Step | Training Loss | foundational_eval_cosine_ndcg@10 |
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+ |:------:|:----:|:-------------:|:--------------------------------:|
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+ | 0.0518 | 100 | 1.0162 | - |
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+ | 0.1035 | 200 | 0.7522 | - |
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+ | 0.1553 | 300 | 0.644 | - |
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+ | 0.2070 | 400 | 0.5971 | - |
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+ | 0.2588 | 500 | 0.5651 | - |
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+ | 0.3105 | 600 | 0.5391 | - |
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+ | 0.3297 | 637 | - | 0.8536 |
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+ | 0.3623 | 700 | 0.5306 | - |
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+ | 0.4140 | 800 | 0.5122 | - |
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+ | 0.4658 | 900 | 0.5024 | - |
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+ | 0.5175 | 1000 | 0.494 | - |
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+ | 0.5693 | 1100 | 0.4907 | - |
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+ | 0.6210 | 1200 | 0.48 | - |
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+ | 0.6593 | 1274 | - | 0.8639 |
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+ | 0.6728 | 1300 | 0.47 | - |
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+ | 0.7245 | 1400 | 0.4657 | - |
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+ | 0.7763 | 1500 | 0.4643 | - |
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+ | 0.8281 | 1600 | 0.4573 | - |
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+ | 0.8798 | 1700 | 0.4555 | - |
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+ | 0.9316 | 1800 | 0.4537 | - |
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+ | 0.9833 | 1900 | 0.4431 | - |
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+ | 0.9890 | 1911 | - | 0.8693 |
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+ | 1.0347 | 2000 | 0.4356 | - |
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+ | 1.0864 | 2100 | 0.4299 | - |
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+ | 1.1382 | 2200 | 0.4278 | - |
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+ | 1.1899 | 2300 | 0.4307 | - |
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+ | 1.2417 | 2400 | 0.4242 | - |
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+ | 1.2934 | 2500 | 0.4279 | - |
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+ | 1.3183 | 2548 | - | 0.8723 |
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+ | 1.3452 | 2600 | 0.4185 | - |
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+ | 1.3969 | 2700 | 0.42 | - |
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+ | 1.4487 | 2800 | 0.4189 | - |
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+ | 1.5005 | 2900 | 0.4183 | - |
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+ | 1.5522 | 3000 | 0.4143 | - |
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+ | 1.6040 | 3100 | 0.4147 | - |
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+ | 1.6479 | 3185 | - | 0.8748 |
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+ | 1.6557 | 3200 | 0.413 | - |
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+ | 1.7075 | 3300 | 0.4107 | - |
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+ | 1.7592 | 3400 | 0.4114 | - |
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+ | 1.8110 | 3500 | 0.4111 | - |
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+ | 1.8627 | 3600 | 0.4073 | - |
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+ | 1.9145 | 3700 | 0.4093 | - |
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+ | 1.9662 | 3800 | 0.4057 | - |
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+ | 1.9776 | 3822 | - | 0.8766 |
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+ | 2.0176 | 3900 | 0.3993 | - |
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+ | 2.0693 | 4000 | 0.3996 | - |
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+ | 2.1211 | 4100 | 0.3987 | - |
450
+ | 2.1729 | 4200 | 0.4012 | - |
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+ | 2.2246 | 4300 | 0.3979 | - |
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+ | 2.2764 | 4400 | 0.3977 | - |
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+ | 2.3069 | 4459 | - | 0.8774 |
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+ | 2.3281 | 4500 | 0.3981 | - |
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+ | 2.3799 | 4600 | 0.394 | - |
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+ | 2.4316 | 4700 | 0.3946 | - |
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+ | 2.4834 | 4800 | 0.395 | - |
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+ | 2.5351 | 4900 | 0.3971 | - |
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+ | 2.5869 | 5000 | 0.3963 | - |
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+ | 2.6366 | 5096 | - | 0.8776 |
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+ | 2.6386 | 5100 | 0.396 | - |
462
+ | 2.6904 | 5200 | 0.3976 | - |
463
+ | 2.7421 | 5300 | 0.3963 | - |
464
+ | 2.7939 | 5400 | 0.3985 | - |
465
+ | 2.8456 | 5500 | 0.3968 | - |
466
+ | 2.8974 | 5600 | 0.3973 | - |
467
+ | 2.9492 | 5700 | 0.3981 | - |
468
+ | 2.9662 | 5733 | - | 0.8778 |
469
+
470
+
471
+ ### Framework Versions
472
+ - Python: 3.11.11
473
+ - Sentence Transformers: 3.4.1
474
+ - Transformers: 4.53.2
475
+ - PyTorch: 2.6.0+cu124
476
+ - Accelerate: 1.5.2
477
+ - Datasets: 3.2.0
478
+ - Tokenizers: 0.21.0
479
+
480
+ ## Citation
481
+
482
+ ### BibTeX
483
+
484
+ #### Sentence Transformers
485
+ ```bibtex
486
+ @inproceedings{reimers-2019-sentence-bert,
487
+ title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
488
+ author = "Reimers, Nils and Gurevych, Iryna",
489
+ booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
490
+ month = "11",
491
+ year = "2019",
492
+ publisher = "Association for Computational Linguistics",
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+ url = "https://arxiv.org/abs/1908.10084",
494
+ }
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+ ```
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+
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+ <!--
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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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+
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+ <!--
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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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+
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+ <!--
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+ ## Model Card Contact
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+
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+ *Provides a way for people who have updates to the Model Card, suggestions, or questions, to contact the Model Card authors.*
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+ -->
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