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Add new SentenceTransformer model

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1_Pooling/config.json ADDED
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+ {
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+ "word_embedding_dimension": 768,
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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:360886
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+ - loss:CoSENTLoss
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+ base_model: sentence-transformers/all-mpnet-base-v2
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+ widget:
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+ - source_sentence: '|Immunosuppressant drug therapy (procedure)| : { |Method (attribute)|
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+ = |Administration - action (qualifier value)|, |Direct substance (attribute)|
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+ = |Auranofin (substance)| }, { |Has intent (attribute)| = |Therapeutic intent
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+ (qualifier value)| }'
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+ sentences:
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+ - Tofacitinib therapy (procedure)
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+ - Mural thrombus of right ventricle following acute myocardial infarction (disorder)
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+ - Neonatal botulism (disorder)
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+ - source_sentence: '|Injury of finger of left hand (disorder)| + |Traumatic blister
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+ of index finger (disorder)| + |Traumatic blister of left hand (disorder)| : {
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+ |Finding site (attribute)| = |Skin structure of left index finger (body structure)|,
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+ |Associated morphology (attribute)| = |Blister (morphologic abnormality)| }, {
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+ |Due to (attribute)| = |Traumatic event (event)| }'
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+ sentences:
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+ - Cardiovascular system closure (procedure)
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+ - Entire skin of lower eyelid and periocular area (body structure)
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+ - Avulsion of nail unit of left little finger (disorder)
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+ - source_sentence: '|Evaluation finding (finding)| : { |Interprets (attribute)| =
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+ |Interferon gamma assay (procedure)|, |Has interpretation (attribute)| = |Positive
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+ (qualifier value)| }'
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+ sentences:
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+ - Gleason pattern (observable entity)
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+ - Interferon gamma assay positive (finding)
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+ - Intentional melphalan overdose (disorder)
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+ - source_sentence: '|Finding of specific antibody level (finding)| : { |Interprets
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+ (attribute)| = |Measurement of viral antibody (procedure)| }'
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+ sentences:
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+ - Lyme detected by immunoblot (finding)
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+ - Primary malignant neoplasm of accessory sinus (disorder)
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+ - Perfusion of lymphatics with hyperthermia (procedure)
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+ - source_sentence: '|Neoplasm of anterior wall of nasopharynx (disorder)| + |Neoplasm
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+ of uncertain behavior of nasopharynx (disorder)| : { |Finding site (attribute)|
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+ = |Structure of anterior wall of nasopharynx (body structure)|, |Associated morphology
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+ (attribute)| = |Neoplasm of uncertain behavior (morphologic abnormality)| }'
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+ sentences:
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+ - Secondary angle-closure glaucoma - synechial (disorder)
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+ - Neoplasm of uncertain behavior of lateral wall of nasopharynx (disorder)
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+ - Product containing precisely cefamandole (as cefamandole nafate) 1 gram/1 vial
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+ powder for conventional release solution for injection (clinical drug)
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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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+ - pearson_cosine
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+ - spearman_cosine
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+ model-index:
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+ - name: SentenceTransformer based on sentence-transformers/all-mpnet-base-v2
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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: sts dev
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+ type: sts-dev
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+ metrics:
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+ - type: pearson_cosine
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+ value: 0.9048593944190657
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+ name: Pearson Cosine
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+ - type: spearman_cosine
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+ value: 0.8556279874385214
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+ name: Spearman Cosine
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+ ---
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+
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+ # SentenceTransformer based on sentence-transformers/all-mpnet-base-v2
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+
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+ This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [sentence-transformers/all-mpnet-base-v2](https://huggingface.co/sentence-transformers/all-mpnet-base-v2) on the csv dataset. It maps sentences & paragraphs to a 768-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:** [sentence-transformers/all-mpnet-base-v2](https://huggingface.co/sentence-transformers/all-mpnet-base-v2) <!-- at revision 9a3225965996d404b775526de6dbfe85d3368642 -->
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+ - **Maximum Sequence Length:** 384 tokens
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+ - **Output Dimensionality:** 768 dimensions
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+ - **Similarity Function:** Cosine Similarity
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+ - **Training Dataset:**
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+ - csv
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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': 384, 'do_lower_case': False}) with Transformer model: MPNetModel
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+ (1): Pooling({'word_embedding_dimension': 768, '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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+ (2): Normalize()
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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("yyzheng00/all-mpnet-base-v2_snomed_expression")
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+ # Run inference
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+ sentences = [
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+ '|Neoplasm of anterior wall of nasopharynx (disorder)| + |Neoplasm of uncertain behavior of nasopharynx (disorder)| : { |Finding site (attribute)| = |Structure of anterior wall of nasopharynx (body structure)|, |Associated morphology (attribute)| = |Neoplasm of uncertain behavior (morphologic abnormality)| }',
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+ 'Neoplasm of uncertain behavior of lateral wall of nasopharynx (disorder)',
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+ 'Secondary angle-closure glaucoma - synechial (disorder)',
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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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+
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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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+
138
+ <!--
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+ ### Direct Usage (Transformers)
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+
141
+ <details><summary>Click to see the direct usage in Transformers</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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+ ### 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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+
153
+ </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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+
162
+ ## Evaluation
163
+
164
+ ### Metrics
165
+
166
+ #### Semantic Similarity
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+
168
+ * Dataset: `sts-dev`
169
+ * Evaluated with [<code>EmbeddingSimilarityEvaluator</code>](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.EmbeddingSimilarityEvaluator)
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+
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+ | Metric | Value |
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+ |:--------------------|:-----------|
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+ | pearson_cosine | 0.9049 |
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+ | **spearman_cosine** | **0.8556** |
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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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+
182
+ <!--
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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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+
188
+ ## Training Details
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+
190
+ ### Training Dataset
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+
192
+ #### csv
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+
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+ * Dataset: csv
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+ * Size: 360,886 training samples
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+ * Columns: <code>text_a</code>, <code>text_b</code>, and <code>label</code>
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+ * Approximate statistics based on the first 1000 samples:
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+ | | text_a | text_b | label |
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+ |:--------|:-------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:------------------------------------------------|
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+ | type | string | string | int |
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+ | details | <ul><li>min: 28 tokens</li><li>mean: 101.13 tokens</li><li>max: 357 tokens</li></ul> | <ul><li>min: 7 tokens</li><li>mean: 15.29 tokens</li><li>max: 60 tokens</li></ul> | <ul><li>0: ~51.40%</li><li>1: ~48.60%</li></ul> |
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+ * Samples:
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+ | text_a | text_b | label |
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+ |:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------|:---------------|
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+ | <code>|Risk assessment (procedure)| : { |Method (attribute)| = |Evaluation - action (qualifier value)| }, { |Has focus (attribute)| = |At increased risk of ineffective tissue perfusion (finding)| }</code> | <code>Assessment of risk of ineffective tissue perfusion (procedure)</code> | <code>1</code> |
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+ | <code>|Chronic inflammatory disorder (disorder)| + |Chronic nervous system disorder (disorder)| + |Meningitis (disorder)| : { |Finding site (attribute)| = |Meninges structure (body structure)|, |Associated morphology (attribute)| = |Chronic inflammatory morphology (morphologic abnormality)| }, { |Clinical course (attribute)| = |Chronic (qualifier value)| }</code> | <code>Chronic meningitis (disorder)</code> | <code>1</code> |
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+ | <code>|Imaging of head (procedure)| + |Ultrasound procedure on topographic region (procedure)| : { |Method (attribute)| = |Ultrasound imaging - action (qualifier value)|, |Procedure site - Direct (attribute)| = |Head structure (body structure)| }</code> | <code>Imaging of brain (procedure)</code> | <code>0</code> |
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+ * Loss: [<code>CoSENTLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#cosentloss) with these parameters:
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+ ```json
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+ {
211
+ "scale": 20.0,
212
+ "similarity_fct": "pairwise_cos_sim"
213
+ }
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+ ```
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+
216
+ ### Evaluation Dataset
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+
218
+ #### csv
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+
220
+ * Dataset: csv
221
+ * Size: 360,886 evaluation samples
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+ * Columns: <code>text_a</code>, <code>text_b</code>, and <code>label</code>
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+ * Approximate statistics based on the first 1000 samples:
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+ | | text_a | text_b | label |
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+ |:--------|:-------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:------------------------------------------------|
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+ | type | string | string | int |
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+ | details | <ul><li>min: 25 tokens</li><li>mean: 101.18 tokens</li><li>max: 366 tokens</li></ul> | <ul><li>min: 7 tokens</li><li>mean: 15.21 tokens</li><li>max: 52 tokens</li></ul> | <ul><li>0: ~51.30%</li><li>1: ~48.70%</li></ul> |
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+ * Samples:
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+ | text_a | text_b | label |
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+ |:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------|:---------------|
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+ | <code>|Disorder of fetal abdominal region (disorder)| + |Fetal genitourinary abnormality (disorder)| + |Kidney disease (disorder)| : { |Occurrence (attribute)| = |Fetal period (qualifier value)|, |Finding site (attribute)| = |Kidney structure (body structure)|, |Associated morphology (attribute)| = |Morphologically abnormal structure (morphologic abnormality)|, |Pathological process (attribute)| = |Pathological developmental process (qualifier value)| }</code> | <code>Early urethral obstruction sequence (disorder)</code> | <code>0</code> |
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+ | <code>|Computed tomography of pelvis for brachytherapy planning (procedure)| + |Computed tomography of prostate for radiotherapy planning (procedure)| : { |Has focus (attribute)| = |Treatment planning for brachytherapy (procedure)| }, { |Method (attribute)| = |Computed tomography imaging - action (qualifier value)|, |Procedure site - Direct (attribute)| = |Prostatic structure (body structure)| }</code> | <code>Computed tomography of prostate with contrast for radiotherapy planning (procedure)</code> | <code>0</code> |
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+ | <code>|Product containing only hydroxyzine in oral dose form (medicinal product form)| : |Has manufactured dose form (attribute)| = |Conventional release oral capsule (dose form)|, |Has unit of presentation (attribute)| = |Capsule (unit of presentation)|, |Count of base of active ingredient (attribute)| = #1, { |Has precise active ingredient (attribute)| = |Hydroxyzine pamoate (substance)|, |Has basis of strength substance (attribute)| = |Hydroxyzine pamoate (substance)|, |Has presentation strength numerator value (attribute)| = #100, |Has presentation strength numerator unit (attribute)| = |milligram (qualifier value)|, |Has presentation strength denominator value (attribute)| = #1, |Has presentation strength denominator unit (attribute)| = |Capsule (unit of presentation)| }</code> | <code>Hydroxyzine pamoate 100mg capsule (product)</code> | <code>1</code> |
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+ * Loss: [<code>CoSENTLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#cosentloss) with these parameters:
235
+ ```json
236
+ {
237
+ "scale": 20.0,
238
+ "similarity_fct": "pairwise_cos_sim"
239
+ }
240
+ ```
241
+
242
+ ### Training Hyperparameters
243
+ #### Non-Default Hyperparameters
244
+
245
+ - `eval_strategy`: steps
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+ - `per_device_train_batch_size`: 16
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+ - `per_device_eval_batch_size`: 16
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+ - `num_train_epochs`: 1
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+ - `warmup_ratio`: 0.1
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+ - `fp16`: True
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+ - `batch_sampler`: no_duplicates
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+
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+ #### All Hyperparameters
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+ <details><summary>Click to expand</summary>
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+
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+ - `overwrite_output_dir`: False
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+ - `do_predict`: False
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+ - `eval_strategy`: steps
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+ - `prediction_loss_only`: True
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+ - `per_device_train_batch_size`: 16
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+ - `per_device_eval_batch_size`: 16
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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`: 1
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+ - `eval_accumulation_steps`: None
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+ - `torch_empty_cache_steps`: None
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+ - `learning_rate`: 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`: 1
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+ - `max_steps`: -1
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+ - `lr_scheduler_type`: linear
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+ - `lr_scheduler_kwargs`: {}
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+ - `warmup_ratio`: 0.1
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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
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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`: False
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+ - `fp16`: True
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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`: 0
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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`: False
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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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+ - `gradient_checkpointing`: False
341
+ - `gradient_checkpointing_kwargs`: None
342
+ - `include_inputs_for_metrics`: False
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+ - `include_for_metrics`: []
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+ - `eval_do_concat_batches`: True
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+ - `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`:
349
+ - `auto_find_batch_size`: False
350
+ - `full_determinism`: False
351
+ - `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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+ - `dispatch_batches`: None
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+ - `split_batches`: 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
364
+ - `eval_on_start`: False
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+ - `use_liger_kernel`: False
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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`: no_duplicates
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+ - `multi_dataset_batch_sampler`: proportional
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+
372
+ </details>
373
+
374
+ ### Training Logs
375
+ <details><summary>Click to expand</summary>
376
+
377
+ | Epoch | Step | Training Loss | Validation Loss | sts-dev_spearman_cosine |
378
+ |:------:|:-----:|:-------------:|:---------------:|:-----------------------:|
379
+ | 0.0055 | 100 | 5.2922 | 3.9427 | 0.6159 |
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+ | 0.0111 | 200 | 3.2766 | 2.8638 | 0.7437 |
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+ | 0.0166 | 300 | 2.8445 | 2.4816 | 0.7833 |
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+ | 0.0222 | 400 | 2.5209 | 2.2995 | 0.7974 |
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+ | 0.0277 | 500 | 2.5298 | 2.1033 | 0.8072 |
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+ | 0.0333 | 600 | 2.0427 | 2.1055 | 0.8114 |
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+ | 0.0388 | 700 | 2.1367 | 2.0634 | 0.8121 |
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+ | 0.0443 | 800 | 2.2486 | 1.7848 | 0.8210 |
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+ | 0.0499 | 900 | 1.921 | 1.9666 | 0.8190 |
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+ | 0.0554 | 1000 | 1.9962 | 1.9688 | 0.8180 |
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+ | 0.0610 | 1100 | 1.5203 | 2.0695 | 0.8187 |
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+ | 0.0665 | 1200 | 2.0616 | 1.7060 | 0.8223 |
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+ | 0.0720 | 1300 | 2.0793 | 1.8158 | 0.8254 |
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+ | 0.0776 | 1400 | 2.0766 | 1.8549 | 0.8213 |
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+ | 0.0831 | 1500 | 1.5608 | 1.8045 | 0.8241 |
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+ | 0.0887 | 1600 | 1.7671 | 1.9724 | 0.8196 |
395
+ | 0.0942 | 1700 | 2.1665 | 2.2623 | 0.8033 |
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+ | 0.9975 | 18000 | 0.7509 | 0.6400 | 0.8556 |
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+
560
+ </details>
561
+
562
+ ### Framework Versions
563
+ - Python: 3.11.1
564
+ - Sentence Transformers: 3.3.1
565
+ - Transformers: 4.47.0
566
+ - PyTorch: 2.1.1+cu121
567
+ - Accelerate: 1.2.0
568
+ - Datasets: 2.18.0
569
+ - Tokenizers: 0.21.0
570
+
571
+ ## Citation
572
+
573
+ ### BibTeX
574
+
575
+ #### Sentence Transformers
576
+ ```bibtex
577
+ @inproceedings{reimers-2019-sentence-bert,
578
+ title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
579
+ author = "Reimers, Nils and Gurevych, Iryna",
580
+ booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
581
+ month = "11",
582
+ year = "2019",
583
+ publisher = "Association for Computational Linguistics",
584
+ url = "https://arxiv.org/abs/1908.10084",
585
+ }
586
+ ```
587
+
588
+ #### CoSENTLoss
589
+ ```bibtex
590
+ @online{kexuefm-8847,
591
+ title={CoSENT: A more efficient sentence vector scheme than Sentence-BERT},
592
+ author={Su Jianlin},
593
+ year={2022},
594
+ month={Jan},
595
+ url={https://kexue.fm/archives/8847},
596
+ }
597
+ ```
598
+
599
+ <!--
600
+ ## Glossary
601
+
602
+ *Clearly define terms in order to be accessible across audiences.*
603
+ -->
604
+
605
+ <!--
606
+ ## Model Card Authors
607
+
608
+ *Lists the people who create the model card, providing recognition and accountability for the detailed work that goes into its construction.*
609
+ -->
610
+
611
+ <!--
612
+ ## Model Card Contact
613
+
614
+ *Provides a way for people who have updates to the Model Card, suggestions, or questions, to contact the Model Card authors.*
615
+ -->
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67
+ "strip_accents": null,
68
+ "tokenize_chinese_chars": true,
69
+ "tokenizer_class": "MPNetTokenizer",
70
+ "truncation_side": "right",
71
+ "truncation_strategy": "longest_first",
72
+ "unk_token": "[UNK]"
73
+ }
vocab.txt ADDED
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