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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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+ base_model: allenai/specter2_base
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+ library_name: sentence-transformers
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+ pipeline_tag: sentence-similarity
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+ tags:
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+ - sentence-transformers
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+ - sentence-similarity
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+ - feature-extraction
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+ - generated_from_trainer
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+ - dataset_size:9988
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+ - loss:MultipleNegativesRankingLoss
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+ widget:
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+ - source_sentence: Splenomegaly in Malta fever
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+ sentences:
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+ - 'TROPICAL SPLENOMEGALY. '
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+ - '[Voluminous migrating spleen in the course of Malta fever: effects of splenectomy]. '
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+ - '[Adenoma of appendix]. '
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+ - source_sentence: sRNA regulation
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+ sentences:
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+ - 'SR proteins control a complex network of RNA-processing events. '
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+ - 'Convergence of submodality-specific input onto neurons in primary somatosensory
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+ cortex. '
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+ - 'Dynamic features of gene expression control by small regulatory RNAs. '
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+ - source_sentence: Foley catheter hysterosalpingography
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+ sentences:
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+ - 'Hysterosalpingography using a Foley catheter. '
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+ - '[Long-term follow-up of adult patients with isolated congenital AV block]. '
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+ - 'Hysterosalpingography. '
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+ - source_sentence: Anti-endoglin monoclonal antibodies
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+ sentences:
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+ - 'Cortisol response to general anaesthesia for medical imaging in children. '
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+ - 'Anti-endoglin monoclonal antibodies are effective for suppressing metastasis
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+ and the primary tumors by targeting tumor vasculature. '
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+ - 'Endoglin: Beyond the Endothelium. '
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+ - source_sentence: Alternariol Methyl Ether Quantitation
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+ sentences:
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+ - 'Stable isotope dilution assays of alternariol and alternariol monomethyl ether
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+ in beverages. '
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+ - 'The roles of eotaxin and the STAT6 signalling pathway in eosinophil recruitment
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+ and host resistance to the nematodes Nippostrongylus brasiliensis and Heligmosomoides
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+ bakeri. '
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+ - 'Mechanisms of Action and Toxicity of the Mycotoxin Alternariol: A Review. '
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+ ---
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+
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+ # SentenceTransformer based on allenai/specter2_base
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+
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+ This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [allenai/specter2_base](https://huggingface.co/allenai/specter2_base) on the json 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:** [allenai/specter2_base](https://huggingface.co/allenai/specter2_base) <!-- at revision 3447645e1def9117997203454fa4495937bfbd83 -->
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+ - **Maximum Sequence Length:** 512 tokens
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+ - **Output Dimensionality:** 768 tokens
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+ - **Similarity Function:** Cosine Similarity
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+ - **Training Dataset:**
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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': 512, 'do_lower_case': False}) with Transformer model: BertModel
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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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+ )
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+ ```
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+
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+ ## Usage
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+
79
+ ### Direct Usage (Sentence Transformers)
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+
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+ First install the Sentence Transformers library:
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+
83
+ ```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("sentence_transformers_model_id")
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+ # Run inference
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+ sentences = [
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+ 'Alternariol Methyl Ether Quantitation',
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+ 'Stable isotope dilution assays of alternariol and alternariol monomethyl ether in beverages. ',
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+ 'Mechanisms of Action and Toxicity of the Mycotoxin Alternariol: A Review. ',
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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)
105
+ print(similarities.shape)
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+ # [3, 3]
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+ ```
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+
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+ <!--
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+ ### Direct Usage (Transformers)
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+
112
+ <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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+
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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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+ <!--
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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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+
139
+ <!--
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+ ### Recommendations
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+
142
+ *What are recommendations with respect to the foreseeable issues? For example, filtering explicit content.*
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+ -->
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+
145
+ ## Training Details
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+
147
+ ### Training Dataset
148
+
149
+ #### json
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+
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+ * Dataset: json
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+ * Size: 9,988 training samples
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+ * Columns: <code>anchor</code>, <code>positive</code>, and <code>negative</code>
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+ * Approximate statistics based on the first 1000 samples:
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+ | | anchor | positive | negative |
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+ |:--------|:---------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|
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+ | type | string | string | string |
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+ | details | <ul><li>min: 4 tokens</li><li>mean: 7.66 tokens</li><li>max: 34 tokens</li></ul> | <ul><li>min: 6 tokens</li><li>mean: 19.05 tokens</li><li>max: 42 tokens</li></ul> | <ul><li>min: 4 tokens</li><li>mean: 11.84 tokens</li><li>max: 48 tokens</li></ul> |
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+ * Samples:
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+ | anchor | positive | negative |
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+ |:-----------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------|
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+ | <code>mechanotransduction pathways</code> | <code>Signalling cascades in mechanotransduction: cell-matrix interactions and mechanical loading. </code> | <code>Mechanotransduction: May the force be with you. </code> |
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+ | <code>FSR-tunable comb filter</code> | <code>Multiwavelength Raman fiber laser with a continuously-tunable spacing. </code> | <code>Tunable multiwavelength fiber laser using a comb filter based on erbium-ytterbium co-doped polarization maintaining fiber loop mirror. </code> |
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+ | <code>Radiation pneumonitis enhancement</code> | <code>Induction and concurrent taxanes enhance both the pulmonary metabolic radiation response and the radiation pneumonitis response in patients with esophagus cancer. </code> | <code>Imaging of Hypersensitivity Pneumonitis. </code> |
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+ * Loss: [<code>MultipleNegativesRankingLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters:
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+ ```json
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+ {
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+ "scale": 20.0,
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+ "similarity_fct": "cos_sim"
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+ }
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+ ```
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+
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+ ### Training Hyperparameters
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+ #### Non-Default Hyperparameters
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+
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+ - `per_device_train_batch_size`: 32
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+ - `per_device_eval_batch_size`: 32
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+ - `learning_rate`: 2e-05
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+ - `num_train_epochs`: 1
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+ - `lr_scheduler_type`: cosine_with_restarts
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+ - `warmup_ratio`: 0.1
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+ - `bf16`: 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`: no
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+ - `prediction_loss_only`: True
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+ - `per_device_train_batch_size`: 32
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+ - `per_device_eval_batch_size`: 32
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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`: 2e-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`: cosine_with_restarts
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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`: 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`: 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
267
+ - `resume_from_checkpoint`: None
268
+ - `hub_model_id`: None
269
+ - `hub_strategy`: every_save
270
+ - `hub_private_repo`: False
271
+ - `hub_always_push`: False
272
+ - `gradient_checkpointing`: False
273
+ - `gradient_checkpointing_kwargs`: None
274
+ - `include_inputs_for_metrics`: False
275
+ - `eval_do_concat_batches`: True
276
+ - `fp16_backend`: auto
277
+ - `push_to_hub_model_id`: None
278
+ - `push_to_hub_organization`: None
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+ - `mp_parameters`:
280
+ - `auto_find_batch_size`: False
281
+ - `full_determinism`: False
282
+ - `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
287
+ - `torch_compile_mode`: None
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+ - `dispatch_batches`: None
289
+ - `split_batches`: None
290
+ - `include_tokens_per_second`: False
291
+ - `include_num_input_tokens_seen`: False
292
+ - `neftune_noise_alpha`: None
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+ - `optim_target_modules`: None
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+ - `batch_eval_metrics`: False
295
+ - `eval_on_start`: False
296
+ - `use_liger_kernel`: False
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+ - `eval_use_gather_object`: False
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+ - `batch_sampler`: no_duplicates
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+ - `multi_dataset_batch_sampler`: proportional
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+
301
+ </details>
302
+
303
+ ### Training Logs
304
+ <details><summary>Click to expand</summary>
305
+
306
+ | Epoch | Step | Training Loss |
307
+ |:------:|:----:|:-------------:|
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+ | 0.0095 | 1 | 2.9432 |
309
+ | 0.0190 | 2 | 3.0121 |
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+ | 0.0286 | 3 | 2.9051 |
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+ | 0.0381 | 4 | 2.7906 |
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+ | 0.0476 | 5 | 2.6592 |
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+ | 0.0571 | 6 | 2.2835 |
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+ | 0.0667 | 7 | 2.1373 |
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+ | 0.0762 | 8 | 1.7872 |
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+ | 0.0857 | 9 | 1.6329 |
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+ | 0.0952 | 10 | 1.5184 |
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+ | 0.1048 | 11 | 1.234 |
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+ | 0.1143 | 12 | 1.0315 |
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+ | 0.1238 | 13 | 0.9664 |
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+ | 0.1333 | 14 | 0.9369 |
322
+ | 0.1429 | 15 | 0.6871 |
323
+ | 0.1524 | 16 | 0.5633 |
324
+ | 0.1619 | 17 | 0.5141 |
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+ | 0.1714 | 18 | 0.5259 |
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+ | 0.1810 | 19 | 0.4295 |
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+ | 0.1905 | 20 | 0.4585 |
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+ | 0.2 | 21 | 0.2799 |
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+ | 0.2095 | 22 | 0.4226 |
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+ | 0.2190 | 23 | 0.2524 |
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+ | 0.2286 | 24 | 0.2135 |
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+ | 0.2381 | 25 | 0.1958 |
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+ | 0.2476 | 26 | 0.1823 |
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+ | 0.2571 | 27 | 0.393 |
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+ | 0.2667 | 28 | 0.3186 |
336
+ | 0.2762 | 29 | 0.1414 |
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+ | 0.2857 | 30 | 0.1927 |
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+ | 0.2952 | 31 | 0.2597 |
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+ | 0.3048 | 32 | 0.1291 |
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+ | 0.3143 | 33 | 0.1488 |
341
+ | 0.3238 | 34 | 0.1203 |
342
+ | 0.3333 | 35 | 0.2001 |
343
+ | 0.3429 | 36 | 0.1877 |
344
+ | 0.3524 | 37 | 0.0713 |
345
+ | 0.3619 | 38 | 0.1778 |
346
+ | 0.3714 | 39 | 0.1179 |
347
+ | 0.3810 | 40 | 0.147 |
348
+ | 0.3905 | 41 | 0.1158 |
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+ | 0.4 | 42 | 0.1003 |
350
+ | 0.4095 | 43 | 0.158 |
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+ | 0.4190 | 44 | 0.159 |
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+ | 0.4286 | 45 | 0.063 |
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+ | 0.4381 | 46 | 0.1309 |
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+ | 0.4476 | 47 | 0.0327 |
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+ | 0.4571 | 48 | 0.1665 |
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+ | 0.4667 | 49 | 0.1064 |
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+ | 0.4762 | 50 | 0.0699 |
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+ | 0.4857 | 51 | 0.0674 |
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+ | 0.4952 | 52 | 0.0508 |
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+ | 0.5048 | 53 | 0.0493 |
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+ | 0.5143 | 54 | 0.0565 |
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+ | 0.5238 | 55 | 0.0366 |
363
+ | 0.5333 | 56 | 0.0606 |
364
+ | 0.5429 | 57 | 0.0727 |
365
+ | 0.5524 | 58 | 0.092 |
366
+ | 0.5619 | 59 | 0.0628 |
367
+ | 0.5714 | 60 | 0.0369 |
368
+ | 0.5810 | 61 | 0.0889 |
369
+ | 0.5905 | 62 | 0.0409 |
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+ | 0.6 | 63 | 0.0545 |
371
+ | 0.6095 | 64 | 0.0856 |
372
+ | 0.6190 | 65 | 0.0478 |
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+ | 0.6286 | 66 | 0.0584 |
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+ | 0.6381 | 67 | 0.0757 |
375
+ | 0.6476 | 68 | 0.0609 |
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+ | 0.6571 | 69 | 0.0381 |
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+ | 0.6667 | 70 | 0.069 |
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+ | 0.6762 | 71 | 0.0243 |
379
+ | 0.6857 | 72 | 0.0517 |
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+ | 0.6952 | 73 | 0.0332 |
381
+ | 0.7048 | 74 | 0.0662 |
382
+ | 0.7143 | 75 | 0.0753 |
383
+ | 0.7238 | 76 | 0.0914 |
384
+ | 0.7333 | 77 | 0.1094 |
385
+ | 0.7429 | 78 | 0.0557 |
386
+ | 0.7524 | 79 | 0.0436 |
387
+ | 0.7619 | 80 | 0.0137 |
388
+ | 0.7714 | 81 | 0.0399 |
389
+ | 0.7810 | 82 | 0.0278 |
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+ | 0.7905 | 83 | 0.0438 |
391
+ | 0.8 | 84 | 0.1392 |
392
+ | 0.8095 | 85 | 0.0299 |
393
+ | 0.8190 | 86 | 0.0667 |
394
+ | 0.8286 | 87 | 0.0404 |
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+ | 0.8381 | 88 | 0.0166 |
396
+ | 0.8476 | 89 | 0.1679 |
397
+ | 0.8571 | 90 | 0.0282 |
398
+ | 0.8667 | 91 | 0.0628 |
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+ | 0.8762 | 92 | 0.0618 |
400
+ | 0.8857 | 93 | 0.0167 |
401
+ | 0.8952 | 94 | 0.2108 |
402
+ | 0.9048 | 95 | 0.0749 |
403
+ | 0.9143 | 96 | 0.0997 |
404
+ | 0.9238 | 97 | 0.0675 |
405
+ | 0.9333 | 98 | 0.0409 |
406
+ | 0.9429 | 99 | 0.0355 |
407
+ | 0.9524 | 100 | 0.1391 |
408
+ | 0.9619 | 101 | 0.0938 |
409
+ | 0.9714 | 102 | 0.0526 |
410
+ | 0.9810 | 103 | 0.0035 |
411
+ | 0.9905 | 104 | 0.0022 |
412
+ | 1.0 | 105 | 0.0016 |
413
+
414
+ </details>
415
+
416
+ ### Framework Versions
417
+ - Python: 3.9.19
418
+ - Sentence Transformers: 3.1.1
419
+ - Transformers: 4.45.2
420
+ - PyTorch: 2.5.0
421
+ - Accelerate: 1.0.1
422
+ - Datasets: 2.19.0
423
+ - Tokenizers: 0.20.3
424
+
425
+ ## Citation
426
+
427
+ ### BibTeX
428
+
429
+ #### Sentence Transformers
430
+ ```bibtex
431
+ @inproceedings{reimers-2019-sentence-bert,
432
+ title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
433
+ author = "Reimers, Nils and Gurevych, Iryna",
434
+ booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
435
+ month = "11",
436
+ year = "2019",
437
+ publisher = "Association for Computational Linguistics",
438
+ url = "https://arxiv.org/abs/1908.10084",
439
+ }
440
+ ```
441
+
442
+ #### MultipleNegativesRankingLoss
443
+ ```bibtex
444
+ @misc{henderson2017efficient,
445
+ title={Efficient Natural Language Response Suggestion for Smart Reply},
446
+ author={Matthew Henderson and Rami Al-Rfou and Brian Strope and Yun-hsuan Sung and Laszlo Lukacs and Ruiqi Guo and Sanjiv Kumar and Balint Miklos and Ray Kurzweil},
447
+ year={2017},
448
+ eprint={1705.00652},
449
+ archivePrefix={arXiv},
450
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+ }
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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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