anoyinonion commited on
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Add new SentenceTransformer model

Browse files
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:4012
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+ - loss:MultipleNegativesRankingLoss
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+ base_model: sentence-transformers/all-mpnet-base-v2
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+ widget:
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+ - source_sentence: We employed genetic, cytological, and genomic approaches to better
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+ understand the role of PR-Set7 and H4K20 methylation in regulating DNA replication
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+ and genome stability in Drosophila cells. Thus, coordinating the status of H4K20
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+ methylation is pivotal for the proper selection of DNA replication origins in
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+ higher eukaryotes. The methylation state of lysine 20 on histone H4 (H4K20) has
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+ been linked to chromatin compaction, transcription, DNA repair and DNA replication.
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+ Histone turnover is often associated with various histone modifications such as
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+ H3K56 acetylation (H3K56Ac), H3K36 methylation (H3K36me), and H4K20 methylation
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+ (H4K20me). We review the signaling pathways and functions associated with a single
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+ residue, H4K20, as a model chromatin and clinically important mark that regulates
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+ biological processes ranging from the DNA damage response and DNA replication
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+ to gene expression and silencing. <CopyrightInformation>© 2016 by The American
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+ Society for Biochemistry and Molecular Biology, Inc.</C In particular, the methylation
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+ states of H3K4, H3K36 and H4K20 have been associated with establishing active,
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+ repressed or poised origins depending on the timing and extent of methylation.
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+ 5BrC and 5ClC may cause aberrant methylation of cytosine during DNA replication
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+ and mimic the endogenous methylation signal associated with gene silencing.
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+ sentences:
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+ - Is H4K20 methylation associated with DNA replication?
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+ - What is the function of the protein Cuf1?
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+ - Which syndromes are associated with heterochromia iridum?
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+ - source_sentence: 'The Abbreviated Injury Scale (AIS) is an objective anatomically-based
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+ injury severity scoring system that classifies each injury by body region on a
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+ 6 point scale. AIS is the system used to determine the Injury Severity Score (ISS)
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+ of the multiply injured trauma patient.
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+
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+
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+ AIS CLASSIFICATIONS
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+
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+ The AIS classifies individual injuries by body region as follows:
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+
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+ AIS 1 – Minor
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+
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+ AIS 2 – Moderate
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+
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+ AIS 3 – Serious
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+
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+ AIS 4 – Severe
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+
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+ AIS 5 – Critical
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+
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+ AIS 6 – Maximal (currently untreatable)'
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+ sentences:
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+ - What is the role of the Hof1-Cyk3 interaction in yeast?
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+ - Which drugs are included in the MAID chemotherapy regimen for sarcoma?
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+ - What is Abbreviated Injury Scale (AIS) used to determine?
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+ - source_sentence: Multicluster Pcdh diversity is required for mouse olfactory neural
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+ circuit assembly. The vertebrate clustered protocadherin (Pcdh) cell surface proteins
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+ are encoded by three closely linked gene clusters (Pcdhα, Pcdhβ, and Pcdhγ). Although
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+ deletion of individual Pcdh clusters had subtle phenotypic consequences, the loss
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+ of all three clusters (tricluster deletion) led to a severe axonal arborization
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+ defect and loss of self-avoidance.
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+ sentences:
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+ - Does thyroid hormone affect cardiac remodeling?
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+ - What are the effects of the deletion of all three Pcdh clusters (tricluster deletion)
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+ in mice?
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+ - Which R/bioconductor package has been developed to aid in epigenomic analysis?
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+ - source_sentence: Huntington disease (HD; OMIM 143100), a progressive neurodegenerative
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+ disorder, is caused by an expanded trinucleotide CAG (polyQ) motif in the HTT
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+ gene. Mutations of the huntingtin protein (HTT) gene underlie both adult-onset
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+ and juvenile forms of Huntington's disease (HD).
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+ sentences:
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+ - What is resistin?
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+ - Does thyroid hormone signaling affect microRNAs expression in the heart?
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+ - What gene is mutated in Huntington's disease?
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+ - source_sentence: Nusinersen is a modified antisense oligonucleotide that binds to
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+ a specific sequence in the intron, downstream of exon 7 on the pre-messenger ribonucleic
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+ acid (pre-mRNA) of the SMN2 gene. This modulates the splicing of the SMN2 mRNA
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+ transcript to include exon 7, thereby increasing the production of full-length
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+ SMN protein. It is approved for treatment of spinal muscular atrophy.
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+ sentences:
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+ - Describe mechanism of action of Nusinersen.
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+ - What is Mobilome-seq?
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+ - What percentage of currently available drugs are metabolized by CYP3A4?
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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 based on sentence-transformers/all-mpnet-base-v2
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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: sentence transformers/all mpnet base v2
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+ type: sentence-transformers/all-mpnet-base-v2
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+ metrics:
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+ - type: cosine_accuracy@1
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+ value: 0.8472418670438473
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+ name: Cosine Accuracy@1
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+ - type: cosine_accuracy@3
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+ value: 0.9335219236209336
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+ name: Cosine Accuracy@3
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+ - type: cosine_accuracy@5
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+ value: 0.9490806223479491
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+ name: Cosine Accuracy@5
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+ - type: cosine_accuracy@10
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+ value: 0.9603960396039604
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+ name: Cosine Accuracy@10
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+ - type: cosine_precision@1
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+ value: 0.8472418670438473
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+ name: Cosine Precision@1
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+ - type: cosine_precision@3
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+ value: 0.31117397454031115
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+ name: Cosine Precision@3
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+ - type: cosine_precision@5
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+ value: 0.1898161244695898
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+ name: Cosine Precision@5
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+ - type: cosine_precision@10
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+ value: 0.09603960396039603
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+ name: Cosine Precision@10
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+ - type: cosine_recall@1
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+ value: 0.8472418670438473
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+ name: Cosine Recall@1
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+ - type: cosine_recall@3
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+ value: 0.9335219236209336
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+ name: Cosine Recall@3
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+ - type: cosine_recall@5
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+ value: 0.9490806223479491
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+ name: Cosine Recall@5
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+ - type: cosine_recall@10
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+ value: 0.9603960396039604
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+ name: Cosine Recall@10
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+ - type: cosine_ndcg@10
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+ value: 0.9092929874201823
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+ name: Cosine Ndcg@10
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+ - type: cosine_mrr@10
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+ value: 0.8923284165151212
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+ name: Cosine Mrr@10
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+ - type: cosine_map@100
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+ value: 0.8935812728750705
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+ name: Cosine Map@100
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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 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:** [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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+ - 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': 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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+
195
+ ### Direct Usage (Sentence Transformers)
196
+
197
+ First install the Sentence Transformers library:
198
+
199
+ ```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("anoyinonion/all-mpnet-base-v2-bioasq-1epoc-batch32-100")
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+ # Run inference
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+ sentences = [
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+ 'Nusinersen is a modified antisense oligonucleotide that binds to a specific sequence in the intron, downstream of exon 7 on the pre-messenger ribonucleic acid (pre-mRNA) of the SMN2 gene. This modulates the splicing of the SMN2 mRNA transcript to include exon 7, thereby increasing the production of full-length SMN protein. It is approved for treatment of spinal muscular atrophy.',
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+ 'Describe mechanism of action of Nusinersen.',
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+ 'What percentage of currently available drugs are metabolized by CYP3A4?',
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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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+
225
+ <!--
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+ ### Direct Usage (Transformers)
227
+
228
+ <details><summary>Click to see the direct usage in Transformers</summary>
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+
230
+ </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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+
236
+ You can finetune this model on your own dataset.
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+
238
+ <details><summary>Click to expand</summary>
239
+
240
+ </details>
241
+ -->
242
+
243
+ <!--
244
+ ### Out-of-Scope Use
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+
246
+ *List how the model may foreseeably be misused and address what users ought not to do with the model.*
247
+ -->
248
+
249
+ ## Evaluation
250
+
251
+ ### Metrics
252
+
253
+ #### Information Retrieval
254
+
255
+ * Dataset: `sentence-transformers/all-mpnet-base-v2`
256
+ * 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 |
259
+ |:--------------------|:-----------|
260
+ | cosine_accuracy@1 | 0.8472 |
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+ | cosine_accuracy@3 | 0.9335 |
262
+ | cosine_accuracy@5 | 0.9491 |
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+ | cosine_accuracy@10 | 0.9604 |
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+ | cosine_precision@1 | 0.8472 |
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+ | cosine_precision@3 | 0.3112 |
266
+ | cosine_precision@5 | 0.1898 |
267
+ | cosine_precision@10 | 0.096 |
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+ | cosine_recall@1 | 0.8472 |
269
+ | cosine_recall@3 | 0.9335 |
270
+ | cosine_recall@5 | 0.9491 |
271
+ | cosine_recall@10 | 0.9604 |
272
+ | **cosine_ndcg@10** | **0.9093** |
273
+ | cosine_mrr@10 | 0.8923 |
274
+ | cosine_map@100 | 0.8936 |
275
+
276
+ <!--
277
+ ## Bias, Risks and Limitations
278
+
279
+ *What are the known or foreseeable issues stemming from this model? You could also flag here known failure cases or weaknesses of the model.*
280
+ -->
281
+
282
+ <!--
283
+ ### Recommendations
284
+
285
+ *What are recommendations with respect to the foreseeable issues? For example, filtering explicit content.*
286
+ -->
287
+
288
+ ## Training Details
289
+
290
+ ### Training Dataset
291
+
292
+ #### json
293
+
294
+ * Dataset: json
295
+ * Size: 4,012 training samples
296
+ * Columns: <code>positive</code> and <code>anchor</code>
297
+ * Approximate statistics based on the first 1000 samples:
298
+ | | positive | anchor |
299
+ |:--------|:-----------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|
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+ | type | string | string |
301
+ | details | <ul><li>min: 3 tokens</li><li>mean: 63.14 tokens</li><li>max: 384 tokens</li></ul> | <ul><li>min: 5 tokens</li><li>mean: 16.13 tokens</li><li>max: 49 tokens</li></ul> |
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+ * Samples:
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+ | positive | anchor |
304
+ |:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------|
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+ | <code>Aberrant patterns of H3K4, H3K9, and H3K27 histone lysine methylation were shown to result in histone code alterations, which induce changes in gene expression, and affect the proliferation rate of cells in medulloblastoma.</code> | <code>What is the implication of histone lysine methylation in medulloblastoma?</code> |
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+ | <code>STAG1/STAG2 proteins are tumour suppressor proteins that suppress cell proliferation and are essential for differentiation.</code> | <code>What is the role of STAG1/STAG2 proteins in differentiation?</code> |
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+ | <code>The association between cell phone use and incident glioblastoma remains unclear. Some studies have reported that cell phone use was associated with incident glioblastoma, and with reduced survival of patients diagnosed with glioblastoma. However, other studies have repeatedly replicated to find an association between cell phone use and glioblastoma.</code> | <code>What is the association between cell phone use and glioblastoma?</code> |
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+ * Loss: [<code>MultipleNegativesRankingLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters:
309
+ ```json
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+ {
311
+ "scale": 20.0,
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+ "similarity_fct": "cos_sim"
313
+ }
314
+ ```
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+
316
+ ### Training Hyperparameters
317
+ #### Non-Default Hyperparameters
318
+
319
+ - `eval_strategy`: steps
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+ - `per_device_train_batch_size`: 32
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+ - `per_device_eval_batch_size`: 16
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+ - `learning_rate`: 2e-05
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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`: 32
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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`: 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`: 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
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+ - `gradient_checkpointing_kwargs`: None
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+ - `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`:
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+ - `auto_find_batch_size`: False
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+ - `full_determinism`: False
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+ - `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
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+ - `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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+
447
+ </details>
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+
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+ ### Training Logs
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+ | Epoch | Step | Training Loss | sentence-transformers/all-mpnet-base-v2_cosine_ndcg@10 |
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+ |:------:|:----:|:-------------:|:------------------------------------------------------:|
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+ | 0.7937 | 100 | 0.1152 | 0.9093 |
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+
454
+
455
+ ### Framework Versions
456
+ - Python: 3.10.12
457
+ - Sentence Transformers: 3.3.1
458
+ - Transformers: 4.47.1
459
+ - PyTorch: 2.1.2+cu121
460
+ - Accelerate: 1.2.1
461
+ - Datasets: 2.19.1
462
+ - Tokenizers: 0.21.0
463
+
464
+ ## Citation
465
+
466
+ ### BibTeX
467
+
468
+ #### Sentence Transformers
469
+ ```bibtex
470
+ @inproceedings{reimers-2019-sentence-bert,
471
+ title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
472
+ author = "Reimers, Nils and Gurevych, Iryna",
473
+ booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
474
+ month = "11",
475
+ year = "2019",
476
+ publisher = "Association for Computational Linguistics",
477
+ url = "https://arxiv.org/abs/1908.10084",
478
+ }
479
+ ```
480
+
481
+ #### MultipleNegativesRankingLoss
482
+ ```bibtex
483
+ @misc{henderson2017efficient,
484
+ title={Efficient Natural Language Response Suggestion for Smart Reply},
485
+ 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},
486
+ year={2017},
487
+ eprint={1705.00652},
488
+ archivePrefix={arXiv},
489
+ primaryClass={cs.CL}
490
+ }
491
+ ```
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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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