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Grammar-aware phrase dataset generated using a novel python package.

ABSTRACT: The past technique of manual dataset preparation was time-consuming and needed much effort. Another attempt to the data acquisition method was using web scraping. Such web scraping tools also produce a bunch of data errors. For this reason, we developed "Oromo-grammar" a novel Python package that accepts a raw text file from the user, extracts every possible root verb from the text, and stores the verbs into a Python list. Our algorithm then iterates over list of root verbs to form their corresponding list of stems. Finally, our algorithm synthesizes grammatical phrases using the appropriate affixations and personal pronouns. The generated phrase dataset can indicate grammatical elements like numbers, gender, and cases. The output is a grammar-rich dataset, which is applicable to modern NLP applications like machine translation, sentence completion, and grammar and spell checker. The dataset also helps linguists and academia in teaching language grammar structures. The method can easily be reproducible to any other language with a systematic analysis and slight modifications to its affix structures in the algorithm.

SUBMITTER: Gemechu EA

PROVIDER: S-EPMC10293991 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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Grammar-aware phrase dataset generated using a novel python package.

Gemechu Ebisa A EA Kanagachidambaresan G R GR

Data in brief 20230519

The past technique of manual dataset preparation was time-consuming and needed much effort. Another attempt to the data acquisition method was using web scraping. Such web scraping tools also produce a bunch of data errors. For this reason, we developed "Oromo-grammar" a novel Python package that accepts a raw text file from the user, extracts every possible root verb from the text, and stores the verbs into a Python list. Our algorithm then iterates over list of root verbs to form their corresp ...[more]

PMID: 37383805

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Project description:BackgroundMicrosatellite instability (MSI) is a common genomic alteration in colorectal cancer, endometrial carcinoma, and other solid tumors. MSI is characterized by a high degree of polymorphism in microsatellite lengths owing to the deficiency in the mismatch repair system. Based on the degree, MSI can be classified as microsatellite instability-high (MSI-H) and microsatellite stable (MSS). MSI is a predictive biomarker for immunotherapy efficacy in advanced/metastatic solid tumors, especially in colorectal cancer patients. Several computational approaches based on target panel sequencing data have been used to detect MSI; however, they are considerably affected by the sequencing depth and panel size.ResultsWe developed MSIFinder, a python package for automatic MSI classification, using random forest classifier (RFC)-based genome sequencing, which is a machine learning technology. We included 19 MSI-H and 25 MSS samples as training sets. First, we selected 54 feature markers from the training sets, built an RFC model, and validated the classifier using a test set comprising 21 MSI-H and 379 MSS samples. With this test set, MSIFinder achieved a sensitivity (recall) of 1.0, a specificity of 0.997, an accuracy of 0.998, a positive predictive value of 0.954, an F1 score of 0.977, and an area under the curve of 0.999. To further verify the robustness and effectiveness of the model, we used a prospective cohort consisting of 18 MSI-H samples and 122 MSS samples. MSIFinder achieved a sensitivity (recall) of 1.0 and a specificity of 1.0. We discovered that MSIFinder is less affected by a low sequencing depth and can achieve a concordance of 0.993 while exhibiting a sequencing depth of 100×. Furthermore, we realized that MSIFinder is less affected by the panel size and can achieve a concordance of 0.99 when the panel size is 0.5 M (million bases).ConclusionThese results indicate that MSIFinder is a robust and effective MSI classification tool that can provide reliable MSI detection for scientific and clinical purposes.

Dataset Information

Grammar-aware phrase dataset generated using a novel python package.

Publications

Grammar-aware phrase dataset generated using a novel python package.

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