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Normalization is an essential step with considerable impact on high-throughput RNA sequencing (RNA-seq) data analysis. Although there are numerous methods for read count normalization, it remains a challenge to choose an optimal method due to multiple factors contributing to read count variability that affects the overall sensitivity and specificity. In order to properly determine the most appropriate normalization methods, it is critical to compare the performance and shortcomings of a representative set of normalization routines based on different dataset characteristics. Therefore, we set out to evaluate the performance of the commonly used methods (DESeq, TMM-edgeR, FPKM-CuffDiff, TC, Med UQ and FQ) and two new methods we propose: Med-pgQ2 and UQ-pgQ2 (per-gene normalization after per-sample median or upper-quartile global scaling). Our per-gene normalization approach allows for comparisons between conditions based on similar count levels. Using the benchmark Microarray Quality Control Project (MAQC) and simulated datasets, we performed differential gene expression analysis to evaluate these methods. When evaluating MAQC2 with two replicates, we observed that Med-pgQ2 and UQ-pgQ2 achieved a slightly higher area under the Receiver Operating Characteristic Curve (AUC), a specificity rate > 85%, the detection power > 92% and an actual false discovery rate (FDR) under 0.06 given the nominal FDR (≤0.05). Although the top commonly used methods (DESeq and TMM-edgeR) yield a higher power (>93%) for MAQC2 data, they trade off with a reduced specificity (
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TwitterThe technological advances in mass spectrometry allow us to collect more comprehensive data with higher quality and increasing speed. With the rapidly increasing amount of data generated, the need for streamlining analyses becomes more apparent. Proteomics data is known to be often affected by systemic bias from unknown sources, and failing to adequately normalize the data can lead to erroneous conclusions. To allow researchers to easily evaluate and compare different normalization methods via a user-friendly interface, we have developed “proteiNorm”. The current implementation of proteiNorm accommodates preliminary filters on peptide and sample levels followed by an evaluation of several popular normalization methods and visualization of the missing value. The user then selects an adequate normalization method and one of the several imputation methods used for the subsequent comparison of different differential expression methods and estimation of statistical power. The application of proteiNorm and interpretation of its results are demonstrated on two tandem mass tag multiplex (TMT6plex and TMT10plex) and one label-free spike-in mass spectrometry example data set. The three data sets reveal how the normalization methods perform differently on different experimental designs and the need for evaluation of normalization methods for each mass spectrometry experiment. With proteiNorm, we provide a user-friendly tool to identify an adequate normalization method and to select an appropriate method for differential expression analysis.
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Normalization of RNA-Seq data has proven essential to ensure accurate inferences and replication of findings. Hence, various normalization methods have been proposed for various technical artifacts that can be present in high-throughput sequencing transcriptomic studies. In this study, we set out to compare the widely used library size normalization methods (UQ, TMM, and RLE) and across sample normalization methods (SVA, RUV, and PCA) for RNA-Seq data using publicly available data from The Cancer Genome Atlas (TCGA) cervical cancer study. Additionally, an extensive simulation study was completed to compare the performance of the across sample normalization methods in estimating technical artifacts. Lastly, we investigated the effect of reduction in degrees of freedom in the normalized data and their impact on downstream differential expression analysis results. Based on this study, the TMM and RLE library size normalization methods give similar results for CESC dataset. In addition, the simulated datasets results show that the SVA (“BE”) method outperforms the other methods (SVA “Leek”, PCA) by correctly estimating the number of latent artifacts. Moreover, ignoring the loss of degrees of freedom due to normalization results in an inflated type I error rates. We recommend adjusting not only for library size differences but also the assessment of known and unknown technical artifacts in the data, and if needed, complete across sample normalization. In addition, we suggest that one includes the known and estimated latent artifacts in the design matrix to correctly account for the loss in degrees of freedom, as opposed to completing the analysis on the post-processed normalized data.
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This Hospital Management System project features a fully normalized relational database designed to manage hospital data including patients, doctors, appointments, diagnoses, medications, and billing. The schema applies database normalization (1NF, 2NF, 3NF) to reduce redundancy and maintain data integrity, providing an efficient, scalable structure for healthcare data management. Included are SQL scripts to create tables and insert sample data, making it a useful resource for learning practical database design and normalization in a healthcare context.
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Dataset for human osteoarthritis (OA) — microarray gene expression (Affymetrix GPL570) PMC +1
Contains expression data for 7 healthy control (normal) tissue samples and 7 osteoarthritis patient tissue samples from synovial / joint tissue. PMC +1
Pre-processed for normalization (background correction, log-transformation, normalization) to remove technical variation.
Suitable for downstream analyses: differential gene expression (normal vs OA), subtype- or phenotype-based classification, machine learning.
Can act as a validation dataset when combining with other GEO datasets to increase sample size or test reproducibility. SpringerLink +1
Useful for biomarker discovery, pathway enrichment analysis (e.g., GO, KEGG), immune infiltration analysis, and subtype analysis in osteoarthritis research.
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Arabic handwritten paragraph dataset to be used for text normalization and generation using conditional deep generative models, such as:
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Background
The Infinium EPIC array measures the methylation status of > 850,000 CpG sites. The EPIC BeadChip uses a two-array design: Infinium Type I and Type II probes. These probe types exhibit different technical characteristics which may confound analyses. Numerous normalization and pre-processing methods have been developed to reduce probe type bias as well as other issues such as background and dye bias.
Methods
This study evaluates the performance of various normalization methods using 16 replicated samples and three metrics: absolute beta-value difference, overlap of non-replicated CpGs between replicate pairs, and effect on beta-value distributions. Additionally, we carried out Pearson’s correlation and intraclass correlation coefficient (ICC) analyses using both raw and SeSAMe 2 normalized data.
Results
The method we define as SeSAMe 2, which consists of the application of the regular SeSAMe pipeline with an additional round of QC, pOOBAH masking, was found to be the best-performing normalization method, while quantile-based methods were found to be the worst performing methods. Whole-array Pearson’s correlations were found to be high. However, in agreement with previous studies, a substantial proportion of the probes on the EPIC array showed poor reproducibility (ICC < 0.50). The majority of poor-performing probes have beta values close to either 0 or 1, and relatively low standard deviations. These results suggest that probe reliability is largely the result of limited biological variation rather than technical measurement variation. Importantly, normalizing the data with SeSAMe 2 dramatically improved ICC estimates, with the proportion of probes with ICC values > 0.50 increasing from 45.18% (raw data) to 61.35% (SeSAMe 2).
Methods
Study Participants and Samples
The whole blood samples were obtained from the Health, Well-being and Aging (Saúde, Ben-estar e Envelhecimento, SABE) study cohort. SABE is a cohort of census-withdrawn elderly from the city of São Paulo, Brazil, followed up every five years since the year 2000, with DNA first collected in 2010. Samples from 24 elderly adults were collected at two time points for a total of 48 samples. The first time point is the 2010 collection wave, performed from 2010 to 2012, and the second time point was set in 2020 in a COVID-19 monitoring project (9±0.71 years apart). The 24 individuals were 67.41±5.52 years of age (mean ± standard deviation) at time point one; and 76.41±6.17 at time point two and comprised 13 men and 11 women.
All individuals enrolled in the SABE cohort provided written consent, and the ethic protocols were approved by local and national institutional review boards COEP/FSP/USP OF.COEP/23/10, CONEP 2044/2014, CEP HIAE 1263-10, University of Toronto RIS 39685.
Blood Collection and Processing
Genomic DNA was extracted from whole peripheral blood samples collected in EDTA tubes. DNA extraction and purification followed manufacturer’s recommended protocols, using Qiagen AutoPure LS kit with Gentra automated extraction (first time point) or manual extraction (second time point), due to discontinuation of the equipment but using the same commercial reagents. DNA was quantified using Nanodrop spectrometer and diluted to 50ng/uL. To assess the reproducibility of the EPIC array, we also obtained technical replicates for 16 out of the 48 samples, for a total of 64 samples submitted for further analyses. Whole Genome Sequencing data is also available for the samples described above.
Characterization of DNA Methylation using the EPIC array
Approximately 1,000ng of human genomic DNA was used for bisulphite conversion. Methylation status was evaluated using the MethylationEPIC array at The Centre for Applied Genomics (TCAG, Hospital for Sick Children, Toronto, Ontario, Canada), following protocols recommended by Illumina (San Diego, California, USA).
Processing and Analysis of DNA Methylation Data
The R/Bioconductor packages Meffil (version 1.1.0), RnBeads (version 2.6.0), minfi (version 1.34.0) and wateRmelon (version 1.32.0) were used to import, process and perform quality control (QC) analyses on the methylation data. Starting with the 64 samples, we first used Meffil to infer the sex of the 64 samples and compared the inferred sex to reported sex. Utilizing the 59 SNP probes that are available as part of the EPIC array, we calculated concordance between the methylation intensities of the samples and the corresponding genotype calls extracted from their WGS data. We then performed comprehensive sample-level and probe-level QC using the RnBeads QC pipeline. Specifically, we (1) removed probes if their target sequences overlap with a SNP at any base, (2) removed known cross-reactive probes (3) used the iterative Greedycut algorithm to filter out samples and probes, using a detection p-value threshold of 0.01 and (4) removed probes if more than 5% of the samples having a missing value. Since RnBeads does not have a function to perform probe filtering based on bead number, we used the wateRmelon package to extract bead numbers from the IDAT files and calculated the proportion of samples with bead number < 3. Probes with more than 5% of samples having low bead number (< 3) were removed. For the comparison of normalization methods, we also computed detection p-values using out-of-band probes empirical distribution with the pOOBAH() function in the SeSAMe (version 1.14.2) R package, with a p-value threshold of 0.05, and the combine.neg parameter set to TRUE. In the scenario where pOOBAH filtering was carried out, it was done in parallel with the previously mentioned QC steps, and the resulting probes flagged in both analyses were combined and removed from the data.
Normalization Methods Evaluated
The normalization methods compared in this study were implemented using different R/Bioconductor packages and are summarized in Figure 1. All data was read into R workspace as RG Channel Sets using minfi’s read.metharray.exp() function. One sample that was flagged during QC was removed, and further normalization steps were carried out in the remaining set of 63 samples. Prior to all normalizations with minfi, probes that did not pass QC were removed. Noob, SWAN, Quantile, Funnorm and Illumina normalizations were implemented using minfi. BMIQ normalization was implemented with ChAMP (version 2.26.0), using as input Raw data produced by minfi’s preprocessRaw() function. In the combination of Noob with BMIQ (Noob+BMIQ), BMIQ normalization was carried out using as input minfi’s Noob normalized data. Noob normalization was also implemented with SeSAMe, using a nonlinear dye bias correction. For SeSAMe normalization, two scenarios were tested. For both, the inputs were unmasked SigDF Sets converted from minfi’s RG Channel Sets. In the first, which we call “SeSAMe 1”, SeSAMe’s pOOBAH masking was not executed, and the only probes filtered out of the dataset prior to normalization were the ones that did not pass QC in the previous analyses. In the second scenario, which we call “SeSAMe 2”, pOOBAH masking was carried out in the unfiltered dataset, and masked probes were removed. This removal was followed by further removal of probes that did not pass previous QC, and that had not been removed by pOOBAH. Therefore, SeSAMe 2 has two rounds of probe removal. Noob normalization with nonlinear dye bias correction was then carried out in the filtered dataset. Methods were then compared by subsetting the 16 replicated samples and evaluating the effects that the different normalization methods had in the absolute difference of beta values (|β|) between replicated samples.
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This repository contains a sample of the input data for the models of the preprint "Can AI be enabled to dynamical downscaling? Training a Latent Diffusion Model to mimic km-scale COSMO-CLM downscaling of ERA5 over Italy". It allows the user to test and train the models on a reduced dataset (45GB).
This sample dataset comprises ~3 years of normalized hourly data for both low-resolution predictors and high-resolution target variables. Data has been randomly picked from the whole dataset, from 2000 to 2020, with 70% of data coming from the original training dataset, 15% from the original validation dataset, and 15% from the original test dataset. Low-resolution data are preprocessed ERA5 data while high-resolution data are preprocessed VHR-REA CMCC data. Details on the performed preprocessing are available in the paper.
This sample dataset also includes files relative to metadata, static data, normalization, and plotting.
To use the data, clone the corresponding repository and unzip this zip file in the data folder.
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This dataset contains biographical information derived from articles on English Wikipedia as it stood in early June 2024. It was created as part of the Structured Contents initiative at Wikimedia Enterprise and is intended for evaluation and research use.
The beta sample dataset is a subset of the Structured Contents Snapshot focusing on people with infoboxes in EN wikipedia; outputted as json files (compressed in tar.gz).
We warmly welcome any feedback you have. Please share your thoughts, suggestions, and any issues you encounter on the discussion page for this dataset here on Kaggle.
Noteworthy Included Fields: - name - title of the article. - identifier - ID of the article. - image - main image representing the article's subject. - description - one-sentence description of the article for quick reference. - abstract - lead section, summarizing what the article is about. - infoboxes - parsed information from the side panel (infobox) on the Wikipedia article. - sections - parsed sections of the article, including links. Note: excludes other media/images, lists, tables and references or similar non-prose sections.
The Wikimedia Enterprise Data Dictionary explains all of the fields in this dataset.
Infoboxes - Compressed: 2GB - Uncompressed: 11GB
Infoboxes + sections + short description - Size of compressed file: 4.12 GB - Size of uncompressed file: 21.28 GB
Article analysis and filtering breakdown: - total # of articles analyzed: 6,940,949 - # people found with QID: 1,778,226 - # people found with Category: 158,996 - people found with Biography Project: 76,150 - Total # of people articles found: 2,013,372 - Total # people articles with infoboxes: 1,559,985 End stats - Total number of people articles in this dataset: 1,559,985 - that have a short description: 1,416,701 - that have an infobox: 1,559,985 - that have article sections: 1,559,921
This dataset includes 235,146 people articles that exist on Wikipedia but aren't yet tagged on Wikidata as instance of:human.
This dataset was originally extracted from the Wikimedia Enterprise APIs on June 5, 2024. The information in this dataset may therefore be out of date. This dataset isn't being actively updated or maintained, and has been shared for community use and feedback. If you'd like to retrieve up-to-date Wikipedia articles or data from other Wikiprojects, get started with Wikimedia Enterprise's APIs
The dataset is built from the Wikimedia Enterprise HTML “snapshots”: https://enterprise.wikimedia.com/docs/snapshot/ and focuses on the Wikipedia article namespace (namespace 0 (main)).
Wikipedia is a human generated corpus of free knowledge, written, edited, and curated by a global community of editors since 2001. It is the largest and most accessed educational resource in history, accessed over 20 billion times by half a billion people each month. Wikipedia represents almost 25 years of work by its community; the creation, curation, and maintenance of millions of articles on distinct topics. This dataset includes the biographical contents of English Wikipedia language editions: English https://en.wikipedia.org/, written by the community.
Wikimedia Enterprise provides this dataset under the assumption that downstream users will adhere to the relevant free culture licenses when the data is reused. In situations where attribution is required, reusers should identify the Wikimedia project from which the content was retrieved as the source of the content. Any attribution should adhere to Wikimedia’s trademark policy (available at https://foundation.wikimedia.org/wiki/Trademark_policy) and visual identity guidelines (ava...
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Finding a good data source is the first step toward creating a database. Cardiovascular illnesses (CVDs) are the major cause of death worldwide. CVDs include coronary heart disease, cerebrovascular disease, rheumatic heart disease, and other heart and blood vessel problems. According to the World Health Organization, 17.9 million people die each year. Heart attacks and strokes account for more than four out of every five CVD deaths, with one-third of these deaths occurring before the age of 70 A comprehensive database for factors that contribute to a heart attack has been constructed , The main purpose here is to collect characteristics of Heart Attack or factors that contribute to it. As a result, a form is created to accomplish this. Microsoft Excel was used to create this form. Figure 1 depicts the form which It has nine fields, where eight fields for input fields and one field for output field. Age, gender, heart rate, systolic BP, diastolic BP, blood sugar, CK-MB, and Test-Troponin are representing the input fields, while the output field pertains to the presence of heart attack, which is divided into two categories (negative and positive).negative refers to the absence of a heart attack, while positive refers to the presence of a heart attack.Table 1 show the detailed information and max and min of values attributes for 1319 cases in the whole database.To confirm the validity of this data, we looked at the patient files in the hospital archive and compared them with the data stored in the laboratories system. On the other hand, we interviewed the patients and specialized doctors. Table 2 is a sample for 1320 cases, which shows 44 cases and the factors that lead to a heart attack in the whole database,After collecting this data, we checked the data if it has null values (invalid values) or if there was an error during data collection. The value is null if it is unknown. Null values necessitate special treatment. This value is used to indicate that the target isn’t a valid data element. When trying to retrieve data that isn't present, you can come across the keyword null in Processing. If you try to do arithmetic operations on a numeric column with one or more null values, the outcome will be null. An example of a null values processing is shown in Figure 2.The data used in this investigation were scaled between 0 and 1 to guarantee that all inputs and outputs received equal attention and to eliminate their dimensionality. Prior to the use of AI models, data normalization has two major advantages. The first is to avoid overshadowing qualities in smaller numeric ranges by employing attributes in larger numeric ranges. The second goal is to avoid any numerical problems throughout the process.After completion of the normalization process, we split the data set into two parts - training and test sets. In the test, we have utilized1060 for train 259 for testing Using the input and output variables, modeling was implemented.
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TwitterExample data of fusion features and growth indicators after Z-Score normalization.
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RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D. melanogaster that we used here. We investigated the power of existing approaches for quality checking mRNA-seq data and explored additional, quantitative quality checks. To accommodate nested, multi-level experimental designs, we incorporated sample layout into our analyses. We employed a subsampling without replacement-based normalization and an identification of DE that accounted for the hierarchy and amplitude of effect sizes within samples, then evaluated the resulting differential expression call in comparison to existing approaches. In a final step to test for broader applicability, we applied our approaches to a published set of H. sapiens mRNA-seq samples, The dataset-tailored methods improved sample comparability and delivered a robust prediction of subtle gene expression changes. The proposed approaches have the potential to improve key steps in the analysis of RNA-seq data by incorporating the structure and characteristics of biological experiments.
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TwitterIsobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here we introduce two novel algorithms implemented in MaxQuant that substantially improve the data analysis with multiple n-plexes. First, isobaric matching between runs (IMBR) makes use of the three-dimensional MS1 features to transfer identifications from identified to unidentified MS/MS spectra between LC-MS runs in order to utilize reporter ion intensities in unidentified spectra for quantification. On typical datasets, we observe a significant gain in quantifiable n-plexesMS/MS spectra that can be used for quantification. Second, we introduce a novel PSM-level normalization, applicable to data with and without common reference channel. It is a weighted median-based method, in which the weights reflect the number of ions that were used for fragmentation. On a typical dataset, we observe complete removal of batch effects and dominance of the biological sample grouping after normalization. This dataset is one of the datasets used for the study. It is TMT 10-plex with a reference channel.
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Technical biases are introduced in omics data sets during data generation and interfere with the ability to study biological mechanisms. Several normalization approaches have been proposed to minimize the effects of such biases, but fluctuations in the electrospray current during liquid chromatography–mass spectrometry gradients cause local and sample-specific bias not considered by most approaches. Here we introduce a software named NormalyzerDE that includes a generic retention time (RT)-segmented approach compatible with a wide range of global normalization approaches to reduce the effects of time-resolved bias. The software offers straightforward access to multiple normalization methods, allows for data set evaluation and normalization quality assessment as well as subsequent or independent differential expression analysis using the empirical Bayes Limma approach. When evaluated on two spike-in data sets the RT-segmented approaches outperformed conventional approaches by detecting more peptides (8–36%) without loss of precision. Furthermore, differential expression analysis using the Limma approach consistently increased recall (2–35%) compared to analysis of variance. The combination of RT-normalization and Limma was in one case able to distinguish 108% (2597 vs 1249) more spike-in peptides compared to traditional approaches. NormalyzerDE provides widely usable tools for performing normalization and evaluating the outcome and makes calculation of subsequent differential expression statistics straightforward. The program is available as a web server at http://quantitativeproteomics.org/normalyzerde.
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According to our latest research, the global Tick Data Normalization market size reached USD 1.02 billion in 2024, reflecting robust expansion driven by the increasing complexity and volume of financial market data. The market is expected to grow at a CAGR of 13.1% during the forecast period, reaching approximately USD 2.70 billion by 2033. This growth is fueled by the rising adoption of algorithmic trading, regulatory demands for accurate and consistent data, and the proliferation of advanced analytics across financial institutions. As per our analysis, the market’s trajectory underscores the critical role of data normalization in ensuring data integrity and operational efficiency in global financial markets.
The primary growth driver for the tick data normalization market is the exponential surge in financial data generated by modern trading platforms and electronic exchanges. With the proliferation of high-frequency trading and the integration of diverse market data feeds, financial institutions face the challenge of processing vast amounts of tick-by-tick data from multiple sources, each with unique formats and structures. Tick data normalization solutions address this complexity by transforming disparate data streams into consistent, standardized formats, enabling seamless downstream processing for analytics, trading algorithms, and compliance reporting. This standardization is particularly vital in the context of regulatory mandates such as MiFID II and Dodd-Frank, which require accurate data lineage and auditability, further propelling market growth.
Another significant factor contributing to market expansion is the growing reliance on advanced analytics and artificial intelligence within the financial sector. As firms seek to extract actionable insights from historical and real-time tick data, the need for high-quality, normalized datasets becomes paramount. Data normalization not only enhances the accuracy and reliability of predictive models but also facilitates the integration of machine learning algorithms for tasks such as anomaly detection, risk assessment, and portfolio optimization. The increasing sophistication of trading strategies, coupled with the demand for rapid, data-driven decision-making, is expected to sustain robust demand for tick data normalization solutions across asset classes and geographies.
Furthermore, the transition to cloud-based infrastructure has transformed the operational landscape for banks, hedge funds, and asset managers. Cloud deployment offers scalability, flexibility, and cost-efficiency, enabling firms to manage large-scale tick data normalization workloads without the constraints of on-premises hardware. This shift is particularly relevant for smaller institutions and emerging markets, where cloud adoption lowers entry barriers and accelerates the deployment of advanced data management capabilities. At the same time, the availability of managed services and API-driven platforms is fostering innovation and expanding the addressable market, as organizations seek to outsource complex data normalization tasks to specialized vendors.
Regionally, North America continues to dominate the tick data normalization market, accounting for the largest share in terms of revenue and technology adoption. The presence of leading financial centers, advanced IT infrastructure, and a strong regulatory framework underpin the region’s leadership. Meanwhile, Asia Pacific is emerging as the fastest-growing market, driven by rapid digitalization of financial services, burgeoning capital markets, and increasing participation of retail and institutional investors. Europe also maintains a significant market presence, supported by stringent compliance requirements and a mature financial ecosystem. Latin America and the Middle East & Africa are witnessing steady growth, albeit from a lower base, as financial modernization initiatives gain momentum.
The tick data normalizati
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Research Domain/Project:
This dataset was created for a machine learning experiment aimed at developing a classification model to predict outcomes based on a set of features. The primary research domain is disease prediction in patients. The dataset was used in the context of training, validating, and testing.
Purpose of the Dataset:
The purpose of this dataset is to provide training, validation, and testing data for the development of machine learning models. It includes labeled examples that help train classifiers to recognize patterns in the data and make predictions.
Dataset Creation:
Data preprocessing steps involved cleaning, normalization, and splitting the data into training, validation, and test sets. The data was carefully curated to ensure its quality and relevance to the problem at hand. For any missing values or outliers, appropriate handling techniques were applied (e.g., imputation, removal, etc.).
Structure of the Dataset:
The dataset consists of several files organized into folders by data type:
Training Data: Contains the training dataset used to train the machine learning model.
Validation Data: Used for hyperparameter tuning and model selection.
Test Data: Reserved for final model evaluation.
Each folder contains files with consistent naming conventions for easy navigation, such as train_data.csv, validation_data.csv, and test_data.csv. Each file follows a tabular format with columns representing features and rows representing individual data points.
Software Requirements:
To open and work with this dataset, you need VS Code or Jupyter, which could include tools like:
Python (with libraries such as pandas, numpy, scikit-learn, matplotlib, etc.)
Reusability:
Users of this dataset should be aware that it is designed for machine learning experiments involving classification tasks. The dataset is already split into training, validation, and test subsets. Any model trained with this dataset should be evaluated using the test set to ensure proper validation.
Limitations:
The dataset may not cover all edge cases, and it might have biases depending on the selection of data sources. It's important to consider these limitations when generalizing model results to real-world applications.
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Supplementary data 4a: RNA-seq raw read counts to genes in the Foc race1 challenged corm sample (before normalization). Supplementary data 4b: RNA-seq raw read counts to genes in the Foc race1 challenged root sample (before normalization). Supplementary data 4c: RNA-seq raw read counts to genes in the Foc TR4 challenged corm sample (before normalization). Supplementary data 4d: RNA-seq raw read counts to genes in the Foc TR4 challenged root sample (before normalization)
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TwitterThis feature class is part of the Cadastral National Spatial Data Infrastructure (NSDI) CADNSDI publication data set for rectangular and non-rectangular Public Land Survey System (PLSS) data set. The metadata description in the Cadastral Reference System Feature Data Set more fully describes the entire data set. This feature class is the second division of the PLSS is quarter, quarter-quarter, sixteenth or government lot divisions of the PLSS. The second and third divisions are combined into this feature class as an intentional de-normalization of the PLSS hierarchical data. The polygons in this feature class represent the smallest division to the sixteenth that has been defined for the first division. For example In some cases sections have only been divided to the quarter. Divisions below the sixteenth are in the Special Survey or Parcel Feature Class.
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TwitterThis feature class is part of the Cadastral National Spatial Data Infrastructure (NSDI) CADNSDI publication data set for rectangular and non-rectangular Public Land Survey System (PLSS) data set. The metadata description in the Cadastral Reference System Feature Data Set more fully describes the entire data set. This feature class is the second division of the PLSS is quarter, quarter-quarter, sixteenth or government lot divisions of the PLSS. The second and third divisions are combined into this feature class as an intentional de-normalization of the PLSS hierarchical data. The polygons in this feature class represent the smallest division to the sixteenth that has been defined for the first division. For example In some cases sections have only been divided to the quarter. Divisions below the sixteenth are in the Special Survey or Parcel Feature Class.
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Data used in the experiments described in:
Nikola Ljubešić, Katja Zupan, Darja Fišer and Tomaž Erjavec: Normalising Slovene data: historical texts vs. user-generated content. Proceedings of KONVENS 2016, September 19–21, 2016, Bochum, Germany.
https://www.linguistics.rub.de/konvens16/pub/19_konvensproc.pdf
(https://www.linguistics.rub.de/konvens16/)
Data are split into the "token" folder (experiment on normalising individual tokens) and "segment" folder (experiment on normalising whole segments of text, i.e. sentences or tweets). Each experiment folder contains the "train", "dev" and "test" subfolders. Each subfolder contains two files for each sample, the original data (.orig.txt) and the data with hand-normalised words (.norm.txt). The files are aligned by lines.
There are four datasets:
- goo300k-bohoric: historical Slovene, hard case (<1850)
- goo300k-gaj: historical Slovene, easy case (1850 - 1900)
- tweet-L3: Slovene tweets, hard case (non-standard language)
- tweet-L1: Slovene tweets, easy case (mostly standard language)
The goo300k data come from http://hdl.handle.net/11356/1025, while the tweet data originate from the JANES project (http://nl.ijs.si/janes/english/).
The text in the files has been split by inserting spaces between characters, with underscore (_) substituting the space character. Tokens not relevant for normalisation (e.g. URLs, hashtags) have been substituted by the inverted question mark '¿' character.
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Normalization is an essential step with considerable impact on high-throughput RNA sequencing (RNA-seq) data analysis. Although there are numerous methods for read count normalization, it remains a challenge to choose an optimal method due to multiple factors contributing to read count variability that affects the overall sensitivity and specificity. In order to properly determine the most appropriate normalization methods, it is critical to compare the performance and shortcomings of a representative set of normalization routines based on different dataset characteristics. Therefore, we set out to evaluate the performance of the commonly used methods (DESeq, TMM-edgeR, FPKM-CuffDiff, TC, Med UQ and FQ) and two new methods we propose: Med-pgQ2 and UQ-pgQ2 (per-gene normalization after per-sample median or upper-quartile global scaling). Our per-gene normalization approach allows for comparisons between conditions based on similar count levels. Using the benchmark Microarray Quality Control Project (MAQC) and simulated datasets, we performed differential gene expression analysis to evaluate these methods. When evaluating MAQC2 with two replicates, we observed that Med-pgQ2 and UQ-pgQ2 achieved a slightly higher area under the Receiver Operating Characteristic Curve (AUC), a specificity rate > 85%, the detection power > 92% and an actual false discovery rate (FDR) under 0.06 given the nominal FDR (≤0.05). Although the top commonly used methods (DESeq and TMM-edgeR) yield a higher power (>93%) for MAQC2 data, they trade off with a reduced specificity (