Data Mining Techniques in Analyzing Process Data: A Didactic.
Ontology highlight
ABSTRACT:
SUBMITTER: Qiao X
PROVIDER: S-EPMC6265513 | biostudies-literature | 2018
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BACKGROUND:Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagenomic sequencing data. Here we employed the random forest algorithm to develop VirMiner, a web-based phage contig prediction tool especially sensitive for high-abundances phage contigs, trained and validated by paired metagenomic and phagenomic sequencing data from the human gut flora. RESULTS:VirMiner achieved 41.06% ± 17.51% sensitivity and 81.91% ± 4.04% specificity in the prediction of phage contigs. In particular, for the high-abundance phage contigs, VirMiner outperformed other tools (VirFinder and VirSorter) with much higher sensitivity (65.23% ± 16.94%) than VirFinder (34.63% ± 17.96%) and VirSorter (18.75% ± 15.23%) at almost the same specificity. Moreover, VirMiner provides the most comprehensive phage analysis pipeline which is comprised of metagenomic raw reads processing, functional annotation, phage contig identification, and phage-host relationship prediction (CRISPR-spacer recognition) and supports two-group comparison when the input (metagenomic sequence data) includes different conditions (e.g., case and control). Application of VirMiner to an independent cohort of human gut metagenomes obtained from individuals treated with antibiotics revealed that 122 KEGG orthology and 118 Pfam groups had significantly differential abundance in the pre-treatment samples compared to samples at the end of antibiotic administration, including clustered regularly interspaced short palindromic repeats (CRISPR), multidrug resistance, and protein transport. The VirMiner webserver is available at http://sbb.hku.hk/VirMiner/ . CONCLUSIONS:We developed a comprehensive tool for phage prediction and analysis for metagenomic samples. Compared to VirSorter and VirFinder-the most widely used tools-VirMiner is able to capture more high-abundance phage contigs which could play key roles in infecting bacteria and modulating microbial community dynamics. TRIAL REGISTRATION:The European Union Clinical Trials Register, EudraCT Number: 2013-003378-28 . Registered on 9 April 2014.
| S-EPMC6425642 | biostudies-literature
Project description:The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique.
| S-EPMC3526995 | biostudies-literature
Project description:ObjectivesAnalyze a set of data of hydrogen breath tests by use of data mining tools. Identify new patterns of H2 production.MethodsHydrogen breath tests data sets as well as k-means clustering as the data mining technique to a dataset of 2571 patients.ResultsSix different patterns have been extracted upon analysis of the hydrogen breath test data. We have also shown the relevance of each of the samples taken throughout the test.ConclusionsAnalysis of the hydrogen breath test data sets using data mining techniques has identified new patterns of hydrogen generation upon lactose absorption. We can see the potential of application of data mining techniques to clinical data sets. These results offer promising data for future research on the relations between gut microbiota produced hydrogen and its link to clinical symptoms.
| S-EPMC5268498 | biostudies-literature
Project description:Data mining is the process of analyzing a massive amount of data to identify meaningful patterns and detect relations, which can lead to future trend prediction and appropriate decision making. Data mining applications are significant in marketing, banking, medicine, etc. In this paper, we present an overview of data mining applications in medicine to provide a clear view of the challenges and previous works in this area for researchers. Data mining techniques such as Decision Tree, Random Forest, K-means Clustering, Support Vector Machine, Logistic Regression, Neural Network, Naive Bayes, and association rule mining are used for diagnosing, prognosis, classifying, constructing predictive models, and analyzing risk factors of various diseases. The main objective of the paper is to analyze and compare different data mining techniques used in the medical applications. We present a summary of the results and provide comparison analysis of the data mining methods employed by the reviewed articles.Supplementary informationThe online version contains supplementary material available at 10.1007/s40200-021-00884-2.
| S-EPMC8630112 | biostudies-literature
Project description:BackgroundHyperbilirubinemia is emerging as an increasingly common problem in newborns due to a decreasing hospital length of stay after birth. Jaundice is the most common disease of the newborn and although being benign in most cases it can lead to severe neurological consequences if poorly evaluated. In different areas of medicine, data mining has contributed to improve the results obtained with other methodologies.Hence, the aim of this study was to improve the diagnosis of neonatal jaundice with the application of data mining techniques.MethodsThis study followed the different phases of the Cross Industry Standard Process for Data Mining model as its methodology.This observational study was performed at the Obstetrics Department of a central hospital (Centro Hospitalar Tâmega e Sousa--EPE), from February to March of 2011. A total of 227 healthy newborn infants with 35 or more weeks of gestation were enrolled in the study. Over 70 variables were collected and analyzed. Also, transcutaneous bilirubin levels were measured from birth to hospital discharge with maximum time intervals of 8 hours between measurements, using a noninvasive bilirubinometer.Different attribute subsets were used to train and test classification models using algorithms included in Weka data mining software, such as decision trees (J48) and neural networks (multilayer perceptron). The accuracy results were compared with the traditional methods for prediction of hyperbilirubinemia.ResultsThe application of different classification algorithms to the collected data allowed predicting subsequent hyperbilirubinemia with high accuracy. In particular, at 24 hours of life of newborns, the accuracy for the prediction of hyperbilirubinemia was 89%. The best results were obtained using the following algorithms: naive Bayes, multilayer perceptron and simple logistic.ConclusionsThe findings of our study sustain that, new approaches, such as data mining, may support medical decision, contributing to improve diagnosis in neonatal jaundice.
| S-EPMC3557145 | biostudies-literature
Project description:Gene set analyses have become a standard approach for increasing the sensitivity of transcriptomic studies. However, analytical methods incorporating gene sets require the availability of pre-defined gene sets relevant to the underlying physiology being studied. For novel physiological problems, relevant gene sets may be unavailable or existing gene set databases may bias the results towards only the best-studied of the relevant biological processes. We describe a successful attempt to mine novel functional gene sets for translational projects where the underlying physiology is not necessarily well characterized in existing annotation databases. We choose targeted training data from public expression data repositories and define new criteria for selecting biclusters to serve as candidate gene sets. Many of the discovered gene sets show little or no enrichment for informative Gene Ontology terms or other functional annotation. However, we observe that such gene sets show coherent differential expression in new clinical test data sets, even if derived from different species, tissues, and disease states. We demonstrate the efficacy of this method on a human metabolic data set, where we discover novel, uncharacterized gene sets that are diagnostic of diabetes, and on additional data sets related to neuronal processes and human development. Our results suggest that our approach may be an efficient way to generate a collection of gene sets relevant to the analysis of data for novel clinical applications where existing functional annotation is relatively incomplete.
| S-EPMC3201790 | biostudies-literature
Project description:Floods are among the devastating types of disasters in terms of human life, social and financial losses. Authoritative data from flood gauges are scarce in arid regions because of the specific type of dry climate that dysfunctions these measuring devices. Hence, social media data could be a useful tool in this case, where a wealth of information is available online. This study investigates the reliability of flood related data quality collected from social media, particularly for an arid region where the usage of flow gauges is limited. The data (text, images and videos) of social media, related to a flood event, was analyzed using the Machine Learning approach. For this reason, digital data (758 images and 1413 video frames) was converted into numeric values through ResNet50 model using the VGG-16 architecture. Numeric data of images, videos and text was further classified using different Machine Learning algorithms. Receiver operating characteristics (ROC) curve and area under curve (AUC) methods were used to evaluate and compare the performance of the developed machine learning algorithms. This novel approach of studying the quality of social media data could be a reliable alternative in the absence of real-time flow gauges data. A flash flood that occurred in the United Arab Emirates (UAE) from March 7-11, 2016 was selected as the focus of this study. Random forest showed the highest accuracy of 80.18% among the five other classifiers for images and videos. Precipitation/rainfall data were used to validate social media data, which showed a significant relationship between rainfall and the number of posts. The validity of the machine learning models was assessed using the area under the curve, precision-recall curve, root mean square error, and kappa statistics to confirm the validity and accuracy of the model. The data quality of YouTube videos was found to have the highest accuracy followed by Facebook, Flickr, Twitter, and Instagram. These results showed that social media data could be used when gauge data is unavailable.
| S-EPMC9037947 | biostudies-literature
Project description:The thermo-mechanical properties of streptavidin-conjugated gold nanospheres, adhered to a surface via complex molecular chains, are investigated by two-color infrared asynchronous optical sampling pump-probe spectroscopy. Nanospheres with different surface densities have been deposited and exposed to a plasma treatment to modify their polymer binding chains. The aim is to monitor their optical response in complex chemical environments that may be experienced in, e.g., photothermal therapy or drug delivery applications. By applying unsupervised learning techniques to the spectroscopic traces, we identify their thermo-mechanical response variation. This variation discriminates nanospheres in different chemical environments or different surface densities. Such discrimination is not evident based on a standard analysis of the spectroscopic traces. This kind of analysis is important, given the widespread application of conjugated gold nanospheres in medicine and biology.
| S-EPMC7530730 | biostudies-literature
Project description:BackgroundMillennials are exposed to many investment opportunities, and they have shown their interest in gaining more income via investments. One popular investment avenue is unit trusts. However, analysing unit trusts' financial data and gaining valuable insights may not be as simple because not everyone has the required financial knowledge and adequate time to perform in-depth analytics on the numerous financial data. Furthermore, it is not easy to compile the performance of each unit trust available in Malaysia. The primary objective of this research is to identify unit trust funds that provide higher returns than their average peers via performance profiling. Methods: This research proposed a performance profiling on Malaysia unit trust funds using the two data mining techniques, i.e., Expectation Maximisation (EM) and Apriori, to assist amateur retail investors to choose the right unit trust based on their risk tolerance. EM clustered the unit trust funds in Malaysia into several groups based on their annual financial performances. This was then followed by finding the rules associated with each cluster by applying Apriori. The resulted rules shall serve the purpose of profiling the clustered unit trust funds. Retail investors can then select their preferred unit trust funds based on the performance profile of the clusters. Results: The yearly average total return of the financial year 2018 and 2019 was used to evaluate unit trust funds' performance in the clusters. The evaluation results indicated that the profiling could provide valuable and insightful information to retail investors with varying risk appetites. Conclusions: This research has demonstrated that the financial performance profiling of unit trust funds could be acquired via data mining approaches. This valuable information is crucial to unit trust investors for selecting suitable funds in investment.
| S-EPMC9237553 | biostudies-literature
Project description:The present research reports on the use of data mining techniques for differentiating between translated and non-translated original Chinese based on monolingual comparable corpora. We operationalized seven entropy-based metrics including character, wordform unigram, wordform bigram and wordform trigram, POS (Part-of-speech) unigram, POS bigram and POS trigram entropy from two balanced Chinese comparable corpora (translated vs non-translated) for data mining and analysis. We then applied four data mining techniques including Support Vector Machines (SVMs), Linear discriminant analysis (LDA), Random Forest (RF) and Multilayer Perceptron (MLP) to distinguish translated Chinese from original Chinese based on these seven features. Our results show that SVMs is the most robust and effective classifier, yielding an AUC of 90.5% and an accuracy rate of 84.3%. Our results have affirmed the hypothesis that translational language is categorically different from original language. Our research demonstrates that combining information-theoretic indicator of Shannon's entropy together with machine learning techniques can provide a novel approach for studying translation as a unique communicative activity. This study has yielded new insights for corpus-based studies on the translationese phenomenon in the field of translation studies.
| S-EPMC8947138 | biostudies-literature