BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study

2019 ◽  
Author(s):  
Jie Dong ◽  
Min-Feng Zhu ◽  
Yong-Huan Yun ◽  
Ai-Ping Lu ◽  
Ting-Jun Hou ◽  
...  
Keyword(s):  
Data Mining ◽  
Clustering Algorithms ◽  
R Package ◽  
Integrated Analysis ◽  
Analysis Pipeline ◽  
Molecular Fingerprints ◽  
Useful Knowledge ◽  
Data Mining Algorithms ◽  
Mining Methods ◽  
Mining Algorithms

Abstract Background With the increasing development of biotechnology and information technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these resources needs to be extracted and then transformed to useful knowledge by various data mining methods. However, a main computational challenge is how to effectively represent or encode molecular objects under investigation such as chemicals, proteins, DNAs and even complicated interactions when data mining methods are employed. To further explore these complicated data, an integrated toolkit to represent different types of molecular objects and support various data mining algorithms is urgently needed. Results We developed a freely available R/CRAN package, called BioMedR, for molecular representations of chemicals, proteins, DNAs and pairwise samples of their interactions. The current version of BioMedR could calculate 293 molecular descriptors and 13 kinds of molecular fingerprints for small molecules, 9920 protein descriptors based on protein sequences and six types of generalized scale-based descriptors for proteochemometric modeling, more than 6000 DNA descriptors from nucleotide sequences and six types of interaction descriptors using three different combining strategies. Moreover, this package realized five similarity calculation methods and four powerful clustering algorithms as well as several useful auxiliary tools, which aims at building an integrated analysis pipeline for data acquisition, data checking, descriptor calculation and data modeling. Conclusion BioMedR provides a comprehensive and uniform R package to link up different representations of molecular objects with each other and will benefit cheminformatics/bioinformatics and other biomedical users. It is available at: https://CRAN.R-project.org/package=BioMedR and https://github.com/wind22zhu/BioMedR/.

scholarly journals Data Mining algorithms in search of effective conditions for conducting chemical reactions

2021 ◽  
pp. 29-42
Author(s):  
Владимир Арнольдович Биллиг ◽  
Николай Васильевич Звягинцев
Keyword(s):  
Data Mining ◽  
Chemical Reactions ◽  
Software Package ◽  
Maximum Amount ◽  
Minimal Cost ◽  
Useful Knowledge ◽  
Data Mining Algorithms ◽  
Practical Information ◽  
Mining Algorithms ◽  
Effective Conditions

В настоящее время накоплено значительное количество экспериментальных данных, фиксирующих процесс протекания химических реакций. Анализ этих данных комплексом алгоритмов Data Mining дает важную практическую информацию для поиска эффективных условий проведения реакций, при которых получается максимальное количество целевого продукта при минимальных затратах. В данной работе на примере работы с базой, содержащей данные о протекании реакции карбонилирования различных олефинов, показано, как разработанный нами программный комплекс позволяет извлечь полезные знания, способствующие повышению эффективности химических реакций. At present, a significant amount of experimental data has been accumulated, recording the process of the occurrence of chemical reactions. Analysis of these data by a set of Data Mining algorithms provides important practical information for finding effective conditions for carrying out reactions, at which the maximum amount of the target product is obtained at minimal cost. In this paper, using the example of working with a database containing data on the course of the carbonylation reaction of various olefins, it is shown how the software package developed by us allows us to extract useful knowledge that contributes to an increase in the efficiency of chemical reactions.

Determination of Voting Tendencies in Turkey through Data Mining Algorithms

2017 ◽  
Vol 9 (1) ◽  
pp. 50-58
Author(s):  
Ali Bayır ◽  
Sebnem Ozdemir ◽  
Sevinç Gülseçen
Keyword(s):  
Data Mining ◽  
Economic Status ◽  
Educational Status ◽  
Data Set ◽  
Data Mining Algorithms ◽  
C4.5 Decision Tree ◽  
Survey Results ◽  
Mining Methods ◽  
Using Data ◽  
Mining Algorithms

Political elections can be defined as systems that contain political tendencies and voters' perceptions and preferences. The outputs of those systems are formed by specific attributes of individuals such as age, gender, occupancy, educational status, socio-economic status, religious belief, etc. Those attributes can create a data set, which contains hidden information and undiscovered patterns that can be revealed by using data mining methods and techniques. The main purpose of this study is to define voting tendencies in politics by using some of data mining methods. According to that purpose, the survey results, which were prepared and applied before 2011 elections of Turkey by KONDA Research and Consultancy Company, were used as raw data set. After Preprocessing of data, models were generated via data mining algorithms, such as Gini, C4.5 Decision Tree, Naive Bayes and Random Forest. Because of increasing popularity and flexibility in analyzing process, R language and Rstudio environment were used.

Data Mining in Proteomics Using Grid Computing

2011 ◽  
pp. 245-267
Author(s):  
Fotis Psomopoulos ◽  
Pericles Mitkas
Keyword(s):  
Data Mining ◽  
Data Retrieval ◽  
Protein Classification ◽  
Classification Problems ◽  
Proteomics Data ◽  
Grid Environment ◽  
Useful Knowledge ◽  
Domain Specific ◽  
Data Mining Algorithms ◽  
Mining Algorithms

The scope of this chapter is the presentation of Data Mining techniques for knowledge extraction in proteomics, taking into account both the particular features of most proteomics issues (such as data retrieval and system complexity), and the opportunities and constraints found in a Grid environment. The chapter discusses the way new and potentially useful knowledge can be extracted from proteomics data, utilizing Grid resources in a transparent way. Protein classification is introduced as a current research issue in proteomics, which also demonstrates most of the domain – specific traits. An overview of common and custom-made Data Mining algorithms is provided, with emphasis on the specific needs of protein classification problems. A unified methodology is presented for complex Data Mining processes on the Grid, highlighting the different application types and the benefits and drawbacks in each case. Finally, the methodology is validated through real-world case studies, deployed over the EGEE grid environment.

Data Mining in Proteomics Using Grid Computing

2012 ◽  
pp. 918-940
Author(s):  
Fotis Psomopoulos ◽  
Pericles Mitkas
Keyword(s):  
Data Mining ◽  
Data Retrieval ◽  
Protein Classification ◽  
Classification Problems ◽  
Proteomics Data ◽  
Grid Environment ◽  
Useful Knowledge ◽  
Domain Specific ◽  
Data Mining Algorithms ◽  
Mining Algorithms

The scope of this chapter is the presentation of Data Mining techniques for knowledge extraction in proteomics, taking into account both the particular features of most proteomics issues (such as data retrieval and system complexity), and the opportunities and constraints found in a Grid environment. The chapter discusses the way new and potentially useful knowledge can be extracted from proteomics data, utilizing Grid resources in a transparent way. Protein classification is introduced as a current research issue in proteomics, which also demonstrates most of the domain – specific traits. An overview of common and custom-made Data Mining algorithms is provided, with emphasis on the specific needs of protein classification problems. A unified methodology is presented for complex Data Mining processes on the Grid, highlighting the different application types and the benefits and drawbacks in each case. Finally, the methodology is validated through real-world case studies, deployed over the EGEE grid environment.

Trajectory Pattern Mining: Methods and Applications

2014 ◽  
Vol 490-491 ◽  
pp. 1361-1367
Author(s):  
Xin Huang ◽  
Hui Juan Chen ◽  
Mao Gong Zheng ◽  
Ping Liu ◽  
Jing Qian
Keyword(s):  
Data Mining ◽  
Social Media ◽  
Pattern Mining ◽  
Data Sets ◽  
Trajectory Data ◽  
Data Mining Algorithms ◽  
Mining Methods ◽  
Trajectory Pattern ◽  
Mining Algorithms ◽  
Trajectory Pattern Mining

With the advent of location-based social media and locationacquisition technologies, trajectory data are becoming more and more ubiquitous in the real world. A lot of data mining algorithms have been successfully applied to trajectory data sets. Trajectory pattern mining has received a lot of attention in recent years. In this paper, we review the most inuential methods as well as typical applications within the context of trajectory pattern mining.

Data Mining Algorithm and its Application with Massive Text Database

2015 ◽  
Vol 742 ◽  
pp. 395-398
Author(s):  
Chun Ping Wang
Keyword(s):  
Data Mining ◽  
Semantic Analysis ◽  
Data Mining Algorithm ◽  
User Characteristics ◽  
Text Data ◽  
Data Mining Algorithms ◽  
Mining Methods ◽  
Language Characteristics ◽  
Network Language ◽  
Mining Algorithms

Features of large text data mining methods method is avoided semantic analysis from the lexical, syntactic, but by means of statistical analysis and processing large text data, thus maximizing literally ignored similar semantic differences, adapt to network language characteristics. The results of our paper show that data mining algorithms may extract the information in this article can portray the characteristics of vocabulary specific user characteristics and make recommendations based on the characteristics of the user vocabulary.

scholarly journals Analysis And Detection of Diabetes Using Data Mining Techniques – Efficiency Comparison

2021 ◽  
pp. 73-79
Author(s):  
G. Ramadevi ◽  
Srujitha Yeruva ◽  
P. Sravanthi ◽  
P. Eknath Vamsi ◽  
S. Jaya Prakash
Keyword(s):  
Data Mining ◽  
Clustering Algorithms ◽  
Medical Data ◽  
Healthcare Sector ◽  
Data Mining Techniques ◽  
Data Mining Algorithms ◽  
Use Of Data ◽  
Efficiency Comparison ◽  
Using Data ◽  
Mining Algorithms

In a digitized world, data is growing exponentially and it is difficult to analyze the data and give the results. Data mining techniques play an important role in healthcare sector - BigData. By making use of Data mining algorithms it is possible to analyze, detect and predict the presence of disease which helps doctors to detect the disease early and in decision making. The objective of data mining techniques used is to design an automated tool that notifies the patient’s treatment history disease and medical data to doctors. Data mining techniques are very much useful in analyzing medical data to achieve meaningful and practical patterns. This project works on diabetes medical data, classification and clustering algorithms like (OPTICS, NAIVEBAYES, and BRICH) are implemented and the efficiency of the same is examined.

Data Mining Techniques on Earthquake Data

2015 ◽  
pp. 183-199
Author(s):  
Negar Sadat Soleimani Zakeri ◽  
Saeid Pashazadeh
Keyword(s):  
Data Mining ◽  
Seismic Data ◽  
Clustering Algorithms ◽  
Active Faults ◽  
Active Regions ◽  
Tectonic Stress ◽  
Earthquake Hazards ◽  
Data Mining Algorithms ◽  
Proposed Model ◽  
Mining Algorithms

Active faults are sources of earthquakes and one of them is north fault of Tabriz in the northwest of Iran. The activation of faults can harm humans' life and constructions. The analysis of the seismic data in active regions can be helpful in dealing with earthquake hazards and devising prevention strategies. In this chapter, structure of earthquake events along with application of various intelligent data mining algorithms for earthquake prediction are studied. Main focus is on categorizing the seismic data of local regions according to the events' location using clustering algorithms for classification and then using intelligent artificial neural network for cluster prediction. As a result, the target data were clustered to six groups and proposed model with 10 fold cross validation yielded accuracy of 98.3%. Also, as a case study, the tectonic stress on concentration zones of Tabriz fault has been identified and five features of the events were used. Finally, the most important points have been proposed for evaluation of the nonlinear model predictions as future directions.

scholarly journals Sentimental classification analysis of polarity multi-view textual data using data mining techniques

2020 ◽  
Vol 10 (5) ◽  
pp. 5526
Author(s):  
Ali Hameed Yassir ◽  
Ali A. Mohammed ◽  
Adel Abdul-Jabbar Alkhazraji ◽  
Mustafa Emad Hameed ◽  
Mohammed Saad Talib ◽  
...  
Keyword(s):  
Data Mining ◽  
Unstructured Data ◽  
Analytical Models ◽  
Integrated Analysis ◽  
Data Resource ◽  
Data Mining Algorithms ◽  
Data Formats ◽  
Textual Data ◽  
Community Environments ◽  
Mining Algorithms

The data and information available in most community environments is complex in nature. Sentimental data resources may possibly consist of textual data collected from multiple information sources with different representations and usually handled by different analytical models. These types of data resource characteristics can form multi-view polarity textual data. However, knowledge creation from this type of sentimental textual data requires considerable analytical efforts and capabilities. In particular, data mining practices can provide exceptional results in handling textual data formats. Besides, in the case of the textual data exists as multi-view or unstructured data formats, the hybrid and integrated analysis efforts of text data mining algorithms are vital to get helpful results. The objective of this research is to enhance the knowledge discovery from sentimental multi-view textual data which can be considered as unstructured data format to classify the polarity information documents in the form of two different categories or types of useful information. A proposed framework with integrated data mining algorithms has been discussed in this paper, which is achieved through the application of X-means algorithm for clustering and HotSpot algorithm of association rules. The analysis results have shown improved accuracies of classifying the sentimental multi-view textual data into two categories through the application of the proposed framework on online polarity user-reviews dataset upon a given topics.

Data Mining and Privacy

2011 ◽  
pp. 388-393
Author(s):  
Esma Aïmeur
Keyword(s):  
Data Mining ◽  
Data Privacy ◽  
Reconstruction Algorithm ◽  
Learning Task ◽  
Privacy Preserving ◽  
Sources Of Information ◽  
Privacy Preserving Data Mining ◽  
Useful Knowledge ◽  
Data Mining Algorithms ◽  
Mining Algorithms

With the emergence of Internet, it is now possible to connect and access sources of information and databases throughout the world. At the same time, this raises many questions regarding the privacy and the security of the data, in particular how to mine useful information while preserving the privacy of sensible and confidential data. Privacy-preserving data mining is a relatively new but rapidly growing field that studies how data mining algorithms affect the privacy of data and tries to find and analyze new algorithms that preserve this privacy. At first glance, it may seem that data mining and privacy have orthogonal goals, the first one being concerned with the discovery of useful knowledge from data whereas the second is concerned with the protection of data’s privacy. Historically, the interactions between privacy and data mining have been questioned and studied since more than a decade ago, but the name of the domain itself was coined more recently by two seminal papers attacking the subject from two very different perspectives (Agrawal & Srikant, 2000; Lindell & Pinkas, 2000). The first paper (Agrawal & Srikant, 2000) takes the approach of randomizing the data through the injection of noise, and then recovers from it by applying a reconstruction algorithm before a learning task (the induction of a decision tree) is carried out on the reconstructed dataset. The second paper (Lindell & Pinkas, 2000) adopts a cryptographic view of the problem and rephrases it within the general framework of secure multiparty computation. The outline of this chapter is the following. First, the area of privacy-preserving data mining is illustrated through three scenarios, before a classification of privacy- preserving algorithms is described and the three main approaches currently used are detailed. Finally, the future trends and challenges that await the domain are discussed before concluding.

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