RETRACTED ARTICLE: Research on semi supervised K-means clustering algorithm in data mining

BackgroundSerial Analysis of Gene Expression (SAGE) is a DNA sequencing-based method for large-scale gene expression profiling that provides an alternative to microarray analysis. Most analyses of SAGE data aimed at identifying co-expressed genes have been accomplished using various versions of clustering approaches that often result in a number of false positives.Principal FindingsHere we explore the use of seriation, a statistical approach for ordering sets of objects based on their similarity, for large-scale expression pattern discovery in SAGE data. For this specific task we implement a seriation heuristic we term ‘progressive construction of contigs’ that constructs local chains of related elements by sequentially rearranging margins of the correlation matrix. We apply the heuristic to the analysis of simulated and experimental SAGE data and compare our results to those obtained with a clustering algorithm developed specifically for SAGE data. We show using simulations that the performance of seriation compares favorably to that of the clustering algorithm on noisy SAGE data.ConclusionsWe explore the use of a seriation approach for visualization-based pattern discovery in SAGE data. Using both simulations and experimental data, we demonstrate that seriation is able to identify groups of co-expressed genes more accurately than a clustering algorithm developed specifically for SAGE data. Our results suggest that seriation is a useful method for the analysis of gene expression data whose applicability should be further pursued.

PurposeThe K-means (KM) clustering algorithm is extremely responsive to the selection of initial centroids since the initial centroid of clusters determines computational effectiveness, efficiency and local optima issues. Numerous initialization strategies are to overcome these problems through the random and deterministic selection of initial centroids. The random initialization strategy suffers from local optimization issues with the worst clustering performance, while the deterministic initialization strategy achieves high computational cost. Big data clustering aims to reduce computation costs and improve cluster efficiency. The objective of this study is to achieve a better initial centroid for big data clustering on business management data without using random and deterministic initialization that avoids local optima and improves clustering efficiency with effectiveness in terms of cluster quality, computation cost, data comparisons and iterations on a single machine.Design/methodology/approachThis study presents the Normal Distribution Probability Density (NDPD) algorithm for big data clustering on a single machine to solve business management-related clustering issues. The NDPDKM algorithm resolves the KM clustering problem by probability density of each data point. The NDPDKM algorithm first identifies the most probable density data points by using the mean and standard deviation of the datasets through normal probability density. Thereafter, the NDPDKM determines K initial centroid by using sorting and linear systematic sampling heuristics.FindingsThe performance of the proposed algorithm is compared with KM, KM++, Var-Part, Murat-KM, Mean-KM and Sort-KM algorithms through Davies Bouldin score, Silhouette coefficient, SD Validity, S_Dbw Validity, Number of Iterations and CPU time validation indices on eight real business datasets. The experimental evaluation demonstrates that the NDPDKM algorithm reduces iterations, local optima, computing costs, and improves cluster performance, effectiveness, efficiency with stable convergence as compared to other algorithms. The NDPDKM algorithm minimizes the average computing time up to 34.83%, 90.28%, 71.83%, 92.67%, 69.53% and 76.03%, and reduces the average iterations up to 40.32%, 44.06%, 32.02%, 62.78%, 19.07% and 36.74% with reference to KM, KM++, Var-Part, Murat-KM, Mean-KM and Sort-KM algorithms.Originality/valueThe KM algorithm is the most widely used partitional clustering approach in data mining techniques that extract hidden knowledge, patterns and trends for decision-making strategies in business data. Business analytics is one of the applications of big data clustering where KM clustering is useful for the various subcategories of business analytics such as customer segmentation analysis, employee salary and performance analysis, document searching, delivery optimization, discount and offer analysis, chaplain management, manufacturing analysis, productivity analysis, specialized employee and investor searching and other decision-making strategies in business.

Multi-objective local search (MOLS) algorithms are efficient meta-heuristics, which improve a set of solutions by using their neighbourhood to iteratively find better and better solutions. MOLS algorithms are versatile algorithms with many available strategies, first to select the solutions to explore, then to explore them, and finally to update the archive using some of the visited neighbours. In this paper, we propose a new generalisation of MOLS algorithms incorporating new recent ideas and algorithms. To be able to instantiate the many MOLS algorithms of the literature, our generalisation exposes numerous numerical and categorical parameters, raising the possibility of being automatically designed by an automatic algorithm configuration (AAC) mechanism. We investigate the worth of such an automatic design of MOLS algorithms using MO-ParamlLS, a multi-objective AAC configurator, on the permutation flowshop scheduling problem, and demonstrate its worth against a traditional manual design.

ABSTRACTThe K-means clustering method is a widely adopted clustering algorithm in data mining and pattern recognition, where the partitions are made by minimizing the total within group sum of squares based on a given set of variables. Weighted K-means clustering is an extension of the K-means method by assigning nonnegative weights to the set of variables. In this paper, we aim to obtain more meaningful and interpretable clusters by deriving the optimal variable weights for weighted K-means clustering. Specifically, we improve the weighted k-means clustering method by introducing a new algorithm to obtain the globally optimal variable weights based on the Karush-Kuhn-Tucker conditions. We present the mathematical formulation for the clustering problem, derive the structural properties of the optimal weights, and implement an recursive algorithm to calculate the optimal weights. Numerical examples on simulated and real data indicate that our method is superior in both clustering accuracy and computational efficiency.

Clustering of gene expression data is a standard exploratory technique used to identify closely related genes. Many other sources of data are also likely to be of great assistance in the analysis of gene expression data. This data provides a mean to begin elucidating the large-scale modular organization of the cell. The authors consider the challenging task of developing exploratory analytical techniques to deal with multiple complete and incomplete information sources. The Multi-Source Clustering (MSC) algorithm developed performs clustering with multiple, but complete, sources of data. To deal with incomplete data sources, the authors adopted the MPCK-means clustering algorithms to perform exploratory analysis on one complete source and other potentially incomplete sources provided in the form of constraints. This paper presents a new clustering algorithm MSC to perform exploratory analysis using two or more diverse but complete data sources, studies the effectiveness of constraints sets and robustness of the constrained clustering algorithm using multiple sources of incomplete biological data, and incorporates such incomplete data into constrained clustering algorithm in form of constraints sets.

Abstract: The service dramatically affects the number of guests staying at the hotel. Bali is the most visited tourist area by foreign tourists. Therefore, improved service is crucial for determining the rating level of a hotel. This research aims to combine two data mining algorithms: clustering and classification. This research is expected to contribute to hospitality in improving the best services for tourists, especially in the City of Bali. Clustering algorithms are used to group the best number of hotels based on the four clusters selected from the k-means clustering algorithm. The classification algorithm using C4.5 determines the factors most dominant in determining the hotel rating level based on the gain ratio. The data used in this study results from observations on the website agoda.com in Bali of 51 data. The results of this study explained that cluster_0 is the highest-rated cluster, with a total number of 19 hotels found in claster_0. Data cluster0 is used for classification analysis using a decision tree, and the most dominant factor is the service factor, with an accuracy of 80%. Keywords: data mining; kmeans; decision tree; hotel; bali; Abstrak: Pelayanan sangat mempengaruhi jumlah pengunjung yang menginap dihotel. Bali merupakan daerah wisata paling banyak dikunjungi oleh wisatawan mancanegara. Oleh karena itu, peningkatan pelayanan sangat penting untuk penentuan level rating dari hotel. Tujuan dari penelitian ini untuk menggabungkan dua algoritma data mining yaitu clustering dan klasifikasi. Dengan penelitian ini diharapkan dapat memberikan kontribusi bagi perhotelan dalam meningkatkan pelayanan yang terbaik bagi wisatawan khususnya di Kota Bali. Algoritma Clustering digunakan untuk mengelompokkan dari jumlah hotel yang terbaik berdasarkan empat cluster yang dipilih dari algoritma clustering berupa k-means. Algoritma klasifikasi menggunakan C4.5 digunakan untuk mengetahui faktor apa yang paling dominan dalam menentukan level rating hotel berdasarkan gain ratio. Data yang digunakan dalam penelitian ini hasil observasi di website agoda.com di bali sebanyak 51 data. Hasil dari penelitian ini menjelaskan dataset cluster_0 merupakan cluster rating tertinggi dengan jumlah 19 hotel yang terdapat di cluster_0. Data cluster_0 digunakan untuk analisis klasifikasi menggunakan decesion tree, didapat faktor yang paling dominan adalah faktor layanan dengan nilai akurasi sebesar 80%. Kata kunci: data mining; kmeans; decision tree; hotel; bali;

Many clustering algorithms have been proposed for the analysis of gene expression data, but little guidance is available to help choose among them. We provide a systematic framework for assessing the results of clustering algorithms. Clustering algorithms attempt to partition the genes into groups exhibiting similar patterns of variation in expression level. Our methodology is to apply a clustering algorithm to the data from all but one experimental condition. The remaining condition is used to assess the predictive power of the resulting clusters-meaningful clusters should exhibit less variation in the remaining condition than clusters formed by chance. We successfully applied our methodology to compare six clustering algorithms on four gene expression data sets. We found our quantitative measures of cluster quality to be positively correlated with external standards of cluster quality.

There is a growing need for a method to analyze massive gene expression data obtained from DNA microarrays. We introduce a method of combining a self-organizing map (SOM) and a k-means clustering for analyzing and categorizing the gene expression data. The SOM is an unsupervised neural network learning algorithm and forms a mapping the high-dimensional data to two-dimensional space. However, it is difficult to find clustering boundaries from results of the SOM. On the other hand, the k-means clustering can partition the data into the clusters under the assumption of the known number of clusters. In order to understand easily the results of SOM, we apply the k-means clustering to finding the clustering boundaries from results of SOM. We have applied the proposed method to the published data of yeast gene expression and show that the method is effective for categorizing the data.

Objectives: Clustering algorithm is broadly used as spectral algorithm in social media, where a reference of contact is used and mined further for various combinations of suggested friends and lookups. This paper Identifies key lead generation techniques to be used in customer relationship management for sales marketing to decide data gathering. Also to define key merits and demerits of these techniques and to prepare a Matrix of comparison of these techniques to justify the data source and data set. M-Cluster algorithm is used for lead qualification i.e. training set preparation and data evaluation. Methods: Todefine a training set based on various attributes/fields in the data given for classification. This training set is used to run the data process and to produce expected result. This is assessed and accepted for definite data set processing or additional run for interim training data set preparation. Findings: This study is taken to customize clustering algorithm for data mining process in a customer relationship management field as the space of data is more and variant. Also proving the usability of customized clustering algorithm in data mining and the efficiency in processing mechanism compared to other methods used in current situation of data mining in customer relationship management is the part of this study. The customized algorithm developed as part of this study considers the two major areas of data mining using clusters. Applications: The results produced tremendous trends that the clustered algorithm suits to any data mining process when scaling and data classification are diversified and less in control.Keywords: Classification, Clustering Algorithm, Data Mining, K-Means, Lead Generation, M-Clustering Algorithm

The k-means clustering algorithm is a very classical clustering algorithm that is widely used because of its excellent efficiency and performance. The algorithm uses Euclidean distance to calculate the similarity between samples and iteratively updates the membership matrix to obtain clustering results. However, when k-means algorithm clusters datasets containing samples with intra-cluster distances greater than inter-cluster distances, errors often occur when partitioning the boundary samples, which eventually leads to unsatisfactory results. Moreover, although k-means algorithm makes the intra-cluster distance as small as possible, it neglects to maximize the inter-cluster distance, and eventually only finds the local optimal solution. Different from the existing k-means type algorithm, this paper proposes a similarity measure based on the impact factor, which determines the partitioning result by comparing the impact of samples on each cluster. And on the basis of the objective function of k-means algorithm, we combine the inter-cluster distance to solve the defects of local optimality that exist in k-means algorithm. In the paper, we theoretically analyze and prove the proposed method, and compare and analyze the clustering results of the algorithm with the class k-means algorithm on real datasets, and confirm that the proposed algorithm in this paper can effectively avoid the defects of the class k-means algorithm.

Cancer gene search with data-mining and genetic algorithms

Air quality is one of the most popular environmental problems in this globalization era. Air pollution is the poisonous air that comes from car emissions, smog, open burning, chemicals from factories and other particles and gases. This harmful air can give adverse effects to human health and the environment. In order to provide information which areas are better for the residents in Malaysia, cluster analysis is used to determine the areas that can be clustering together based on their a ir quality through several air quality substances. Monthly data from 37 monitoring stations in Peninsular Malaysia from the year 2013 to 2015 were used in this study. K - Means (KM) clustering algorithm, Expectation Maximization (EM) clustering algorithm and Density Based (DB) clustering algorithm have been chosen as the techniques to analyze the cluster analysis by utilizing the Waikato Environment for Knowledge Analysis (WEKA) tools. Results show that K - means clustering algorithm is the best method among ot her algorithms due to its simplicity and time taken to build the model. The output of K - means clustering algorithm shows that it can cluster the area into two clusters, namely as cluster 0 and cluster 1. Clusters 0 consist of 16 monitoring stations and clu ster 1 consists of 36 monitoring stations in Peninsular Malaysia.

Medical datasets hold huge number of records about the patients, the doctors and the diseases. The extraction of useful information which will provide knowledge in decision making process for the diagnosis and treatment of the diseases are becoming increasingly determinant. Knowledge Discovery and data mining make use of Artificial Intelligence (AI) algorithms which are applied to discover hidden patterns and relations in complex datasets using intelligent agents. The existing data mining algorithms and techniques are designed to solve the individual problems, such as classification or clustering. Up till now, no unifying theory is developed.Among the different algorithms in data mining for prediction, classification, interpretation and visualization, ‘k-means clustering’, ‘Decision Trees (C4.5)’, ‘Neural Network (NNs)’ and ‘Data Visualization (2D or 3D scattered graphs)’ algorithms are frequently utilized in data mining tools. The choice of the algorithm depends on the intended use of extracted knowledge.In this paper, the mentioned algorithms are unified into a tool, called Unified Medical Data Miner (UMDM) that will enable prediction, classification, interpretation and visualization on a diabetes dataset.KeywordsMedicineClusteringClassification & PredictionVisualizationAgent Data miningUnified Medical Data Miner

Background - In the NeoTRIPaPDL1 phase III trial, triple-negative breast cancer (TNBC) patients were randomized to receive nab-paclitaxel/carboplatin for 8 cycles (CT arm) with or without atezolizumab (CT/A arm). We previously reported that the majority of patients (65%) with PD-L1- at baseline converted to PD-L1+ (the majority with IC2/IC3) after the first cycle of treatment in the atezolizumab arm. Here we studied treatment associated changes in the molecular tumour features and immune microenvironment by PD-L1 expression. Methods – A total of 158 (56.4%) of patients enrolled in the NeoTRIPaPDL1 trial (76 and 82 from CT/A and CT arm, respectively) were included in this analysis by satisfying the following criteria: i) availability of a paired core biopsy at baseline and at day 1 of the second treatment cycle (D1C2); ii) evaluation of stromal TILs (sTILs) and staining for PD-L1 (Ventana SP142); iii) successful RNA-seq gene expression profiling. PD-L1 groups were defined as IC0/IC1 (<5% PD-L1low) vs IC2/IC3 (>=5% PD-L1high). Presence of different immune cell populations was quantified by gene expression profile deconvolution using ConsensusTME R package. Cancer hallmark gene set collection and custom signature activation status were estimated in each sample using singscore R package. Differences in score distribution were evaluated by 2-sided t-test. Results At baseline, both sTILs and immune cell signatures were upregulated in PD-L1high compared to PD-L1low tumours (p<0.001). No significant differences were found between the two treatment arms in the PD-L1high subpopulation. In the PD-L1low cases, both sTILs and immune related signatures were slightly downregulated in the CT/A arm (p<0.05), suggesting a modest unbalance among treatment arms with CT arm being slightly more inflamed than CT/A arm.At D1C2, PD-L1high tumours in the CT arm systematically had high sTILs (median=70%, range=30-90%), while PD-L1low tumours receiving CT/A had low sTILs in a significant proportion of cases (median=30%, range=0-90%; p<0.001). Similarly, at D1C2 several gene expression-estimated immune cell populations and immune-related signatures were upregulated in the CT arm compared to CT/A arm in PD-L1high tumours, with the weakest association observed for M2 macrophages (p=0.058). No tumour-related signatures were differentially expressed among the two treatment arms within groups with PD-L1high, suggesting that different treatment. modulate PD-L1 by engaging a different immune mileau instead of modulating tumor related features.Considering PD-L1low groups at D1C2, in the CT arm 21 tumors had >30% sTILs (n=21/69, 30.4%), while in the CT/A arm only 2 had sTILs >30% (2/27, 7.4%) (p<0.001). Analysis of gene expression data identified IFN-related signatures as the most upregulated in the CT compared to CT/A arm in PD-L1low cases at D1C2 (p<0.05). Conclusions Integrated dynamic analysis of PD-L1 expression and gene expression data highlighted significant treatment-specific changes of the immune landscape according to PD-L1 expression, when this biomarker is assessed during treatment. This indicates that the immune milieu associated with PD-L1 status is strongly dependent on the time of assessment in relationship to treatment received. Such observation may explain why in the NeoTRIP trial, baseline PD-L1 but not on-treatment PD-L1 was predictive of pCR in CT/A arm. In addition, our findings could have implications related to the use of PD-L1 as a predictive biomarker in pre-treated patients, especially when assessed early on during treatment. Citation Format: Maurizio Callari, Chiun-Sheng Huang, Daniel Egle, Begoña Bermejo, Claudio Zamagni, Matteo Dugo, Marc Thill, Antonio Anton, Marco Barreca, Stefania Russo, Eva Maria Ciruelos, Richard Greil, Stefania Zambelli, Balázs Gyorffy, Chanel Smart, Olivia Biasi, Pinuccia Valagussa, Giuseppe Viale, Luca Gianni, Giampaolo Bianchini. Immune milieu associated with PD-L1 status in TNBC is dependent on time of biomarker assessment and treatment received: A secondary analysis of the NeoTRIPaPDL1 trial [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-04-02.

Recent advances in computing, communications, digital storage technologies, and high-throughput data-acquisition technologies, make it possible to gather and store incredible volumes of data. It creates unprecedented opportunities for large-scale knowledge discovery from huge database. Data mining (DM) technology has emerged as a means of performing this discovery. There are countless researchers working on designing efficient data mining techniques, methods, and algorithms. Many data mining methods and algorithms have been developed and applied in a lot of application fields [1]. Unfortunately, most data mining researchers pay much attention to technique problems for developing data mining models and methods, while little to basic issues of data mining [2]. In this talk, some basic issues of data mining are addressed. What is data mining? What is the product of a data mining process? What are we doing in a data mining process? What is the rule we should obey in a data mining process? Through analyzing existing data mining methods, and domain-driven (or user-driven) data mining models [3-5], we find that we should take a data mining process as a process of knowledge transformation. Based on this understanding of data mining, a conceptual data mining model of domain-oriented data-driven data mining (3DM) is proposed [2]. The relationship between traditional domain-driven (or user-driven) data mining models and our proposed 3DM model is also analyzed. Some domain-oriented data-driven data mining algorithms for mining such knowledge as default rule [6], decision tree [7], and concept lattice [8] from database are proposed. The experiment results for these algorithms are also shown to illustrate the efficiency and performance of the knowledge acquired by our 3DM data mining algorithms.