联合聚类非线性相关的时序基因表达数据

为聚类非线性相关的数据对象,引入广义信息论中二次互信息作为相似性度量,利用矩阵理论降低了二次互信息的计算量,并结合滑动窗口技术,建立了一种时序数据非线性相关模型.在此基础上提出了适用于时序基因表达数据的确定性联合聚类算法MI-TSB.该算法将时序数据转化为抽象字符序列,然后插入到MI-泛化后缀树中,避免了穷举各种组合,从而快速索引全部聚类结果.实验结果显示MI-TSB算法具有良好的运行性能,成功聚类出非线性相关的对象;利用Gene Ontology对聚类结果进行基因注释,也验证了聚类结果的生物学意义.     

融合自动权重学习的深度子空间聚类

子空间聚类算法是一种面向高维数据的聚类方法,具有独特的数据自表示方式和较高的聚类精度。传统子空间聚类算法聚焦于对输入数据构建最优相似图再进行分割,导致聚类效果高度依赖于相似图学习。自适应近邻聚类（CAN）算法改进了相似图学习过程,根据数据间的距离自适应地分配最优邻居以构建相似图和聚类结构。然而,现有CAN算法在进行高维数据非线性聚类时,难以很好地捕获局部数据结构,从而导致聚类准确性及算法泛化能力有限。提出一种融合自动权重学习与结构化信息的深度子空间聚类算法。通过自编码器将数据映射到非线性潜在空间并降维,自适应地赋予潜在特征不同的权重从而处理噪声特征,最小化自编码器的重构误差以保留数据的局部结构信息。通过CAN方法学习相似图,在潜在表示下迭代地增强各特征间的相关性,从而保留数据的全局结构信息。实验结果表明,在ORL、COIL-20、UMIST数据集上该算法的准确率分别达到0.780 1、0.874 3、0.742 1,聚类性能优于LRR、LRSC、SSC、KSSC等算法。     

A probabilistic relaxation labeling framework for reducing the noise effect in geometric biclustering of gene expression data

Biclustering is an important method in DNA microarray analysis which can be applied when only a subset of genes is co-expressed in a subset of conditions. Unlike standard clustering analyses, biclustering methodology can perform simultaneous classification on two dimensions of genes and conditions in a microarray data matrix. However, the performance of biclustering algorithms is affected by the inherent noise in data, types of biclusters and computational complexity. In this paper, we present a geometric biclustering method based on the Hough transform and the relaxation labeling technique. Unlike many existing biclustering algorithms, we first consider the biclustering patterns through geometric interpretation. Such a perspective makes it possible to unify the formulation of different types of biclusters as hyperplanes in spatial space and facilitates the use of a generic plane finding algorithm for bicluster detection. In our algorithm, the Hough transform is employed for hyperplane detection in sub-spaces to reduce the computational complexity. Then sub-biclusters are combined into larger ones under the probabilistic relaxation labeling framework. Our simulation studies demonstrate the robustness of the algorithm against noise and outliers. In addition, our method is able to extract biologically meaningful biclusters from real microarray gene expression data.     

基于自编码器的深度聚类算法综述

聚类分析作为一种常见的分析方法,广泛应用于各种场景。随着机器学习技术的发展,深度聚类算法也成了当下研究的热点,基于自编码器的深度聚类算法是其中的代表算法。为了及时了解掌握基于自编码器的深度聚类算法的发展,介绍了四种自编码器的模型,对近些年代表性的算法依照自编码器的结构进行了分类。在MNIST、USPS、Fashion-MNIST数据集上,针对传统聚类算法和基于自编码器的深度聚类算法进行了实验对比、分析,最后对基于自编码器的深度聚类算法目前存在的问题进行了总结,展望了深度聚类算法的研究方向。     

一种深度自监督聚类集成算法

针对聚类集成中一致性函数设计问题,本文提出一种深度自监督聚类集成算法。该算法首先根据基聚类划分结果采用加权连通三元组算法计算样本之间的相似度矩阵,基于相似度矩阵表达邻接关系,将基聚类由特征空间中的数据表示变换至图数据表示;在此基础上,基聚类的一致性集成问题被转化为对基聚类图数据表示的图聚类问题。为此,本文利用图神经网络构造自监督聚类集成模型,一方面采用图自动编码器学习图的低维嵌入,依据低维嵌入似然分布估计聚类集成的目标分布;另一方面利用聚类集成目标对低维嵌入过程进行指导,确保模型获得的图低维嵌入与聚类集成结果是一致最优的。在大量数据集上进行了仿真实验,结果表明本文算法相比HGPA、CSPA和MCLA等算法可以进一步提高聚类集成结果的准确性。     

基因表达数据的聚类分析研究进展

基因表达数据的爆炸性增长迫切需求自动、有效的数据分析工具. 目前聚类分析已成为分析基因表达数据获取生物学信息的有力工具. 为了更好地挖掘基因表达数据, 近年来提出了许多改进的传统聚类算法和新聚类算法. 本文首先简单介绍了基因表达数据的获取和表示, 之后系统地介绍了近年来应用在基因表达数据分析中的聚类算法. 根据聚类目标的不同将算法分为基于基因的聚类、基于样本的聚类和两路聚类, 并对每类算法介绍了其生物学的含义及其难点, 详细讨论了各种算法的基本原理及优缺点. 最后总结了当前的基因表达数据的聚类分析方法,并对发展趋势作了进一步的展望.     

基于概率无向图模型的近邻传播聚类算法

针对近邻传播聚类算法偏向参数难选定、生成的簇数目偏多等问题,提出一种概率无向图模型的近邻传播聚类算法.首先为样本数据构建概率无向图模型,利用极大团和势函数计算无向图中数据样本的概率密度,将此概率密度作为一种聚类先验知识注入近邻传播算法的偏向参数中,提高算法的聚类效率;并用高斯降噪和簇归并方法进一步提升算法的聚类精度.在UCI数据集上的实验结果表明,所提出算法的聚类效率和精度均优于相比较的同类算法.     

面向混合属性数据集的双重聚类方法

面对复杂信息环境下的数据预处理需求,提出了一种可以处理混合属性数据集的双重聚类方法。这种双重聚类方法由双重近邻无向图的构造算法或其改进算法,基于分离集合并的双重近邻图聚类算法、基于宽度优先搜索的双重近邻图聚类算法、或基于深度优先搜索的双重近邻图聚类算法来实现。通过人工数据集和UCI标准数据集的仿真实验,可以验证,尽管这三个聚类算法所采用的搜索策略不同,但最终的结果是一致的。仿真实验结果还表明,对于一些具有明显聚类分布结构且无近邻噪声干扰的数据集,该方法经常能取得比K-means算法和AP算法更好的聚类精度,从而说明这种双重聚类方法具有一定的有效性。为进一步推广并在实际中发掘出该方法的应用价值,最后给出了一点较有价值的研究展望。     

关键语义信息补足的深度文本聚类算法

针对大多数现有的深度文本聚类方法在特征映射过程中过于依赖原始数据质量以及关键语义信息丢失的问题,提出了一种基于关键语义信息补足的深度文本聚类算法(DCKSC)。该算法首先通过提取关键词数据对原始文本数据进行数据增强;其次,设计了一个关键语义信息补足模块对传统的自动编码器进行改进,补足映射过程中丢失的关键语义信息;最后,通过综合聚类损失与关键词语义自动编码器的重构损失学习适合于聚类的表示特征。实验证明,提出算法在五个现实数据集上的聚类效果均优于当前先进的聚类方法。聚类结果证明了关键语义信息补足方法和文本数据增强方法对深度文本聚类的重要性。     

Experimental correlation analysis of bicluster coherence measures and gene ontology information

Biclustering algorithms have become popular tools for gene expression data analysis. They can identify local patterns defined by subsets of genes and subsets of samples, which cannot be detected by traditional clustering algorithms. In spite of being useful, biclustering is an NP-hard problem. Therefore, the majority of biclustering algorithms look for biclusters optimizing a pre-established coherence measure. Many heuristics and validation measures have been proposed for biclustering over the last 20 years. However, there is a lack of an extensive comparison of bicluster coherence measures on practical scenarios. To deal with this lack, this paper experimentally analyzes 17 bicluster coherence measures and external measures calculated from information obtained in the gene ontologies. In this analysis, results were produced by 10 algorithms from the literature in 19 gene expression datasets. According to the experimental results, a few pairs of strongly correlated coherence measures could be identified, which suggests redundancy. Moreover, the pairs of strongly correlated measures might change when dealing with normalized or non-normalized data and biclusters enriched by different ontologies. Finally, there was no clear relation between coherence measures and assessment using information from gene ontology.     

Clustering based on a near neighbor graph and a grid cell graph

This paper presents two novel graph-clustering algorithms, Clustering based on a Near Neighbor Graph (CNNG) and Clustering based on a Grid Cell Graph (CGCG). CNNG algorithm inspired by the idea of near neighbors is an improved graph-clustering method based on Minimum Spanning Tree (MST). In order to analyze massive data sets more efficiently, CGCG algorithm, which is a kind of graph-clustering method based on MST on the level of grid cells, is presented. To clearly describe the two algorithms, we give some important concepts, such as near neighbor point set, near neighbor undirected graph, grid cell, and so on. To effectively implement the two algorithms, we use some efficient partitioning and index methods, such as multidimensional grid partition method, multidimensional index tree, and so on. From simulation experiments of some artificial data sets and seven real data sets, we observe that the time cost of CNNG algorithm can be decreased by using some improving techniques and approximate methods while attaining an acceptable clustering quality, and CGCG algorithm can approximately analyze some dense data sets with linear time cost. Moreover, comparing some classical clustering algorithms, CNNG algorithm can often get better clustering quality or quicker clustering speed.     

Extensions to the k-Means Algorithm for Clustering Large Data Sets with Categorical Values

The k-means algorithm is well known for its efficiency in clustering large data sets. However, working only on numeric values prohibits it from being used to cluster real world data containing categorical values. In this paper we present two algorithms which extend the k-means algorithm to categorical domains and domains with mixed numeric and categorical values. The k-modes algorithm uses a simple matching dissimilarity measure to deal with categorical objects, replaces the means of clusters with modes, and uses a frequency-based method to update modes in the clustering process to minimise the clustering cost function. With these extensions the k-modes algorithm enables the clustering of categorical data in a fashion similar to k-means. The k-prototypes algorithm, through the definition of a combined dissimilarity measure, further integrates the k-means and k-modes algorithms to allow for clustering objects described by mixed numeric and categorical attributes. We use the well known soybean disease and credit approval data sets to demonstrate the clustering performance of the two algorithms. Our experiments on two real world data sets with half a million objects each show that the two algorithms are efficient when clustering large data sets, which is critical to data mining applications.     

复杂高维数据的密度峰值快速搜索聚类算法

机器学习的无监督聚类算法已被广泛应用于各种目标识别任务。基于密度峰值的快速搜索聚类算法(DPC)能快速有效地确定聚类中心点和类个数,但在处理复杂分布形状的数据和高维图像数据时仍存在聚类中心点不容易确定、类数偏少等问题。为了提高其处理复杂高维数据的鲁棒性,文中提出了一种基于学习特征表示的密度峰值快速搜索聚类算法(AE-MDPC)。该算法采用无监督的自动编码器(AutoEncoder)学出数据的最优特征表示,结合能刻画数据全局一致性的流形相似性,提高了同类数据间的紧致性和不同类数据间的分离性,促使潜在类中心点的密度值成为局部最大。在4个人工数据集和4个真实图像数据集上将AE-MDPC与经典的K-means,DBSCAN,DPC算法以及结合了PCA的DPC算法进行比较。实验结果表明,在外部评价指标聚类精度、内部评价指标调整互信息和调整兰德指数上,AE-MDPC的聚类性能优于对比算法,而且提供了更好的可视化性能。总之,基于特征表示学习且结合流形距离的AE-MDPC算法能有效地处理复杂流形数据和高维图像数据。     

基于逻辑运算的离散人工蜂群优化双聚类算法

基因表达数据是由DNA微阵列实验产生的大规模数据矩阵,双聚类算法是挖掘数据矩阵中具有较高相关性的子矩阵,能有效地提取生物学信息.针对当前多目标双聚类优化算法易于陷入早熟和局部最优解等问题,论文提出了基于逻辑运算的离散人工蜂群优化双聚类算法(LOABCB算法),一方面引入人工蜂群算法增强双聚类的全局寻优能力,另一方面通过...     

Biclustering of human cancer microarray data using co-similarity based co-clustering

Biclustering of gene expression data aims at finding localized patterns in a subspace. A bicluster (sometimes called a co-cluster), in the context of gene expression data, is a set of genes that exhibit similar expression intensity under a subset of experimental features (conditions). Most biclustering algorithms proposed in the literature aim at finding sub-matrices that exhibit some sort of coherence by selecting an initial sub-matrix and iteratively adding or subtracting rows and columns. These algorithms are generally dependent on the initial, hard selection of the gene and condition clusters respectively. In this work, we adapt a recently proposed approach for clustering textual data to find biclusters in gene expression data. Our proposed technique is based on the concept of co-similarity between genes (and between conditions) that exploits weighted higher order paths in a bipartite graph representation of the gene expression data. Therefore, we build statistical relations between genes and between conditions by comparing all genes and conditions before finally extracting biclusters from the data. We show that the proposed technique is able to find meaningful non-overlapping biclusters both on synthetically generated data as well as real cancer data. Our results indicate that the proposed technique is resistant to noise in the data and can successfully retrieve biclusters even in the presence of relatively large amount of noise. We also analyze our results with respect to the discovered genes and observe that our extracted biclusters are supported by biological evidences, such as enrichment of gene functions and biological processes.     

加权PageRank改进地标表示的自编码谱聚类算法

针对传统谱聚类算法在处理大规模数据集时,聚类精度低并且存在相似度矩阵存储开销大和拉普拉斯矩阵特征分解计算复杂度高的问题。提出了一种加权PageRank改进地标表示的自编码谱聚类算法,首先选取数据亲和图中权重最高的节点作为地标点,以选定的地标点与其他数据点之间的相似关系来逼近相似度矩阵作为叠加自动编码器的输入。然后利用聚类损失同时更新自动编码器和聚类中心的参数,从而实现可扩展和精确的聚类。实验表明,在几种典型的数据集上,所提算法与地标点谱聚类算法和深度谱聚类算法相比具有更好的聚类性能。     

Binary matrix factorization for analyzing gene expression data

The advent of microarray technology enables us to monitor an entire genome in a single chip using a systematic approach. Clustering, as a widely used data mining approach, has been used to discover phenotypes from the raw expression data. However traditional clustering algorithms have limitations since they can not identify the substructures of samples and features hidden behind the data. Different from clustering, biclustering is a new methodology for discovering genes that are highly related to a subset of samples. Several biclustering models/methods have been presented and used for tumor clinical diagnosis and pathological research. In this paper, we present a new biclustering model using Binary Matrix Factorization (BMF). BMF is a new variant rooted from non-negative matrix factorization (NMF). We begin by proving a new boundedness property of NMF. Two different algorithms to implement the model and their comparison are then presented. We show that the microarray data biclustering problem can be formulated as a BMF problem and can be solved effectively using our proposed algorithms. Unlike the greedy strategy-based algorithms, our proposed algorithms for BMF are more likely to find the global optima. Experimental results on synthetic and real datasets demonstrate the advantages of BMF over existing biclustering methods. Besides the attractive clustering performance, BMF can generate sparse results (i.e., the number of genes/features involved in each biclustering structure is very small related to the total number of genes/features) that are in accordance with the common practice in molecular biology.     

Fast online graph clustering via Erd?s-Rényi mixture

In the context of graph clustering, we consider the problem of simultaneously estimating both the partition of the graph nodes and the parameters of an underlying mixture of affiliation networks. In numerous applications the rapid increase of data size over time makes classical clustering algorithms too slow because of the high computational cost. In such situations online clustering algorithms are an efficient alternative to classical batch algorithms. We present an original online algorithm for graph clustering based on a Erd?s-Rényi graph mixture. The relevance of the algorithm is illustrated, using both simulated and real data sets. The real data set is a network extracted from the French political blogosphere and presents an interesting community organization.     

采用多样性选择的量子粒子群双向聚类算法

双向聚类已成为分析基因表达数据的一种重要工具,可以同时从基因和条件两个方向寻找具有相同表达波动的簇。但双向聚类是一种多目标优化的局部搜索算法,处理繁杂的基因数据时容易陷入局部最优。为提高算法的全局搜索能力,提出了一种多样性选择的量子粒子群双向聚类算法（Diversify-Optional QPSO,DOQPSO）。算法首先采用DOQPSO处理基因数据,然后用改进的FLOC算法进行贪心迭代寻找双向聚类,以求得更为理想的结果。算法通过实验仿真,并与FLOC算法和QPSO算法进行比较,结果证明DOQPSO双向聚类算法具有更好的全局寻优能力,且聚类效果更佳。