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Single Linkage Clustering
In statistics, single-linkage clustering is one of several methods of hierarchical clustering. It is based on grouping clusters in bottom-up fashion (agglomerative clustering), at each step combining two clusters that contain the closest pair of elements not yet belonging to the same cluster as each other. A drawback of this method is that it tends to produce long thin clusters in which nearby elements of the same cluster have small distances, but elements at opposite ends of a cluster may be much farther from each other than two elements of other clusters. This may lead to difficulties in defining classes that could usefully subdivide the data. Overview of agglomerative clustering methods In the beginning of the agglomerative clustering process, each element is in a cluster of its own. The clusters are then sequentially combined into larger clusters, until all elements end up being in the same cluster. At each step, the two clusters separated by the shortest distance are com ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistics
Statistics (from German: '' Statistik'', "description of a state, a country") is the discipline that concerns the collection, organization, analysis, interpretation, and presentation of data. In applying statistics to a scientific, industrial, or social problem, it is conventional to begin with a statistical population or a statistical model to be studied. Populations can be diverse groups of people or objects such as "all people living in a country" or "every atom composing a crystal". Statistics deals with every aspect of data, including the planning of data collection in terms of the design of surveys and experiments.Dodge, Y. (2006) ''The Oxford Dictionary of Statistical Terms'', Oxford University Press. When census data cannot be collected, statisticians collect data by developing specific experiment designs and survey samples. Representative sampling assures that inferences and conclusions can reasonably extend from the sample to the population as a whole. An ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Minimum Spanning Tree
A minimum spanning tree (MST) or minimum weight spanning tree is a subset of the edges of a connected, edge-weighted undirected graph that connects all the vertices together, without any cycles and with the minimum possible total edge weight. That is, it is a spanning tree whose sum of edge weights is as small as possible. More generally, any edge-weighted undirected graph (not necessarily connected) has a minimum spanning forest, which is a union of the minimum spanning trees for its connected components. There are many use cases for minimum spanning trees. One example is a telecommunications company trying to lay cable in a new neighborhood. If it is constrained to bury the cable only along certain paths (e.g. roads), then there would be a graph containing the points (e.g. houses) connected by those paths. Some of the paths might be more expensive, because they are longer, or require the cable to be buried deeper; these paths would be represented by edges with larger weights ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Clock
The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins. The benchmarks for determining the mutation rate are often fossil or archaeological dates. The molecular clock was first tested in 1962 on the hemoglobin protein variants of various animals, and is commonly used in molecular evolution to estimate times of speciation or radiation. It is sometimes called a gene clock or an evolutionary clock. Early discovery and genetic equidistance The notion of the existence of a so-called "molecular clock" was first attributed to Émile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin between different lineages changes roughly linearly with time, as estimated from fossil evi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cluster Analysis
Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense) to each other than to those in other groups (clusters). It is a main task of exploratory data analysis, and a common technique for statistical data analysis, used in many fields, including pattern recognition, image analysis, information retrieval, bioinformatics, data compression, computer graphics and machine learning. Cluster analysis itself is not one specific algorithm, but the general task to be solved. It can be achieved by various algorithms that differ significantly in their understanding of what constitutes a cluster and how to efficiently find them. Popular notions of clusters include groups with small distances between cluster members, dense areas of the data space, intervals or particular statistical distributions. Clustering can therefore be formulated as a multi-objective optimization problem. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Prim's Algorithm
In computer science, Prim's algorithm (also known as Jarník's algorithm) is a greedy algorithm that finds a minimum spanning tree for a weighted undirected graph. This means it finds a subset of the edges that forms a tree that includes every vertex, where the total weight of all the edges in the tree is minimized. The algorithm operates by building this tree one vertex at a time, from an arbitrary starting vertex, at each step adding the cheapest possible connection from the tree to another vertex. The algorithm was developed in 1930 by Czech mathematician Vojtěch Jarník and later rediscovered and republished by computer scientists Robert C. Prim in 1957 and Edsger W. Dijkstra in 1959. Therefore, it is also sometimes called the Jarník's algorithm, Prim–Jarník algorithm, Prim–Dijkstra algorithm. or the DJP algorithm.. Other well-known algorithms for this problem include Kruskal's algorithm and Borůvka's algorithm. These algorithms find the minimum spanning forest ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Complete-linkage Clustering
Complete-linkage clustering is one of several methods of agglomerative hierarchical clustering. At the beginning of the process, each element is in a cluster of its own. The clusters are then sequentially combined into larger clusters until all elements end up being in the same cluster. The method is also known as farthest neighbour clustering. The result of the clustering can be visualized as a dendrogram, which shows the sequence of cluster fusion and the distance at which each fusion took place. Clustering procedure At each step, the two clusters separated by the shortest distance are combined. The definition of 'shortest distance' is what differentiates between the different agglomerative clustering methods. In complete-linkage clustering, the link between two clusters contains all element pairs, and the distance between clusters equals the distance between those two elements (one in each cluster) that are farthest away from each other. The shortest of these links that r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UPGMA Dendrogram 5S Data
UPGMA (unweighted pair group method with arithmetic mean) is a simple agglomerative (bottom-up) hierarchical clustering method. The method is generally attributed to Sokal and Michener. The UPGMA method is similar to its ''weighted'' variant, the WPGMA method. Note that the unweighted term indicates that all distances contribute equally to each average that is computed and does not refer to the math by which it is achieved. Thus the simple averaging in WPGMA produces a weighted result and the proportional averaging in UPGMA produces an unweighted result ('' see the working example''). Algorithm The UPGMA algorithm constructs a rooted tree (dendrogram) that reflects the structure present in a pairwise similarity matrix (or a dissimilarity matrix). At each step, the nearest two clusters are combined into a higher-level cluster. The distance between any two clusters \mathcal and \mathcal, each of size (''i.e.'', cardinality) and , is taken to be the average of all distances d(x,y ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
WPGMA Dendrogram 5S Data
WPGMA (Weighted Pair Group Method with Arithmetic Mean) is a simple agglomerative (bottom-up) hierarchical clustering method, generally attributed to Sokal and Michener. The WPGMA method is similar to its ''unweighted'' variant, the UPGMA method. Algorithm The WPGMA algorithm constructs a rooted tree (dendrogram) that reflects the structure present in a pairwise distance matrix (or a similarity matrix). At each step, the nearest two clusters, say i and j, are combined into a higher-level cluster i \cup j. Then, its distance to another cluster k is simply the arithmetic mean of the average distances between members of k and i and k and j : d_ = \frac The WPGMA algorithm produces rooted dendrograms and requires a constant-rate assumption: it produces an ultrametric tree in which the distances from the root to every branch tip are equal. This ultrametricity assumption is called the molecular clock when the tips involve DNA, RNA and protein data. Working example This wo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Complete Linkage Dendrogram 5S Data
Complete may refer to: Logic * Completeness (logic) * Completeness of a theory, the property of a theory that every formula in the theory's language or its negation is provable Mathematics * The completeness of the real numbers, which implies that there are no "holes" in the real numbers * Complete metric space, a metric space in which every Cauchy sequence converges * Complete uniform space, a uniform space where every Cauchy net in converges (or equivalently every Cauchy filter converges) * Complete measure, a measure space where every subset of every null set is measurable * Completion (algebra), at an ideal * Completeness (cryptography) * Completeness (statistics), a statistic that does not allow an unbiased estimator of zero * Complete graph, an undirected graph in which every pair of vertices has exactly one edge connecting them * Complete category, a category ''C'' where every diagram from a small category to ''C'' has a limit; it is ''cocomplete'' if every such functor h ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Distance Matrix1
Distance is a numerical or occasionally qualitative measurement of how far apart objects or points are. In physics or everyday usage, distance may refer to a physical length or an estimation based on other criteria (e.g. "two counties over"). Since spatial cognition is a rich source of conceptual metaphors in human thought, the term is also frequently used metaphorically to mean a measurement of the amount of difference between two similar objects (such as statistical distance between probability distributions or edit distance between strings of text) or a degree of separation (as exemplified by distance between people in a social network). Most such notions of distance, both physical and metaphorical, are formalized in mathematics using the notion of a metric space. In the social sciences, distance can refer to a qualitative measurement of separation, such as social distance or psychological distance. Distances in physics and geometry The distance between physical l ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ward's Method
In statistics, Ward's method is a criterion applied in hierarchical cluster analysis. Ward's minimum variance method is a special case of the objective function approach originally presented by Joe H. Ward, Jr. Ward suggested a general agglomerative hierarchical clustering procedure, where the criterion for choosing the pair of clusters to merge at each step is based on the optimal value of an objective function. This objective function could be "any function that reflects the investigator's purpose." Many of the standard clustering procedures are contained in this very general class. To illustrate the procedure, Ward used the example where the objective function is the error sum of squares, and this example is known as ''Ward's method'' or more precisely ''Ward's minimum variance method''. The nearest-neighbor chain algorithm can be used to find the same clustering defined by Ward's method, in time proportional to the size of the input distance matrix and space linear in the num ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
WPGMA
WPGMA (Weighted Pair Group Method with Arithmetic Mean) is a simple agglomerative (bottom-up) hierarchical clustering method, generally attributed to Sokal and Michener. The WPGMA method is similar to its ''unweighted'' variant, the UPGMA method. Algorithm The WPGMA algorithm constructs a rooted tree (dendrogram) that reflects the structure present in a pairwise distance matrix (or a similarity matrix). At each step, the nearest two clusters, say i and j, are combined into a higher-level cluster i \cup j. Then, its distance to another cluster k is simply the arithmetic mean of the average distances between members of k and i and k and j : d_ = \frac The WPGMA algorithm produces rooted dendrograms and requires a constant-rate assumption: it produces an ultrametric tree in which the distances from the root to every branch tip are equal. This ultrametricity assumption is called the molecular clock when the tips involve DNA, RNA and protein data. Working example This wor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
