Cultural algorithms (CA) are a branch of evolutionary computation where there is a knowledge component that is called the belief space in addition to the population component. In this sense, cultural algorithms can be seen as an extension to a conventional genetic algorithm. Cultural algorithms were introduced by Reynolds (see references). == Belief space == The belief space of a cultural algorithm is divided into distinct categories. These categories represent different domains of knowledge that the population has of the search space. The belief space is updated after each iteration by the best individuals of the population. The best individuals can be selected using a fitness function that assesses the performance of each individual in population much like in genetic algorithms. === List of belief space categories === Normative knowledge A collection of desirable value ranges for the individuals in the population component e.g. acceptable behavior for the agents in population. Domain specific knowledge Information about the domain of the cultural algorithm problem is applied to. Situational knowledge Specific examples of important events - e.g. successful/unsuccessful solutions Temporal knowledge History of the search space - e.g. the temporal patterns of the search process Spatial knowledge Information about the topography of the search space == Population == The population component of the cultural algorithm is approximately the same as that of the genetic algorithm. == Communication protocol == Cultural algorithms require an interface between the population and belief space. The best individuals of the population can update the belief space via the update function. Also, the knowledge categories of the belief space can affect the population component via the influence function. The influence function can affect population by altering the genome or the actions of the individuals. == Pseudocode for cultural algorithms == Initialize population space (choose initial population) Initialize belief space (e.g. set domain specific knowledge and normative value-ranges) Repeat until termination condition is met Perform actions of the individuals in population space Evaluate each individual by using the fitness function Select the parents to reproduce a new generation of offspring Let the belief space alter the genome of the offspring by using the influence function Update the belief space by using the accept function (this is done by letting the best individuals to affect the belief space) == Applications == Various optimization problems Social simulation Real-parameter optimization
Randomized Hough transform
Hough transforms are techniques for object detection, a critical step in many implementations of computer vision, or data mining from images. Specifically, the Randomized Hough transform is a probabilistic variant to the classical Hough transform, and is commonly used to detect curves (straight line, circle, ellipse, etc.) The basic idea of Hough transform (HT) is to implement a voting procedure for all potential curves in the image, and at the termination of the algorithm, curves that do exist in the image will have relatively high voting scores. Randomized Hough transform (RHT) is different from HT in that it tries to avoid conducting the computationally expensive voting process for every nonzero pixel in the image by taking advantage of the geometric properties of analytical curves, and thus improve the time efficiency and reduce the storage requirement of the original algorithm. == Motivation == Although Hough transform (HT) has been widely used in curve detection, it has two major drawbacks: First, for each nonzero pixel in the image, the parameters for the existing curve and redundant ones are both accumulated during the voting procedure. Second, the accumulator array (or Hough space) is predefined in a heuristic way. The more accuracy needed, the higher parameter resolution should be defined. These two needs usually result in a large storage requirement and low speed for real applications. Therefore, RHT was brought up to tackle this problem. == Implementation == In comparison with HT, RHT takes advantage of the fact that some analytical curves can be fully determined by a certain number of points on the curve. For example, a straight line can be determined by two points, and an ellipse (or a circle) can be determined by three points. The case of ellipse detection can be used to illustrate the basic idea of RHT. The whole process generally consists of three steps: Fit ellipses with randomly selected points. Update the accumulator array and corresponding scores. Output the ellipses with scores higher than some predefined threshold. === Ellipse fitting === One general equation for defining ellipses is: a ( x − p ) 2 + 2 b ( x − p ) ( y − q ) + c ( y − q ) 2 = 1 {\displaystyle a(x-p)^{2}+2b(x-p)(y-q)+c(y-q)^{2}=1} with restriction: a c − b 2 > 0 {\displaystyle ac-b^{2}>0} However, an ellipse can be fully determined if one knows three points on it and the tangents in these points. RHT starts by randomly selecting three points on the ellipse. Let them be X 1 {\displaystyle X_{1}} , X 2 {\displaystyle X_{2}} and X 3 {\displaystyle X_{3}} . The first step is to find the tangents of these three points. They can be found by fitting a straight line using least squares technique for a small window of neighboring pixels. The next step is to find the intersection points of the tangent lines. This can be easily done by solving the line equations found in the previous step. Then let the intersection points be T 12 {\displaystyle T_{12}} and T 23 {\displaystyle T_{23}} , the midpoints of line segments X 1 X 2 {\displaystyle X_{1}X_{2}} and X 2 X 3 {\displaystyle X_{2}X_{3}} be M 12 {\displaystyle M_{12}} and M 23 {\displaystyle M_{23}} . Then the center of the ellipse will lie in the intersection of T 12 M 12 {\displaystyle T_{12}M_{12}} and T 23 M 23 {\displaystyle T_{23}M_{23}} . Again, the coordinates of the intersected point can be determined by solving line equations and the detailed process is skipped here for conciseness. Let the coordinates of ellipse center found in previous step be ( x 0 , y 0 ) {\displaystyle (x_{0},y_{0})} . Then the center can be translated to the origin with x ′ = x − x 0 {\displaystyle x'=x-x_{0}} and y ′ = y − y 0 {\displaystyle y'=y-y_{0}} so that the ellipse equation can be simplified to: a x ′ 2 + 2 b x ′ y ′ + c y ′ 2 = 1 {\displaystyle ax'^{2}+2bx'y'+cy'^{2}=1} Now we can solve for the rest of ellipse parameters: a {\displaystyle a} , b {\displaystyle b} and c {\displaystyle c} by substituting the coordinates of X 1 {\displaystyle X_{1}} , X 2 {\displaystyle X_{2}} and X 3 {\displaystyle X_{3}} into the equation above. === Accumulating === With the ellipse parameters determined from previous stage, the accumulator array can be updated correspondingly. Different from classical Hough transform, RHT does not keep "grid of buckets" as the accumulator array. Rather, it first calculates the similarities between the newly detected ellipse and the ones already stored in accumulator array. Different metrics can be used to calculate the similarity. As long as the similarity exceeds some predefined threshold, replace the one in the accumulator with the average of both ellipses and add 1 to its score. Otherwise, initialize this ellipse to an empty position in the accumulator and assign a score of 1. === Termination === Once the score of one candidate ellipse exceeds the threshold, it is determined as existing in the image (in other words, this ellipse is detected), and should be removed from the image and accumulator array so that the algorithm can detect other potential ellipses faster. The algorithm terminates when the number of iterations reaches a maximum limit or all the ellipses have been detected. Pseudo code for RHT: while (we find ellipses AND not reached the maximum epoch) { for (a fixed number of iterations) { Find a potential ellipse. if (the ellipse is similar to an ellipse in the accumulator) then Replace the one in the accumulator with the average of two ellipses and add 1 to the score; else Insert the ellipse into an empty position in the accumulator with a score of 1; } Select the ellipse with the best score and save it in a best ellipse table; Eliminate the pixels of the best ellipse from the image; Empty the accumulator; }
Sum of absolute differences
In digital image processing, the sum of absolute differences (SAD) is a measure of the similarity between image blocks. It is calculated by taking the absolute difference between each pixel in the original block and the corresponding pixel in the block being used for comparison. These differences are summed to create a simple metric of block similarity, the L1 norm of the difference image or Manhattan distance between two image blocks. The sum of absolute differences may be used for a variety of purposes, such as object recognition, the generation of disparity maps for stereo images, and motion estimation for video compression. == Example == This example uses the sum of absolute differences to identify which part of a search image is most similar to a template image. In this example, the template image is 3 by 3 pixels in size, while the search image is 3 by 5 pixels in size. Each pixel is represented by a single integer from 0 to 9. Template Search image 2 5 5 2 7 5 8 6 4 0 7 1 7 4 2 7 7 5 9 8 4 6 8 5 There are exactly three unique locations within the search image where the template may fit: the left side of the image, the center of the image, and the right side of the image. To calculate the SAD values, the absolute value of the difference between each corresponding pair of pixels is used: the difference between 2 and 2 is 0, 4 and 1 is 3, 7 and 8 is 1, and so forth. Calculating the values of the absolute differences for each pixel, for the three possible template locations, gives the following: Left Center Right 0 2 0 5 0 3 3 3 1 3 7 3 3 4 5 0 2 0 1 1 3 3 1 1 1 3 4 For each of these three image patches, the 9 absolute differences are added together, giving SAD values of 20, 25, and 17, respectively. From these SAD values, it could be asserted that the right side of the search image is the most similar to the template image, because it has the lowest sum of absolute differences as compared to the other two locations. == Comparison to other metrics == === Object recognition === The sum of absolute differences provides a simple way to automate the searching for objects inside an image, but may be unreliable due to the effects of contextual factors such as changes in lighting, color, viewing direction, size, or shape. The SAD may be used in conjunction with other object recognition methods, such as edge detection, to improve the reliability of results. === Video compression === SAD is an extremely fast metric due to its simplicity; it is effectively the simplest possible metric that takes into account every pixel in a block. Therefore, it is very effective for a wide motion search of many different blocks. SAD is also easily parallelizable since it analyzes each pixel separately, making it easily implementable with such instructions as ARM NEON or x86 SSE2. For example, SSE has packed sum of absolute differences instruction (PSADBW) specifically for this purpose. Once candidate blocks are found, the final refinement of the motion estimation process is often done with other slower but more accurate metrics, which better take into account human perception. These include the sum of absolute transformed differences (SATD), the sum of squared differences (SSD), and rate–distortion optimization.
Blockmodeling
Blockmodeling is a set or a coherent framework, that is used for analyzing social structure and also for setting procedure(s) for partitioning (clustering) social network's units (nodes, vertices, actors), based on specific patterns, which form a distinctive structure through interconnectivity. It is primarily used in statistics, machine learning and network science. As an empirical procedure, blockmodeling assumes that all the units in a specific network can be grouped together to such extent to which they are equivalent. Regarding equivalency, it can be structural, regular or generalized. Using blockmodeling, a network can be analyzed using newly created blockmodels, which transforms large and complex network into a smaller and more comprehensible one. At the same time, the blockmodeling is used to operationalize social roles. While some contend that the blockmodeling is just clustering methods, Bonacich and McConaghy state that "it is a theoretically grounded and algebraic approach to the analysis of the structure of relations". Blockmodeling's unique ability lies in the fact that it considers the structure not just as a set of direct relations, but also takes into account all other possible compound relations that are based on the direct ones. The principles of blockmodeling were first introduced by Francois Lorrain and Harrison C. White in 1971. Blockmodeling is considered as "an important set of network analytic tools" as it deals with delineation of role structures (the well-defined places in social structures, also known as positions) and the discerning the fundamental structure of social networks. According to Batagelj, the primary "goal of blockmodeling is to reduce a large, potentially incoherent network to a smaller comprehensible structure that can be interpreted more readily". Blockmodeling was at first used for analysis in sociometry and psychometrics, but has now spread also to other sciences. == Definition == A network as a system is composed of (or defined by) two different sets: one set of units (nodes, vertices, actors) and one set of links between the units. Using both sets, it is possible to create a graph, describing the structure of the network. During blockmodeling, the researcher is faced with two problems: how to partition the units (e.g., how to determine the clusters (or classes), that then form vertices in a blockmodel) and then how to determine the links in the blockmodel (and at the same time the values of these links). In the social sciences, the networks are usually social networks, composed of several individuals (units) and selected social relationships among them (links). Real-world networks can be large and complex; blockmodeling is used to simplify them into smaller structures that can be easier to interpret. Specifically, blockmodeling partitions the units into clusters and then determines the ties among the clusters. At the same time, blockmodeling can be used to explain the social roles existing in the network, as it is assumed that the created cluster of units mimics (or is closely associated with) the units' social roles. Blockmodeling can thus be defined as a set of approaches for partitioning units into clusters (also known as positions) and links into blocks, which are further defined by the newly obtained clusters. A block (also blockmodel) is defined as a submatrix, that shows interconnectivity (links) between nodes, present in the same or different clusters. Each of these positions in the cluster is defined by a set of (in)direct ties to and from other social positions. These links (connections) can be directed or undirected; there can be multiple links between the same pair of objects or they can have weights on them. If there are not any multiple links in a network, it is called a simple network. A matrix representation of a graph is composed of ordered units, in rows and columns, based on their names. The ordered units with similar patterns of links are partitioned together in the same clusters. Clusters are then arranged together so that units from the same clusters are placed next to each other, thus preserving interconnectivity. In the next step, the units (from the same clusters) are transformed into a blockmodel. With this, several blockmodels are usually formed, one being core cluster and others being cohesive; a core cluster is always connected to cohesive ones, while cohesive ones cannot be linked together. Clustering of nodes is based on the equivalence, such as structural and regular. The primary objective of the matrix form is to visually present relations between the persons included in the cluster. These ties are coded dichotomously (as present or absent), and the rows in the matrix form indicate the source of the ties, while the columns represent the destination of the ties. Equivalence can have two basic approaches: the equivalent units have the same connection pattern to the same neighbors or these units have same or similar connection pattern to different neighbors. If the units are connected to the rest of network in identical ways, then they are structurally equivalent. Units can also be regularly equivalent, when they are equivalently connected to equivalent others. With blockmodeling, it is necessary to consider the issue of results being affected by measurement errors in the initial stage of acquiring the data. == Different approaches == Regarding what kind of network is undergoing blockmodeling, a different approach is necessary. Networks can be one–mode or two–mode. In the former all units can be connected to any other unit and where units are of the same type, while in the latter the units are connected only to the unit(s) of a different type. Regarding relationships between units, they can be single–relational or multi–relational networks. Further more, the networks can be temporal or multilevel and also binary (only 0 and 1) or signed (allowing negative ties)/values (other values are possible) networks. Different approaches to blockmodeling can be grouped into two main classes: deterministic blockmodeling and stochastic blockmodeling approaches. Deterministic blockmodeling is then further divided into direct and indirect blockmodeling approaches. Among direct blockmodeling approaches are: structural equivalence and regular equivalence. Structural equivalence is a state, when units are connected to the rest of the network in an identical way(s), while regular equivalence occurs when units are equally related to equivalent others (units are not necessarily sharing neighbors, but have neighbour that are themselves similar). Indirect blockmodeling approaches, where partitioning is dealt with as a traditional cluster analysis problem (measuring (dis)similarity results in a (dis)similarity matrix), are: conventional blockmodeling, generalized blockmodeling: generalized blockmodeling of binary networks, generalized blockmodeling of valued networks and generalized homogeneity blockmodeling, prespecified blockmodeling. According to Brusco and Steinley (2011), the blockmodeling can be categorized (using a number of dimensions): deterministic or stochastic blockmodeling, one–mode or two–mode networks, signed or unsigned networks, exploratory or confirmatory blockmodeling. == Blockmodels == Blockmodels (sometimes also block models) are structures in which: vertices (e.g., units, nodes) are assembled within a cluster, with each cluster identified as a vertex; from such vertices a graph can be constructed; combinations of all the links (ties), represented in a block as a single link between positions, while at the same time constructing one tie for each block. In a case, when there are no ties in a block, there will be no ties between the two positions that define the block. Computer programs can partition the social network according to pre-set conditions. When empirical blocks can be reasonably approximated in terms of ideal blocks, such blockmodels can be reduced to a blockimage, which is a representation of the original network, capturing its underlying 'functional anatomy'. Thus, blockmodels can "permit the data to characterize their own structure", and at the same time not seek to manifest a preconceived structure imposed by the researcher. Blockmodels can be created indirectly or directly, based on the construction of the criterion function. Indirect construction refers to a function, based on "compatible (dis)similarity measure between paris of units", while the direct construction is "a function measuring the fit of real blocks induced by a given clustering to the corresponding ideal blocks with perfect relations within each cluster and between clusters according to the considered types of connections (equivalence)". === Types === Blockmodels can be specified regarding the intuition, substance or the insight into the nature of the studied network; this can result in such models as follows: parent-child role systems, organizational hierarchies, systems of
Bioz
Bioz is a search engine for life science experimentation. == History == Bioz was founded by Karin Lachmi and Daniel Levitt. Lachmi is a scientist who completed her postdoc in molecular and cellular biology at the Stanford University School of Medicine. During her lab work she found little available data regarding preferable lab tools, reagents and related products for experimentation. There are 50,000 vendors selling 300 million scientific products. She decided to start the company in order to provide researchers with adequate information for that purpose. Co-founder Daniel Levitt is an entrepreneur who sold his company WebAppoint to Microsoft in the year 2000. He also co-founded the company StemRad. At Bioz, Lachmi serves as the Chief Scientific Officer and Levitt serves as the chief executive officer. Bioz claims to have over a million researcher-users from 196 countries. Among the investors are Esther Dyson and the Stanford-StartX Fund. The company's advisory board includes Nobel Laureates in Chemistry Michael Levitt, Roger Kornberg, and Ada Yonath. == Technology == The company uses artificial intelligence, machine learning and natural language processing in order to extract experimentation data from scientific articles, such as the products that researchers used, the companies that supply the products, the protocol conditions that researchers selected, and the types of experiments and techniques. The algorithm ranks products based on how frequently they were used by researchers in their experiments, how recently a product was used, and the impact factor of the journal. The algorithm's output is a Bioz stars score for each product that was mentioned in an article. Bioz is a data-driven platform for product recommendations, which is contrary to platforms such as TripAdvisor and OpenTable that are based on user-generated reviews and ratings. The recommendations and scoring system that the company has developed are meant to assist researchers with the process of developing future medications and finding cures for diseases. They are guided towards products and techniques that were previously used by other researchers when planning and performing experiments. The company's revenue is based on selling SaaS subscriptions to researchers in biopharma companies. They also charge product suppliers for content syndication.
Natural language processing
Natural language processing (NLP) is the processing of natural language information by a computer. NLP is a subfield of computer science and is closely associated with artificial intelligence. NLP is also related to information retrieval, knowledge representation, computational linguistics, and linguistics more broadly. Major processing tasks in an NLP system include: speech recognition, text classification, natural language understanding, and natural language generation. == History == Natural language processing has its roots in the 1950s. Already in 1950, Alan Turing published an article titled "Computing Machinery and Intelligence," which proposed what is now called the Turing test as a criterion of intelligence, though at the time that was not articulated as a problem separate from artificial intelligence. The proposed test includes a task that involves the automated interpretation and generation of natural language. === Symbolic NLP (1950s – early 1990s) === The premise of symbolic NLP is often illustrated using John Searle's Chinese room thought experiment: Given a collection of rules (e.g., a Chinese phrasebook, with questions and matching answers), the computer emulates natural language understanding (or other NLP tasks) by applying those rules to the data it confronts. 1950s: The Georgetown experiment in 1954 involved fully automatic translation of more than sixty Russian sentences into English. The authors claimed that within three or five years, machine translation would be a solved problem. However, real progress was much slower, and after the ALPAC report in 1966, which found that ten years of research had failed to fulfill the expectations, funding for machine translation was dramatically reduced. Little further research in machine translation was conducted in America (though some research continued elsewhere, such as Japan and Europe) until the late 1980s when the first statistical machine translation systems were developed. 1960s: Some notably successful natural language processing systems developed in the 1960s were SHRDLU, a natural language system working in restricted "blocks worlds" with restricted vocabularies, and ELIZA, a simulation of Rogerian psychotherapy, written by Joseph Weizenbaum between 1964 and 1966. Despite using minimal information about human thought or emotion, ELIZA was able to produce interactions that appeared human-like. When the "patient" exceeded the very small knowledge base, ELIZA might provide a generic response, for example, responding to "My head hurts" with "Why do you say your head hurts?". Ross Quillian's successful work on natural language was demonstrated with a vocabulary of only twenty words, because that was all that would fit in a computer memory at the time. 1970s: During the 1970s, many programmers began to write "conceptual ontologies", which structured real-world information into computer-understandable data. Examples are MARGIE (Schank, 1975), SAM (Cullingford, 1978), PAM (Wilensky, 1978), TaleSpin (Meehan, 1976), QUALM (Lehnert, 1977), Politics (Carbonell, 1979), and Plot Units (Lehnert 1981). During this time, the first chatterbots were written (e.g., PARRY). 1980s: The 1980s and early 1990s mark the heyday of symbolic methods in NLP. Focus areas of the time included research on rule-based parsing (e.g., the development of HPSG as a computational operationalization of generative grammar), morphology (e.g., two-level morphology), semantics (e.g., Lesk algorithm), reference (e.g., within Centering Theory) and other areas of natural language understanding (e.g., in the Rhetorical Structure Theory). Other lines of research were continued, e.g., the development of chatterbots with Racter and Jabberwacky. An important development (that eventually led to the statistical turn in the 1990s) was the rising importance of quantitative evaluation in this period. === Statistical NLP (1990s–present) === Up until the 1980s, most natural language processing systems were based on complex sets of hand-written rules. Starting in the late 1980s, however, there was a revolution in natural language processing with the introduction of machine learning algorithms for language processing. This shift was influenced by increasing computational power (see Moore's law) and a decline in the dominance of Chomskyan linguistic theories (e.g. transformational grammar), whose theoretical underpinnings discouraged the sort of corpus linguistics that underlies the machine-learning approach to language processing. 1990s: Many of the notable early successes in statistical methods in NLP occurred in the field of machine translation, due especially to work at IBM Research, such as IBM alignment models. These systems were able to take advantage of existing multilingual textual corpora that had been produced by the Parliament of Canada and the European Union as a result of laws calling for the translation of all governmental proceedings into all official languages of the corresponding systems of government. However, many systems relied on corpora that were specifically developed for the tasks they were designed to perform. This reliance has been a major limitation to their broader effectiveness and continues to affect similar systems. Consequently, significant research has focused on methods for learning effectively from limited amounts of data. 2000s: With the growth of the web, increasing amounts of raw (unannotated) language data have become available since the mid-1990s. Research has thus increasingly focused on unsupervised and semi-supervised learning algorithms. Such algorithms can learn from data that has not been hand-annotated with the desired answers or using a combination of annotated and non-annotated data. Generally, this task is much more difficult than supervised learning, and typically produces less accurate results for a given amount of input data. However, large quantities of non-annotated data are available (including, among other things, the entire content of the World Wide Web), which can often make up for the worse efficiency if the algorithm used has a low enough time complexity to be practical. 2003: word n-gram model, at the time the best statistical algorithm, is outperformed by a multi-layer perceptron (with a single hidden layer and context length of several words, trained on up to 14 million words, by Bengio et al.) 2010: Tomáš Mikolov (then a PhD student at Brno University of Technology) with co-authors applied a simple recurrent neural network with a single hidden layer to language modeling, and in the following years he went on to develop Word2vec. In the 2010s, representation learning and deep neural network-style (featuring many hidden layers) machine learning methods became widespread in natural language processing. This shift gained momentum due to results showing that such techniques can achieve state-of-the-art results in many natural language tasks, e.g., in language modeling and parsing. This is increasingly important in medicine and healthcare, where NLP helps analyze notes and text in electronic health records that would otherwise be inaccessible for study when seeking to improve care or protect patient privacy. == Approaches: Symbolic, statistical, neural networks == Symbolic approach, i.e., the hand-coding of a set of rules for manipulating symbols, coupled with a dictionary lookup, was historically the first approach used both by AI in general and by NLP in particular: such as by writing grammars or devising heuristic rules for stemming. Machine learning approaches, which include both statistical and neural networks, on the other hand, have many advantages over the symbolic approach: both statistical and neural network methods tend to focus more on the most common cases extracted from a corpus of texts, whereas the rule-based approach needs to provide rules for both rare and common cases equally. language models, produced by either statistical or neural networks methods, are more robust to both unfamiliar (e.g. containing words or structures that have not been seen before) and erroneous input (e.g. with misspelled words or words accidentally omitted) in comparison to the rule-based systems, which are also more costly to produce. the larger such a (probabilistic) language model is, the more accurate it becomes, in contrast to rule-based systems that can gain accuracy only by increasing the amount and complexity of the rules leading to intractability problems. Rule-based systems are commonly used: when the amount of training data is insufficient to successfully apply machine learning methods, e.g., for the machine translation of low-resource languages such as provided by the Apertium system, for preprocessing in NLP pipelines, e.g., tokenization, or for post-processing and transforming the output of NLP pipelines, e.g., for knowledge extraction from syntactic parses. === Statistical approach === In the late 1980s and mid-1990s, the statistical approach ended a peri
Detrended correspondence analysis
Detrended correspondence analysis (DCA) is a multivariate statistical technique widely used by ecologists to find the main factors or gradients in large, species-rich but usually sparse data matrices that typify ecological community data. DCA is frequently used to suppress artifacts inherent in most other multivariate analyses when applied to gradient data. == History == DCA was created in 1979 by Mark Hill of the United Kingdom's Institute for Terrestrial Ecology (now merged into Centre for Ecology and Hydrology) and implemented in FORTRAN code package called DECORANA (Detrended Correspondence Analysis), a correspondence analysis method. DCA is sometimes erroneously referred to as DECORANA; however, DCA is the underlying algorithm, while DECORANA is a tool implementing it. == Issues addressed == According to Hill and Gauch, DCA suppresses two artifacts inherent in most other multivariate analyses when applied to gradient data. An example is a time-series of plant species colonising a new habitat; early successional species are replaced by mid-successional species, then by late successional ones (see example below). When such data are analysed by a standard ordination such as a correspondence analysis: the ordination scores of the samples will exhibit the 'edge effect', i.e. the variance of the scores at the beginning and the end of a regular succession of species will be considerably smaller than that in the middle, when presented as a graph the points will be seen to follow a horseshoe shaped curve rather than a straight line ('arch effect'), even though the process under analysis is a steady and continuous change that human intuition would prefer to see as a linear trend. Outside ecology, the same artifacts occur when gradient data are analysed (e.g. soil properties along a transect running between 2 different geologies, or behavioural data over the lifespan of an individual) because the curved projection is an accurate representation of the shape of the data in multivariate space. Ter Braak and Prentice (1987, p. 121) cite a simulation study analysing two-dimensional species packing models resulting in a better performance of DCA compared to CA. == Method == DCA is an iterative algorithm that has shown itself to be a highly reliable and useful tool for data exploration and summary in community ecology (Shaw 2003). It starts by running a standard ordination (CA or reciprocal averaging) on the data, to produce the initial horse-shoe curve in which the 1st ordination axis distorts into the 2nd axis. It then divides the first axis into segments (default = 26), and rescales each segment to have mean value of zero on the 2nd axis - this effectively squashes the curve flat. It also rescales the axis so that the ends are no longer compressed relative to the middle, so that 1 DCA unit approximates to the same rate of turnover all the way through the data: the rule of thumb is that 4 DCA units mean that there has been a total turnover in the community. Ter Braak and Prentice (1987, p. 122) warn against the non-linear rescaling of the axes due to robustness issues and recommend using detrending-by-polynomials only. == Drawbacks == No significance tests are available with DCA, although there is a constrained (canonical) version called DCCA in which the axes are forced by Multiple linear regression to correlate optimally with a linear combination of other (usually environmental) variables; this allows testing of a null model by Monte-Carlo permutation analysis. == Example == The example shows an ideal data set: The species data is in rows, samples in columns. For each sample along the gradient, a new species is introduced but another species is no longer present. The result is a sparse matrix. Ones indicate the presence of a species in a sample. Except at the edges each sample contains five species. The plot of the first two axes of the correspondence analysis result on the right hand side clearly shows the disadvantages of this procedure: the edge effect, i.e. the points are clustered at the edges of the first axis, and the arch effect. == Software == An open source implementation of DCA, based on the original FORTRAN code, is available in the vegan R-package.