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  Crucible (software)

  Crucible is a collaborative code review application by Australian software company Atlassian. Like other Atlassian products, Crucible is a Web-based application primarily aimed at enterprise, and certain features that enable peer review of a codebase may be considered enterprise social software. Crucible is particularly tailored to remote workers, and facilitates asynchronous review and commenting on code. Crucible also integrates with popular source control tools, such as Git and Subversion. Crucible is not open source, but customers are allowed to view and modify the code for their own use.

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  Clustering illusion

  The clustering illusion is the tendency to erroneously consider the inevitable "streaks" or "clusters" arising in small samples from random distributions to be non-random. The illusion is caused by a human tendency to underpredict the amount of variability likely to appear in a small sample of random or pseudorandom data. Thomas Gilovich, an early author on the subject, argued that the effect occurs for different types of random dispersions. Some might perceive patterns in stock market price fluctuations over time, or clusters in two-dimensional data such as the locations of impact of World War II V-1 flying bombs on maps of London. Although Londoners developed specific theories about the pattern of impacts within London, a statistical analysis by R. D. Clarke originally published in 1946 showed that the impacts of V-2 rockets on London were a close fit to a random distribution. == Similar biases == Using this cognitive bias in causal reasoning may result in the Texas sharpshooter fallacy, in which differences in data are ignored and similarities are overemphasized. More general forms of erroneous pattern recognition are pareidolia and apophenia. Related biases are the illusion of control which the clustering illusion could contribute to, and insensitivity to sample size in which people don't expect greater variation in smaller samples. A different cognitive bias involving misunderstanding of chance streams is the gambler's fallacy. == Possible causes == Daniel Kahneman and Amos Tversky explained this kind of misprediction as being caused by the representativeness heuristic (which itself they also first proposed).

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  Persian Speech Corpus

  The Persian Speech Corpus is a Modern Persian speech corpus for speech synthesis. The corpus contains phonetic and orthographic transcriptions of about 2.5 hours of Persian speech aligned with recorded speech on the phoneme level, including annotations of word boundaries. Previous spoken corpora of Persian include FARSDAT, which consists of read aloud speech from newspaper texts from 100 Persian speakers and the Telephone FARsi Spoken language DATabase (TFARSDAT) which comprises seven hours of read and spontaneous speech produced by 60 native speakers of Persian from ten regions of Iran. The Persian Speech Corpus was built using the same methodologies laid out in the doctoral project on Modern Standard Arabic of Nawar Halabi at the University of Southampton. The work was funded by MicroLinkPC, who own an exclusive license to commercialise the corpus, though the corpus is available for non-commercial use through the corpus' website. It is distributed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The corpus was built for speech synthesis purposes, but has been used for building HMM based voices in Persian. It can also be used to automatically align other speech corpora with their phonetic transcript and could be used as part of a larger corpus for training speech recognition systems. == Contents == The corpus is downloadable from its website, and contains the following: 396 .wav files containing spoken utterances 396 .lab files containing text utterances 396 .TextGrid files containing the phoneme labels with time stamps of the boundaries where these occur in the .wav files. phonetic-transcript.txt which has the form "[wav_filename]" "[Phoneme Sequence]" in every line orthographic-transcript.txt which has the form "[wav_filename]" "[Orthographic Transcript]" in every line

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  Logic learning machine

  Logic learning machine (LLM) is a machine learning method based on the generation of intelligible rules. LLM is an efficient implementation of the Switching Neural Network (SNN) paradigm, developed by Marco Muselli, Senior Researcher at the Italian National Research Council CNR-IEIIT in Genoa. LLM has been employed in many different sectors, including the field of medicine (orthopedic patient classification, DNA micro-array analysis and Clinical Decision Support Systems), financial services and supply chain management. == History == The Switching Neural Network approach was developed in the 1990s to overcome the drawbacks of the most commonly used machine learning methods. In particular, black box methods, such as multilayer perceptron and support vector machine, had good accuracy but could not provide deep insight into the studied phenomenon. On the other hand, decision trees were able to describe the phenomenon but often lacked accuracy. Switching Neural Networks made use of Boolean algebra to build sets of intelligible rules able to obtain very good performance. In 2014, an efficient version of Switching Neural Network was developed and implemented in the Rulex suite with the name Logic Learning Machine. Also, an LLM version devoted to regression problems was developed. == General == Like other machine learning methods, LLM uses data to build a model able to perform a good forecast about future behaviors. LLM starts from a table including a target variable (output) and some inputs and generates a set of rules that return the output value y {\displaystyle y} corresponding to a given configuration of inputs. A rule is written in the form: if premise then consequence where consequence contains the output value whereas premise includes one or more conditions on the inputs. According to the input type, conditions can have different forms: for categorical variables the input value must be in a given subset: x 1 ∈ { A , B , C , . . . } {\displaystyle x_{1}\in \{A,B,C,...\}} . for ordered variables the condition is written as an inequality or an interval: x 2 ≤ α {\displaystyle x_{2}\leq \alpha } or β ≤ x 3 ≤ γ {\displaystyle \beta \leq x_{3}\leq \gamma } A possible rule is therefore in the form if x 1 ∈ { A , B , C , . . . } {\displaystyle x_{1}\in \{A,B,C,...\}} AND x 2 ≤ α {\displaystyle x_{2}\leq \alpha } AND β ≤ x 3 ≤ γ {\displaystyle \beta \leq x_{3}\leq \gamma } then y = y ¯ {\displaystyle y={\bar {y}}} == Types == According to the output type, different versions of the Logic Learning Machine have been developed: Logic Learning Machine for classification, when the output is a categorical variable, which can assume values in a finite set Logic Learning Machine for regression, when the output is an integer or real number.

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  Xara Designer Pro+

  Xara Designer Pro+ is an image editing program incorporating photo editing and vector illustration tools created by British software company Xara. Xara Xtreme LX was an early open source version for Linux. The Windows version was previously sold under the names Xara Studio, Xara X and Xara Xtreme, and traces its origin in the late 1980s to a title called ArtWorks for the Acorn Archimedes line of computers using RISC OS. There is a pro version called Xara Designer Pro (formerly Xara Xtreme Pro). The current commercial version of Xara Photo & Graphic Designer runs only on Windows, although Xara documents can be edited in a web browser on any platform using the Xara Cloud service. Versions up to 4.x can be run on Linux using Wine. == History == ArtWorks, the predecessor of Xara Photo and Graphic Designer, was developed on Acorn Archimedes and Risc PC 32-bit RISC computers running RISC OS by Computer Concepts during the late 1980s. The first version, developed for Microsoft Windows was initially called Xara Studio. It was licensed to Corel Corporation before wide-scale public availability, and from 1995 to 2000 was released as CorelXARA. Corel ceded the licensing rights back to Xara in 2000. The first Xara X version released in 2000 by its original owner. The next version, Xara X¹, was released in 2004. Xara Xtreme was released in 2005. In November 2006, Xara Xtreme PRO (an enhanced version of Xara Xtreme) was released. Xara Xtreme 3.2 and Xtreme Pro 3.2 were released in May 2007. 3.2 Pro included Xara3D, and both versions had more robust typography. In April 2008, Xara Xtreme 4.0 was released. Xara Xtreme and Xara Xtreme Pro 5.1 were released in June 2009. Features included more text-area enhancements, content-aware scaling of bitmap images, improved file import and export, master-page (repeated) objects, an object gallery (replacing the layer gallery), website-creation tools, and multi-stage graduated transparency. In June 2010, Xara Photo & Graphic Designer 6 and Xara Designer Pro 6 were released. Xtreme was renamed Photo & Graphic Designer, and Xtreme Pro was renamed Designer Pro. In May 2011, Xara Photo & Graphic Designer 7 and Xara Designer Pro 7 were released. Features included "magic" photo erase, user interface improvements to docking galleries and snapping alignment, and (in Pro) new webpage and website-design features. In May 2012, Xara Photo & Graphic Designer 2013 and Xara Designer Pro X (v8) were released. Xara Photo & Graphic Designer 9 was released in May 2013. In July of that year, Xara Designer Pro X9 was released. Xara Photo & Graphic Designer 10 was released on 16 July 2014, and Xara Designer Pro X10 on 23 July. Xara Photo & Graphic Designer 11 was released on 29 June 2015, and Xara Designer Pro X11 was released the following month. In 2016, the delivery model was changed to an update service which can be renewed annually. Users are entitled to any updates released while the update service is active. The first update-service updates were in May 2016 for Xara Photo & Graphic Designer, and July 2016 for Xara Designer Pro X. == Features == Xara Photo & Graphic Designer is known for its usability and fast renderer. It provides a fully anti-aliased display, advanced gradient fill, and transparency tools. Among vector editors, Xara Photo & Graphic Designer is considered to be fairly easy to learn, with similarities to CorelDRAW and Inkscape in terms of interface. Alongside the vector illustration tools, Xara Photo & Graphic Designer also includes an integrated photo tool offering manual and automatic photo enhance, cropping, adjustment of brightness levels, red-eye fix, 'magic' erase, photo healing, color and background erase, panoramas and content aware resizing. Designer Pro includes a wider range of tools for other design tasks including the creation of web pages and websites, and text and page layout tools for DTP with the aim of providing a single solution for all graphic and web design tasks.

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  Random forest

  Random forests or random decision forests is an ensemble learning method for classification, regression and other tasks that works by creating a multitude of decision trees during training. For classification tasks, the output of the random forest is the class selected by most trees. For regression tasks, the output is the average of the predictions of the trees. Random forests correct for decision trees' habit of overfitting to their training set. The first algorithm for random decision forests was created in 1995 by Tin Kam Ho using the random subspace method, which, in Ho's formulation, is a way to implement the "stochastic discrimination" approach to classification proposed by Eugene Kleinberg. An extension of the algorithm was developed by Leo Breiman and Adele Cutler, who registered "Random Forests" as a trademark in 2006 (as of 2019, owned by Minitab, Inc.). The extension combines Breiman's "bagging" idea and random selection of features, introduced first by Ho and later independently by Amit and Geman in order to construct a collection of decision trees with controlled variance. == History == The general method of random decision forests was first proposed by Salzberg and Heath in 1993, with a method that used a randomized decision tree algorithm to create multiple trees and then combine them using majority voting. This idea was developed further by Ho in 1995. Ho established that forests of trees splitting with oblique hyperplanes can gain accuracy as they grow without suffering from overtraining, as long as the forests are randomly restricted to be sensitive to only selected feature dimensions. A subsequent work along the same lines concluded that other splitting methods behave similarly, as long as they are randomly forced to be insensitive to some feature dimensions. This observation that a more complex classifier (a larger forest) gets more accurate nearly monotonically is in sharp contrast to the common belief that the complexity of a classifier can only grow to a certain level of accuracy before being hurt by overfitting. The explanation of the forest method's resistance to overtraining can be found in Kleinberg's theory of stochastic discrimination. The early development of Breiman's notion of random forests was influenced by the work of Amit and Geman who introduced the idea of searching over a random subset of the available decisions when splitting a node, in the context of growing a single tree. The idea of random subspace selection from Ho was also influential in the design of random forests. This method grows a forest of trees, and introduces variation among the trees by projecting the training data into a randomly chosen subspace before fitting each tree or each node. Finally, the idea of randomized node optimization, where the decision at each node is selected by a randomized procedure, rather than a deterministic optimization was first introduced by Thomas G. Dietterich. The proper introduction of random forests was made in a paper by Leo Breiman, that has become one of the world's most cited papers. This paper describes a method of building a forest of uncorrelated trees using a CART like procedure, combined with randomized node optimization and bagging. In addition, this paper combines several ingredients, some previously known and some novel, which form the basis of the modern practice of random forests, in particular: Using out-of-bag error as an estimate of the generalization error. Measuring variable importance through permutation. The report also offers the first theoretical result for random forests in the form of a bound on the generalization error which depends on the strength of the trees in the forest and their correlation. == Algorithm == === Preliminaries: decision tree learning === Decision trees are a popular method for various machine learning tasks. Tree learning is almost "an off-the-shelf procedure for data mining", say Hastie et al., "because it is invariant under scaling and various other transformations of feature values, is robust to inclusion of irrelevant features, and produces inspectable models. However, they are seldom accurate". In particular, trees that are grown very deep tend to learn highly irregular patterns: they overfit their training sets, i.e. have low bias, but very high variance. Random forests are a way of averaging multiple deep decision trees, trained on different parts of the same training set, with the goal of reducing the variance. This comes at the expense of a small increase in the bias and some loss of interpretability, but generally greatly boosts the performance in the final model. === Bagging === The training algorithm for random forests applies the general technique of bootstrap aggregating, or bagging, to tree learners. Given a training set X = x1, ..., xn with responses Y = y1, ..., yn, bagging repeatedly (B times) selects a random sample with replacement of the training set and fits trees to these samples: After training, predictions for unseen samples x' can be made by averaging the predictions from all the individual regression trees on x': f ^ = 1 B ∑ b = 1 B f b ( x ′ ) {\displaystyle {\hat {f}}={\frac {1}{B}}\sum _{b=1}^{B}f_{b}(x')} or by taking the plurality vote in the case of classification trees. This bootstrapping procedure leads to better model performance because it decreases the variance of the model, without increasing the bias. This means that while the predictions of a single tree are highly sensitive to noise in its training set, the average of many trees is not, as long as the trees are not correlated. Simply training many trees on a single training set would give strongly correlated trees (or even the same tree many times, if the training algorithm is deterministic); bootstrap sampling is a way of de-correlating the trees by showing them different training sets. Additionally, an estimate of the uncertainty of the prediction can be made as the standard deviation of the predictions from all the individual regression trees on x′: σ = ∑ b = 1 B ( f b ( x ′ ) − f ^ ) 2 B − 1 . {\displaystyle \sigma ={\sqrt {\frac {\sum _{b=1}^{B}(f_{b}(x')-{\hat {f}})^{2}}{B-1}}}.} The number B of samples (equivalently, of trees) is a free parameter. Typically, a few hundred to several thousand trees are used, depending on the size and nature of the training set. B can be optimized using cross-validation, or by observing the out-of-bag error: the mean prediction error on each training sample xi, using only the trees that did not have xi in their bootstrap sample. The training and test error tend to level off after some number of trees have been fit. === From bagging to random forests === The above procedure describes the original bagging algorithm for trees. Random forests also include another type of bagging scheme: they use a modified tree learning algorithm that selects, at each candidate split in the learning process, a random subset of the features. This process is sometimes called "feature bagging". The reason for doing this is the correlation of the trees in an ordinary bootstrap sample: if one or a few features are very strong predictors for the response variable (target output), these features will be selected in many of the B trees, causing them to become correlated. An analysis of how bagging and random subspace projection contribute to accuracy gains under different conditions is given by Ho. Typically, for a classification problem with p {\displaystyle p} features, p {\displaystyle {\sqrt {p}}} (rounded down) features are used in each split. For regression problems the inventors recommend p / 3 {\displaystyle p/3} (rounded down) with a minimum node size of 5 as the default. In practice, the best values for these parameters should be tuned on a case-to-case basis for every problem. === ExtraTrees === Adding one further step of randomization yields extremely randomized trees, or ExtraTrees. As with ordinary random forests, they are an ensemble of individual trees, but there are two main differences: (1) each tree is trained using the whole learning sample (rather than a bootstrap sample), and (2) the top-down splitting is randomized: for each feature under consideration, a number of random cut-points are selected, instead of computing the locally optimal cut-point (based on, e.g., information gain or the Gini impurity). The values are chosen from a uniform distribution within the feature's empirical range (in the tree's training set). Then, of all the randomly chosen splits, the split that yields the highest score is chosen to split the node. Similar to ordinary random forests, the number of randomly selected features to be considered at each node can be specified. Default values for this parameter are p {\displaystyle {\sqrt {p}}} for classification and p {\displaystyle p} for regression, where p {\displaystyle p} is the number of features in the model. === Random forests for high-dimensional data === The basic random forest procedure may

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  Weka (software)

  Waikato Environment for Knowledge Analysis (Weka) is a collection of machine learning and data analysis free software licensed under the GNU General Public License. It was developed at the University of Waikato, New Zealand, and is the companion software to the book "Data Mining: Practical Machine Learning Tools and Techniques". == Description == Weka contains a collection of visualization tools and algorithms for data analysis and predictive modeling, together with graphical user interfaces for easy access to these functions. The original non-Java version of Weka was a Tcl/Tk front-end to (mostly third-party) modeling algorithms implemented in other programming languages, plus data preprocessing utilities in C, and a makefile-based system for running machine learning experiments. This original version was primarily designed as a tool for analyzing data from agricultural domains, but the more recent fully Java-based version (Weka 3), for which development started in 1997, is now used in many different application areas, in particular for educational purposes and research. Advantages of Weka include: Free availability under the GNU General Public License. Portability, since it is fully implemented in the Java programming language and thus runs on almost any modern computing platform. A comprehensive collection of data preprocessing and modeling techniques. Ease of use due to its graphical user interfaces. Weka supports several standard data mining tasks, more specifically, data preprocessing, clustering, classification, regression, visualization, and feature selection. Input to Weka is expected to be formatted according the Attribute-Relational File Format and with the filename bearing the .arff extension. All of Weka's techniques are predicated on the assumption that the data is available as one flat file or relation, where each data point is described by a fixed number of attributes (normally, numeric or nominal attributes, but some other attribute types are also supported). Weka provides access to SQL databases using Java Database Connectivity and can process the result returned by a database query. Weka provides access to deep learning with Deeplearning4j. It is not capable of multi-relational data mining, but there is separate software for converting a collection of linked database tables into a single table that is suitable for processing using Weka. Another important area that is currently not covered by the algorithms included in the Weka distribution is sequence modeling. == Extension packages == In version 3.7.2, a package manager was added to allow the easier installation of extension packages. Some functionality that used to be included with Weka prior to this version has since been moved into such extension packages, but this change also makes it easier for others to contribute extensions to Weka and to maintain the software, as this modular architecture allows independent updates of the Weka core and individual extensions. == History == In 1993, the University of Waikato in New Zealand began development of the original version of Weka, which became a mix of Tcl/Tk, C, and makefiles. In 1997, the decision was made to redevelop Weka from scratch in Java, including implementations of modeling algorithms. In 2005, Weka received the SIGKDD Data Mining and Knowledge Discovery Service Award. In 2006, Pentaho Corporation acquired an exclusive licence to use Weka for business intelligence. It forms the data mining and predictive analytics component of the Pentaho business intelligence suite. Pentaho has since been acquired by Hitachi Vantara, and Weka now underpins the PMI (Plugin for Machine Intelligence) open source component. == Related tools == Auto-WEKA is an automated machine learning system for Weka. Environment for DeveLoping KDD-Applications Supported by Index-Structures (ELKI) is a similar project to Weka with a focus on cluster analysis, i.e., unsupervised methods. H2O.ai is an open-source data science and machine learning platform KNIME is a machine learning and data mining software implemented in Java. Massive Online Analysis (MOA) is an open-source project for large scale mining of data streams, also developed at the University of Waikato in New Zealand. Neural Designer is a data mining software based on deep learning techniques written in C++. Orange is a similar open-source project for data mining, machine learning and visualization based on scikit-learn. RapidMiner is a commercial machine learning framework implemented in Java which integrates Weka. scikit-learn is a popular machine learning library in Python.

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  Relief (feature selection)

  Relief is an algorithm developed by Kenji Kira and Larry Rendell in 1992 that takes a filter-method approach to feature selection that is notably sensitive to feature interactions. It was originally designed for application to binary classification problems with discrete or numerical features. Relief calculates a feature score for each feature which can then be applied to rank and select top scoring features for feature selection. Alternatively, these scores may be applied as feature weights to guide downstream modeling. Relief feature scoring is based on the identification of feature value differences between nearest neighbor instance pairs. If a feature value difference is observed in a neighboring instance pair with the same class (a 'hit'), the feature score decreases. Alternatively, if a feature value difference is observed in a neighboring instance pair with different class values (a 'miss'), the feature score increases. The original Relief algorithm has since inspired a family of Relief-based feature selection algorithms (RBAs), including the ReliefF algorithm. Beyond the original Relief algorithm, RBAs have been adapted to (1) perform more reliably in noisy problems, (2) generalize to multi-class problems (3) generalize to numerical outcome (i.e. regression) problems, and (4) to make them robust to incomplete (i.e. missing) data. To date, the development of RBA variants and extensions has focused on four areas; (1) improving performance of the 'core' Relief algorithm, i.e. examining strategies for neighbor selection and instance weighting, (2) improving scalability of the 'core' Relief algorithm to larger feature spaces through iterative approaches, (3) methods for flexibly adapting Relief to different data types, and (4) improving Relief run efficiency. Their strengths are that they are not dependent on heuristics, they run in low-order polynomial time, and they are noise-tolerant and robust to feature interactions, as well as being applicable for binary or continuous data; however, it does not discriminate between redundant features, and low numbers of training instances fool the algorithm. == Relief Algorithm == Take a data set with n instances of p features, belonging to two known classes. Within the data set, each feature should be scaled to the interval [0 1] (binary data should remain as 0 and 1). The algorithm will be repeated m times. Start with a p-long weight vector (W) of zeros. At each iteration, take the feature vector (X) belonging to one random instance, and the feature vectors of the instance closest to X (by Euclidean distance) from each class. The closest same-class instance is called 'near-hit', and the closest different-class instance is called 'near-miss'. Update the weight vector such that W i = W i − ( x i − n e a r H i t i ) 2 + ( x i − n e a r M i s s i ) 2 , {\displaystyle W_{i}=W_{i}-(x_{i}-\mathrm {nearHit} _{i})^{2}+(x_{i}-\mathrm {nearMiss} _{i})^{2},} where i {\displaystyle i} indexes the components and runs from 1 to p. Thus the weight of any given feature decreases if it differs from that feature in nearby instances of the same class more than nearby instances of the other class, and increases in the reverse case. After m iterations, divide each element of the weight vector by m. This becomes the relevance vector. Features are selected if their relevance is greater than a threshold τ. Kira and Rendell's experiments showed a clear contrast between relevant and irrelevant features, allowing τ to be determined by inspection. However, it can also be determined by Chebyshev's inequality for a given confidence level (α) that a τ of 1/sqrt(αm) is good enough to make the probability of a Type I error less than α, although it is stated that τ can be much smaller than that. Relief was also described as generalizable to multinomial classification by decomposition into a number of binary problems. == ReliefF Algorithm == Kononenko et al. propose a number of updates to Relief. Firstly, they find the near-hit and near-miss instances using the Manhattan (L1) norm rather than the Euclidean (L2) norm, although the rationale is not specified. Furthermore, they found taking the absolute differences between xi and near-hiti, and xi and near-missi to be sufficient when updating the weight vector (rather than the square of those differences). === Reliable probability estimation === Rather than repeating the algorithm m times, implement it exhaustively (i.e. n times, once for each instance) for relatively small n (up to one thousand). Furthermore, rather than finding the single nearest hit and single nearest miss, which may cause redundant and noisy attributes to affect the selection of the nearest neighbors, ReliefF searches for k nearest hits and misses and averages their contribution to the weights of each feature. k can be tuned for any individual problem. === Incomplete data === In ReliefF, the contribution of missing values to the feature weight is determined using the conditional probability that two values should be the same or different, approximated with relative frequencies from the data set. This can be calculated if one or both features are missing. === Multi-class problems === Rather than use Kira and Rendell's proposed decomposition of a multinomial classification into a number of binomial problems, ReliefF searches for k near misses from each different class and averages their contributions for updating W, weighted with the prior probability of each class. == Other Relief-based Algorithm Extensions/Derivatives == The following RBAs are arranged chronologically from oldest to most recent. They include methods for improving (1) the core Relief algorithm concept, (2) iterative approaches for scalability, (3) adaptations to different data types, (4) strategies for computational efficiency, or (5) some combination of these goals. For more on RBAs see these book chapters or this most recent review paper. === RRELIEFF === Robnik-Šikonja and Kononenko propose further updates to ReliefF, making it appropriate for regression. === Relieved-F === Introduced deterministic neighbor selection approach and a new approach for incomplete data handling. === Iterative Relief === Implemented method to address bias against non-monotonic features. Introduced the first iterative Relief approach. For the first time, neighbors were uniquely determined by a radius threshold and instances were weighted by their distance from the target instance. === I-RELIEF === Introduced sigmoidal weighting based on distance from target instance. All instance pairs (not just a defined subset of neighbors) contributed to score updates. Proposed an on-line learning variant of Relief. Extended the iterative Relief concept. Introduced local-learning updates between iterations for improved convergence. === TuRF (a.k.a. Tuned ReliefF) === Specifically sought to address noise in large feature spaces through the recursive elimination of features and the iterative application of ReliefF. === Evaporative Cooling ReliefF === Similarly seeking to address noise in large feature spaces. Utilized an iterative `evaporative' removal of lowest quality features using ReliefF scores in association with mutual information. === EReliefF (a.k.a. Extended ReliefF) === Addressing issues related to incomplete and multi-class data. === VLSReliefF (a.k.a. Very Large Scale ReliefF) === Dramatically improves the efficiency of detecting 2-way feature interactions in very large feature spaces by scoring random feature subsets rather than the entire feature space. === ReliefMSS === Introduced calculation of feature weights relative to average feature 'diff' between instance pairs. === SURF === SURF identifies nearest neighbors (both hits and misses) based on a distance threshold from the target instance defined by the average distance between all pairs of instances in the training data. Results suggest improved power to detect 2-way epistatic interactions over ReliefF. === SURF (a.k.a. SURFStar) === SURF extends the SURF algorithm to not only utilized 'near' neighbors in scoring updates, but 'far' instances as well, but employing inverted scoring updates for 'far instance pairs. Results suggest improved power to detect 2-way epistatic interactions over SURF, but an inability to detect simple main effects (i.e. univariate associations). === SWRF === SWRF extends the SURF algorithm adopting sigmoid weighting to take distance from the threshold into account. Also introduced a modular framework for further developing RBAs called MoRF. === MultiSURF (a.k.a. MultiSURFStar) === MultiSURF extends the SURF algorithm adapting the near/far neighborhood boundaries based on the average and standard deviation of distances from the target instance to all others. MultiSURF uses the standard deviation to define a dead-band zone where 'middle-distance' instances do not contribute to scoring. Evidence suggests MultiSURF performs best in detecting pure 2-way feature interactions. === Reli

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  IEEE Transactions on Visualization and Computer Graphics

  IEEE Transactions on Visualization and Computer Graphics is a peer-reviewed scientific journal published by the IEEE Computer Society. It covers subjects related to computer graphics and visualization techniques, systems, software, hardware, and user interface issues. TVCG has been considered the top journal in the field of visualization. Since 2011, TVCG has allowed authors to present recently accepted papers at partner conferences. These include: IEEE Visualization (VIS), including VAST, InfoVis, and SciVis. IEEE Virtual Reality Conference (IEEE VR) IEEE International Symposium on Mixed and Augmented Reality (ISMAR) ACM Symposium on Interactive 3D Graphics and Games (I3D) IEEE Pacific Visualization Conference (IEEE PacificVis) ACM SIGGRAPH/Eurographics Symposium on Computer Animation (SCA) Eurographics Symposium on Geometry Processing (SGP) Pacific Graphics Conference (PG) Eurovis - The EG and VGTC Conference on Visualization Graphics Interfaces (GI)

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  Bondy's theorem

  In mathematics, Bondy's theorem is a bound on the number of elements needed to distinguish the sets in a family of sets from each other. It belongs to the field of combinatorics, and is named after John Adrian Bondy, who published it in 1972. == Statement == The theorem is as follows: Let X be a set with n elements and let A1, A2, ..., An be distinct subsets of X. Then there exists a subset S of X with n − 1 elements such that the sets Ai ∩ S are all distinct. In other words, if we have a 0-1 matrix with n rows and n columns such that each row is distinct, we can remove one column such that the rows of the resulting n × (n − 1) matrix are distinct. == Example == Consider the 4 × 4 matrix [ 1 1 0 1 0 1 0 1 0 0 1 1 0 1 1 0 ] {\displaystyle {\begin{bmatrix}1&1&0&1\\0&1&0&1\\0&0&1&1\\0&1&1&0\end{bmatrix}}} where all rows are pairwise distinct. If we delete, for example, the first column, the resulting matrix [ 1 0 1 1 0 1 0 1 1 1 1 0 ] {\displaystyle {\begin{bmatrix}1&0&1\\1&0&1\\0&1&1\\1&1&0\end{bmatrix}}} no longer has this property: the first row is identical to the second row. Nevertheless, by Bondy's theorem we know that we can always find a column that can be deleted without introducing any identical rows. In this case, we can delete the third column: all rows of the 3 × 4 matrix [ 1 1 1 0 1 1 0 0 1 0 1 0 ] {\displaystyle {\begin{bmatrix}1&1&1\\0&1&1\\0&0&1\\0&1&0\end{bmatrix}}} are distinct. Another possibility would have been deleting the fourth column. == Learning theory application == From the perspective of computational learning theory, Bondy's theorem can be rephrased as follows: Let C be a concept class over a finite domain X. Then there exists a subset S of X with the size at most |C| − 1 such that S is a witness set for every concept in C. This implies that every finite concept class C has its teaching dimension bounded by |C| − 1.

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  Kernel principal component analysis

  In the field of multivariate statistics, kernel principal component analysis (kernel PCA) is an extension of principal component analysis (PCA) using techniques of kernel methods. Using a kernel, the originally linear operations of PCA are performed in a reproducing kernel Hilbert space. == Background: Linear PCA == Recall that conventional PCA operates on zero-centered data; that is, 1 N ∑ i = 1 N x i = 0 {\displaystyle {\frac {1}{N}}\sum _{i=1}^{N}\mathbf {x} _{i}=\mathbf {0} } , where x i {\displaystyle \mathbf {x} _{i}} is one of the N {\displaystyle N} multivariate observations. It operates by diagonalizing the covariance matrix, C = 1 N ∑ i = 1 N x i x i ⊤ {\displaystyle C={\frac {1}{N}}\sum _{i=1}^{N}\mathbf {x} _{i}\mathbf {x} _{i}^{\top }} in other words, it gives an eigendecomposition of the covariance matrix: λ v = C v {\displaystyle \lambda \mathbf {v} =C\mathbf {v} } which can be rewritten as λ x i ⊤ v = x i ⊤ C v for i = 1 , … , N {\displaystyle \lambda \mathbf {x} _{i}^{\top }\mathbf {v} =\mathbf {x} _{i}^{\top }C\mathbf {v} \quad {\textrm {for}}~i=1,\ldots ,N} . (See also: Covariance matrix as a linear operator) == Introduction of the Kernel to PCA == To understand the utility of kernel PCA, particularly for clustering, observe that, while N points cannot, in general, be linearly separated in d < N {\displaystyle d Read more →

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  Liquid state machine

  A liquid state machine (LSM) is a type of reservoir computer that uses a spiking neural network. An LSM consists of a large collection of units (called nodes, or neurons). Each node receives time varying input from external sources (the inputs) as well as from other nodes. Nodes are randomly connected to each other. The recurrent nature of the connections turns the time varying input into a spatio-temporal pattern of activations in the network nodes. The spatio-temporal patterns of activation are read out by linear discriminant units. The soup of recurrently connected nodes will end up computing a large variety of nonlinear functions on the input. Given a large enough variety of such nonlinear functions, it is theoretically possible to obtain linear combinations (using the read out units) to perform whatever mathematical operation is needed to perform a certain task, such as speech recognition or computer vision. The word liquid in the name comes from the analogy drawn to dropping a stone into a still body of water or other liquid. The falling stone will generate ripples in the liquid. The input (motion of the falling stone) has been converted into a spatio-temporal pattern of liquid displacement (ripples). LSMs have been put forward as a way to explain the operation of brains. LSMs are argued to be an improvement over the theory of artificial neural networks because: Circuits are not hard coded to perform a specific task. Continuous time inputs are handled "naturally". Computations on various time scales can be done using the same network. The same network can perform multiple computations. Criticisms of LSMs as used in computational neuroscience are that LSMs don't actually explain how the brain functions. At best they can replicate some parts of brain functionality. There is no guaranteed way to dissect a working network and figure out how or what computations are being performed. There is very little control over the process. == Universal function approximation == If a reservoir has fading memory and input separability, with help of a readout, it can be proven the liquid state machine is a universal function approximator using Stone–Weierstrass theorem.

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  Visual analytics

  Visual analytics is a multidisciplinary science and technology field that emerged from information visualization and scientific visualization. It focuses on how analytical reasoning can be facilitated by interactive visual interfaces. == Overview == Visual analytics is "the science of analytical reasoning facilitated by interactive visual interfaces." It can address problems whose size, complexity, and need for closely coupled human and machine analysis may make them otherwise intractable. Visual analytics advances scientific and technological development across multiple domains, including analytical reasoning, human–computer interaction, data transformations, visual representation for computation and analysis, analytic reporting, and the transition of new technologies into practice. As a research agenda, visual analytics brings together several scientific and technical communities from computer science, information visualization, cognitive and perceptual sciences, interactive design, graphic design, and social sciences. Visual analytics integrates new computational and theory-based tools with innovative interactive techniques and visual representations to enable human-information discourse. The design of the tools and techniques is based on cognitive, design, and perceptual principles. This science of analytical reasoning provides the reasoning framework upon which one can build both strategic and tactical visual analytics technologies for threat analysis, prevention, and response. Analytical reasoning is central to the analyst's task of applying human judgments to reach conclusions from a combination of evidence and assumptions. Visual analytics has some overlapping goals and techniques with information visualization and scientific visualization. There is currently no clear consensus on the boundaries between these fields, but broadly speaking the three areas can be distinguished as follows: Scientific visualization deals with data that has a natural geometric structure (e.g., MRI data, wind flows). Information visualization handles abstract data structures such as trees or graphs. Visual analytics is especially concerned with coupling interactive visual representations with underlying analytical processes (e.g., statistical procedures, data mining techniques) such that high-level, complex activities can be effectively performed (e.g., sense making, reasoning, decision making). Visual analytics seeks to marry techniques from information visualization with techniques from computational transformation and analysis of data. Information visualization forms part of the direct interface between user and machine, amplifying human cognitive capabilities in six basic ways: by increasing cognitive resources, such as by using a visual resource to expand human working memory, by reducing search, such as by representing a large amount of data in a small space, by enhancing the recognition of patterns, such as when information is organized in space by its time relationships, by supporting the easy perceptual inference of relationships that are otherwise more difficult to induce, by perceptual monitoring of a large number of potential events, and by providing a manipulable medium that, unlike static diagrams, enables the exploration of a space of parameter values These capabilities of information visualization, combined with computational data analysis, can be applied to analytic reasoning to support the sense-making process. == History == As an interdisciplinary approach, visual analytics has its roots in information visualization, cognitive sciences, and computer science. The term and scope of the field was defined in the early 2000s through researchers such as Jim Thomas, Kristin A. Cook, John Stasko, Pak Chung Wong, Daniel A. Keim and David S. Ebert. As a reaction to the September 11, 2001 attacks the United States Department of Homeland Security was established in late 2002, combining dozens of previously separated government agencies. Building upon earlier work on visual data mining by Daniel A. Keim starting in the late 1990s, this simultaneously lead to the development of a research agenda for visual analytics. As part of these efforts the National Visualization and Analytics Center (NVAC) at Pacific Northwest National Laboratory was established in 2004, whose charter was to develop system to mitigate information overload after the September 11, 2001 attacks in the intelligence community. Their research work determined core challenges, posed open research questions, and positioned visual analytics as a new research domain, in particular through the 2005 research agenda Illuminating the Path. In 2006, the IEEE VIS community led by Pak Chung Wong and Daniel A. Keim launched the annual IEEE Conference on Visual Analytics Science and Technology (VAST), providing a dedicated venue for research into visual analytics, which in 2020 merged to form the IEEE Visualization conference. In 2008, scope and challenges of visual analytics were conceptually defined by Daniel A. Keim and Jim Thomas in their influential book about visual data mining. The domain was further refined as part of the European Commissions FP7 VisMaster program in the late 2000s. == Topics == === Scope === Visual analytics is a multidisciplinary field that includes the following focus areas: Analytical reasoning techniques that enable users to obtain deep insights that directly support assessment, planning, and decision making Data representations and transformations that convert all types of conflicting and dynamic data in ways that support visualization and analysis Techniques to support production, presentation, and dissemination of the results of an analysis to communicate information in the appropriate context to a variety of audiences. Visual representations and interaction techniques that take advantage of the human eye's broad bandwidth pathway into the mind to allow users to see, explore, and understand large amounts of information at once. === Analytical reasoning techniques === Analytical reasoning techniques are the method by which users obtain deep insights that directly support situation assessment, planning, and decision making. Visual analytics must facilitate high-quality human judgment with a limited investment of the analysts’ time. Visual analytics tools must enable diverse analytical tasks such as: Understanding past and present situations quickly, as well as the trends and events that have produced current conditions Identifying possible alternative futures and their warning signs Monitoring current events for emergence of warning signs as well as unexpected events Determining indicators of the intent of an action or an individual Supporting the decision maker in times of crisis. These tasks will be conducted through a combination of individual and collaborative analysis, often under extreme time pressure. Visual analytics must enable hypothesis-based and scenario-based analytical techniques, providing support for the analyst to reason based on the available evidence. === Data representations === Data representations are structured forms suitable for computer-based transformations. These structures must exist in the original data or be derivable from the data themselves. They must retain the information and knowledge content and the related context within the original data to the greatest degree possible. The structures of underlying data representations are generally neither accessible nor intuitive to the user of the visual analytics tool. They are frequently more complex in nature than the original data and are not necessarily smaller in size than the original data. The structures of the data representations may contain hundreds or thousands of dimensions and be unintelligible to a person, but they must be transformable into lower-dimensional representations for visualization and analysis. === Theories of visualization === Theories of visualization include: Jacques Bertin's Semiology of Graphics (1967) Nelson Goodman's Languages of Art (1977) Jock D. Mackinlay's Automated design of optimal visualization (APT) (1986) Leland Wilkinson's Grammar of Graphics (1998) Hadley Wickham's Layered Grammar of Graphics (2010) === Visual representations === Visual representations translate data into a visible form that highlights important features, including commonalities and anomalies. These visual representations make it easy for users to perceive salient aspects of their data quickly. Augmenting the cognitive reasoning process with perceptual reasoning through visual representations permits the analytical reasoning process to become faster and more focused. == Process == The input for the data sets used in the visual analytics process are heterogeneous data sources (i.e., the internet, newspapers, books, scientific experiments, expert systems). From these rich sources, the data sets S = S1, ..., Sm are chosen, whereas each Si , i ∈ (1, ..., m) consists of attrib

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  Ilastik

  ilastik is free open source software for image classification and segmentation. No previous experience in image processing is required to run the software. Since 2018 ilastik is further developed and maintained by Anna Kreshuk's group at European Molecular Biology Laboratory. == Features == ilastik allows user to annotate an arbitrary number of classes in images with a mouse interface. Using these user annotations and the generic (nonlinear) image features, the user can train a random forest classifier. Trained ilastik classifiers can be applied new data not included in the training set in ilastik via its batch processing functionality, or without using the graphical user interface, in headless mode. ilastik can be integrated into various related tools: Pre-trained workflows can be executed directly from ImageJ/Fiji using the ilastik-ImageJ plugin. Pre-trained ilastik Pixel Classification workflows can be run directly in Python with the ilastik Python package, which is available via conda. ilastik has a CellProfiler module to use ilastik classifiers to process images within a CellProfiler framework. == History == ilastik was first released in 2011 by scientists at the Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg. == Application == The Interactive Learning and Segmentation Toolkit Carving Cell classification and neuron classification Synapse detection Cell tracking Neural Network Classification == Resources == ilastik project is hosted on GitHub. It is a collaborative project, any contributions such as comments, bug reports, bug fixes or code contributions are welcome. The ilastik team can be contacted for user support on the image.sc forum.

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  Fitness approximation

  Fitness approximation aims to approximate the objective or fitness functions in evolutionary optimization by building up machine learning models based on data collected from numerical simulations or physical experiments. The machine learning models for fitness approximation are also known as meta-models or surrogates, and evolutionary optimization based on approximated fitness evaluations are also known as surrogate-assisted evolutionary approximation. Fitness approximation in evolutionary optimization can be seen as a sub-area of data-driven evolutionary optimization. == Approximate models in function optimization == === Motivation === In many real-world optimization problems including engineering problems, the number of fitness function evaluations needed to obtain a good solution dominates the optimization cost. In order to obtain efficient optimization algorithms, it is crucial to use prior information gained during the optimization process. Conceptually, a natural approach to utilizing the known prior information is building a model of the fitness function to assist in the selection of candidate solutions for evaluation. A variety of techniques for constructing such a model, often also referred to as surrogates, metamodels or approximation models – for computationally expensive optimization problems have been considered. === Approaches === Common approaches to constructing approximate models based on learning and interpolation from known fitness values of a small population include: Low-degree polynomials and regression models Fourier surrogate modeling Artificial neural networks including Multilayer perceptrons Radial basis function network Support vector machines Due to the limited number of training samples and high dimensionality encountered in engineering design optimization, constructing a globally valid approximate model remains difficult. As a result, evolutionary algorithms using such approximate fitness functions may converge to local optima. Therefore, it can be beneficial to selectively use the original fitness function together with the approximate model.

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