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  Morphobank

  MorphoBank is a web application for collaborative evolutionary research, specifically phylogenetic systematics or cladistics, on the phenotype. Historically, scientists conducting research on phylogenetic systematics have worked individually or in small groups employing traditional single-user software applications such as MacClade, Mesquite and Nexus Data Editor. As the hypotheses under study have grown more complex, large research teams have assembled to tackle the problem of discovering the Tree of Life for the estimated 4-100 million living species(Wilson 2003, pp. 77–80) and the many thousands more extinct species known from fossils. Because the phenotype is fundamentally visual, and as phenotype-based phylogenetic studies have continued to increase in size, it becomes important that observations be backed up by labeled images. Traditional desktop software applications currently in wide use do not provide robust support for team-based research or for image manipulation and storage. MorphoBank is a particularly important tool for the growing scientific field of phenomics. The development of MorphoBank, which began in 2001, has been funded by the National Science Foundation's Directorates for Geosciences, Biological Sciences and Computer and Information Science and Engineering. The significance of the scientific work on MorphoBank has been featured in the New York Times(here and here), among other publications. == Advantages == Teams of scientists studying phylogenetics to build the Tree of Life assemble large spreadsheets of observations about species (referred to as "matrices"). These teams require simultaneous access by each team member to a single and secure copy of the team's data during a scientific research project. This single copy of the data also changes with great frequency during the data collection phase. Images that can be very helpful for documenting homology statements must be displayed, labeled and shared as homology statements develop. This cannot be accomplished elegantly with a desktop software package alone because in a desktop environment each collaborator is working on his own private copy of project data. Changes made by one participant cannot automatically propagate to others, preventing collaborators from seeing each other's data edits until they are manually (and due to the effort involved, often only periodically) merged into a single "true" dataset. In all but the smallest and most disciplined of teams, file version control and the reconciliation of changes made on multiple copies of the data emerge quickly as significant drags on productivity. MorphoBank is an attempt to address these issues by leveraging the ubiquity of the web and modern web-based application techniques, including Ajax, web service layers, and rich web applications to provide a full-featured, net-accessible collaborative workspace for phylogenetic research. In particular, MorphoBank makes it easy to: Share all kinds of data with geographically separated team members, including taxonomy, character and specimen data, media (including images, video and audio), phylogenetic matrices (including data in the widely used NEXUS and TNT format) and other data such as documents and genetic sequences. Label high-resolution images using a web-based image annotation application. Collaboratively edit project data such as phylogenetic matrices using a built-in web-based matrix editor. The editor allows the linking of labeled images to individual cells of a matrix. Manage access to project data. Access ranges from full-access for team members to anonymous read-only access for potential reviewers. Publish completed project data on the web in support of a published paper with a persistent URL. Search The Encyclopedia of Life for taxon exemplar images. Store high resolution CT data Create ontologies for updating and populating matrix cells. These tasks are difficult or impossible in most existing software applications. == History == In 2001 the National Science Foundation (NSF) sponsored a workshop, at the American Museum of Natural History in New York to develop the outlines of a web-based system for a collaborative, media-rich research tool for morphological phylogenetics. An application prototype presented at the workshop was later refined with feedback from the workshop and became MorphoBank version 1.0. A grant from the US National Oceanic and Atmospheric Administration funded further revisions resulting in version 2.0, released in 2005. Current support from the NSF is funding current feature enhancements to MorphoBank. MorphoBank was hosted by Stony Brook University until late October 2021 and received back up support from the American Museum of Natural History. The current version is 3.0. Rationale for the software was described in the journal Cladistics. MorphoBank has also received support from NESCENT and the San Diego Supercomputer Center. Since 2018, MorphoBank has been supported in part by Phoenix Bioinformatics, a non-profit company founded to sustain databases for the basic sciences. A permanent move of MorphoBank from Stony Brook University to Phoenix Bioinformatics was complete in late October 2021. The San Diego Supercomputer Center has previously provided technical and hosting resources to the MorphoBank project. == Usage == MorphoBank hosts the products of peer-reviewed scientific research on phenotypes. An increasing volume of systematics data is "born digital" and MorphoBank is well suited to handle this type of material. On August 24, 2007, 62 active research projects were hosted by MorphoBank, as well as 6 completed (and published) projects. By 2017 over 2000 scientists and their students were registered content builders (users are not required to register and are even more numerous) and has more than 500 publicly available projects with approximately 80,000 images that are the products of scientific research. Over 1,500 active research projects are hosted by MorphoBank. The software has been used to assemble phylogenetic research on such groups as mammals, from bats to whales, bivalve molluscs, arachnids, fossil plants and living and extinct amniotes. It has also been used more broadly in evolutionary and paleontological research to host curated images associated with published research on lacewing insects geckos, raptor birds, dinosaurs, frogs and nematodes. MorphoBank is increasingly used in conjunction with the Paleobiology Database. Example published projects: Project 1097: Blank CE, 2013 Origin and early evolution of photosynthetic eukaryotes in freshwater environments – reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution Project 2520: Carvalho, T. P., R. E. Reis, and J. P. Friel, 2017 A new species of Hoplomyzon (Siluriformes: Aspredinidae) from Maracaibo Basin, Venezuela: osteological description using high-resolution Project 2651: Baron, M. G., Norman, D. B., Barrett, P. M., 2017 A new hypothesis of dinosaur relationships and early dinosaur evolution MorphoBank has been particularly important to the Assembling the Tree of Life initiative sponsored by the National Science Foundation. MorphoBank is well-suited to such projects because of its tools for merging taxonomic, character and matrix-based data, as well as its collaborative features. Highlights of this research include a collaborative matrix on mammal evolution published in Science that included over 4,000 phenomic characters scored for over 80 species, a matrix on extant baleen whales featuring nearly 600 images, and more.

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  Exploratory blockmodeling

  Exploratory blockmodeling is an (inductive) approach (or a group of approaches) in blockmodeling regarding the specification of an ideal blockmodel. This approach, also known as hypotheses-generating, is the simplest approach, as it "merely involves the definition of the block types permitted as well as of the number of clusters." With this approach, researcher usually defines the best possible blockmodel, which then represent the base for the analysis of the whole network. This approach is usually based on: previous analyses and theoretical considerations, using stricker blockmodel and block types, where the structural equivalence is stricker than the regular equivalence and using smaller number of classes. The opposite approach is called a confirmatory blockmodeling.

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  Hinge loss

  In machine learning, the hinge loss is a loss function used for training classifiers. The hinge loss is used for "maximum-margin" classification, most notably for support vector machines (SVMs). For an intended output t = ±1 and a classifier score y, the hinge loss of the prediction y is defined as ℓ ( y ) = max ( 0 , 1 − t ⋅ y ) {\displaystyle \ell (y)=\max(0,1-t\cdot y)} Note that y {\displaystyle y} should be the "raw" output of the classifier's decision function, not the predicted class label. For instance, in linear SVMs, y = w ⋅ x + b {\displaystyle y=\mathbf {w} \cdot \mathbf {x} +b} , where ( w , b ) {\displaystyle (\mathbf {w} ,b)} are the parameters of the hyperplane and x {\displaystyle \mathbf {x} } is the input variable(s). When t and y have the same sign (meaning y predicts the right class) and | y | ≥ 1 {\displaystyle |y|\geq 1} , the hinge loss ℓ ( y ) = 0 {\displaystyle \ell (y)=0} . When they have opposite signs, ℓ ( y ) {\displaystyle \ell (y)} increases linearly with y, and similarly if | y | < 1 {\displaystyle |y|<1} , even if it has the same sign (correct prediction, but not by enough margin). The Hinge loss is not a proper scoring rule. == Extensions == While binary SVMs are commonly extended to multiclass classification in a one-vs.-all or one-vs.-one fashion, it is also possible to extend the hinge loss itself for such an end. Several different variations of multiclass hinge loss have been proposed. For example, Crammer and Singer defined it for a linear classifier as ℓ ( y ) = max ( 0 , 1 + max y ≠ t w y x − w t x ) {\displaystyle \ell (y)=\max(0,1+\max _{y\neq t}\mathbf {w} _{y}\mathbf {x} -\mathbf {w} _{t}\mathbf {x} )} , where t {\displaystyle t} is the target label, w t {\displaystyle \mathbf {w} _{t}} and w y {\displaystyle \mathbf {w} _{y}} are the model parameters. Weston and Watkins provided a similar definition, but with a sum rather than a max: ℓ ( y ) = ∑ y ≠ t max ( 0 , 1 + w y x − w t x ) {\displaystyle \ell (y)=\sum _{y\neq t}\max(0,1+\mathbf {w} _{y}\mathbf {x} -\mathbf {w} _{t}\mathbf {x} )} . In structured prediction, the hinge loss can be further extended to structured output spaces. Structured SVMs with margin rescaling use the following variant, where w denotes the SVM's parameters, y the SVM's predictions, φ the joint feature function, and Δ the Hamming loss: ℓ ( y ) = max ( 0 , Δ ( y , t ) + ⟨ w , ϕ ( x , y ) ⟩ − ⟨ w , ϕ ( x , t ) ⟩ ) = max ( 0 , max y ∈ Y ( Δ ( y , t ) + ⟨ w , ϕ ( x , y ) ⟩ ) − ⟨ w , ϕ ( x , t ) ⟩ ) {\displaystyle {\begin{aligned}\ell (\mathbf {y} )&=\max(0,\Delta (\mathbf {y} ,\mathbf {t} )+\langle \mathbf {w} ,\phi (\mathbf {x} ,\mathbf {y} )\rangle -\langle \mathbf {w} ,\phi (\mathbf {x} ,\mathbf {t} )\rangle )\\&=\max(0,\max _{y\in {\mathcal {Y}}}\left(\Delta (\mathbf {y} ,\mathbf {t} )+\langle \mathbf {w} ,\phi (\mathbf {x} ,\mathbf {y} )\rangle \right)-\langle \mathbf {w} ,\phi (\mathbf {x} ,\mathbf {t} )\rangle )\end{aligned}}} . == Optimization == The hinge loss is a convex function, so many of the usual convex optimizers used in machine learning can work with it. It is not differentiable, but has a subgradient with respect to model parameters w of a linear SVM with score function y = w ⋅ x {\displaystyle y=\mathbf {w} \cdot \mathbf {x} } that is given by ∂ ℓ ∂ w i = { − t ⋅ x i if t ⋅ y < 1 , 0 otherwise . {\displaystyle {\frac {\partial \ell }{\partial w_{i}}}={\begin{cases}-t\cdot x_{i}&{\text{if }}t\cdot y<1,\\0&{\text{otherwise}}.\end{cases}}} However, since the derivative of the hinge loss at t y = 1 {\displaystyle ty=1} is undefined, smoothed versions may be preferred for optimization, such as Rennie and Srebro's ℓ ( y ) = { 1 2 − t y if t y ≤ 0 , 1 2 ( 1 − t y ) 2 if 0 < t y < 1 , 0 if 1 ≤ t y {\displaystyle \ell (y)={\begin{cases}{\frac {1}{2}}-ty&{\text{if}}~~ty\leq 0,\\{\frac {1}{2}}(1-ty)^{2}&{\text{if}}~~0 Read more →

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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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  Concept drift

  In predictive analytics, data science, machine learning and related fields, concept drift or drift is an evolution of data that invalidates the data model. It happens when the statistical properties of the target variable, which the model is trying to predict, change over time in unforeseen ways. This causes problems because the predictions become less accurate as time passes. Drift detection and drift adaptation are of paramount importance in the fields that involve dynamically changing data and data models. == Predictive model decay == In machine learning and predictive analytics this drift phenomenon is called concept drift. In machine learning, a common element of a data model are the statistical properties, such as probability distribution of the actual data. If they deviate from the statistical properties of the training data set, then the learned predictions may become invalid, if the drift is not addressed. == Data configuration decay == Another important area is software engineering, where three types of data drift affecting data fidelity may be recognized. Changes in the software environment ("infrastructure drift") may invalidate software infrastructure configuration. "Structural drift" happens when the data schema changes, which may invalidate databases. "Semantic drift" is changes in the meaning of data while the structure does not change. In many cases this may happen in complicated applications when many independent developers introduce changes without proper awareness of the effects of their changes in other areas of the software system. For many application systems, the nature of data on which they operate are subject to changes for various reasons, e.g., due to changes in business model, system updates, or switching the platform on which the system operates. In the case of cloud computing, infrastructure drift that may affect the applications running on cloud may be caused by the updates of cloud software. There are several types of detrimental effects of data drift on data fidelity. Data corrosion is passing the drifted data into the system undetected. Data loss happens when valid data are ignored due to non-conformance with the applied schema. Squandering is the phenomenon when new data fields are introduced upstream in the data processing pipeline, but somewhere downstream these data fields are absent. == Inconsistent data == "Data drift" may refer to the phenomenon when database records fail to match the real-world data due to the changes in the latter over time. This is a common problem with databases involving people, such as customers, employees, citizens, residents, etc. Human data drift may be caused by unrecorded changes in personal data, such as place of residence or name, as well as due to errors during data input. "Data drift" may also refer to inconsistency of data elements between several replicas of a database. The reasons can be difficult to identify. A simple drift detection is to run checksum regularly. However the remedy may be not so easy. == Examples == The behavior of the customers in an online shop may change over time. For example, if weekly merchandise sales are to be predicted, and a predictive model has been developed that works satisfactorily. The model may use inputs such as the amount of money spent on advertising, promotions being run, and other metrics that may affect sales. The model is likely to become less and less accurate over time – this is concept drift. In the merchandise sales application, one reason for concept drift may be seasonality, which means that shopping behavior changes seasonally. Perhaps there will be higher sales in the winter holiday season than during the summer, for example. Concept drift generally occurs when the covariates that comprise the data set begin to explain the variation of your target set less accurately — there may be some confounding variables that have emerged, and that one simply cannot account for, which renders the model accuracy to progressively decrease with time. Generally, it is advised to perform health checks as part of the post-production analysis and to re-train the model with new assumptions upon signs of concept drift. == Possible remedies == To prevent deterioration in prediction accuracy because of concept drift, reactive and tracking solutions can be adopted. Reactive solutions retrain the model in reaction to a triggering mechanism, such as a change-detection test or control charts from statistical process control, to explicitly detect concept drift as a change in the statistics of the data-generating process. When concept drift is detected, the current model is no longer up-to-date and must be replaced by a new one to restore prediction accuracy. A shortcoming of reactive approaches is that performance may decay until the change is detected. Tracking solutions seek to track the changes in the concept by continually updating the model. Methods for achieving this include online machine learning, frequent retraining on the most recently observed samples, and maintaining an ensemble of classifiers where one new classifier is trained on the most recent batch of examples and replaces the oldest classifier in the ensemble. Contextual information, when available, can be used to better explain the causes of the concept drift: for instance, in the sales prediction application, concept drift might be compensated by adding information about the season to the model. By providing information about the time of the year, the rate of deterioration of your model is likely to decrease, but concept drift is unlikely to be eliminated altogether. This is because actual shopping behavior does not follow any static, finite model. New factors may arise at any time that influence shopping behavior, the influence of the known factors or their interactions may change. Concept drift cannot be avoided for complex phenomena that are not governed by fixed laws of nature. All processes that arise from human activity, such as socioeconomic processes, and biological processes are likely to experience concept drift. Therefore, periodic retraining, also known as refreshing, of any model is necessary. === Remedy methods === DDM (Drift Detection Method): detects drift by monitoring the model's error rate over time. When the error rate passes a set threshold, it enters a warning phase, and if it passes another threshold, it enters a drift phase. EDDM (Early Drift Detection Method): improves DDM's detection rate by tracking the average distance between two errors instead of only the error rate. ADWIN (Adaptive Windowing): dynamically stores a window of recent data and warns the user if it detects a significant change between the statistics of the window's earlier data compared to more recent data. KSWIN (Kolmogorov–Smirnov Windowing): detects drift based on the Kolmogorov-Smirnov statistical test. DDM and EDDM: Concept Drift Detection online supervised methods that rely on sequential error monitoring to estimate the evolving error rate. ADWIN and KSWIN: Windowing maintain a "window", a subset of the most recent data, of the data stream, which it checks for statistical differences across the window. == Applications in security == Concept drift is a recurring issue in security analytics, especially in malware and intrusion detection. In these systems, models are often trained on past logs, binaries or network traces, but the behaviour of attackers changes over time as new malware families, obfuscation techniques and campaigns appear. When the data no longer resemble the training set, the decision boundaries learned by classifiers or anomaly detectors can become misaligned with the current threat landscape and detection performance can drop unless the models are updated or replaced. Several studies on Windows malware model detection as an evolving data stream and track how performance changes as time passes. They show that classifiers trained on a fixed time window can perform well on nearby data but deteriorate quickly when evaluated on samples collected months or years later, even when large amounts of training data are available. In order to keep up with this, security systems often use sliding or adaptive windows, which restrict training to the most recent portion of the data so that older, less relevant examples are gradually discarded. They also employ drift detectors such as ADWIN and KSWIN that monitor error rates or changes in the distribution of recent observations and signal when the statistics of the incoming stream differ significantly from the past, prompting retraining or model replacement. Related problems appear in spam filtering, fraud detection and intrusion detection, where adversaries change content, patterns of activity or network behavior to evade models trained on historical data. In these settings drift can be gradual, as new types of spam or fraud emerge, or abrupt, after a sudden shift in attack techniques. Common strategies to remain eff

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  CN2 algorithm

  The CN2 induction algorithm is a learning algorithm for rule induction. It is designed to work even when the training data is imperfect. It is based on ideas from the AQ algorithm and the ID3 algorithm. As a consequence it creates a rule set like that created by AQ but is able to handle noisy data like ID3. == Description of algorithm == The algorithm must be given a set of examples, TrainingSet, which have already been classified in order to generate a list of classification rules. A set of conditions, SimpleConditionSet, which can be applied, alone or in combination, to any set of examples is predefined to be used for the classification. routine CN2(TrainingSet) let the ClassificationRuleList be empty repeat let the BestConditionExpression be Find_BestConditionExpression(TrainingSet) if the BestConditionExpression is not nil then let the TrainingSubset be the examples covered by the BestConditionExpression remove from the TrainingSet the examples in the TrainingSubset let the MostCommonClass be the most common class of examples in the TrainingSubset append to the ClassificationRuleList the rule 'if ' the BestConditionExpression ' then the class is ' the MostCommonClass until the TrainingSet is empty or the BestConditionExpression is nil return the ClassificationRuleList routine Find_BestConditionExpression(TrainingSet) let the ConditionalExpressionSet be empty let the BestConditionExpression be nil repeat let the TrialConditionalExpressionSet be the set of conditional expressions, {x and y where x belongs to the ConditionalExpressionSet and y belongs to the SimpleConditionSet}. remove all formulae in the TrialConditionalExpressionSet that are either in the ConditionalExpressionSet (i.e., the unspecialized ones) or null (e.g., big = y and big = n) for every expression, F, in the TrialConditionalExpressionSet if F is statistically significant and F is better than the BestConditionExpression by user-defined criteria when tested on the TrainingSet then replace the current value of the BestConditionExpression by F while the number of expressions in the TrialConditionalExpressionSet > user-defined maximum remove the worst expression from the TrialConditionalExpressionSet let the ConditionalExpressionSet be the TrialConditionalExpressionSet until the ConditionalExpressionSet is empty return the BestConditionExpression

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  Perceptron

  In machine learning, the perceptron is an algorithm for supervised learning of binary classifiers. A binary classifier is a function that can decide whether or not an input, represented by a vector of numbers, belongs to some specific class. It is a type of linear classifier, i.e. a classification algorithm that makes its predictions based on a linear predictor function combining a set of weights with the feature vector. == History == The artificial neuron and artificial neural network were invented in 1943 by Warren McCulloch and Walter Pitts in their seminal paper "A Logical Calculus of the Ideas Immanent in Nervous Activity". In 1957, Frank Rosenblatt was at the Cornell Aeronautical Laboratory. He simulated the perceptron on an IBM 704. Later, he obtained funding by the Information Systems Branch of the United States Office of Naval Research and the Rome Air Development Center, to build a custom-made computer, the Mark I Perceptron. It was first publicly demonstrated on 23 June 1960. The machine was "part of a previously secret four-year NPIC [the US' National Photographic Interpretation Center] effort from 1963 through 1966 to develop this algorithm into a useful tool for photo-interpreters". Rosenblatt described the details of the perceptron in a 1958 paper. His organization of a perceptron is constructed of three kinds of cells ("units"): S, A, R, which stand for "sensory", "association" and "response". He presented at the first international symposium on AI, Mechanisation of Thought Processes, which took place in 1958 November. Rosenblatt's project was funded under Contract Nonr-401(40) "Cognitive Systems Research Program", which lasted from 1959 to 1970, and Contract Nonr-2381(00) "Project PARA" ("PARA" means "Perceiving and Recognition Automata"), which lasted from 1957 to 1963. In 1959, the Institute for Defense Analysis awarded his group a $10,000 contract. By September 1961, the ONR awarded further $153,000 worth of contracts, with $108,000 committed for 1962. The ONR research manager, Marvin Denicoff, stated that ONR, instead of ARPA, funded the Perceptron project, because the project was unlikely to produce technological results in the near or medium term. Funding from ARPA go up to the order of millions dollars, while from ONR are on the order of 10,000 dollars. Meanwhile, the head of IPTO at ARPA, J.C.R. Licklider, was interested in 'self-organizing', 'adaptive' and other biologically-inspired methods in the 1950s; but by the mid-1960s he was openly critical of these, including the perceptron. Instead he strongly favored the logical AI approach of Simon and Newell. === Mark I Perceptron machine === The perceptron was intended to be a machine, rather than a program, and while its first implementation was in software for the IBM 704, it was subsequently implemented in custom-built hardware as the Mark I Perceptron with the project name "Project PARA", designed for image recognition. The machine is currently in Smithsonian National Museum of American History. The Mark I Perceptron had three layers. One version was implemented as follows: An array of 400 photocells arranged in a 20x20 grid, named "sensory units" (S-units), or "input retina". Each S-unit can connect to up to 40 A-units. A hidden layer of 512 perceptrons, named "association units" (A-units). An output layer of eight perceptrons, named "response units" (R-units). Rosenblatt called this three-layered perceptron network the alpha-perceptron, to distinguish it from other perceptron models he experimented with. The S-units are connected to the A-units randomly (according to a table of random numbers) via a plugboard (see photo), to "eliminate any particular intentional bias in the perceptron". The connection weights are fixed, not learned. Rosenblatt was adamant about the random connections, as he believed the retina was randomly connected to the visual cortex, and he wanted his perceptron machine to resemble human visual perception. The A-units are connected to the R-units, with adjustable weights encoded in potentiometers, and weight updates during learning were performed by electric motors.The hardware details are in an operators' manual. In a 1958 press conference organized by the US Navy, Rosenblatt made statements about the perceptron that caused a heated controversy among the fledgling AI community; based on Rosenblatt's statements, The New York Times reported the perceptron to be "the embryo of an electronic computer that [the Navy] expects will be able to walk, talk, see, write, reproduce itself and be conscious of its existence." The Photo Division of Central Intelligence Agency, from 1960 to 1964, studied the use of Mark I Perceptron machine for recognizing militarily interesting silhouetted targets (such as planes and ships) in aerial photos. === Principles of Neurodynamics (1962) === Rosenblatt described his experiments with many variants of the Perceptron machine in a book Principles of Neurodynamics (1962). The book is a published version of the 1961 report. Among the variants are: "cross-coupling" (connections between units within the same layer) with possibly closed loops, "back-coupling" (connections from units in a later layer to units in a previous layer), four-layer perceptrons where the last two layers have adjustable weights (and thus a proper multilayer perceptron), incorporating time-delays to perceptron units, to allow for processing sequential data, analyzing audio (instead of images). The machine was shipped from Cornell to Smithsonian in 1967, under a government transfer administered by the Office of Naval Research. === Perceptrons (1969) === Although the perceptron initially seemed promising, it was quickly proved that perceptrons could not be trained to recognise many classes of patterns. This caused the field of neural network research to stagnate for many years, before it was recognised that a feedforward neural network with two or more layers (also called a multilayer perceptron) had greater processing power than perceptrons with one layer (also called a single-layer perceptron). Single-layer perceptrons are only capable of learning linearly separable patterns. For a classification task with some step activation function, a single node will have a single line dividing the data points forming the patterns. More nodes can create more dividing lines, but those lines must somehow be combined to form more complex classifications. A second layer of perceptrons, or even linear nodes, are sufficient to solve many otherwise non-separable problems. In 1969, a famous book entitled Perceptrons by Marvin Minsky and Seymour Papert showed that it was impossible for these classes of network to learn an XOR function. It is often incorrectly believed that they also conjectured that a similar result would hold for a multi-layer perceptron network. However, this is not true, as both Minsky and Papert already knew that multi-layer perceptrons were capable of producing an XOR function. (See the page on Perceptrons (book) for more information.) Nevertheless, the often-miscited Minsky and Papert text caused a significant decline in interest and funding of neural network research. It took ten more years until neural network research experienced a resurgence in the 1980s. This text was reprinted in 1987 as "Perceptrons - Expanded Edition" where some errors in the original text are shown and corrected. === Subsequent work === Rosenblatt continued working on perceptrons despite diminishing funding. The last attempt was Tobermory, built between 1961 and 1967, built for speech recognition. It occupied an entire room. It had 4 layers with 12,000 weights implemented by toroidal magnetic cores. By the time of its completion, simulation on digital computers had become faster than purpose-built perceptron machines. He died in a boating accident in 1971. A simulation program for neural networks was written for IBM 7090/7094, and was used to study various pattern recognition applications, such as character recognition, particle tracks in bubble-chamber photographs; phoneme, isolated word, and continuous speech recognition; speaker verification; and center-of-attention mechanisms for image processing. The kernel perceptron algorithm was already introduced in 1964 by Aizerman et al. Margin bounds guarantees were given for the Perceptron algorithm in the general non-separable case first by Freund and Schapire (1998), and more recently by Mohri and Rostamizadeh (2013) who extend previous results and give new and more favorable L1 bounds. The perceptron is a simplified model of a biological neuron. While the complexity of biological neuron models is often required to fully understand neural behavior, research suggests a perceptron-like linear model can produce some behavior seen in real neurons. The solution spaces of decision boundaries for all binary functions and learning behaviors are studied in. == Definition == In the modern sense, the perceptron is an algori

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  Multidimensional analysis

  In statistics, econometrics and related fields, multidimensional analysis (MDA) is a data analysis process that groups data into two categories: data dimensions and measurements. For example, a data set consisting of the number of wins for a single football team at each of several years is a single-dimensional (in this case, longitudinal) data set. A data set consisting of the number of wins for several football teams in a single year is also a single-dimensional (in this case, cross-sectional) data set. A data set consisting of the number of wins for several football teams over several years is a two-dimensional data set. == Higher dimensions == In many disciplines, two-dimensional data sets are also called panel data. While, strictly speaking, two- and higher-dimensional data sets are "multi-dimensional", the term "multidimensional" tends to be applied only to data sets with three or more dimensions. For example, some forecast data sets provide forecasts for multiple target periods, conducted by multiple forecasters, and made at multiple horizons. The three dimensions provide more information than can be gleaned from two-dimensional panel data sets. == Software == Computer software for MDA include Online analytical processing (OLAP) for data in relational databases, pivot tables for data in spreadsheets, and Array DBMSs for general multi-dimensional data (such as raster data) in science, engineering, and business.

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  JDoodle

  JDoodle is a cloud-based online integrated development environment and compiler platform that supports execution of source code in 70+ programming languages including Java, Python, C/C++, PHP, Ruby, Perl, HTML, and more. It provides zero‑setup code for compilation, execution, and sharing via a web browser interface. == Features == Provides real‑time collaboration and code embedding via shareable URLs and APIs Offers an integrated terminal interface supporting database engines such as MySQL and MongoDB. JDroid — AI‑assistant to generate code snippets, optimize code, and assist debugging. == Languages and frameworks supported ==

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  Facial recognition system

  A facial recognition system is a technology potentially capable of matching a human face from a digital image or a video frame against a database of faces. Such a system is typically employed to authenticate users through ID verification services, and works by pinpointing and measuring facial features from a given image. Development on similar systems began in the 1960s as a form of computer application. Since their inception, facial recognition systems have seen wider uses in recent times on smartphones and in other forms of technology, such as robotics. Because computerized facial recognition involves the measurement of a human's physiological characteristics, facial recognition systems are categorized as biometrics. Although the accuracy of facial recognition systems as a biometric technology is lower than iris recognition, fingerprint image acquisition, palm recognition or voice recognition, it is widely adopted due to its contactless process. Facial recognition systems have been deployed in advanced human–computer interaction, video surveillance, law enforcement, passenger screening, decisions on employment and housing, and automatic indexing of images. Facial recognition systems are employed throughout the world today by governments and private companies. Their effectiveness varies, and some systems have previously been scrapped because of their ineffectiveness. The use of facial recognition systems has also raised controversy, with claims that the systems violate citizens' privacy, commonly make incorrect identifications, encourage gender norms and racial profiling, and do not protect important biometric data. The appearance of synthetic media such as deepfakes has also raised concerns about its security. These claims have led to the ban of facial recognition systems in several cities in the United States. Growing societal concerns led social networking company Meta Platforms to shut down its Facebook facial recognition system in 2021, deleting the face-scan data of more than one billion users. The change represented one of the largest shifts in facial recognition usage in the technology's history. IBM also stopped offering facial recognition technology due to similar concerns. == History of facial recognition technology == Automated facial recognition was pioneered in the 1960s by Woody Bledsoe, Helen Chan Wolf, and Charles Bisson, whose work focused on teaching computers to recognize human faces. Their early facial recognition project was dubbed "man-machine" because a human first needed to establish the coordinates of facial features in a photograph before they could be used by a computer for recognition. Using a graphics tablet, a human would pinpoint facial features coordinates, such as the pupil centers, the inside and outside corners of eyes, and the widows peak in the hairline. The coordinates were used to calculate 20 individual distances, including the width of the mouth and of the eyes. A human could process about 40 pictures an hour, building a database of these computed distances. A computer would then automatically compare the distances for each photograph, calculate the difference between the distances, and return the closed records as a possible match. In 1970, Takeo Kanade publicly demonstrated a face-matching system that located anatomical features such as the chin and calculated the distance ratio between facial features without human intervention. Later tests revealed that the system could not always reliably identify facial features. Nonetheless, interest in the subject grew and in 1977 Kanade published the first detailed book on facial recognition technology. In 1993, the Defense Advanced Research Project Agency (DARPA) and the Army Research Laboratory (ARL) established the face recognition technology program FERET to develop "automatic face recognition capabilities" that could be employed in a productive real life environment "to assist security, intelligence, and law enforcement personnel in the performance of their duties." Face recognition systems that had been trialled in research labs were evaluated. The FERET tests found that while the performance of existing automated facial recognition systems varied, a handful of existing methods could viably be used to recognize faces in still images taken in a controlled environment. The FERET tests spawned three US companies that sold automated facial recognition systems. Vision Corporation and Miros Inc were founded in 1994, by researchers who used the results of the FERET tests as a selling point. Viisage Technology was established by an identification card defense contractor in 1996 to commercially exploit the rights to the facial recognition algorithm developed by Alex Pentland at MIT. Following the 1993 FERET face-recognition vendor test, the Department of Motor Vehicles (DMV) offices in West Virginia and New Mexico became the first DMV offices to use automated facial recognition systems to prevent people from obtaining multiple driving licenses using different names. Driver's licenses in the United States were at that point a commonly accepted form of photo identification. DMV offices across the United States were undergoing a technological upgrade and were in the process of establishing databases of digital ID photographs. This enabled DMV offices to deploy the facial recognition systems on the market to search photographs for new driving licenses against the existing DMV database. DMV offices became one of the first major markets for automated facial recognition technology and introduced US citizens to facial recognition as a standard method of identification. The increase of the US prison population in the 1990s prompted U.S. states to established connected and automated identification systems that incorporated digital biometric databases, in some instances this included facial recognition. In 1999, Minnesota incorporated the facial recognition system FaceIT by Visionics into a mug shot booking system that allowed police, judges and court officers to track criminals across the state. Until the 1990s, facial recognition systems were developed primarily by using photographic portraits of human faces. Research on face recognition to reliably locate a face in an image that contains other objects gained traction in the early 1990s with the principal component analysis (PCA). The PCA method of face detection is also known as Eigenface and was developed by Matthew Turk and Alex Pentland. Turk and Pentland combined the conceptual approach of the Karhunen–Loève theorem and factor analysis, to develop a linear model. Eigenfaces are determined based on global and orthogonal features in human faces. A human face is calculated as a weighted combination of a number of Eigenfaces. Because few Eigenfaces were used to encode human faces of a given population, Turk and Pentland's PCA face detection method greatly reduced the amount of data that had to be processed to detect a face. Pentland in 1994 defined Eigenface features, including eigen eyes, eigen mouths and eigen noses, to advance the use of PCA in facial recognition. In 1997, the PCA Eigenface method of face recognition was improved upon using linear discriminant analysis (LDA) to produce Fisherfaces. LDA Fisherfaces became dominantly used in PCA feature based face recognition. While Eigenfaces were also used for face reconstruction. In these approaches no global structure of the face is calculated which links the facial features or parts. Purely feature based approaches to facial recognition were overtaken in the late 1990s by the Bochum system, which used Gabor filter to record the face features and computed a grid of the face structure to link the features. Christoph von der Malsburg and his research team at the University of Bochum developed Elastic Bunch Graph Matching in the mid-1990s to extract a face out of an image using skin segmentation. By 1997, the face detection method developed by Malsburg outperformed most other facial detection systems on the market. The so-called "Bochum system" of face detection was sold commercially on the market as ZN-Face to operators of airports and other busy locations. The software was "robust enough to make identifications from less-than-perfect face views. It can also often see through such impediments to identification as mustaches, beards, changed hairstyles and glasses—even sunglasses". Real-time face detection in video footage became possible in 2001 with the Viola–Jones object detection framework for faces. Paul Viola and Michael Jones combined their face detection method with the Haar-like feature approach to object recognition in digital images to launch AdaBoost, the first real-time frontal-view face detector. By 2015, the Viola–Jones algorithm had been implemented using small low power detectors on handheld devices and embedded systems. Therefore, the Viola–Jones algorithm has not only broadened the practical application of face recognition systems but

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  Facial recognition system

  A facial recognition system is a technology potentially capable of matching a human face from a digital image or a video frame against a database of faces. Such a system is typically employed to authenticate users through ID verification services, and works by pinpointing and measuring facial features from a given image. Development on similar systems began in the 1960s as a form of computer application. Since their inception, facial recognition systems have seen wider uses in recent times on smartphones and in other forms of technology, such as robotics. Because computerized facial recognition involves the measurement of a human's physiological characteristics, facial recognition systems are categorized as biometrics. Although the accuracy of facial recognition systems as a biometric technology is lower than iris recognition, fingerprint image acquisition, palm recognition or voice recognition, it is widely adopted due to its contactless process. Facial recognition systems have been deployed in advanced human–computer interaction, video surveillance, law enforcement, passenger screening, decisions on employment and housing, and automatic indexing of images. Facial recognition systems are employed throughout the world today by governments and private companies. Their effectiveness varies, and some systems have previously been scrapped because of their ineffectiveness. The use of facial recognition systems has also raised controversy, with claims that the systems violate citizens' privacy, commonly make incorrect identifications, encourage gender norms and racial profiling, and do not protect important biometric data. The appearance of synthetic media such as deepfakes has also raised concerns about its security. These claims have led to the ban of facial recognition systems in several cities in the United States. Growing societal concerns led social networking company Meta Platforms to shut down its Facebook facial recognition system in 2021, deleting the face-scan data of more than one billion users. The change represented one of the largest shifts in facial recognition usage in the technology's history. IBM also stopped offering facial recognition technology due to similar concerns. == History of facial recognition technology == Automated facial recognition was pioneered in the 1960s by Woody Bledsoe, Helen Chan Wolf, and Charles Bisson, whose work focused on teaching computers to recognize human faces. Their early facial recognition project was dubbed "man-machine" because a human first needed to establish the coordinates of facial features in a photograph before they could be used by a computer for recognition. Using a graphics tablet, a human would pinpoint facial features coordinates, such as the pupil centers, the inside and outside corners of eyes, and the widows peak in the hairline. The coordinates were used to calculate 20 individual distances, including the width of the mouth and of the eyes. A human could process about 40 pictures an hour, building a database of these computed distances. A computer would then automatically compare the distances for each photograph, calculate the difference between the distances, and return the closed records as a possible match. In 1970, Takeo Kanade publicly demonstrated a face-matching system that located anatomical features such as the chin and calculated the distance ratio between facial features without human intervention. Later tests revealed that the system could not always reliably identify facial features. Nonetheless, interest in the subject grew and in 1977 Kanade published the first detailed book on facial recognition technology. In 1993, the Defense Advanced Research Project Agency (DARPA) and the Army Research Laboratory (ARL) established the face recognition technology program FERET to develop "automatic face recognition capabilities" that could be employed in a productive real life environment "to assist security, intelligence, and law enforcement personnel in the performance of their duties." Face recognition systems that had been trialled in research labs were evaluated. The FERET tests found that while the performance of existing automated facial recognition systems varied, a handful of existing methods could viably be used to recognize faces in still images taken in a controlled environment. The FERET tests spawned three US companies that sold automated facial recognition systems. Vision Corporation and Miros Inc were founded in 1994, by researchers who used the results of the FERET tests as a selling point. Viisage Technology was established by an identification card defense contractor in 1996 to commercially exploit the rights to the facial recognition algorithm developed by Alex Pentland at MIT. Following the 1993 FERET face-recognition vendor test, the Department of Motor Vehicles (DMV) offices in West Virginia and New Mexico became the first DMV offices to use automated facial recognition systems to prevent people from obtaining multiple driving licenses using different names. Driver's licenses in the United States were at that point a commonly accepted form of photo identification. DMV offices across the United States were undergoing a technological upgrade and were in the process of establishing databases of digital ID photographs. This enabled DMV offices to deploy the facial recognition systems on the market to search photographs for new driving licenses against the existing DMV database. DMV offices became one of the first major markets for automated facial recognition technology and introduced US citizens to facial recognition as a standard method of identification. The increase of the US prison population in the 1990s prompted U.S. states to established connected and automated identification systems that incorporated digital biometric databases, in some instances this included facial recognition. In 1999, Minnesota incorporated the facial recognition system FaceIT by Visionics into a mug shot booking system that allowed police, judges and court officers to track criminals across the state. Until the 1990s, facial recognition systems were developed primarily by using photographic portraits of human faces. Research on face recognition to reliably locate a face in an image that contains other objects gained traction in the early 1990s with the principal component analysis (PCA). The PCA method of face detection is also known as Eigenface and was developed by Matthew Turk and Alex Pentland. Turk and Pentland combined the conceptual approach of the Karhunen–Loève theorem and factor analysis, to develop a linear model. Eigenfaces are determined based on global and orthogonal features in human faces. A human face is calculated as a weighted combination of a number of Eigenfaces. Because few Eigenfaces were used to encode human faces of a given population, Turk and Pentland's PCA face detection method greatly reduced the amount of data that had to be processed to detect a face. Pentland in 1994 defined Eigenface features, including eigen eyes, eigen mouths and eigen noses, to advance the use of PCA in facial recognition. In 1997, the PCA Eigenface method of face recognition was improved upon using linear discriminant analysis (LDA) to produce Fisherfaces. LDA Fisherfaces became dominantly used in PCA feature based face recognition. While Eigenfaces were also used for face reconstruction. In these approaches no global structure of the face is calculated which links the facial features or parts. Purely feature based approaches to facial recognition were overtaken in the late 1990s by the Bochum system, which used Gabor filter to record the face features and computed a grid of the face structure to link the features. Christoph von der Malsburg and his research team at the University of Bochum developed Elastic Bunch Graph Matching in the mid-1990s to extract a face out of an image using skin segmentation. By 1997, the face detection method developed by Malsburg outperformed most other facial detection systems on the market. The so-called "Bochum system" of face detection was sold commercially on the market as ZN-Face to operators of airports and other busy locations. The software was "robust enough to make identifications from less-than-perfect face views. It can also often see through such impediments to identification as mustaches, beards, changed hairstyles and glasses—even sunglasses". Real-time face detection in video footage became possible in 2001 with the Viola–Jones object detection framework for faces. Paul Viola and Michael Jones combined their face detection method with the Haar-like feature approach to object recognition in digital images to launch AdaBoost, the first real-time frontal-view face detector. By 2015, the Viola–Jones algorithm had been implemented using small low power detectors on handheld devices and embedded systems. Therefore, the Viola–Jones algorithm has not only broadened the practical application of face recognition systems but

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  Soft independent modelling of class analogies

  Soft independent modelling by class analogy (SIMCA) is a statistical method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes. == Method == In order to build the classification models, the samples belonging to each class need to be analysed using principal component analysis (PCA); only the significant components are retained. For a given class, the resulting model then describes either a line (for one Principal Component or PC), plane (for two PCs) or hyper-plane (for more than two PCs). For each modelled class, the mean orthogonal distance of training data samples from the line, plane, or hyper-plane (calculated as the residual standard deviation) is used to determine a critical distance for classification. This critical distance is based on the F-distribution and is usually calculated using 95% or 99% confidence intervals. New observations are projected into each PC model and the residual distances calculated. An observation is assigned to the model class when its residual distance from the model is below the statistical limit for the class. The observation may be found to belong to multiple classes and a measure of goodness of the model can be found from the number of cases where the observations are classified into multiple classes. The classification efficiency is usually indicated by Receiver operating characteristics. In the original SIMCA method, the ends of the hyper-plane of each class are closed off by setting statistical control limits along the retained principal components axes (i.e., score value between plus and minus 0.5 times score standard deviation). More recent adaptations of the SIMCA method close off the hyper-plane by construction of ellipsoids (e.g. Hotelling's T2 or Mahalanobis distance). With such modified SIMCA methods, classification of an object requires both that its orthogonal distance from the model and its projection within the model (i.e. score value within the region defined by the ellipsoid) are not significant. == Application == SIMCA as a method of classification has gained widespread use especially in applied statistical fields such as chemometrics and spectroscopic data analysis.

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  Fatpaint

  Fatpaint is a free, online (web-based) graphic design and desktop publishing software product and image editor. It includes integrated tools for creating page layout, painting, coloring and editing pictures and photos, drawing vector images, using dingbat vector clipart, writing rich text, creating ray traced 3D text logos and displaying graphics on products from Zazzle that can be purchased or sold. Fatpaint integrates desktop publishing features with brush painting, vector drawing and custom printed products in a single Flash application. It supports the use of a pressure-sensitive pen tablet and allows the user to add images by searching Wikimedia, Picasa, Flickr, Google, Yahoo, Bing, and Fatpaint's own collection of public domain images. The completed project can be saved on Fatpaint's server or locally. Fatpaint is affiliated with Zazzle, and owned by Mersica (also the developer of MakeWebVideo). == History == Fatpaint was launched in May 2010, after five years of development by Danish-Brazilian software developer, Mario Gomes Cavalcanti. After his departure, he was involved in the development of two of Denmark's most visited websites and is responsible for developing and running Fatpaint. Partner Kenneth Christensen mastered assembler and graphics programming on the Amiga computer. He spent years with Mario on the Amiga demo scene. According to the CEO, Kenneth helped him with the Linux servers while he handled the development, administration, promotion, video production, testing and content. The founder of Fatpaint also created "Make Web Video" (or Video Maker), a web application for creating video presentations for business, families and individuals. Video Maker allows users to give out the videos for personal or business use in a simple and affordable way. == Tools == Fatpaint provides free online logo maker, graphic design, vector drawing, photo editor and paint design in English, Danish and Portuguese. === Photo Editor === Users can change photo colours by manipulating R, G, B and A channels, saturation, contrast, brightness, hue, gamma, sharpness, tint and RGBA matrix. Users can also remove unwanted background and other artifacts by using the paint tools with added effects or by cloning. Multiple photos can be combined into a single image. Users can pick different blend modes and multiple layers. Users can also extract or change parts of the photo by cropping, resizing, skewing, bending, distorting and rotating in 2D and 3D. Hence, users' graphics can be printed on custom products that can be bought and sold for personal and business purposes. === Vector Drawing === Users can choose from 5000 vector images or draw vector graphics and art from scratch, using Fatpaint's vector shape creation tools. It also provides advanced symmetric vector transformation in 2D and 3D, as well as support for colour gradients. Multiple drawings can be combined to form complex vector shapes. Different blend modes and effects are supported. Vector drawings can be cropped, resized, skewed, distorted and rotated in 2D and 3D. Similar to Fatpaint's photo editor, vector graphics can be displayed on custom printed products that can be purchased and sold by the users for personal or business uses. === Paint Design === Fatpaint has full support for Pen Tablets and users can pick pen, brush, airbrush, paint bucket, clone painting, eraser and smudging tools. Fatpaint offers 8 palettes for painting, plus 13 palettes when clone painting. Fatpaint allows users to import or create their own brushes and thousands of free clipart drawings and brush sets that have dynamic brushes, effects and blend modes. Paintings can be combined in different layers and objects. Similarly, paintings can be cropped, resized, skewed, bent, distorted and rotated in 2D and 3D. Moreover, the graphics can be displayed on custom printed products, which users can buy or sell for personal or business uses. == Top Features == 3D Text objects: Create photorealistic, ray-traced 3D text logos and images. Image objects: Paint on multiple layers, import or create your own brushes, clone painting, and painting with effects. Vector drawing objects: Create vector images using multiple paths. Rich text objects with 981 fonts. Effect objects: Blur, Drop Shadow, Glow, Gradient Glow, Bevel, Gradient Bevel, Color manipulations. Page layout: Create multiple pages with a size limit of 64 megapixels, and arrange graphical objects on created pages (each object can be up to 7.8 megapixels in size). Nest graphical objects and transform them into 2D and 3D. Skew, bend and distort images and text. Design, purchase and sell custom-printed products. Fatpaint can send the projects to a printing company. Supports pressure-sensitive pen tablets. Fonts, public domain images, cliparts, and brushes. == Compatibility == Fatpaint supports Firefox, Google Chrome, Opera, and Internet Explorer with cookies and JavaScript enabled. Other browsers may not work correctly due to their support of Java Applets. Fatpaint requires Adobe's Flash 10 or newer and Sun's Java 6 or newer. It is recommended to run on Windows 7 and on Apple and Linux if Java has been disabled. The editor only works on Firefox on Linux. Java and Flash integration do not work on Linux and Apple browsers. WikiMedia search is disabled on those browsers. Fatpaint works best with at least 2 GB RAM and 1 GB video memory, as well as a decent graphics card.

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  Linguamatics

  Linguamatics, headquartered in Cambridge, England, with offices in the United States and UK, is a provider of text mining systems through software licensing and services, primarily for pharmaceutical and healthcare applications. Founded in 2001, the company was purchased by IQVIA in January 2019. == Technology == The company develops enterprise search tools for the life sciences sector. The core natural language processing engine (I2E) uses a federated architecture to incorporate data from 3rd party resources. Initially developed to be used interactively through a graphic user interface, the core software also has an application programming interface that can be used to automate searches. LabKey, Penn Medicine, Atrius Health and Mercy all use Linguamatics software to extract electronic health record data into data warehouses. Linguamatics software is used by 17 of the top 20 global pharmaceutical companies, the US Food and Drug Administration, as well as healthcare providers. == Software community == The core software, "I2E", is used by a number of companies to either extend their own software or to publish their data. Copyright Clearance Center uses I2E to produce searchable indexes of material that would otherwise be unsearchable due to copyright. Thomson Reuters produces Cortellis Informatics Clinical Text Analytics, which depends on I2E to make clinical data accessible and searchable. Pipeline Pilot can integrate I2E as part of a workflow. ChemAxon can be used alongside I2E to allow named entity recognition of chemicals within unstructured data. Data sources include MEDLINE, ClinicalTrials.gov, FDA Drug Labels, PubMed Central, and Patent Abstracts.

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  Statistical classification

  When classification is performed by a computer, statistical methods are normally used to develop the algorithm. Often, the individual observations are analyzed into a set of quantifiable properties, known variously as explanatory variables or features. These properties may variously be categorical (e.g. "A", "B", "AB" or "O", for blood type), ordinal (e.g. "large", "medium" or "small"), integer-valued (e.g. the number of occurrences of a particular word in an email) or real-valued (e.g. a measurement of blood pressure). Other classifiers work by comparing observations to previous observations by means of a similarity or distance function. An algorithm that implements classification, especially in a concrete implementation, is known as a classifier. The term "classifier" sometimes also refers to the mathematical function, implemented by a classification algorithm, that maps input data to a category. Terminology across fields is quite varied. In statistics, where classification is often done with logistic regression or a similar procedure, the properties of observations are termed explanatory variables (or independent variables, regressors, etc.), and the categories to be predicted are known as outcomes, which are considered to be possible values of the dependent variable. In machine learning, the observations are often known as instances, the explanatory variables are termed features (grouped into a feature vector), and the possible categories to be predicted are classes. Other fields may use different terminology: e.g. in community ecology, the term "classification" normally refers to cluster analysis. == Relation to other problems == Classification and clustering are examples of the more general problem of pattern recognition, which is the assignment of some sort of output value to a given input value. Other examples are regression, which assigns a real-valued output to each input; sequence labeling, which assigns a class to each member of a sequence of values (for example, part of speech tagging, which assigns a part of speech to each word in an input sentence); parsing, which assigns a parse tree to an input sentence, describing the syntactic structure of the sentence; etc. A common subclass of classification is probabilistic classification. Algorithms of this nature use statistical inference to find the best class for a given instance. Unlike other algorithms, which simply output a "best" class, probabilistic algorithms output a probability of the instance being a member of each of the possible classes. The best class is normally then selected as the one with the highest probability. However, such an algorithm has numerous advantages over non-probabilistic classifiers: It can output a confidence value associated with its choice (in general, a classifier that can do this is known as a confidence-weighted classifier). Correspondingly, it can abstain when its confidence of choosing any particular output is too low. Because of the probabilities which are generated, probabilistic classifiers can be more effectively incorporated into larger machine-learning tasks, in a way that partially or completely avoids the problem of error propagation. == Frequentist procedures == Early work on statistical classification was undertaken by Fisher, in the context of two-group problems, leading to Fisher's linear discriminant function as the rule for assigning a group to a new observation. This early work assumed that data-values within each of the two groups had a multivariate normal distribution. The extension of this same context to more than two groups has also been considered with a restriction imposed that the classification rule should be linear. Later work for the multivariate normal distribution allowed the classifier to be nonlinear: several classification rules can be derived based on different adjustments of the Mahalanobis distance, with a new observation being assigned to the group whose centre has the lowest adjusted distance from the observation. == Bayesian procedures == Unlike frequentist procedures, Bayesian classification procedures provide a natural way of taking into account any available information about the relative sizes of the different groups within the overall population. Bayesian procedures tend to be computationally expensive and, in the days before Markov chain Monte Carlo computations were developed, approximations for Bayesian clustering rules were devised. Some Bayesian procedures involve the calculation of group-membership probabilities: these provide a more informative outcome than a simple attribution of a single group-label to each new observation. == Binary and multiclass classification == Classification can be thought of as two separate problems – binary classification and multiclass classification. In binary classification, a better understood task, only two classes are involved, whereas multiclass classification involves assigning an object to one of several classes. Since many classification methods have been developed specifically for binary classification, multiclass classification often requires the combined use of multiple binary classifiers. == Feature vectors == Most algorithms describe an individual instance whose category is to be predicted using a feature vector of individual, measurable properties of the instance. Each property is termed a feature, also known in statistics as an explanatory variable (or independent variable, although features may or may not be statistically independent). Features may variously be binary (e.g. "on" or "off"); categorical (e.g. "A", "B", "AB" or "O", for blood type); ordinal (e.g. "large", "medium" or "small"); integer-valued (e.g. the number of occurrences of a particular word in an email); or real-valued (e.g. a measurement of blood pressure). If the instance is an image, the feature values might correspond to the pixels of an image; if the instance is a piece of text, the feature values might be occurrence frequencies of different words. Some algorithms work only in terms of discrete data and require that real-valued or integer-valued data be discretized into groups (e.g. less than 5, between 5 and 10, or greater than 10). == Linear classifiers == A large number of algorithms for classification can be phrased in terms of a linear function that assigns a score to each possible category k by combining the feature vector of an instance with a vector of weights, using a dot product. The predicted category is the one with the highest score. This type of score function is known as a linear predictor function and has the following general form: score ⁡ ( X i , k ) = β k ⋅ X i , {\displaystyle \operatorname {score} (\mathbf {X} _{i},k)={\boldsymbol {\beta }}_{k}\cdot \mathbf {X} _{i},} where Xi is the feature vector for instance i, βk is the vector of weights corresponding to category k, and score(Xi, k) is the score associated with assigning instance i to category k. In discrete choice theory, where instances represent people and categories represent choices, the score is considered the utility associated with person i choosing category k. Algorithms with this basic setup are known as linear classifiers. What distinguishes them is the procedure for determining (training) the optimal weights/coefficients and the way that the score is interpreted. Examples of such algorithms include Logistic regression – Statistical model for a binary dependent variable Multinomial logistic regression – Regression for more than two discrete outcomes Probit regression – Statistical regression where the dependent variable can take only two valuesPages displaying short descriptions of redirect targets The perceptron algorithm Support vector machine – Set of methods for supervised statistical learning Linear discriminant analysis – Method used in statistics, pattern recognition, and other fields == Algorithms == Since no single form of classification is appropriate for all data sets, a large toolkit of classification algorithms has been developed. The most commonly used include: Artificial neural networks – Computational model used in machine learningPages displaying short descriptions of redirect targets Boosting (machine learning) – Ensemble learning method Random forest – Tree-based ensemble machine learning methods Genetic programming – Evolving computer programs with techniques analogous to natural genetic processes Gene expression programming – Evolutionary algorithm Multi expression programming Linear genetic programming Kernel estimation – Concept in statisticsPages displaying short descriptions of redirect targets k-nearest neighbor – Non-parametric classification methodPages displaying short descriptions of redirect targets Learning vector quantization Linear classifier – Statistical classification in machine learning Fisher's linear discriminant – Method used in statistics, pattern recognition, and other fieldsPages displaying short descriptions of redirect targets Logistic r

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