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  Amira (software)

  Amira (ah-MEER-ah) is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo. == Overview == Amira is an extendable software system for scientific visualization, data analysis, and presentation of 3D and 4D data. It is used by researchers and engineers in academia and industry. It is a tool for processing, analysis and visualization of data from various modalities; e.g. micro-CT, PET, Ultrasound. It is used in many fields, such as microscopy in biology and materials science, molecular biology, quantum physics, astrophysics, computational fluid dynamics (CFD), finite element modeling (FEM), non-destructive testing (NDT), and many more. One of the key features, besides data visualization, is Amira's set of tools for image segmentation and geometry reconstruction. This allows the user to mark (or segment) structures and regions of interest in 3D image volumes using automatic, semi-automatic, and manual tools. The segmentation can then be used for a variety of subsequent tasks, such as volumetric analysis, density analysis, shape analysis, or the generation of 3D computer models for visualization, numerical simulations, or rapid prototyping or 3D printing. Other key Amira features are multi-planar and volume visualization, image registration, filament tracing, cell separation and analysis, tetrahedral mesh generation, fiber-tracking from diffusion tensor imaging (DTI) data, skeletonization, spatial graph analysis, and stereoscopic rendering of 3D data over multiple displays and immersive virtual reality environments, including CAVEs. As a commercial product Amira requires the purchase of a license or an academic subscription. A time-limited, but full-featured evaluation version is available for download free of charge. == History == === 1993–1998: Research software === Amira's roots go back to 1993 and the Department for Scientific Visualization, headed by Hans-Christian Hege at the Zuse Institute Berlin (ZIB). The ZIB is a research institute for mathematics and informatics. The Scientific Visualization department's mission is to help solve computationally and scientifically challenging tasks in medicine, biology, engineering and materials science. For this purpose, it develops algorithms and software for 2D, 3D, and 4D data visualization and visually supported exploration and analysis. At that time, the young visualization group at the ZIB had experience with the extendable, data flow-oriented visualization environments apE, IRIS Explorer, and Advanced Visualization Studio (AVS), but was not satisfied with these products' interactivity, flexibility, and ease-of-use for non-computer scientists. Therefore, the development of a new software system was started in a research project within a medically oriented, multi-disciplinary collaborative research center. Based on experiences that Tobias Höllerer had gained in late 1993 with the new graphics library IRIS Inventor, it was decided to utilize that library. The development of the medical planning system was performed by Detlev Stalling, who later became the chief software architect of Amira. The new software was called "HyperPlan", highlighting its initial target application – a planning system for hyperthermia cancer treatment. The system was being developed on Silicon Graphics (SGI) computers, which at the time were the standard workstations used for high-end graphics computing. The software was based on libraries such as OpenGL (originally IRIS GL), Open Inventor (originally IRIS Inventor), and the graphical user interface libraries X11, Motif (software), and ViewKit. In 1998, X11/Motif/Viewkit were replaced by the Qt toolkit. The HyperPlan framework served as the base for more and more projects at the ZIB and was used by a growing number of researchers in collaborating institutions. The projects included applications in medical image computing, medical visualization, neurobiology, confocal microscopy, flow visualization, molecular analytics and computational astrophysics. === 1998–today: Commercially supported product === The growing number of users of the system started to exceed the capacities that ZIB could spare for software distribution and support, as ZIB's primary mission was algorithmic research. Therefore, the spin-off company Indeed – Visual Concepts GmbH was founded by Hans-Christian Hege, Detlev Stalling, and Malte Westerhoff. In Feb 1998 the HyperPlan software was given the new, application-neutral name "Amira". This name is not an acronym, but was chosen for being pronounceable in different languages and providing a suitable connotation, namely "to look at" or "to wonder at", from the Latin verb "admirare" (to admire), which reflects a basic situation in data visualization. A major re-design of the software was undertaken by Detlev Stalling and Malte Westerhoff in order to make it a commercially supportable product and to make it available on non-SGI computers as well. In March 1999, the first version of the commercial Amira was exhibited at the CeBIT tradeshow in Hannover, Germany on SGI IRIX and Hewlett-Packard UniX (HP-UX) booths. Versions for Linux and Microsoft Windows followed within the following twelve months. Later Mac OS X support was added. Indeed – Visual Concepts GmbH selected the Bordeaux, France and San Diego, United States based company TGS, Inc. as the worldwide distributor for Amira and completed five major releases (up to version 3.1) in the subsequent four years. In 2003 both Indeed – Visual Concepts GmbH, as well as TGS, Inc. were acquired by Massachusetts-based Mercury Computer Systems, Inc. (NASDAQ:MRCY) and became part of Mercury's newly formed life sciences business unit, later branded Visage Imaging. In 2009, Mercury Computer Systems, Inc. spun off Visage Imaging again and sold it to Melbourne, Australia based Promedicus Ltd (ASX:PME), a leading provider of radiology information systems and medical IT solutions. During this time, Amira continued to be developed in Berlin, Germany and in close collaboration with the ZIB, still headed by the original creators of Amira. TGS, located in Bordeaux, France was sold by Mercury Computer systems to a French investor and renamed to Visualization Sciences Group (VSG). VSG continued the work on a complementary product named Avizo, based on the same source code but customized for material sciences. In August 2012, FEI, to that date the largest OEM reseller of Amira, purchased VSG and the Amira business from Promedicus. This brought the two software sisters Amira and Avizo back into one hand. In August 2013, Visualization Sciences Group (VSG) became a business unit of FEI. In 2016 FEI has been bought by Thermo Fisher Scientific and became part of its Materials & Structural Analysis division in early 2017. Amira and Avizo are still being marketed as two different products; Amira for life sciences and Avizo for materials science, but the development efforts are now joined once again. In the meantime, the number of scientific articles using the Amira / Avizo software, is in the order of 10 thousands. == Amira options == === Microscopy option === Specific readers for microscopy data Image deconvolution Exploration of 3D imagery obtained from virtually any microscope Extraction and editing of filament networks from microscopy images === DICOM reader === Import of clinical and preclinical data in DICOM format === Mesh option === Generation of 3D finite element (FE) meshes from segmented image data Support for many state-of-the-art FE solver formats High-quality visualization of simulation mesh-based results, using scalar, vector, and tensor field display modules === Skeletonization option === Reconstruction and analysis of neural and vascular networks Visualization of skeletonized networks Length and diameter quantification of network segments Ordering of segments in a tree graph Skeletonization of very large image stacks === Molecular option === Advanced tools for the visualization of molecule models Hardware-accelerated volume rendering Powerful molecule editor Specific tools for complex molecular visualization === Developer option === Creation of new custom components for visualizing or data processing Implementation of new file readers or writers C++ programming language Development wizard for getting started quickly === Neuro option === Medical image analysis for DTI and brain perfusion Fiber tracking supporting several stream-line based algorithms Fiber separation into fiber bundles based on user defined source and destination regions Computation of tensor fields, diffusion weighted maps Eigenvalue decomposition of tensor fields Computation of mean transit time, cerebral blood flow, and cerebral blood volume === VR option === Visualization of data on large tiled displays

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  Constrained clustering

  In computer science, constrained clustering is a class of semi-supervised learning algorithms. Typically, constrained clustering incorporates either a set of must-link constraints, cannot-link constraints, or both, with a data clustering algorithm. A cluster in which the members conform to all must-link and cannot-link constraints is called a chunklet. == Types of constraints == Both a must-link and a cannot-link constraint define a relationship between two data instances. Together, the sets of these constraints act as a guide for which a constrained clustering algorithm will attempt to find chunklets (clusters in the dataset which satisfy the specified constraints). A must-link constraint is used to specify that the two instances in the must-link relation should be associated with the same cluster. A cannot-link constraint is used to specify that the two instances in the cannot-link relation should not be associated with the same cluster. Some constrained clustering algorithms will abort if no such clustering exists which satisfies the specified constraints. Others will try to minimize the amount of constraint violation should it be impossible to find a clustering which satisfies the constraints. Constraints could also be used to guide the selection of a clustering model among several possible solutions. == Examples == Examples of constrained clustering algorithms include: COP K-means PCKmeans (Pairwise Constrained K-means) CMWK-Means (Constrained Minkowski Weighted K-Means)

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  Population model (evolutionary algorithm)

  The population model of an evolutionary algorithm (EA) describes the structural properties of its population to which its members are subject. A population is the set of all proposed solutions of an EA considered in one iteration, which are also called individuals according to the biological role model. The individuals of a population can generate further individuals as offspring with the help of the genetic operators of the procedure. The simplest and widely used population model in EAs is the global or panmictic model, which corresponds to an unstructured population. It allows each individual to choose any other individual of the population as a partner for the production of offspring by crossover, whereby the details of the selection are irrelevant as long as the fitness of the individuals plays a significant role. Due to global mate selection, the genetic information of even slightly better individuals can prevail in a population after a few generations (iteration of an EA), provided that no better other offspring have emerged in this phase. If the solution found in this way is not the optimum sought, that is called premature convergence. This effect can be observed more often in panmictic populations. In nature global mating pools are rarely found. What prevails is a certain and limited isolation due to spatial distance. The resulting local neighbourhoods initially evolve independently and mutants have a higher chance of persisting over several generations. As a result, genotypic diversity in the gene pool is preserved longer than in a panmictic population. It is therefore obvious to divide the previously global population by substructures. Two basic models were introduced for this purpose, the island models, which are based on a division of the population into fixed subpopulations that exchange individuals from time to time, and the neighbourhood models, which assign individuals to overlapping neighbourhoods, also known as cellular genetic or evolutionary algorithms (cGA or cEA). The associated division of the population also suggests a corresponding parallelization of the procedure. For this reason, the topic of population models is also frequently discussed in the literature in connection with the parallelization of EAs. == Island models == In the island model, also called the migration model or coarse grained model, evolution takes place in strictly divided subpopulations. These can be organised panmictically, but do not have to be. From time to time an exchange of individuals takes place, which is called migration. The time between an exchange is called an epoch and its end can be triggered by various criteria: E.g. after a given time or given number of completed generations, or after the occurrence of stagnation. Stagnation can be detected, for example, by the fact that no fitness improvement has occurred in the island for a given number of generations. Island models introduce a variety of new strategy parameters: Number of subpopulations Size of the subpopulations Neighbourhood relations between islands: they determine which islands are considered neighbouring and can thus exchange individuals, see picture of a simple unidirectional ring (black arrows) and its extension by additional bidirectional neighbourhood relations (additional green arrows) Criteria for the termination of an epoch, synchronous or asynchronous migration Migration rate: number or proportion of individuals involved in migration. Migrant selection: There are many alternatives for this. E.g. the best individuals can replace the worst or randomly selected ones. Depending on the migration rate, this can affect one or more individuals at a time. With these parameters, the selection pressure can be influenced to a considerable extent. For example, it increases with the interconnectedness of the islands and decreases with the number of subpopulations or the epoch length. == Neighbourhood models or cellular evolutionary algorithms == The neighbourhood model, also called diffusion model or fine grained model, defines a topological neighbouhood relation between the individuals of a population that is independent of their phenotypic properties. The fundamental idea of this model is to provide the EA population with a special structure defined as a connected graph, in which each vertex is an individual that communicates with its nearest neighbours. Particularly, individuals are conceptually set in a toroidal mesh, and are only allowed to recombine with close individuals. This leads to a kind of locality known as isolation by distance. The set of potential mates of an individual is called its neighbourhood or deme. The adjacent figure illustrates that by showing two slightly overlapping neighbourhoods of two individuals marked yellow, through which genetic information can spread between the two demes. It is known that in this kind of algorithm, similar individuals tend to cluster and create niches that are independent of the deme boundaries and, in particular, can be larger than a deme. There is no clear borderline between adjacent groups, and close niches could be easily colonized by competitive ones and maybe merge solution contents during this process. Simultaneously, farther niches can be affected more slowly. EAs with this type of population are also well known as cellular EAs (cEA) or cellular genetic algorithms (cGA). A commonly used structure for arranging the individuals of a population is a 2D toroidal grid, although the number of dimensions can be easily extended (to 3D) or reduced (to 1D, e.g. a ring, see the figure on the right). The neighbourhood of a particular individual in the grid is defined in terms of the Manhattan distance from it to others in the population. In the basic algorithm, all the neighbourhoods have the same size and identical shapes. The two most commonly used neighbourhoods for two-dimensional cEAs are L5 and C9, see the figure on the left. Here, L stands for Linear while C stands for Compact. Each deme represents a panmictic subpopulation within which mate selection and the acceptance of offspring takes place by replacing the parent. The rules for the acceptance of offspring are local in nature and based on the neighbourhood: for example, it can be specified that the best offspring must be better than the parent being replaced or, less strictly, only better than the worst individual in the deme. The first rule is elitist and creates a higher selective pressure than the second non-elitist rule. In elitist EAs, the best individual of a population always survives. In this respect, they deviate from the biological model. The overlap of the neighbourhoods causes a mostly slow spread of genetic information across the neighbourhood boundaries, hence the name diffusion model. A better offspring now needs more generations than in panmixy to spread in the population. This promotes the emergence of local niches and their local evolution, thus preserving genotypic diversity over a longer period of time. The result is a better and dynamic balance between breadth and depth search adapted to the search space during a run. Depth search takes place in the niches and breadth search in the niche boundaries and through the evolution of the different niches of the whole population. For the same neighbourhood size, the spread of genetic information is larger for elongated figures like L9 than for a block like C9, and again significantly larger than for a ring. This means that ring neighbourhoods are well suited for achieving high quality results, even if this requires comparatively long run times. On the other hand, if one is primarily interested in fast and good, but possibly suboptimal results, 2D topologies are more suitable. == Comparison == When applying both population models to genetic algorithms, evolutionary strategy and other EAs, the splitting of a total population into subpopulations usually reduces the risk of premature convergence and leads to better results overall more reliably and faster than would be expected with panmictic EAs. Island models have the disadvantage compared to neighbourhood models that they introduce a large number of new strategy parameters. Despite the existing studies on this topic in the literature, a certain risk of unfavourable settings remains for the user. With neighbourhood models, on the other hand, only the size of the neighbourhood has to be specified and, in the case of the two-dimensional model, the choice of the neighbourhood figure is added. == Parallelism == Since both population models imply population partitioning, they are well suited as a basis for parallelizing an EA. This applies even more to cellular EAs, since they rely only on locally available information about the members of their respective demes. Thus, in the extreme case, an independent execution thread can be assigned to each individual, so that the entire cEA can run on a parallel hardware platform. The island model also supports p

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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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  Reciprocal human machine learning

  Reciprocal Human Machine Learning (RHML) is an interdisciplinary approach to designing human-AI interaction systems. RHML aims to enable continual learning between humans and machine learning models by having them learn from each other. This approach keeps the human expert "in the loop" to oversee and enhance machine learning performance and simultaneously support the human expert continue learning. == Background == RHML emerged in the context of the rise of big data analytics and artificial intelligence for intelligent tasks like sense-making and decision-making. As machine learning advanced to take on more roles, researchers realized fully autonomous systems had limitations and needed human guidance. RHML extends the concept of human-in-the-loop systems by promoting reciprocal learning. Humans learn from their interactions with machine learning models, staying up-to-date on evolving technology. The models also learn from human feedback and oversight. This amplification of learning on both sides is a key focus of RHML. The approach draws on theories of learning in dyads from education and psychology. It also builds on human-computer interaction and human-centered design principles. Implementing RHML requires developing specialized tools and interfaces tailored to the application == Applications == RHML has been explored across diverse domains including: Cybersecurity - Software to enable reciprocal learning between experts and AI models for social media threat detection. Organizational decision-making - RHML to structure collaboration between humans and AI systems. Workplace training - Using RHML for workers to learn from AI technologies on the job. Open science - Using human and AI collaboration to promote open science. Production and logistics - turning workers and intelligent machines into teammates. RHML maintains human oversight and control over AI systems, while enabling cutting-edge machine learning performance. This collaborative approach highlights the importance of keeping the human expert involved in the loop. An example of RHML in application is Free Spirit (AFSFCV), an open-source architecture first published in early 2025 as a whitepaper, proposing a visually structured approach to intent-based human–AI interaction.

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  Extremal Ensemble Learning

  Extremal Ensemble Learning (EEL) is a machine learning algorithmic paradigm for graph partitioning. EEL creates an ensemble of partitions and then uses information contained in the ensemble to find new and improved partitions. The ensemble evolves and learns how to form improved partitions through extremal updating procedure. The final solution is found by achieving consensus among its member partitions about what the optimal partition is. == Reduced-Network Extremal Ensemble Learning (RenEEL) == A particular implementation of the EEL paradigm is the Reduced-Network Extremal Ensemble Learning (RenEEL) scheme for partitioning a graph. RenEEL uses consensus across many partitions in an ensemble to create a reduced network that can be efficiently analyzed to find more accurate partitions. These better quality partitions are subsequently used to update the ensemble. An algorithm that utilizes the RenEEL scheme is currently the best algorithm for finding the graph partition with maximum modularity, which is an NP-hard problem.

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  Joseph Nechvatal

  Joseph Nechvatal (born January 15, 1951) is an American post-conceptual digital artist and art theoretician who creates computer-assisted paintings and computer animations, often using custom computer viruses. == Life and work == Joseph Nechvatal was born in Chicago. He studied fine art and philosophy at Southern Illinois University Carbondale, Cornell University, and Columbia University. He earned a Doctor of Philosophy in Philosophy of Art and Technology at the Planetary Collegium at University of Wales, Newport and has taught art theory and art history at the School of Visual Arts. He has had many solo exhibitions and is one of five artists that art historian Patrick Frank examines in his 2024 book Art of the 1980s: As If the Digital Mattered. His work in the late 1970s and early 1980s chiefly consisted of postminimal gray palimpsest-like drawings that were often photo-mechanically enlarged. Beginning in 1979 he became associated with the artist group Colab, organized the Public Arts International/Free Speech series, and helped established the non-profit group ABC No Rio. In 1983 he co-founded the avant-garde electronic art music audio project Tellus Audio Cassette Magazine. In 1984, Nechvatal began work on an opera called XS: The Opera Opus (1984-6) with the no wave musical composer Rhys Chatham. He began using computers and robotics to make post-conceptual paintings in 1986 and later, in his signature work, began to employ self-created computer viruses. From 1991 to 1993, he was artist-in-residence at the Louis Pasteur Atelier in Arbois, France and at the Saline Royale/Ledoux Foundation's computer lab. There he worked on The Computer Virus Project, his first artistic experiment with computer viruses and computer virus animation. He exhibited computer-robotic paintings at Documenta 8 in 1987. In 2002 he extended his experimentation into viral artificial life through a collaboration with the programmer Stephane Sikora of music2eye in a work called the Computer Virus Project II. Nechvatal has also created a noise music work called viral symphOny, a collaborative sound symphony created by using his computer virus software at the Institute for Electronic Arts at Alfred University. In 2021 Pentiments released Nechvatal's retrospective audio cassette called Selected Sound Works (1981-2021) and in 2022 his The Viral Tempest, a double vinyl LP of new audio work. In 2025, he joined the roster of artists/musicians at Table of the Elements with two CD/book releases: Selected Sound Works (1981-2021) and The Marriage of Orlando and Artaud, Even. From 1999 to 2013, Nechvatal taught art theories of immersive virtual reality and the viractual at the School of Visual Arts in New York City (SVA). A book of his collected essays entitled Towards an Immersive Intelligence: Essays on the Work of Art in the Age of Computer Technology and Virtual Reality (1993–2006) was published by Edgewise Press in 2009. Also in 2009, his virtual reality art theory and art history book Immersive Ideals / Critical Distances was published. In 2011, his book Immersion Into Noise was published by Open Humanities Press in conjunction with the University of Michigan Library's Scholarly Publishing Office. Nechvatal has also published three books with Punctum Books: Minóy (noise music—ed.—2014), Destroyer of Naivetés (poetry—2015), and Styling Sagaciousness (poetry—2022). In 2023 his art theory cybersex farce novella venus©~Ñ~vibrator, even was published by Orbis Tertius Press The Joseph Nechvatal archive is housed at The Fales Library Downtown Collection at the NYU Special Collections Library in New York City. === Viractualism === Viractualism is an art theory concept developed by Nechvatal in 1999 from Ph.D. research Nechvatal conducted at the Planetary Collegium at University of Wales, Newport. There he developed his concept of the viractual, which strives to create an interface between the actual and the virtual.

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  Relationship square

  In statistics, the relationship square is a graphical representation for use in the factorial analysis of a table individuals x variables. This representation completes classical representations provided by principal component analysis (PCA) or multiple correspondence analysis (MCA), namely those of individuals, of quantitative variables (correlation circle) and of the categories of qualitative variables (at the centroid of the individuals who possess them). It is especially important in factor analysis of mixed data (FAMD) and in multiple factor analysis (MFA). == Definition of relationship square in the MCA frame == The first interest of the relationship square is to represent the variables themselves, not their categories, which is all the more valuable as there are many variables. For this, we calculate for each qualitative variable j {\displaystyle j} and each factor F s {\displaystyle F_{s}} ( F s {\displaystyle F_{s}} , rank s {\displaystyle s} factor, is the vector of coordinates of the individuals along the axis of rank s {\displaystyle s} ; in PCA, F s {\displaystyle F_{s}} is called principal component of rank s {\displaystyle s} ), the square of the correlation ratio between the F s {\displaystyle F_{s}} and the variable j {\displaystyle j} , usually denoted : η 2 ( j , F s ) {\displaystyle \eta ^{2}(j,F_{s})} Thus, to each factorial plane, we can associate a representation of qualitative variables themselves. Their coordinates being between 0 and 1, the variables appear in the square having as vertices the points (0,0), ( 0,1), (1,0) and (1,1). == Example in MCA == Six individuals ( i 1 , … , i 6 ) {\displaystyle i_{1},\ldots ,i_{6})} are described by three variables ( q 1 , q 2 , q 3 ) {\displaystyle (q_{1},q_{2},q_{3})} having respectively 3, 2 and 3 categories. Example : the individual i 1 {\displaystyle i_{1}} possesses the category a {\displaystyle a} of q 1 {\displaystyle q_{1}} , d {\displaystyle d} of q 2 {\displaystyle q_{2}} and f {\displaystyle f} of q 3 {\displaystyle q_{3}} . Applied to these data, the MCA function included in the R Package FactoMineR provides to the classical graph in Figure 1. The relationship square (Figure 2) makes easier the reading of the classic factorial plane. It indicates that: The first factor is related to the three variables but especially q 3 {\displaystyle q_{3}} (which have a very high coordinate along the first axis) and then q 2 {\displaystyle q_{2}} . The second factor is related only to q 1 {\displaystyle q_{1}} and q 3 {\displaystyle q_{3}} (and not to q 2 {\displaystyle q_{2}} which has a coordinate along axis 2 equal to 0) and that in a strong and equal manner. All this is visible on the classic graphic but not so clearly. The role of the relationship square is first to assist in reading a conventional graphic. This is precious when the variables are numerous and possess numerous coordinates. == Extensions == This representation may be supplemented with those of quantitative variables, the coordinates of the latter being the square of correlation coefficients (and not of correlation ratios). Thus, the second advantage of the relationship square lies in the ability to represent simultaneously quantitative and qualitative variables. The relationship square can be constructed from any factorial analysis of a table individuals x variables. In particular, it is (or should be) used systematically: in multiple correspondences analysis (MCA); in principal components analysis (PCA) when there are many supplementary variables; in factor analysis of mixed data (FAMD). An extension of this graphic to groups of variables (how to represent a group of variables by a single point ?) is used in Multiple Factor Analysis (MFA) == History == The idea of representing the qualitative variables themselves by a point (and not the categories) is due to Brigitte Escofier. The graphic as it is used now has been introduced by Brigitte Escofier and Jérôme Pagès in the framework of multiple factor analysis == Conclusion == In MCA, the relationship square provides a synthetic view of the connections between mixed variables, all the more valuable as there are many variables having many categories. This representation iscan be useful in any factorial analysis when there are numerous mixed variables, active and/or supplementary.

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  Knowledge integration

  Knowledge integration is the process of synthesizing multiple knowledge models (or representations) into a common model (representation). Compared to information integration, which involves merging information having different schemas and representation models, knowledge integration focuses more on synthesizing the understanding of a given subject from different perspectives. For example, multiple interpretations are possible of a set of student grades, typically each from a certain perspective. An overall, integrated view and understanding of this information can be achieved if these interpretations can be put under a common model, say, a student performance index. The Web-based Inquiry Science Environment (WISE), from the University of California at Berkeley has been developed along the lines of knowledge integration theory. Knowledge integration has also been studied as the process of incorporating new information into a body of existing knowledge with an interdisciplinary approach. This process involves determining how the new information and the existing knowledge interact, how existing knowledge should be modified to accommodate the new information, and how the new information should be modified in light of the existing knowledge. A learning agent that actively investigates the consequences of new information can detect and exploit a variety of learning opportunities; e.g., to resolve knowledge conflicts and to fill knowledge gaps. By exploiting these learning opportunities the learning agent is able to learn beyond the explicit content of the new information. The machine learning program KI, developed by Murray and Porter at the University of Texas at Austin, was created to study the use of automated and semi-automated knowledge integration to assist knowledge engineers constructing a large knowledge base. A possible technique which can be used is semantic matching. More recently, a technique useful to minimize the effort in mapping validation and visualization has been presented which is based on Minimal Mappings. Minimal mappings are high quality mappings such that i) all the other mappings can be computed from them in time linear in the size of the input graphs, and ii) none of them can be dropped without losing property i). The University of Waterloo operates a Bachelor of Knowledge Integration undergraduate degree program as an academic major or minor. The program started in 2008.

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  Robust principal component analysis

  Robust Principal Component Analysis (RPCA) is a modification of the widely used statistical procedure of principal component analysis (PCA) which works well with respect to grossly corrupted observations. A number of different approaches exist for Robust PCA, including an idealized version of Robust PCA, which aims to recover a low-rank matrix L0 from highly corrupted measurements M = L0 +S0. This decomposition in low-rank and sparse matrices can be achieved by techniques such as Principal Component Pursuit method (PCP), Stable PCP, Quantized PCP, Block based PCP, and Local PCP. Then, optimization methods are used such as the Augmented Lagrange Multiplier Method (ALM), Alternating Direction Method (ADM), Fast Alternating Minimization (FAM), Iteratively Reweighted Least Squares (IRLS ) or alternating projections (AP). == Algorithms == === Non-convex method === The 2014 guaranteed algorithm for the robust PCA problem (with the input matrix being M = L + S {\displaystyle M=L+S} ) is an alternating minimization type algorithm. The computational complexity is O ( m n r 2 log ⁡ 1 ϵ ) {\displaystyle O\left(mnr^{2}\log {\frac {1}{\epsilon }}\right)} where the input is the superposition of a low-rank (of rank r {\displaystyle r} ) and a sparse matrix of dimension m × n {\displaystyle m\times n} and ϵ {\displaystyle \epsilon } is the desired accuracy of the recovered solution, i.e., ‖ L ^ − L ‖ F ≤ ϵ {\displaystyle \|{\widehat {L}}-L\|_{F}\leq \epsilon } where L {\displaystyle L} is the true low-rank component and L ^ {\displaystyle {\widehat {L}}} is the estimated or recovered low-rank component. Intuitively, this algorithm performs projections of the residual onto the set of low-rank matrices (via the SVD operation) and sparse matrices (via entry-wise hard thresholding) in an alternating manner - that is, low-rank projection of the difference the input matrix and the sparse matrix obtained at a given iteration followed by sparse projection of the difference of the input matrix and the low-rank matrix obtained in the previous step, and iterating the two steps until convergence. This alternating projections algorithm is later improved by an accelerated version, coined AccAltProj. The acceleration is achieved by applying a tangent space projection before projecting the residue onto the set of low-rank matrices. This trick improves the computational complexity to O ( m n r log ⁡ 1 ϵ ) {\displaystyle O\left(mnr\log {\frac {1}{\epsilon }}\right)} with a much smaller constant in front while it maintains the theoretically guaranteed linear convergence. Another fast version of accelerated alternating projections algorithm is IRCUR. It uses the structure of CUR decomposition in alternating projections framework to dramatically reduces the computational complexity of RPCA to O ( max { m , n } r 2 log ⁡ ( m ) log ⁡ ( n ) log ⁡ 1 ϵ ) {\displaystyle O\left(\max\{m,n\}r^{2}\log(m)\log(n)\log {\frac {1}{\epsilon }}\right)} === Convex relaxation === This method consists of relaxing the rank constraint r a n k ( L ) {\displaystyle rank(L)} in the optimization problem to the nuclear norm ‖ L ‖ ∗ {\displaystyle \|L\|_{}} and the sparsity constraint ‖ S ‖ 0 {\displaystyle \|S\|_{0}} to ℓ 1 {\displaystyle \ell _{1}} -norm ‖ S ‖ 1 {\displaystyle \|S\|_{1}} . The resulting program can be solved using methods such as the method of Augmented Lagrange Multipliers. === Deep-learning augmented method === Some recent works propose RPCA algorithms with learnable/training parameters. Such a learnable/trainable algorithm can be unfolded as a deep neural network whose parameters can be learned via machine learning techniques from a given dataset or problem distribution. The learned algorithm will have superior performance on the corresponding problem distribution. == Applications == RPCA has many real life important applications particularly when the data under study can naturally be modeled as a low-rank plus a sparse contribution. Following examples are inspired by contemporary challenges in computer science, and depending on the applications, either the low-rank component or the sparse component could be the object of interest: === Video surveillance === Given a sequence of surveillance video frames, it is often required to identify the activities that stand out from the background. If we stack the video frames as columns of a matrix M, then the low-rank component L0 naturally corresponds to the stationary background and the sparse component S0 captures the moving objects in the foreground. === Face recognition === Images of a convex, Lambertian surface under varying illuminations span a low-dimensional subspace. This is one of the reasons for effectiveness of low-dimensional models for imagery data. In particular, it is easy to approximate images of a human's face by a low-dimensional subspace. To be able to correctly retrieve this subspace is crucial in many applications such as face recognition and alignment. It turns out that RPCA can be applied successfully to this problem to exactly recover the face.

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  Effective fitness

  In natural evolution and artificial evolution (e.g. artificial life and evolutionary computation) the fitness (or performance or objective measure) of a schema is rescaled to give its effective fitness which takes into account crossover and mutation. Effective fitness is used in Evolutionary Computation to understand population dynamics. While a biological fitness function only looks at reproductive success, an effective fitness function tries to encompass things that are needed to be fulfilled for survival on population level. In homogeneous populations, reproductive fitness and effective fitness are equal. When a population moves away from homogeneity a higher effective fitness is reached for the recessive genotype. This advantage will decrease while the population moves toward an equilibrium. The deviation from this equilibrium displays how close the population is to achieving a steady state. When this equilibrium is reached, the maximum effective fitness of the population is achieved. Problem solving with evolutionary computation is realized with a cost function. If cost functions are applied to swarm optimization they are called a fitness function. Strategies like reinforcement learning and NEAT neuroevolution are creating a fitness landscape which describes the reproductive success of cellular automata. The effective fitness function models the number of fit offspring and is used in calculations that include evolutionary processes, such as mutation and crossover, important on the population level. The effective fitness model is superior to its predecessor, the standard reproductive fitness model. It advances in the qualitatively and quantitatively understanding of evolutionary concepts like bloat, self-adaptation, and evolutionary robustness. While reproductive fitness only looks at pure selection, effective fitness describes the flow of a population and natural selection by taking genetic operators into account. A normal fitness function fits to a problem, while an effective fitness function is an assumption if the objective was reached. The difference is important for designing fitness functions with algorithms like novelty search in which the objective of the agents is unknown. In the case of bacteria effective fitness could include production of toxins and rate of mutation of different plasmids, which are mostly stochastically determined == Applications == When evolutionary equations of the studied population dynamics are available, one can algorithmically compute the effective fitness of a given population. Though the perfect effective fitness model is yet to be found, it is already known to be a good framework to the better understanding of the moving of the genotype-phenotype map, population dynamics, and the flow on fitness landscapes. Models using a combination of Darwinian fitness functions and effective functions are better at predicting population trends. Effective models could be used to determine therapeutic outcomes of disease treatment. Other models could determine effective protein engineering and works towards finding novel or heightened biochemistry.

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  Mathematics of neural networks in machine learning

  An artificial neural network (ANN) or neural network combines biological principles with advanced statistics to solve problems in domains such as pattern recognition and game-play. ANNs adopt the basic model of neuron analogues connected to each other in a variety of ways. == Structure == === Neuron === A neuron with label j {\displaystyle j} receiving an input p j ( t ) {\displaystyle p_{j}(t)} from predecessor neurons consists of the following components: an activation a j ( t ) {\displaystyle a_{j}(t)} , the neuron's state, depending on a discrete time parameter, an optional threshold θ j {\displaystyle \theta _{j}} , which stays fixed unless changed by learning, an activation function f {\displaystyle f} that computes the new activation at a given time t + 1 {\displaystyle t+1} from a j ( t ) {\displaystyle a_{j}(t)} , θ j {\displaystyle \theta _{j}} and the net input p j ( t ) {\displaystyle p_{j}(t)} giving rise to the relation a j ( t + 1 ) = f ( a j ( t ) , p j ( t ) , θ j ) , {\displaystyle a_{j}(t+1)=f(a_{j}(t),p_{j}(t),\theta _{j}),} and an output function f out {\displaystyle f_{\text{out}}} computing the output from the activation o j ( t ) = f out ( a j ( t ) ) . {\displaystyle o_{j}(t)=f_{\text{out}}(a_{j}(t)).} Often the output function is simply the identity function. An input neuron has no predecessor but serves as input interface for the whole network. Similarly an output neuron has no successor and thus serves as output interface of the whole network. === Propagation function === The propagation function computes the input p j ( t ) {\displaystyle p_{j}(t)} to the neuron j {\displaystyle j} from the outputs o i ( t ) {\displaystyle o_{i}(t)} and typically has the form p j ( t ) = ∑ i o i ( t ) w i j . {\displaystyle p_{j}(t)=\sum _{i}o_{i}(t)w_{ij}.} === Bias === A bias term can be added, changing the form to the following: p j ( t ) = ∑ i o i ( t ) w i j + w 0 j , {\displaystyle p_{j}(t)=\sum _{i}o_{i}(t)w_{ij}+w_{0j},} where w 0 j {\displaystyle w_{0j}} is a bias. == Neural networks as functions == Neural network models can be viewed as defining a function that takes an input (observation) and produces an output (decision) f : X → Y {\displaystyle \textstyle f:X\rightarrow Y} or a distribution over X {\displaystyle \textstyle X} or both X {\displaystyle \textstyle X} and Y {\displaystyle \textstyle Y} . Sometimes models are intimately associated with a particular learning rule. A common use of the phrase "ANN model" is really the definition of a class of such functions (where members of the class are obtained by varying parameters, connection weights, or specifics of the architecture such as the number of neurons, number of layers or their connectivity). Mathematically, a neuron's network function f ( x ) {\displaystyle \textstyle f(x)} is defined as a composition of other functions g i ( x ) {\displaystyle \textstyle g_{i}(x)} , that can further be decomposed into other functions. This can be conveniently represented as a network structure, with arrows depicting the dependencies between functions. A widely used type of composition is the nonlinear weighted sum, where f ( x ) = K ( ∑ i w i g i ( x ) ) {\displaystyle \textstyle f(x)=K\left(\sum _{i}w_{i}g_{i}(x)\right)} , where K {\displaystyle \textstyle K} (commonly referred to as the activation function) is some predefined function, such as the hyperbolic tangent, sigmoid function, softmax function, or rectifier function. The important characteristic of the activation function is that it provides a smooth transition as input values change, i.e. a small change in input produces a small change in output. The following refers to a collection of functions g i {\displaystyle \textstyle g_{i}} as a vector g = ( g 1 , g 2 , … , g n ) {\displaystyle \textstyle g=(g_{1},g_{2},\ldots ,g_{n})} . This figure depicts such a decomposition of f {\displaystyle \textstyle f} , with dependencies between variables indicated by arrows. These can be interpreted in two ways. The first view is the functional view: the input x {\displaystyle \textstyle x} is transformed into a 3-dimensional vector h {\displaystyle \textstyle h} , which is then transformed into a 2-dimensional vector g {\displaystyle \textstyle g} , which is finally transformed into f {\displaystyle \textstyle f} . This view is most commonly encountered in the context of optimization. The second view is the probabilistic view: the random variable F = f ( G ) {\displaystyle \textstyle F=f(G)} depends upon the random variable G = g ( H ) {\displaystyle \textstyle G=g(H)} , which depends upon H = h ( X ) {\displaystyle \textstyle H=h(X)} , which depends upon the random variable X {\displaystyle \textstyle X} . This view is most commonly encountered in the context of graphical models. The two views are largely equivalent. In either case, for this particular architecture, the components of individual layers are independent of each other (e.g., the components of g {\displaystyle \textstyle g} are independent of each other given their input h {\displaystyle \textstyle h} ). This naturally enables a degree of parallelism in the implementation. Networks such as the previous one are commonly called feedforward, because their graph is a directed acyclic graph. Networks with cycles are commonly called recurrent. Such networks are commonly depicted in the manner shown at the top of the figure, where f {\displaystyle \textstyle f} is shown as dependent upon itself. However, an implied temporal dependence is not shown. == Backpropagation == Backpropagation training algorithms fall into three categories: steepest descent (with variable learning rate and momentum, resilient backpropagation); quasi-Newton (Broyden–Fletcher–Goldfarb–Shanno, one step secant); Levenberg–Marquardt and conjugate gradient (Fletcher–Reeves update, Polak–Ribiére update, Powell–Beale restart, scaled conjugate gradient). === Algorithm === Let N {\displaystyle N} be a network with e {\displaystyle e} connections, m {\displaystyle m} inputs and n {\displaystyle n} outputs. Below, x 1 , x 2 , … {\displaystyle x_{1},x_{2},\dots } denote vectors in R m {\displaystyle \mathbb {R} ^{m}} , y 1 , y 2 , … {\displaystyle y_{1},y_{2},\dots } vectors in R n {\displaystyle \mathbb {R} ^{n}} , and w 0 , w 1 , w 2 , … {\displaystyle w_{0},w_{1},w_{2},\ldots } vectors in R e {\displaystyle \mathbb {R} ^{e}} . These are called inputs, outputs and weights, respectively. The network corresponds to a function y = f N ( w , x ) {\displaystyle y=f_{N}(w,x)} which, given a weight w {\displaystyle w} , maps an input x {\displaystyle x} to an output y {\displaystyle y} . In supervised learning, a sequence of training examples ( x 1 , y 1 ) , … , ( x p , y p ) {\displaystyle (x_{1},y_{1}),\dots ,(x_{p},y_{p})} produces a sequence of weights w 0 , w 1 , … , w p {\displaystyle w_{0},w_{1},\dots ,w_{p}} starting from some initial weight w 0 {\displaystyle w_{0}} , usually chosen at random. These weights are computed in turn: first compute w i {\displaystyle w_{i}} using only ( x i , y i , w i − 1 ) {\displaystyle (x_{i},y_{i},w_{i-1})} for i = 1 , … , p {\displaystyle i=1,\dots ,p} . The output of the algorithm is then w p {\displaystyle w_{p}} , giving a new function x ↦ f N ( w p , x ) {\displaystyle x\mapsto f_{N}(w_{p},x)} . The computation is the same in each step, hence only the case i = 1 {\displaystyle i=1} is described. w 1 {\displaystyle w_{1}} is calculated from ( x 1 , y 1 , w 0 ) {\displaystyle (x_{1},y_{1},w_{0})} by considering a variable weight w {\displaystyle w} and applying gradient descent to the function w ↦ E ( f N ( w , x 1 ) , y 1 ) {\displaystyle w\mapsto E(f_{N}(w,x_{1}),y_{1})} to find a local minimum, starting at w = w 0 {\displaystyle w=w_{0}} . This makes w 1 {\displaystyle w_{1}} the minimizing weight found by gradient descent. == Learning pseudocode == To implement the algorithm above, explicit formulas are required for the gradient of the function w ↦ E ( f N ( w , x ) , y ) {\displaystyle w\mapsto E(f_{N}(w,x),y)} where the function is E ( y , y ′ ) = | y − y ′ | 2 {\displaystyle E(y,y')=|y-y'|^{2}} . The learning algorithm can be divided into two phases: propagation and weight update. === Propagation === Propagation involves the following steps: Propagation forward through the network to generate the output value(s) Calculation of the cost (error term) Propagation of the output activations back through the network using the training pattern target to generate the deltas (the difference between the targeted and actual output values) of all output and hidden neurons. === Weight update === For each weight: Multiply the weight's output delta and input activation to find the gradient of the weight. Subtract the ratio (percentage) of the weight's gradient from the weight. The learning rate is the ratio (percentage) that influences the speed and quality of learning. The greater the ratio, the faster the neuron trains, but the lower the ratio, the more accurat

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  Simulation noise

  Simulation noise is a function that creates a divergence-free vector field. This signal can be used in artistic simulations for the purpose of increasing the perception of extra detail. The function can be calculated in three dimensions by dividing the space into a regular lattice grid. With each edge is associated a random value, indicating a rotational component of material revolving around the edge. By following rotating material into and out of faces, one can quickly sum the flux passing through each face of the lattice. Flux values at lattice faces are then interpolated to create a field value for all positions. Perlin noise is the earliest form of lattice noise, which has become very popular in computer graphics. Perlin Noise is not suited for simulation because it is not divergence-free. Noises based on lattices, such as simulation noise and Perlin noise, are often calculated at different frequencies and summed together to form band-limited fractal signals. Other approaches developed later that use vector calculus identities to produce divergence free fields, such as "Curl-Noise" as suggested by Rook Bridson, and "Divergence-Free Noise" due to Ivan DeWolf. These often require calculation of lattice noise gradients, which sometimes are not readily available. A naive implementation would call a lattice noise function several times to calculate its gradient, resulting in more computation than is strictly necessary. Unlike these noises, simulation noise has a geometric rationale in addition to its mathematical properties. It simulates vortices scattered in space, to produce its pleasing aesthetic. == Curl noise == The vector field is created as follows, for every point (x,y,z) in the space a vector field G is created, every component x, y and z of the vector field (Gx, Gy, Gz) is defined by a 3D perlin or simplex noise function with x, y and z as parameters. The partial derivative of Gx, Gy, and Gz respect to x, y and z is obtained with the gradient of the perlin or simplex noise by finite differences of implicit calculation inside the simplex noise. The partial derivatives are used to calculate F as the curl of G given by F = ( ∂ G z ∂ y − ∂ G y ∂ z , ∂ G x ∂ z − ∂ G z ∂ x , ∂ G y ∂ x − ∂ G x ∂ y ) {\displaystyle F=({\frac {\partial Gz}{\partial y}}-{\frac {\partial Gy}{\partial z}},{\frac {\partial Gx}{\partial z}}-{\frac {\partial Gz}{\partial x}},{\frac {\partial Gy}{\partial x}}-{\frac {\partial Gx}{\partial y}})} == Bitangent noise == This method is based in the fact that the curl of the gradient of scalar field is zero and the identity that expand the divergence of a cross product of two vectors A and B as the difference of the dot products of each vector with the curl of the other: ∇ × ( ∇ φ ) = 0 . {\displaystyle \nabla \times (\nabla \varphi )=\mathbf {0} .} ∇ ⋅ ( A × B ) = ( ∇ × A ) ⋅ B − A ⋅ ( ∇ × B ) {\displaystyle \nabla \cdot (\mathbf {A} \times \mathbf {B} )=\ (\nabla {\times }\mathbf {A} )\cdot \mathbf {B} \,-\,\mathbf {A} \cdot (\nabla {\times }\mathbf {B} )} which means that if the curl of both vector fields is zero then the divergence of the product of two vectors that are the gradients of scalar fields is zero too. This result in a divergence free vector field by construction only calling two noise functions to create the scalar fields. The vector field es created as follows, two scalar fields are calculated ϕ {\displaystyle \phi } and ψ {\displaystyle \psi } using 3D perlin or simplex noise functions, then the gradients A and B of each of this fields is calculated, the cross product of A and B gives a divergence free vector field. == Signed distance noise == The vector field is created based on a closed and differentiable implicit surface S = F(x,y,z) = 0. For every point in the space, frequently outside or near the surface, we get a vector g that is normal to the surface, this is the gradient of S or the partial derivatives respect to x, y and z, this vector is not unitary, but we can get a unitary normal n by dividing each component of the point by the magnitude of the gradient g. Outside of the surface all these normals point away from the surface. g = ∇ F ( x , y , z ) = ( ∂ F ∂ x , ∂ F ∂ y , ∂ F ∂ z ) {\displaystyle g=\nabla F(x,y,z)=\left({\frac {\partial F}{\partial x}},{\frac {\partial F}{\partial y}},{\frac {\partial F}{\partial z}}\right)} n = g ( x , y , z ) ‖ ∇ F ( x , y , z ) ‖ {\displaystyle \mathbf {n} ={\frac {g(x,y,z)}{\|\nabla F(x,y,z)\|}}} ‖ ∇ F ( x , y , z ) ‖ = ( ∂ F ∂ x ) 2 + ( ∂ F ∂ y ) 2 + ( ∂ F ∂ z ) 2 {\displaystyle \|\nabla F(x,y,z)\|={\sqrt {\left({\frac {\partial F}{\partial x}}\right)^{2}+\left({\frac {\partial F}{\partial y}}\right)^{2}+\left({\frac {\partial F}{\partial z}}\right)^{2}}}} Afterwards we calculate a scalar value p for that point in the space using a 3D perlin or simplex noise function. Now we create a vector field V = pn pointing outside of the surface. The curl of this vector field gives the direction in every point in the space where the particles should move. S D N = ( ∂ V z ∂ y − ∂ V y ∂ z , ∂ V x ∂ z − ∂ V z ∂ x , ∂ V y ∂ x − ∂ V x ∂ y ) {\displaystyle SDN=({\frac {\partial Vz}{\partial y}}-{\frac {\partial Vy}{\partial z}},{\frac {\partial Vx}{\partial z}}-{\frac {\partial Vz}{\partial x}},{\frac {\partial Vy}{\partial x}}-{\frac {\partial Vx}{\partial y}})} By construction this vector SDN will point in a tangent direction to an isosurface at the level of the signed distance to the original surface and can be used to confine the movements of the particles to stay in that surface.

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  Radial basis function kernel

  In machine learning, the radial basis function kernel, or RBF kernel, is a popular kernel function used in various kernelized learning algorithms. In particular, it is commonly used in support vector machine classification. The RBF kernel on two samples x , x ′ ∈ R k {\displaystyle \mathbf {x} ,\mathbf {x'} \in \mathbb {R} ^{k}} , represented as feature vectors in some input space, is defined as K ( x , x ′ ) = exp ⁡ ( − ‖ x − x ′ ‖ 2 2 σ 2 ) {\displaystyle K(\mathbf {x} ,\mathbf {x'} )=\exp \left(-{\frac {\|\mathbf {x} -\mathbf {x'} \|^{2}}{2\sigma ^{2}}}\right)} ‖ x − x ′ ‖ 2 {\displaystyle \textstyle \|\mathbf {x} -\mathbf {x'} \|^{2}} may be recognized as the squared Euclidean distance between the two feature vectors. σ {\displaystyle \sigma } is a free parameter. An equivalent definition involves a parameter γ = 1 2 σ 2 {\displaystyle \textstyle \gamma ={\tfrac {1}{2\sigma ^{2}}}} : K ( x , x ′ ) = exp ⁡ ( − γ ‖ x − x ′ ‖ 2 ) {\displaystyle K(\mathbf {x} ,\mathbf {x'} )=\exp(-\gamma \|\mathbf {x} -\mathbf {x'} \|^{2})} Since the value of the RBF kernel decreases with distance and ranges between zero (in the infinite-distance limit) and one (when x = x'), it has a ready interpretation as a similarity measure. The feature space of the kernel has an infinite number of dimensions; for σ = 1 {\displaystyle \sigma =1} , its expansion using the multinomial theorem is: exp ⁡ ( − 1 2 ‖ x − x ′ ‖ 2 ) = exp ⁡ ( 2 2 x ⊤ x ′ − 1 2 ‖ x ‖ 2 − 1 2 ‖ x ′ ‖ 2 ) = exp ⁡ ( x ⊤ x ′ ) exp ⁡ ( − 1 2 ‖ x ‖ 2 ) exp ⁡ ( − 1 2 ‖ x ′ ‖ 2 ) = ∑ j = 0 ∞ ( x ⊤ x ′ ) j j ! exp ⁡ ( − 1 2 ‖ x ‖ 2 ) exp ⁡ ( − 1 2 ‖ x ′ ‖ 2 ) = ∑ j = 0 ∞ ∑ n 1 + n 2 + ⋯ + n k = j exp ⁡ ( − 1 2 ‖ x ‖ 2 ) x 1 n 1 ⋯ x k n k n 1 ! ⋯ n k ! exp ⁡ ( − 1 2 ‖ x ′ ‖ 2 ) x ′ 1 n 1 ⋯ x ′ k n k n 1 ! ⋯ n k ! = ⟨ φ ( x ) , φ ( x ′ ) ⟩ {\displaystyle {\begin{alignedat}{2}\exp \left(-{\frac {1}{2}}\|\mathbf {x} -\mathbf {x'} \|^{2}\right)&=\exp \left({\frac {2}{2}}\mathbf {x} ^{\top }\mathbf {x'} -{\frac {1}{2}}\|\mathbf {x} \|^{2}-{\frac {1}{2}}\|\mathbf {x'} \|^{2}\right)\\[5pt]&=\exp \left(\mathbf {x} ^{\top }\mathbf {x'} \right)\exp \left(-{\frac {1}{2}}\|\mathbf {x} \|^{2}\right)\exp \left(-{\frac {1}{2}}\|\mathbf {x'} \|^{2}\right)\\[5pt]&=\sum _{j=0}^{\infty }{\frac {(\mathbf {x} ^{\top }\mathbf {x'} )^{j}}{j!}}\exp \left(-{\frac {1}{2}}\|\mathbf {x} \|^{2}\right)\exp \left(-{\frac {1}{2}}\|\mathbf {x'} \|^{2}\right)\\[5pt]&=\sum _{j=0}^{\infty }\quad \sum _{n_{1}+n_{2}+\dots +n_{k}=j}\exp \left(-{\frac {1}{2}}\|\mathbf {x} \|^{2}\right){\frac {x_{1}^{n_{1}}\cdots x_{k}^{n_{k}}}{\sqrt {n_{1}!\cdots n_{k}!}}}\exp \left(-{\frac {1}{2}}\|\mathbf {x'} \|^{2}\right){\frac {{x'}_{1}^{n_{1}}\cdots {x'}_{k}^{n_{k}}}{\sqrt {n_{1}!\cdots n_{k}!}}}\\[5pt]&=\langle \varphi (\mathbf {x} ),\varphi (\mathbf {x'} )\rangle \end{alignedat}}} φ ( x ) = exp ⁡ ( − 1 2 ‖ x ‖ 2 ) ( a ℓ 0 ( 0 ) , a 1 ( 1 ) , … , a ℓ 1 ( 1 ) , … , a 1 ( j ) , … , a ℓ j ( j ) , … ) {\displaystyle \varphi (\mathbf {x} )=\exp \left(-{\frac {1}{2}}\|\mathbf {x} \|^{2}\right)\left(a_{\ell _{0}}^{(0)},a_{1}^{(1)},\dots ,a_{\ell _{1}}^{(1)},\dots ,a_{1}^{(j)},\dots ,a_{\ell _{j}}^{(j)},\dots \right)} where ℓ j = ( k + j − 1 j ) {\displaystyle \ell _{j}={\tbinom {k+j-1}{j}}} , a ℓ ( j ) = x 1 n 1 ⋯ x k n k n 1 ! ⋯ n k ! | n 1 + n 2 + ⋯ + n k = j ∧ 1 ≤ ℓ ≤ ℓ j {\displaystyle a_{\ell }^{(j)}={\frac {x_{1}^{n_{1}}\cdots x_{k}^{n_{k}}}{\sqrt {n_{1}!\cdots n_{k}!}}}\quad |\quad n_{1}+n_{2}+\dots +n_{k}=j\wedge 1\leq \ell \leq \ell _{j}} == Approximations == Because support vector machines and other models employing the kernel trick do not scale well to large numbers of training samples or large numbers of features in the input space, several approximations to the RBF kernel (and similar kernels) have been introduced. Typically, these take the form of a function z that maps a single vector to a vector of higher dimensionality, approximating the kernel: ⟨ z ( x ) , z ( x ′ ) ⟩ ≈ ⟨ φ ( x ) , φ ( x ′ ) ⟩ = K ( x , x ′ ) {\displaystyle \langle z(\mathbf {x} ),z(\mathbf {x'} )\rangle \approx \langle \varphi (\mathbf {x} ),\varphi (\mathbf {x'} )\rangle =K(\mathbf {x} ,\mathbf {x'} )} where φ {\displaystyle \textstyle \varphi } is the implicit mapping embedded in the RBF kernel. === Fourier random features === One way to construct such a z is to randomly sample from the Fourier transformation of the kernel φ ( x ) = 1 D [ cos ⁡ ⟨ w 1 , x ⟩ , sin ⁡ ⟨ w 1 , x ⟩ , … , cos ⁡ ⟨ w D , x ⟩ , sin ⁡ ⟨ w D , x ⟩ ] T {\displaystyle \varphi (x)={\frac {1}{\sqrt {D}}}[\cos \langle w_{1},x\rangle ,\sin \langle w_{1},x\rangle ,\ldots ,\cos \langle w_{D},x\rangle ,\sin \langle w_{D},x\rangle ]^{T}} where w 1 , . . . , w D {\displaystyle w_{1},...,w_{D}} are independent samples from the normal distribution N ( 0 , σ − 2 I ) {\displaystyle N(0,\sigma ^{-2}I)} . Theorem: E ⁡ [ ⟨ φ ( x ) , φ ( y ) ⟩ ] = e ‖ x − y ‖ 2 / ( 2 σ 2 ) . {\displaystyle \operatorname {E} [\langle \varphi (x),\varphi (y)\rangle ]=e^{\|x-y\|^{2}/(2\sigma ^{2})}.} Proof: It suffices to prove the case of D = 1 {\displaystyle D=1} . Use the trigonometric identity cos ⁡ ( a − b ) = cos ⁡ ( a ) cos ⁡ ( b ) + sin ⁡ ( a ) sin ⁡ ( b ) {\displaystyle \cos(a-b)=\cos(a)\cos(b)+\sin(a)\sin(b)} , the spherical symmetry of Gaussian distribution, then evaluate the integral ∫ − ∞ ∞ cos ⁡ ( k x ) e − x 2 / 2 2 π d x = e − k 2 / 2 . {\displaystyle \int _{-\infty }^{\infty }{\frac {\cos(kx)e^{-x^{2}/2}}{\sqrt {2\pi }}}dx=e^{-k^{2}/2}.} Theorem: Var ⁡ [ ⟨ φ ( x ) , φ ( y ) ⟩ ] = O ( D − 1 ) {\displaystyle \operatorname {Var} [\langle \varphi (x),\varphi (y)\rangle ]=O(D^{-1})} . (Appendix A.2). === Nyström method === Another approach uses the Nyström method to approximate the eigendecomposition of the Gram matrix K, using only a random sample of the training set.

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  Genetic representation

  In computer programming, genetic representation is a way of presenting solutions/individuals in evolutionary computation methods. The term encompasses both the concrete data structures and data types used to realize the genetic material of the candidate solutions in the form of a genome, and the relationships between search space and problem space. In the simplest case, the search space corresponds to the problem space (direct representation). The choice of problem representation is tied to the choice of genetic operators, both of which have a decisive effect on the efficiency of the optimization. Genetic representation can encode appearance, behavior, physical qualities of individuals. Difference in genetic representations is one of the major criteria drawing a line between known classes of evolutionary computation. Terminology is often analogous with natural genetics. The block of computer memory that represents one candidate solution is called an individual. The data in that block is called a chromosome. Each chromosome consists of genes. The possible values of a particular gene are called alleles. A programmer may represent all the individuals of a population using binary encoding, permutational encoding, encoding by tree, or any one of several other representations. == Representations in some popular evolutionary algorithms == Genetic algorithms (GAs) are typically linear representations; these are often, but not always, binary. Holland's original description of GA used arrays of bits. Arrays of other types and structures can be used in essentially the same way. The main property that makes these genetic representations convenient is that their parts are easily aligned due to their fixed size. This facilitates simple crossover operation. Depending on the application, variable-length representations have also been successfully used and tested in evolutionary algorithms (EA) in general and genetic algorithms in particular, although the implementation of crossover is more complex in this case. Evolution strategy uses linear real-valued representations, e.g., an array of real values. It uses mostly gaussian mutation and blending/averaging crossover. Genetic programming (GP) pioneered tree-like representations and developed genetic operators suitable for such representations. Tree-like representations are used in GP to represent and evolve functional programs with desired properties. Human-based genetic algorithm (HBGA) offers a way to avoid solving hard representation problems by outsourcing all genetic operators to outside agents, in this case, humans. The algorithm has no need for knowledge of a particular fixed genetic representation as long as there are enough external agents capable of handling those representations, allowing for free-form and evolving genetic representations. === Common genetic representations === binary array integer or real-valued array binary tree natural language parse tree directed graph == Distinction between search space and problem space == Analogous to biology, EAs distinguish between problem space (corresponds to phenotype) and search space (corresponds to genotype). The problem space contains concrete solutions to the problem being addressed, while the search space contains the encoded solutions. The mapping from search space to problem space is called genotype-phenotype mapping. The genetic operators are applied to elements of the search space, and for evaluation, elements of the search space are mapped to elements of the problem space via genotype-phenotype mapping. == Relationships between search space and problem space == The importance of an appropriate choice of search space for the success of an EA application was recognized early on. The following requirements can be placed on a suitable search space and thus on a suitable genotype-phenotype mapping: === Completeness === All possible admissible solutions must be contained in the search space. === Redundancy === When more possible genotypes exist than phenotypes, the genetic representation of the EA is called redundant. In nature, this is termed a degenerate genetic code. In the case of a redundant representation, neutral mutations are possible. These are mutations that change the genotype but do not affect the phenotype. Thus, depending on the use of the genetic operators, there may be phenotypically unchanged offspring, which can lead to unnecessary fitness determinations, among other things. Since the evaluation in real-world applications usually accounts for the lion's share of the computation time, it can slow down the optimization process. In addition, this can cause the population to have higher genotypic diversity than phenotypic diversity, which can also hinder evolutionary progress. In biology, the Neutral Theory of Molecular Evolution states that this effect plays a dominant role in natural evolution. This has motivated researchers in the EA community to examine whether neutral mutations can improve EA functioning by giving populations that have converged to a local optimum a way to escape that local optimum through genetic drift. This is discussed controversially and there are no conclusive results on neutrality in EAs. On the other hand, there are other proven measures to handle premature convergence. === Locality === The locality of a genetic representation corresponds to the degree to which distances in the search space are preserved in the problem space after genotype-phenotype mapping. That is, a representation has a high locality exactly when neighbors in the search space are also neighbors in the problem space. In order for successful schemata not to be destroyed by genotype-phenotype mapping after a minor mutation, the locality of a representation must be high. === Scaling === In genotype-phenotype mapping, the elements of the genotype can be scaled (weighted) differently. The simplest case is uniform scaling: all elements of the genotype are equally weighted in the phenotype. A common scaling is exponential. If integers are binary coded, the individual digits of the resulting binary number have exponentially different weights in representing the phenotype. Example: The number 90 is written in binary (i.e., in base two) as 1011010. If now one of the front digits is changed in the binary notation, this has a significantly greater effect on the coded number than any changes at the rear digits (the selection pressure has an exponentially greater effect on the front digits). For this reason, exponential scaling has the effect of randomly fixing the "posterior" locations in the genotype before the population gets close enough to the optimum to adjust for these subtleties. == Hybridization and repair in genotype-phenotype mapping == When mapping the genotype to the phenotype being evaluated, domain-specific knowledge can be used to improve the phenotype and/or ensure that constraints are met. This is a commonly used method to improve EA performance in terms of runtime and solution quality. It is illustrated below by two of the three examples. == Examples == === Example of a direct representation === An obvious and commonly used encoding for the traveling salesman problem and related tasks is to number the cities to be visited consecutively and store them as integers in the chromosome. The genetic operators must be suitably adapted so that they only change the order of the cities (genes) and do not cause deletions or duplications. Thus, the gene order corresponds to the city order and there is a simple one-to-one mapping. === Example of a complex genotype-phenotype mapping === In a scheduling task with heterogeneous and partially alternative resources to be assigned to a set of subtasks, the genome must contain all necessary information for the individual scheduling operations or it must be possible to derive them from it. In addition to the order of the subtasks to be executed, this includes information about the resource selection. A phenotype then consists of a list of subtasks with their start times and assigned resources. In order to be able to create this, as many allocation matrices must be created as resources can be allocated to one subtask at most. In the simplest case this is one resource, e.g., one machine, which can perform the subtask. An allocation matrix is a two-dimensional matrix, with one dimension being the available time units and the other being the resources to be allocated. Empty matrix cells indicate availability, while an entry indicates the number of the assigned subtask. The creation of allocation matrices ensures firstly that there are no inadmissible multiple allocations. Secondly, the start times of the subtasks can be read from it as well as the assigned resources. A common constraint when scheduling resources to subtasks is that a resource can only be allocated once per time unit and that the reservation must be for a contiguous period of time. To achieve this in a timely manner, which is a c

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