AI Generator Outfit

AI Generator Outfit — independent reviews, comparisons, pricing and step-by-step guides on Aizhi.

  • Research software engineering

    Research software engineering

    Research software engineering is the application of software engineering practices, methods and techniques for research software, i.e. software that was made for and is mainly used within research projects. As usual for software engineering, this also includes knowledge of other (and in this case varying) research fields as well as open science that need to be incorporated into a software development process. The term was proposed in a research paper in 2010 in response to an empirical survey on tools used for software development in research projects. It started to be used in United Kingdom in 2012, when it was needed to define the type of software development needed in research. This focuses on reproducibility, reusability, and accuracy of data analysis and applications created for research. == Support == Various type of associations and organisations have been created around this role to support the creation of posts in universities and research institutes. In 2014 a Research Software Engineer Association was created in UK, which attracted 160 members in the first three months and which lead to the creation of the Society of Research Software Engineering in 2019. Other countries like the Netherlands, Germany, and the USA followed creating similar communities and there are similar efforts being pursued in Asia, Australia, Canada, New Zealand, the Nordic countries, and Belgium. In January 2021 the International Council of RSE Associations was introduced. UK counts over 40 universities and institutes with groups that provide access to software expertise to different areas of research. Additionally, the Engineering and Physical Sciences Research Council created a Research Software Engineer fellowship to promote this role and help the creation of RSE groups across UK, with calls in 2015, 2017, and 2020. The world first RSE conference took place in UK in September 2016 and it has been repeated annually (except for a gap in 2020) since. In 2019 the first national RSE conferences in Germany and the Netherlands were held, next editions were planned for 2020 and then cancelled. US-RSE held its first national conference in 2023. The Research Software Alliance was formed in 2019 to advance the global research software ecosystem by collaborating with decision makers and key influencers. The SORSE (A Series of Online Research Software Events) community was established in late‑2020 in response to the COVID-19 pandemic and ran its first online event in September 2020.

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  • Evolutionary multimodal optimization

    Evolutionary multimodal optimization

    In applied mathematics, multimodal optimization deals with optimization tasks that involve finding all or most of the multiple (at least locally optimal) solutions of a problem, as opposed to a single best solution. Evolutionary multimodal optimization is a branch of evolutionary computation, which is closely related to machine learning. Wong provides a short survey, wherein the chapter of Shir and the book of Preuss cover the topic in more detail. == Motivation == Knowledge of multiple solutions to an optimization task is especially helpful in engineering, when due to physical (and/or cost) constraints, the best results may not always be realizable. In such a scenario, if multiple solutions (locally and/or globally optimal) are known, the implementation can be quickly switched to another solution and still obtain the best possible system performance. Multiple solutions could also be analyzed to discover hidden properties (or relationships) of the underlying optimization problem, which makes them important for obtaining domain knowledge. In addition, the algorithms for multimodal optimization usually not only locate multiple optima in a single run, but also preserve their population diversity, resulting in their global optimization ability on multimodal functions. Moreover, the techniques for multimodal optimization are usually borrowed as diversity maintenance techniques to other problems. == Background == Classical techniques of optimization would need multiple restart points and multiple runs in the hope that a different solution may be discovered every run, with no guarantee however. Evolutionary algorithms (EAs) due to their population based approach, provide a natural advantage over classical optimization techniques. They maintain a population of possible solutions, which are processed every generation, and if the multiple solutions can be preserved over all these generations, then at termination of the algorithm we will have multiple good solutions, rather than only the best solution. Note that this is against the natural tendency of classical optimization techniques, which will always converge to the best solution, or a sub-optimal solution (in a rugged, “badly behaving” function). Finding and maintenance of multiple solutions is wherein lies the challenge of using EAs for multi-modal optimization. Niching is a generic term referred to as the technique of finding and preserving multiple stable niches, or favorable parts of the solution space possibly around multiple solutions, so as to prevent convergence to a single solution. The field of Evolutionary algorithms encompasses genetic algorithms (GAs), evolution strategy (ES), differential evolution (DE), particle swarm optimization (PSO), and other methods. Attempts have been made to solve multi-modal optimization in all these realms and most, if not all the various methods implement niching in some form or the other. == Multimodal optimization using genetic algorithms/evolution strategies == De Jong's crowding method, Goldberg's sharing function approach, Petrowski's clearing method, restricted mating, maintaining multiple subpopulations are some of the popular approaches that have been proposed by the community. The first two methods are especially well studied, however, they do not perform explicit separation into solutions belonging to different basins of attraction. The application of multimodal optimization within ES was not explicit for many years, and has been explored only recently. A niching framework utilizing derandomized ES was introduced by Shir, proposing the CMA-ES as a niching optimizer for the first time. The underpinning of that framework was the selection of a peak individual per subpopulation in each generation, followed by its sampling to produce the consecutive dispersion of search-points. The biological analogy of this machinery is an alpha-male winning all the imposed competitions and dominating thereafter its ecological niche, which then obtains all the sexual resources therein to generate its offspring. Recently, an evolutionary multiobjective optimization (EMO) approach was proposed, in which a suitable second objective is added to the originally single objective multimodal optimization problem, so that the multiple solutions form a weak pareto-optimal front. Hence, the multimodal optimization problem can be solved for its multiple solutions using an EMO algorithm. Improving upon their work, the same authors have made their algorithm self-adaptive, thus eliminating the need for pre-specifying the parameters. An approach that does not use any radius for separating the population into subpopulations (or species) but employs the space topology instead is proposed in.

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  • Premature convergence

    Premature convergence

    Premature convergence is an unwanted effect in evolutionary algorithms (EA), a metaheuristic that mimics the basic principles of biological evolution as a computer algorithm for solving an optimization problem. The effect means that the population of an EA has converged too early, resulting in being suboptimal. In this context, the parental solutions, through the aid of genetic operators, are not able to generate offspring that are superior to, or outperform, their parents. Premature convergence is a common problem found in evolutionary algorithms, as it leads to a loss, or convergence of, a large number of alleles, subsequently making it very difficult to search for a specific gene in which the alleles were present. An allele is considered lost if, in a population, a gene is present, where all individuals are sharing the same value for that particular gene. An allele is, as defined by De Jong, considered to be a converged allele, when 95% of a population share the same value for a certain gene. == Strategies for preventing premature convergence == Strategies to regain genetic variation can be: a mating strategy called incest prevention, uniform crossover, mimicking sexual selection, favored replacement of similar individuals (preselection or crowding), segmentation of individuals of similar fitness (fitness sharing), increasing population size niche and specie The genetic variation can also be regained by mutation though this process is highly random. A general strategy to reduce the risk of premature convergence is to use structured populations instead of the commonly used panmictic ones. == Identification of the occurrence of premature convergence == It is hard to determine when premature convergence has occurred, and it is equally hard to predict its presence in the future. One measure is to use the difference between the average and maximum fitness values, as used by Patnaik & Srinivas, to then vary the crossover and mutation probabilities. Population diversity is another measure which has been extensively used in studies to measure premature convergence. However, although it has been widely accepted that a decrease in the population diversity directly leads to premature convergence, there have been little studies done on the analysis of population diversity. In other words, by using the term population diversity, the argument for a study in preventing premature convergence lacks robustness, unless specified what their definition of population diversity is. There are models to counter the effect and risk of premature convergence that do not compromise core GA parameters like population size, mutation rate, and other core mechanisms. These models were inspired by biological ecology, where genetic interactions are limited by external mechanisms such as spatial topologies or speciation. These ecological models, such as the Eco-GA, adopt diffusion-based strategies to improve the robustness of GA runs and increase the likelihood of reaching near-global optima. == Causes for premature convergence == There are a number of presumed or hypothesized causes for the occurrence of premature convergence. === Self-adaptive mutations === Rechenberg introduced the idea of self-adaptation of mutation distributions in evolution strategies. According to Rechenberg, the control parameters for these mutation distributions evolved internally through self-adaptation, rather than predetermination. He called it the 1/5-success rule of evolution strategies (1 + 1)-ES: The step size control parameter would be increased by some factor if the relative frequency of positive mutations through a determined period of time is larger than 1/5, vice versa if it is smaller than 1/5. Self-adaptive mutations may very well be one of the causes for premature convergence. Accurately locating of optima can be enhanced by self-adaptive mutation, as well as accelerating the search for this optima. This has been widely recognized, though the mechanism's underpinnings of this have been poorly studied, as it is often unclear whether the optima is found locally or globally. Self-adaptive methods can cause global convergence to global optimum, provided that the selection methods used are using elitism, as well as that the rule of self-adaptation doesn't interfere with the mutation distribution, which has the property of ensuring a positive minimum probability when hitting a random subset. This is for non-convex objective functions with sets that include bounded lower levels of non-zero measurements. A study by Rudolph suggests that self-adaption mechanisms among elitist evolution strategies do resemble the 1/5-success rule, and could very well get caught by a local optimum that include a positive probability. === Panmictic populations === Most EAs use unstructured or panmictic populations where basically every individual in the population is eligible for mate selection based on fitness. Thus, The genetic information of an only slightly better individual can spread in a population within a few generations, provided that no better other offspring is produced during this time. Especially in comparatively small populations, this can quickly lead to a loss of genotypic diversity and thus to premature convergence. A well-known countermeasure is to switch to alternative population models which introduce substructures into the population that preserve genotypic diversity over a longer period of time and thus counteract the tendency towards premature convergence. This has been shown for various EAs such as genetic algorithms, the evolution strategy, other EAs or memetic algorithms.

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  • One-class classification

    One-class classification

    In machine learning, one-class classification (OCC), also known as unary classification or class-modelling, is an approach to the training of binary classifiers in which only examples of one of the two classes are used. Examples include the monitoring of helicopter gearboxes, motor failure prediction, or assessing the operational status of a nuclear plant as 'normal': In such scenarios, there are few, if any, examples of the catastrophic system states – rare outliers – that comprise the second class. Alternatively, the class that is being focused on may cover a small, coherent subset of the data and the training may rely on an information bottleneck approach. In practice, counter-examples from the second class may be used in later rounds of training to further refine the algorithm. == Overview == The term one-class classification (OCC) was coined by Moya & Hush (1996) and many applications can be found in scientific literature, for example outlier detection, anomaly detection, novelty detection. A feature of OCC is that it uses only sample points from the assigned class, so that a representative sampling is not strictly required for non-target classes. == Introduction == SVM based one-class classification (OCC) relies on identifying the smallest hypersphere (with radius r, and center c) consisting of all the data points. This method is called Support Vector Data Description (SVDD). Formally, the problem can be defined in the following constrained optimization form, min r , c r 2 subject to, | | Φ ( x i ) − c | | 2 ≤ r 2 ∀ i = 1 , 2 , . . . , n {\displaystyle \min _{r,c}r^{2}{\text{ subject to, }}||\Phi (x_{i})-c||^{2}\leq r^{2}\;\;\forall i=1,2,...,n} However, the above formulation is highly restrictive, and is sensitive to the presence of outliers. Therefore, a flexible formulation, that allow for the presence of outliers is formulated as shown below, min r , c , ζ r 2 + 1 ν n ∑ i = 1 n ζ i {\displaystyle \min _{r,c,\zeta }r^{2}+{\frac {1}{\nu n}}\sum _{i=1}^{n}\zeta _{i}} subject to, | | Φ ( x i ) − c | | 2 ≤ r 2 + ζ i ∀ i = 1 , 2 , . . . , n {\displaystyle {\text{subject to, }}||\Phi (x_{i})-c||^{2}\leq r^{2}+\zeta _{i}\;\;\forall i=1,2,...,n} From the Karush–Kuhn–Tucker conditions for optimality, we get c = ∑ i = 1 n α i Φ ( x i ) , {\displaystyle c=\sum _{i=1}^{n}\alpha _{i}\Phi (x_{i}),} where the α i {\displaystyle \alpha _{i}} 's are the solution to the following optimization problem: max α ∑ i = 1 n α i κ ( x i , x i ) − ∑ i , j = 1 n α i α j κ ( x i , x j ) {\displaystyle \max _{\alpha }\sum _{i=1}^{n}\alpha _{i}\kappa (x_{i},x_{i})-\sum _{i,j=1}^{n}\alpha _{i}\alpha _{j}\kappa (x_{i},x_{j})} subject to, ∑ i = 1 n α i = 1 and 0 ≤ α i ≤ 1 ν n for all i = 1 , 2 , . . . , n . {\displaystyle \sum _{i=1}^{n}\alpha _{i}=1{\text{ and }}0\leq \alpha _{i}\leq {\frac {1}{\nu n}}{\text{for all }}i=1,2,...,n.} The introduction of kernel function provide additional flexibility to the One-class SVM (OSVM) algorithm. === PU (Positive Unlabeled) learning === A similar problem is PU learning, in which a binary classifier is constructed by semi-supervised learning from only positive and unlabeled sample points. In PU learning, two sets of examples are assumed to be available for training: the positive set P {\displaystyle P} and a mixed set U {\displaystyle U} , which is assumed to contain both positive and negative samples, but without these being labeled as such. This contrasts with other forms of semisupervised learning, where it is assumed that a labeled set containing examples of both classes is available in addition to unlabeled samples. A variety of techniques exist to adapt supervised classifiers to the PU learning setting, including variants of the EM algorithm. PU learning has been successfully applied to text, time series, bioinformatics tasks, and remote sensing data. == Approaches == Several approaches have been proposed to solve one-class classification (OCC). The approaches can be distinguished into three main categories, density estimation, boundary methods, and reconstruction methods. === Density estimation methods === Density estimation methods rely on estimating the density of the data points, and set the threshold. These methods rely on assuming distributions, such as Gaussian, or a Poisson distribution. Following which discordancy tests can be used to test the new objects. These methods are robust to scale variance. Gaussian model is one of the simplest methods to create one-class classifiers. Due to Central Limit Theorem (CLT), these methods work best when large number of samples are present, and they are perturbed by small independent error values. The probability distribution for a d-dimensional object is given by: p N ( z ; μ ; Σ ) = 1 ( 2 π ) d 2 | Σ | 1 2 exp ⁡ { − 1 2 ( z − μ ) T Σ − 1 ( z − μ ) } {\displaystyle p_{\mathcal {N}}(z;\mu ;\Sigma )={\frac {1}{(2\pi )^{\frac {d}{2}}|\Sigma |^{\frac {1}{2}}}}\exp \left\{-{\frac {1}{2}}(z-\mu )^{T}\Sigma ^{-1}(z-\mu )\right\}} Where, μ {\displaystyle \mu } is the mean and Σ {\displaystyle \Sigma } is the covariance matrix. Computing the inverse of covariance matrix ( Σ − 1 {\displaystyle \Sigma ^{-1}} ) is the costliest operation, and in the cases where the data is not scaled properly, or data has singular directions pseudo-inverse Σ + {\displaystyle \Sigma ^{+}} is used to approximate the inverse, and is calculated as Σ T ( Σ Σ T ) − 1 {\displaystyle \Sigma ^{T}(\Sigma \Sigma ^{T})^{-1}} . === Boundary methods === Boundary methods focus on setting boundaries around a few set of points, called target points. These methods attempt to optimize the volume. Boundary methods rely on distances, and hence are not robust to scale variance. K-centers method, NN-d, and SVDD are some of the key examples. K-centers In K-center algorithm, k {\displaystyle k} small balls with equal radius are placed to minimize the maximum distance of all minimum distances between training objects and the centers. Formally, the following error is minimized, ε k − c e n t e r = max i ( min k | | x i − μ k | | 2 ) {\displaystyle \varepsilon _{k-center}=\max _{i}(\min _{k}||x_{i}-\mu _{k}||^{2})} The algorithm uses forward search method with random initialization, where the radius is determined by the maximum distance of the object, any given ball should capture. After the centers are determined, for any given test object z {\displaystyle z} the distance can be calculated as, d k − c e n t r ( z ) = min k | | z − μ k | | 2 {\displaystyle d_{k-centr}(z)=\min _{k}||z-\mu _{k}||^{2}} === Reconstruction methods === Reconstruction methods use prior knowledge and generating process to build a generating model that best fits the data. New objects can be described in terms of a state of the generating model. Some examples of reconstruction methods for OCC are, k-means clustering, learning vector quantization, self-organizing maps, etc. == Applications == === Document classification === The basic Support Vector Machine (SVM) paradigm is trained using both positive and negative examples, however studies have shown there are many valid reasons for using only positive examples. When the SVM algorithm is modified to only use positive examples, the process is considered one-class classification. One situation where this type of classification might prove useful to the SVM paradigm is in trying to identify a web browser's sites of interest based only off of the user's browsing history. === Biomedical studies === One-class classification can be particularly useful in biomedical studies where often data from other classes can be difficult or impossible to obtain. In studying biomedical data it can be difficult and/or expensive to obtain the set of labeled data from the second class that would be necessary to perform a two-class classification. A study from The Scientific World Journal found that the typicality approach is the most useful in analysing biomedical data because it can be applied to any type of dataset (continuous, discrete, or nominal). The typicality approach is based on the clustering of data by examining data and placing it into new or existing clusters. To apply typicality to one-class classification for biomedical studies, each new observation, y 0 {\displaystyle y_{0}} , is compared to the target class, C {\displaystyle C} , and identified as an outlier or a member of the target class. === Unsupervised Concept Drift Detection === One-class classification has similarities with unsupervised concept drift detection, where both aim to identify whether the unseen data share similar characteristics to the initial data. A concept is referred to as the fixed probability distribution which data is drawn from. In unsupervised concept drift detection, the goal is to detect if the data distribution changes without utilizing class labels. In one-class classification, the flow of data is not important. Unseen data is classified as typical or outlier depending on its characteristics, whether it is from the initi

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  • Avid DS

    Avid DS

    Avid DS (which was called Avid DS Nitris until early 2008) is a high-end offline and finishing system comprising a non-linear editing system and visual effects software. It was developed by Softimage (this company was owned by Microsoft at the time of DS v1.0's launch before being acquired from Microsoft by Avid Technology, Inc. shortly thereafter) in Montreal. DS was discontinued on September 30, 2013 with support ending on the same date the following year. == Software == DS was called ‘Digital Studio’ in development. It was envisioned to be a complete platform for video/audio work. The first previews of the system were on the SGI platform, but this version was never released. The system was rewritten on Windows NT with different video hardware platforms (Matrox DigiSuite or Play Trinity running on a NetPower system) before the final system was released on Intergraph/StudioZ hardware in January 1998. After its acquisition by Avid, DS was always positioned as a high end video finishing tool. However, many users found it to be uniquely soup-to-nuts in its capabilities. From version 1.0 of the product, it competed with products like Autodesk Smoke, Quantel and Avid Symphony. The toolset in DS offered video timeline editing, an object-oriented vector-based paint tool, 2D layer compositing, sample based audio and starting with version 3.01 of the product, a 3D environment. Originally, a subset of the Softimage|XSI 3D software was planned to become part of the DS toolset, both were built on the same software foundation, but over time the code bases divided between the applications and the integration never happened. While the first version of the DS still lacked a few key features (no 3D, poor keying, no real-time effects), it had some significant features compared to the competing products at the time. It offered a large number of built in effects. Avid OMF import was available, positioning Softimage DS as a strong finishing tool for then typical off-line Avid systems. Lastly the integration of the toolset of Softimage DS was beyond what other product offered. A Softimage DS user could quickly go from editing, to paint, to compositing with a few mouse clicks all inside the same interface. Some of the lacking features were quickly resolved, within months of version 1.0 a new chroma keyer was released. Early versions of the software (up thru 4.0) added additional key features. Development continued with one of the first uncompressed HD editing systems (version 4.01) and an attempt to make the system more friendly to Media Composer editors in version 6. In later versions (v7.5 on beyond) DS was criticized for slow development of compositing tools, mainly lack of a new 3D environment and better tracking tools. Many DS users felt that Avid had not been giving DS the attention that it deserved. On July 7, 2013, Avid sent out an email marking the end of life of the DS product. "To Our Avid DS customers, We are writing to inform you that Avid will be realigning our business strategy to focus on a core suite of products to best leverage our developmental and creative resources. As part of this transition, we will be ceasing future development of Avid DS with a final sale date of September 30th, 2013" == Hardware == Up until version 10.5, DS was sold as a turn-key system; the software was not available without purchasing CPU, I/O and storage hardware from Avid. Beginning with 10.5, customers were able to configure their own systems using widely available components, based on recommended system requirements. In turn-key systems, there were many hardware refreshes over time. StudioZ single stream: Intergraph TDZ-425 with 30 minutes of uncompressed SCSI storage. CPUs at the time were Pentium II/300 MHz. StudioZ dual stream: Intergraph TDZ-2000 GT1 with one hour of fibre channel storage. CPUs on first systems were Pentium II/400 MHz, but last shipping systems had Pentium III/1 GHz. DS was one of the first applications to show that real-time effects could be processed with just the CPUs of the system, not requiring special video cards with real-time effect hardware. Equinox: Developed by Avid, it was one of the first uncompressed HD video cards available. Systems were available on CPUs from Pentium III/1 GHz to Pentium 4/2.8 GHz. Storage was typically SCSI, but fibre channel was also supported. Nitris DNA: Developed by Avid, the Nitris hardware was probably the largest hardware update to the system since it was released. 10-bit HD and SD support was standard. Real-time down and cross convert. This was the only hardware for DS that had on-board effect processing. This allowed a system at the time to play back dual-stream uncompressed HD effects in real-time at 16-bit precision. This was also the first hardware from Avid to support the DNxHD codec. Starting with Pentium 4, Intel Core Xeons were supported. SCSI storage was primarily used. AJA Video Systems: First available as a 4:4:4 option to be used in conjunction with Nitris hardware. Final-generation DS systems used the AJA Video Systems Kona 3 (Xena 2K) card as the only I/O for the system. The last systems shipped with two Intel Core Xeon 6-core processors. SAS is the recommended storage for these systems. == History ==

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  • Linguamatics

    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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  • Andrej Mrvar

    Andrej Mrvar

    Andrej Mrvar is a Slovenian computer scientist and a professor at the University of Ljubljana's Faculty of Social Sciences. He is known for his work in network analysis, graph drawing, decision making, virtual reality, timing and data processing of sports competitions. == Education and career == He is well known for his work on Pajek, a free software for analysis and visualization of large networks. Mrvar began work on Pajek in 1996 with Vladimir Batagelj. His book Exploratory Social Network Analysis with Pajek, coauthored with Wouter de Nooy and Vladimir Batagelj, is his most cited work. It was published by Cambridge University Press in three editions (first 2005, second 2011, and third 2018). The book was translated into Japanese (2009) and Chinese (first edition 2012, second 2014). With Anuška Ferligoj, he was a founding co-editor-in-chief of the Metodološki zvezki - Advances in Methodology and Statistics journal. == Awards and honors == Vidmar Award (Faculty of Electrical and Computer Engineering, University of Ljubljana): 1988, 1990 First prizes for contributions (with Vladimir Batagelj) to Graph Drawing Contests in years: 1995, 1996, 1997, 1998, 1999, 2000 and 2005 / Graph Drawing Hall of Fame. Award of University of Ljubljana for contributions in education and research (Svečana listina Univerze v Ljubljani za pomembne dosežke na področju vzgojnoizobraževalnega in znanstvenoraziskovalega dela): 2001 The INSNA's William D. Richards Software award for work on Pajek (with Vladimir Batagelj): 2013 Award of Faculty of Social Sciences, University of Ljubljana for scientific excellence (Priznanje za znanstveno odličnost): 2013 == Selected publications == Wouter de Nooy, Andrej Mrvar, Vladimir Batagelj, Mark Granovetter (Series Editor), Exploratory Social Network Analysis with Pajek (Structural Analysis in the Social Sciences), Cambridge University Press (First Edition: 2005, Second Edition: 2011, Third Edition: 2018 ). Japanese Translation (2010). Chinese Translation (First Edition: 2012, Second Edition: 2014) Andrej Mrvar and Vladimir Batagelj, Analysis and visualization of large networks with program package Pajek. Complex Adaptive Systems Modeling, 4:6. SpringerOpen, 2016 Vladimir Batagelj and Andrej Mrvar, Some Analyses of Erdős Collaboration Graph, Social Networks, 22, 173–186, 2000 Vladimir Batagelj and Andrej Mrvar, A Subquadratic Triad Census Algorithm for Large Sparse Networks with Small Maximum Degree. Social Networks, 23, 237–243, 2001 Patrick Doreian and Andrej Mrvar, A Partitioning Approach to Structural Balance, Social Networks, 18, 149–168, 1996 Patrick Doreian and Andrej Mrvar, Partitioning Signed Social Networks, Social Networks, 31, 1–11, 2009 Andrej Mrvar and Patrick Doreian, Partitioning Signed Two-Mode Networks, Journal of Mathematical Sociology, 33, 196–221, 2009 Patrick Doreian and Andrej Mrvar, The international reach of the Koch brothers network. In: Antonyuk, A. and Basov, N. (Eds.): Networks in the Global World V. NetGloW 2020. Lecture Notes in Networks and Systems, 181, 225–235. Springer, 2021 Patrick Doreian and Andrej Mrvar, Delineating Changes in the Fundamental Structure of Signed Networks, Frontiers in Physics, 294, 1–11, 2021 Patrick Doreian and Andrej Mrvar, Hubs and Authorities in the Koch Brothers Network. Social Networks, Social Networks, 64, 148–157, 2021 Patrick Doreian and Andrej Mrvar, Public issues, policy proposals, social movements, and the interests of the Koch Brothers network of allies, Quality and Quantity, 56, 305–322, 2022 Douglas R. White, Vladimir Batagelj, Andrej Mrvar, Analyzing Large Kinship and Marriage Networks with Pgraph and Pajek. Social Science Computer Review, 17, 245–274, 1999 Ion Georgiou, Ronald Concer, Andrej Mrvar, A Systemic Approach to Sociometric Group Research: Advancing The Work of Leslie Day Zeleny, 1939–1947, Social Networks, 63, 174–200, 2020

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  • Absorbing Markov chain

    Absorbing Markov chain

    In the mathematical theory of probability, an absorbing Markov chain is a Markov chain in which every state can reach an absorbing state. An absorbing state is a state that, once entered, cannot be left. Like general Markov chains, there can be continuous-time absorbing Markov chains with an infinite state space. However, this article concentrates on the discrete-time discrete-state-space case. == Formal definition == A Markov chain is an absorbing chain if there is at least one absorbing state and it is possible to go from any state to at least one absorbing state in a finite number of steps. In an absorbing Markov chain, a state that is not absorbing is called transient. === Canonical form === Let an absorbing Markov chain with transition matrix P have t transient states and r absorbing states. The rows of P represent sources, while columns represent destinations. By ordering the transient states before the absorbing states, it can be assumed that P has the form P = [ Q R 0 I r ] , {\displaystyle P={\begin{bmatrix}Q&R\\\mathbf {0} &I_{r}\end{bmatrix}},} where Q is a t-by-t matrix, R is a nonzero t-by-r matrix, 0 is an r-by-t zero matrix, and Ir is the r-by-r identity matrix. Thus, Q describes the probability of transitioning from some transient state to another while R describes the probability of transitioning from some transient state to some absorbing state. The probability of transitioning from i to j in exactly k steps is the (i,j)-entry of Pk, further computed below. When considering only transient states, the probability is found in the upper left of Pk, the (i,j)-entry of Qk. == Fundamental matrix == === Expected number of visits to a transient state === A basic property about an absorbing Markov chain is the expected number of visits to a transient state j starting from a transient state i (before being absorbed). This can be established to be given by the (i, j) entry of so-called fundamental matrix N, obtained by summing Qk for all k (from 0 to ∞). It can be proven that N := ∑ k = 0 ∞ Q k = ( I t − Q ) − 1 , {\displaystyle N:=\sum _{k=0}^{\infty }Q^{k}=(I_{t}-Q)^{-1},} where It is the t-by-t identity matrix. The computation of this formula is the matrix equivalent of the geometric series of scalars, ∑ k = 0 ∞ q k = 1 1 − q {\displaystyle {\textstyle \sum }_{k=0}^{\infty }q^{k}={\tfrac {1}{1-q}}} . With the matrix N in hand, also other properties of the Markov chain are easy to obtain. === Expected number of steps before being absorbed === The expected number of steps before being absorbed in any absorbing state, when starting in transient state i can be computed via a sum over transient states. The value is given by the ith entry of the vector t := N 1 , {\displaystyle \mathbf {t} :=N\mathbf {1} ,} where 1 is a length-t column vector whose entries are all 1. === Absorbing probabilities === By induction, P k = [ Q k ( I t − Q k ) N R 0 I r ] . {\displaystyle P^{k}={\begin{bmatrix}Q^{k}&(I_{t}-Q^{k})NR\\\mathbf {0} &I_{r}\end{bmatrix}}.} The probability of eventually being absorbed in the absorbing state j when starting from transient state i is given by the (i,j)-entry of the matrix B := N R {\displaystyle B:=NR} . The number of columns of this matrix equals the number of absorbing states r. An approximation of those probabilities can also be obtained directly from the (i,j)-entry of P k {\displaystyle P^{k}} for a large enough value of k, when i is the index of a transient, and j the index of an absorbing state. This is because ( lim k → ∞ P k ) i , t + j = B i , j {\displaystyle \left(\lim _{k\to \infty }P^{k}\right)_{i,t+j}=B_{i,j}} . === Transient visiting probabilities === The probability of visiting transient state j when starting at a transient state i is the (i,j)-entry of the matrix H := ( N − I t ) ( N dg ) − 1 , {\displaystyle H:=(N-I_{t})(N_{\operatorname {dg} })^{-1},} where Ndg is the diagonal matrix with the same diagonal as N. === Variance on number of transient visits === The variance on the number of visits to a transient state j with starting at a transient state i (before being absorbed) is the (i,j)-entry of the matrix N 2 := N ( 2 N dg − I t ) − N sq , {\displaystyle N_{2}:=N(2N_{\operatorname {dg} }-I_{t})-N_{\operatorname {sq} },} where Nsq is the Hadamard product of N with itself (i.e. each entry of N is squared). === Variance on number of steps === The variance on the number of steps before being absorbed when starting in transient state i is the ith entry of the vector ( 2 N − I t ) t − t sq , {\displaystyle (2N-I_{t})\mathbf {t} -\mathbf {t} _{\operatorname {sq} },} where tsq is the Hadamard product of t with itself (i.e., as with Nsq, each entry of t is squared). == Examples == === String generation === Consider the process of repeatedly flipping a fair coin until the sequence (heads, tails, heads) appears. This process is modeled by an absorbing Markov chain with transition matrix P = [ 1 / 2 1 / 2 0 0 0 1 / 2 1 / 2 0 1 / 2 0 0 1 / 2 0 0 0 1 ] . {\displaystyle P={\begin{bmatrix}1/2&1/2&0&0\\0&1/2&1/2&0\\1/2&0&0&1/2\\0&0&0&1\end{bmatrix}}.} The first state represents the empty string, the second state the string "H", the third state the string "HT", and the fourth state the string "HTH". Although in reality, the coin flips cease after the string "HTH" is generated, the perspective of the absorbing Markov chain is that the process has transitioned into the absorbing state representing the string "HTH" and, therefore, cannot leave. For this absorbing Markov chain, the fundamental matrix is N = ( I − Q ) − 1 = ( [ 1 0 0 0 1 0 0 0 1 ] − [ 1 / 2 1 / 2 0 0 1 / 2 1 / 2 1 / 2 0 0 ] ) − 1 = [ 1 / 2 − 1 / 2 0 0 1 / 2 − 1 / 2 − 1 / 2 0 1 ] − 1 = [ 4 4 2 2 4 2 2 2 2 ] . {\displaystyle {\begin{aligned}N&=(I-Q)^{-1}=\left({\begin{bmatrix}1&0&0\\0&1&0\\0&0&1\end{bmatrix}}-{\begin{bmatrix}1/2&1/2&0\\0&1/2&1/2\\1/2&0&0\end{bmatrix}}\right)^{-1}\\[4pt]&={\begin{bmatrix}1/2&-1/2&0\\0&1/2&-1/2\\-1/2&0&1\end{bmatrix}}^{-1}={\begin{bmatrix}4&4&2\\2&4&2\\2&2&2\end{bmatrix}}.\end{aligned}}} The expected number of steps starting from each of the transient states is t = N 1 = [ 4 4 2 2 4 2 2 2 2 ] [ 1 1 1 ] = [ 10 8 6 ] . {\displaystyle \mathbf {t} =N\mathbf {1} ={\begin{bmatrix}4&4&2\\2&4&2\\2&2&2\end{bmatrix}}{\begin{bmatrix}1\\1\\1\end{bmatrix}}={\begin{bmatrix}10\\8\\6\end{bmatrix}}.} Therefore, the expected number of coin flips before observing the sequence (heads, tails, heads) is 10, the entry for the state representing the empty string. === Games of chance === Games based entirely on chance can be modeled by an absorbing Markov chain. A classic example of this is the ancient Indian board game Snakes and Ladders. The graph on the left plots the probability mass in the lone absorbing state that represents the final square as the transition matrix is raised to larger and larger powers. To determine the expected number of turns to complete the game, compute the vector t as described above and examine tstart, which is approximately 39.2. === Infectious disease testing === Infectious disease testing, either of blood products or in medical clinics, is often taught as an example of an absorbing Markov chain. The public U.S. Centers for Disease Control and Prevention (CDC) model for HIV and for hepatitis B, for example, illustrates the property that absorbing Markov chains can lead to the detection of disease, versus the loss of detection through other means. In the standard CDC model, the Markov chain has five states, a state in which the individual is uninfected, then a state with infected but undetectable virus, a state with detectable virus, and absorbing states of having quit/been lost from the clinic, or of having been detected (the goal). The typical rates of transition between the Markov states are the probability p per unit time of being infected with the virus, w for the rate of window period removal (time until virus is detectable), q for quit/loss rate from the system, and d for detection, assuming a typical rate λ {\displaystyle \lambda } at which the health system administers tests of the blood product or patients in question. It follows that we can "walk along" the Markov model to identify the overall probability of detection for a person starting as undetected, by multiplying the probabilities of transition to each next state of the model as: p ( p + q ) w ( w + q ) d ( d + q ) {\displaystyle {\frac {p}{(p+q)}}{\frac {w}{(w+q)}}{\frac {d}{(d+q)}}} . The subsequent total absolute number of false negative tests—the primary CDC concern—would then be the rate of tests, multiplied by the probability of reaching the infected but undetectable state, times the duration of staying in the infected undetectable state: p ( p + q ) 1 ( w + q ) λ {\displaystyle {\frac {p}{(p+q)}}{\frac {1}{(w+q)}}\lambda } .

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  • Artificial intelligence in hiring

    Artificial intelligence in hiring

    Artificial intelligence can be used to automate aspects of the job recruitment process. Advances in artificial intelligence, such as the advent of machine learning and the growth of big data, enable AI to be utilized to recruit, screen, and predict the success of applicants. Proponents of artificial intelligence in hiring claim it reduces bias, assists with finding qualified candidates, and frees up human resource workers' time for other tasks, while opponents worry that AI perpetuates inequalities in the workplace and will eliminate jobs. Despite the potential benefits, the ethical implications of AI in hiring remain a subject of debate, with concerns about algorithmic transparency, accountability, and the need for ongoing oversight to ensure fair and unbiased decision-making throughout the recruitment process. == Background == It is common for companies to use AI to automate aspects of their hiring process, especially the hospitality, finance, and tech industries. == Uses == === Screeners === Screeners are tests that allow companies to sift through a large applicant pool and extract applicants that have desirable features. What factors are used to screen applicants is a concern to ethicists and civil rights activists. A screener that favors people who have similar characteristics to those already employed at a company may perpetuate inequalities. For example, if a company that is predominantly white and male uses its employees' data to train its screener it may accidentally create a screening process that favors white, male applicants. The automation of screeners also has the potential to reduce biases. Biases against applicants with African American sounding names have been shown in multiple studies. An AI screener has the potential to limit human bias and error in the hiring process, allowing more minority applicants to be successful. === Recruitment === Recruitment involves the identification of potential applicants and the marketing of positions. AI is commonly utilized in the recruitment process because it can help boost the number of qualified applicants for positions. Companies are able to use AI to target their marketing to applicants who are likely to be good fits for a position. This often involves the use of social media sites advertising tools, which rely on AI. Facebook allows advertisers to target ads based on demographics, location, interests, behavior, and connections. Facebook also allows companies to target a "look-a-like" audience, that is the company supplies Facebook with a data set, typically the company's current employees, and Facebook will target the ad to profiles that are similar to the profiles in the data set. Additionally, job sites like Indeed, Glassdoor, and ZipRecruiter target job listings to applicants that have certain characteristics employers are looking for. Targeted advertising has many advantages for companies trying to recruit such being a more efficient use of resources, reaching a desired audience, and boosting qualified applicants. This has helped make it a mainstay in modern hiring. Who receives a targeted ad can be controversial. In hiring, the implications of targeted ads have to do with who is able to find out about and then apply to a position. Most targeted ad algorithms are proprietary information. Some platforms, like Facebook and Google, allow users to see why they were shown a specific ad, but users who do not receive the ad likely never know of its existence and also have no way of knowing why they were not shown the ad. === Interviews === Chatbots were one of the first applications of AI and are commonly used in the hiring process. Interviewees interact with chatbots to answer interview questions, and an analysis of their responses can be generated by AI. HireVue has created technology that analyzes interviewees' responses and gestures during recorded video interviews. Over 12 million interviewees have been screened by the more than 700 companies that utilize the service. == Controversies == Artificial intelligence in hiring confers many benefits, but it also has some challenges that have concerned experts. AI is only as good as the data it is using. Biases can inadvertently be baked into the data used in AI. Often companies will use data from their employees to decide what people to recruit or hire. This can perpetuate bias and lead to more homogenous workforces. Facebook Ads was an example of a platform that created such controversy for allowing business owners to specify what type of employee they are looking for. For example, job advertisements for nursing and teach could be set such that only women of a specific age group would see the advertisements. Facebook Ads has since then removed this function from its platform, citing the potential problems with the function in perpetuating biases and stereotypes against minorities. The growing use of Artificial Intelligence-enabled hiring systems has become an important component of modern talent hiring, particularly through social networks such as LinkedIn and Facebook. However, data overflow embedded in the hiring systems, based on Natural Language Processing (NLP) methods, may result in unconscious gender bias. Utilizing data driven methods may mitigate some bias generated from these systems It can also be hard to quantify what makes a good employee. This poses a challenge for training AI to predict which employees will be best. Commonly used metrics like performance reviews can be subjective and have been shown to favor white employees over black employees and men over women. Another challenge is the limited amount of available data. Employers only collect certain details about candidates during the initial stages of the hiring process. This requires AI to make determinations about candidates with very limited information to go off of. Additionally, many employers do not hire employees frequently and so have limited firm specific data to go off. To combat this, many firms will use algorithms and data from other firms in their industry. AI's reliance on applicant and current employees personal data raises privacy issues. These issues effect both the applicants and current employees, but also may have implications for third parties who are linked through social media to applicants or current employees. For example, a sweep of someone's social media will also show their friends and people they have tagged in photos or posts. == AI and the future of hiring == Artificial intelligence along with other technological advances such as improvements in robotics have placed 47% of jobs at risk of being eliminated in the near future. In 2016 the founder of the World Economic Forum, Klaus Schwab, called AI and related technology the "Fourth Industrial Revolution". According to some scholars, however, the transformative impact of AI on labor has been overstated. The "no-real-change" theory holds that an IT revolution has already occurred, but that the benefits of implementing new technologies does not outweigh the costs associated with adopting them. This theory claims that the result of the IT revolution is thus much less impactful than had originally been forecasted. Other scholars refute this theory claiming that AI has already led to significant job loss for unskilled labor and that it will eliminate middle skill and high skill jobs in the future. This position is based around the idea that AI is not yet a technology of general use and that any potential 4th industrial revolution has not fully occurred. A third theory holds that the effect of AI and other technological advances is too complicated to yet be understood. This theory is centered around the idea that while AI will likely eliminate jobs in the short term it will also likely increase the demand for other jobs. The question then becomes will the new jobs be accessible to people and will they emerge near when jobs are eliminated. == AI use in hiring for candidates == Job seekers now commonly encounter AI-driven tools at multiple stages, including automated resume parsing, video interview analysis, chatbots for frequently asked questions, and real‑time application updates. Some candidates also employ AI career agents, designed to optimize job searches, tailor applications, and interface with hiring teams. A 2025 Australian study found that AI-driven video interviews exhibited transcription error rates of up to 22% for non‑native speakers and those with speech-related disabilities, raising concerns of discrimination. A 2017 study in the Journal of Sociology found persistent gender and racial disparities in AI screening tools, even when fairness interventions are applied. Industry observers describe a growing “AI arms race” in recruitment, where both employers and candidates increasingly rely on automated agents. Employers use recruiting systems to source and filter applicants, while candidates deploy AI agents to prepare and submit applications. == Regulations == The Artifici

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  • Multispectral pattern recognition

    Multispectral pattern recognition

    Multispectral remote sensing is the collection and analysis of reflected, emitted, or back-scattered energy from an object or an area of interest in multiple bands of regions of the electromagnetic spectrum (Jensen, 2005). Subcategories of multispectral remote sensing include hyperspectral, in which hundreds of bands are collected and analyzed, and ultraspectral remote sensing where many hundreds of bands are used (Logicon, 1997). The main purpose of multispectral imaging is the potential to classify the image using multispectral classification. This is a much faster method of image analysis than is possible by human interpretation. == Multispectral remote sensing systems == Remote sensing systems gather data via instruments typically carried on satellites in orbit around the Earth. The remote sensing scanner detects the energy that radiates from the object or area of interest. This energy is recorded as an analog electrical signal and converted into a digital value though an A-to-D conversion. There are several multispectral remote sensing systems that can be categorized in the following way: === Multispectral imaging using discrete detectors and scanning mirrors === Landsat Multispectral Scanner (MSS) Landsat Thematic Mapper (TM) NOAA Geostationary Operational Environmental Satellite (GOES) NOAA Advanced Very High Resolution Radiometer (AVHRR) NASA and ORBIMAGE, Inc., Sea-viewing Wide field-of-view Sensor (SeaWiFS) Daedalus, Inc., Aircraft Multispectral Scanner (AMS) NASA Airborne Terrestrial Applications Sensor (ATLAS) === Multispectral imaging using linear arrays === SPOT 1, 2, and 3 High Resolution Visible (HRV) sensors and Spot 4 and 5 High Resolution Visible Infrared (HRVIR) and vegetation sensor Indian Remote Sensing System (IRS) Linear Imaging Self-scanning Sensor (LISS) Space Imaging, Inc. (IKONOS) Digital Globe, Inc. (QuickBird) ORBIMAGE, Inc. (OrbView-3) ImageSat International, Inc. (EROS A1) NASA Terra Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) NASA Terra Multiangle Imaging Spectroradiometer (MISR) === Imaging spectrometry using linear and area arrays === NASA Jet Propulsion Laboratory Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) Compact Airborne Spectrographic Imager 3 (CASI 3) NASA Terra Moderate Resolution Imaging Spectrometer (MODIS) NASA Earth Observer (EO-1) Advanced Land Imager (ALI), Hyperion, and LEISA Atmospheric Corrector (LAC) === Satellite analog and digital photographic systems === Russian SPIN-2 TK-350, and KVR-1000 NASA Space Shuttle and International Space Station Imagery == Multispectral classification methods == A variety of methods can be used for the multispectral classification of images: Algorithms based on parametric and nonparametric statistics that use ratio-and interval-scaled data and nonmetric methods that can also incorporate nominal scale data (Duda et al., 2001), Supervised or unsupervised classification logic, Hard or soft (fuzzy) set classification logic to create hard or fuzzy thematic output products, Per-pixel or object-oriented classification logic, and Hybrid approaches == Supervised classification == In this classification method, the identity and location of some of the land-cover types are obtained beforehand from a combination of fieldwork, interpretation of aerial photography, map analysis, and personal experience. The analyst would locate sites that have similar characteristics to the known land-cover types. These areas are known as training sites because the known characteristics of these sites are used to train the classification algorithm for eventual land-cover mapping of the remainder of the image. Multivariate statistical parameters (means, standard deviations, covariance matrices, correlation matrices, etc.) are calculated for each training site. All pixels inside and outside of the training sites are evaluated and allocated to the class with the more similar characteristics. === Classification scheme === The first step in the supervised classification method is to identify the land-cover and land-use classes to be used. Land-cover refers to the type of material present on the site (e.g. water, crops, forest, wet land, asphalt, and concrete). Land-use refers to the modifications made by people to the land cover (e.g. agriculture, commerce, settlement). All classes should be selected and defined carefully to properly classify remotely sensed data into the correct land-use and/or land-cover information. To achieve this purpose, it is necessary to use a classification system that contains taxonomically correct definitions of classes. If a hard classification is desired, the following classes should be used: Mutually exclusive: there is not any taxonomic overlap of any classes (i.e., rain forest and evergreen forest are distinct classes). Exhaustive: all land-covers in the area have been included. Hierarchical: sub-level classes (e.g., single-family residential, multiple-family residential) are created, allowing that these classes can be included in a higher category (e.g., residential). Some examples of hard classification schemes are: American Planning Association Land-Based Classification System United States Geological Survey Land-use/Land-cover Classification System for Use with Remote Sensor Data U.S. Department of the Interior Fish and Wildlife Service U.S. National Vegetation and Classification System International Geosphere-Biosphere Program IGBP Land Cover Classification System === Training sites === Once the classification scheme is adopted, the image analyst may select training sites in the image that are representative of the land-cover or land-use of interest. If the environment where the data was collected is relatively homogeneous, the training data can be used. If different conditions are found in the site, it would not be possible to extend the remote sensing training data to the site. To solve this problem, a geographical stratification should be done during the preliminary stages of the project. All differences should be recorded (e.g. soil type, water turbidity, crop species, etc.). These differences should be recorded on the imagery and the selection training sites made based on the geographical stratification of this data. The final classification map would be a composite of the individual stratum classifications. After the data are organized in different training sites, a measurement vector is created. This vector would contain the brightness values for each pixel in each band in each training class. The mean, standard deviation, variance-covariance matrix, and correlation matrix are calculated from the measurement vectors. Once the statistics from each training site are determined, the most effective bands for each class should be selected. The objective of this discrimination is to eliminate the bands that can provide redundant information. Graphical and statistical methods can be used to achieve this objective. Some of the graphic methods are: Bar graph spectral plots Cospectral mean vector plots Feature space plots Cospectral parallelepiped or ellipse plots === Classification algorithm === The last step in supervised classification is selecting an appropriate algorithm. The choice of a specific algorithm depends on the input data and the desired output. Parametric algorithms are based on the fact that the data is normally distributed. If the data is not normally distributed, nonparametric algorithms should be used. The more common nonparametric algorithms are: One-dimensional density slicing Parallelipiped Minimum distance Nearest-neighbor Expert system analysis Convolutional neural network == Unsupervised classification == Unsupervised classification (also known as clustering) is a method of partitioning remote sensor image data in multispectral feature space and extracting land-cover information. Unsupervised classification require less input information from the analyst compared to supervised classification because clustering does not require training data. This process consists in a series of numerical operations to search for the spectral properties of pixels. From this process, a map with m spectral classes is obtained. Using the map, the analyst tries to assign or transform the spectral classes into thematic information of interest (i.e. forest, agriculture, urban). This process may not be easy because some spectral clusters represent mixed classes of surface materials and may not be useful. The analyst has to understand the spectral characteristics of the terrain to be able to label clusters as a specific information class. There are hundreds of clustering algorithms. Two of the most conceptually simple algorithms are the chain method and the ISODATA method. === Chain method === The algorithm used in this method operates in a two-pass mode (it passes through the multispectral dataset two times. In the first pass, the program reads through the dataset and sequentially builds clusters (groups of p

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  • Nonlinear dimensionality reduction

    Nonlinear dimensionality reduction

    Nonlinear dimensionality reduction (NLDR), also known as manifold learning, is any of various related techniques that aim to project high-dimensional data, potentially existing across non-linear manifolds which cannot be adequately captured by linear decomposition methods, onto lower-dimensional latent manifolds, with the goal of either visualizing the data in the low-dimensional space, or learning the mapping (either from the high-dimensional space to the low-dimensional embedding or vice versa) itself. The techniques described below can be understood as generalizations of linear decomposition methods used for dimensionality reduction, such as singular value decomposition and principal component analysis. == Applications of NLDR == High dimensional data can be hard for machines to work with, requiring significant time and space for analysis. It also presents a challenge for humans, since it's hard to visualize or understand data in more than three dimensions. Reducing the dimensionality of a data set, while keeping its essential features relatively intact, can make algorithms more efficient and allow analysts to visualize trends and patterns. The reduced-dimensional representations of data are often referred to as "intrinsic variables". This description implies that these are the values from which the data was produced. For example, consider a dataset that contains images of a letter 'A', which has been scaled and rotated by varying amounts. Each image has 32×32 pixels. Each image can be represented as a vector of 1024 pixel values. Each row is a sample on a two-dimensional manifold in 1024-dimensional space (a Hamming space). The intrinsic dimensionality is two, because two variables (rotation and scale) were varied in order to produce the data. Information about the shape or look of a letter 'A' is not part of the intrinsic variables because it is the same in every instance. Nonlinear dimensionality reduction will discard the correlated information (the letter 'A') and recover only the varying information (rotation and scale). By comparison, if principal component analysis, which is a linear dimensionality reduction algorithm, is used to reduce this same dataset into two dimensions, the resulting values are not so well organized. This demonstrates that the high-dimensional vectors (each representing a letter 'A') that sample this manifold vary in a non-linear manner. It should be apparent, therefore, that NLDR has several applications in the field of computer-vision. For example, consider a robot that uses a camera to navigate in a closed static environment. The images obtained by that camera can be considered to be samples on a manifold in high-dimensional space, and the intrinsic variables of that manifold will represent the robot's position and orientation. Invariant manifolds are of general interest for model order reduction in dynamical systems. In particular, if there is an attracting invariant manifold in the phase space, nearby trajectories will converge onto it and stay on it indefinitely, rendering it a candidate for dimensionality reduction of the dynamical system. While such manifolds are not guaranteed to exist in general, the theory of spectral submanifolds (SSM) gives conditions for the existence of unique attracting invariant objects in a broad class of dynamical systems. Active research in NLDR seeks to unfold the observation manifolds associated with dynamical systems to develop modeling techniques. Some of the more prominent nonlinear dimensionality reduction techniques are listed below. == Important concepts == === Sammon's mapping === Sammon's mapping is one of the first and most popular NLDR techniques. === Self-organizing map === The self-organizing map (SOM, also called Kohonen map) and its probabilistic variant generative topographic mapping (GTM) use a point representation in the embedded space to form a latent variable model based on a non-linear mapping from the embedded space to the high-dimensional space. These techniques are related to work on density networks, which also are based around the same probabilistic model. === Kernel principal component analysis === Perhaps the most widely used algorithm for dimensional reduction is kernel PCA. PCA begins by computing the covariance matrix of the m × n {\displaystyle m\times n} matrix X {\displaystyle \mathbf {X} } C = 1 m ∑ i = 1 m x i x i T . {\displaystyle C={\frac {1}{m}}\sum _{i=1}^{m}{\mathbf {x} _{i}\mathbf {x} _{i}^{\mathsf {T}}}.} It then projects the data onto the first k eigenvectors of that matrix. By comparison, KPCA begins by computing the covariance matrix of the data after being transformed into a higher-dimensional space, C = 1 m ∑ i = 1 m Φ ( x i ) Φ ( x i ) T . {\displaystyle C={\frac {1}{m}}\sum _{i=1}^{m}{\Phi (\mathbf {x} _{i})\Phi (\mathbf {x} _{i})^{\mathsf {T}}}.} It then projects the transformed data onto the first k eigenvectors of that matrix, just like PCA. It uses the kernel trick to factor away much of the computation, such that the entire process can be performed without actually computing Φ ( x ) {\displaystyle \Phi (\mathbf {x} )} . Of course Φ {\displaystyle \Phi } must be chosen such that it has a known corresponding kernel. Unfortunately, it is not trivial to find a good kernel for a given problem, so KPCA does not yield good results with some problems when using standard kernels. For example, it is known to perform poorly with these kernels on the Swiss roll manifold. However, one can view certain other methods that perform well in such settings (e.g., Laplacian Eigenmaps, LLE) as special cases of kernel PCA by constructing a data-dependent kernel matrix. KPCA has an internal model, so it can be used to map points onto its embedding that were not available at training time. === Principal curves and manifolds === Principal curves and manifolds give the natural geometric framework for nonlinear dimensionality reduction and extend the geometric interpretation of PCA by explicitly constructing an embedded manifold, and by encoding using standard geometric projection onto the manifold. This approach was originally proposed by Trevor Hastie in his 1984 thesis, which he formally introduced in 1989. This idea has been explored further by many authors. How to define the "simplicity" of the manifold is problem-dependent, however, it is commonly measured by the intrinsic dimensionality and/or the smoothness of the manifold. Usually, the principal manifold is defined as a solution to an optimization problem. The objective function includes a quality of data approximation and some penalty terms for the bending of the manifold. The popular initial approximations are generated by linear PCA and Kohonen's SOM. === Laplacian eigenmaps === Laplacian eigenmaps uses spectral techniques to perform dimensionality reduction. This technique relies on the basic assumption that the data lies in a low-dimensional manifold in a high-dimensional space. This algorithm cannot embed out-of-sample points, but techniques based on Reproducing kernel Hilbert space regularization exist for adding this capability. Such techniques can be applied to other nonlinear dimensionality reduction algorithms as well. Traditional techniques like principal component analysis do not consider the intrinsic geometry of the data. Laplacian eigenmaps builds a graph from neighborhood information of the data set. Each data point serves as a node on the graph and connectivity between nodes is governed by the proximity of neighboring points (using e.g. the k-nearest neighbor algorithm). The graph thus generated can be considered as a discrete approximation of the low-dimensional manifold in the high-dimensional space. Minimization of a cost function based on the graph ensures that points close to each other on the manifold are mapped close to each other in the low-dimensional space, preserving local distances. The eigenfunctions of the Laplace–Beltrami operator on the manifold serve as the embedding dimensions, since under mild conditions this operator has a countable spectrum that is a basis for square integrable functions on the manifold (compare to Fourier series on the unit circle manifold). Attempts to place Laplacian eigenmaps on solid theoretical ground have met with some success, as under certain nonrestrictive assumptions, the graph Laplacian matrix has been shown to converge to the Laplace–Beltrami operator as the number of points goes to infinity. === Isomap === Isomap is a combination of the Floyd–Warshall algorithm with classic Multidimensional Scaling (MDS). Classic MDS takes a matrix of pair-wise distances between all points and computes a position for each point. Isomap assumes that the pair-wise distances are only known between neighboring points, and uses the Floyd–Warshall algorithm to compute the pair-wise distances between all other points. This effectively estimates the full matrix of pair-wise geodesic distances between all of the points. Isomap th

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  • Sliced inverse regression

    Sliced inverse regression

    Sliced inverse regression (SIR) is a tool for dimensionality reduction in the field of multivariate statistics. In statistics, regression analysis is a method of studying the relationship between a response variable y and its input variable x _ {\displaystyle {\underline {x}}} , which is a p-dimensional vector. There are several approaches in the category of regression. For example, parametric methods include multiple linear regression, and non-parametric methods include local smoothing. As the number of observations needed to use local smoothing methods scales exponentially with high-dimensional data (as p grows), reducing the number of dimensions can make the operation computable. Dimensionality reduction aims to achieve this by showing only the most important dimension of the data. SIR uses the inverse regression curve, E ( x _ | y ) {\displaystyle E({\underline {x}}\,|\,y)} , to perform a weighted principal component analysis. == Model == Given a response variable Y {\displaystyle \,Y} and a (random) vector X ∈ R p {\displaystyle X\in \mathbb {R} ^{p}} of explanatory variables, SIR is based on the model Y = f ( β 1 ⊤ X , … , β k ⊤ X , ε ) ( 1 ) {\displaystyle Y=f(\beta _{1}^{\top }X,\ldots ,\beta _{k}^{\top }X,\varepsilon )\quad \quad \quad \quad \quad (1)} where β 1 , … , β k {\displaystyle \beta _{1},\ldots ,\beta _{k}} are unknown projection vectors, k {\displaystyle \,k} is an unknown number smaller than p {\displaystyle \,p} , f {\displaystyle \;f} is an unknown function on R k + 1 {\displaystyle \mathbb {R} ^{k+1}} as it only depends on k {\displaystyle \,k} arguments, and ε {\displaystyle \varepsilon } is a random variable representing error with E [ ε | X ] = 0 {\displaystyle E[\varepsilon |X]=0} and a finite variance of σ 2 {\displaystyle \sigma ^{2}} . The model describes an ideal solution, where Y {\displaystyle \,Y} depends on X ∈ R p {\displaystyle X\in \mathbb {R} ^{p}} only through a k {\displaystyle \,k} dimensional subspace; i.e., one can reduce the dimension of the explanatory variables from p {\displaystyle \,p} to a smaller number k {\displaystyle \,k} without losing any information. An equivalent version of ( 1 ) {\displaystyle \,(1)} is: the conditional distribution of Y {\displaystyle \,Y} given X {\displaystyle \,X} depends on X {\displaystyle \,X} only through the k {\displaystyle \,k} dimensional random vector ( β 1 ⊤ X , … , β k ⊤ X ) {\displaystyle (\beta _{1}^{\top }X,\ldots ,\beta _{k}^{\top }X)} . It is assumed that this reduced vector is as informative as the original X {\displaystyle \,X} in explaining Y {\displaystyle \,Y} . The unknown β i ′ s {\displaystyle \,\beta _{i}'s} are called the effective dimension reducing directions (EDR-directions). The space that is spanned by these vectors is denoted by the effective dimension reducing space (EDR-space). == Relevant linear algebra background == Given a _ 1 , … , a _ r ∈ R n {\displaystyle {\underline {a}}_{1},\ldots ,{\underline {a}}_{r}\in \mathbb {R} ^{n}} , then V := L ( a _ 1 , … , a _ r ) {\displaystyle V:=L({\underline {a}}_{1},\ldots ,{\underline {a}}_{r})} , the set of all linear combinations of these vectors is called a linear subspace and is therefore a vector space. The equation says that vectors a _ 1 , … , a _ r {\displaystyle {\underline {a}}_{1},\ldots ,{\underline {a}}_{r}} span V {\displaystyle \,V} , but the vectors that span space V {\displaystyle \,V} are not unique. The dimension of V ( ∈ R n ) {\displaystyle \,V(\in \mathbb {R} ^{n})} is equal to the maximum number of linearly independent vectors in V {\displaystyle \,V} . A set of n {\displaystyle \,n} linear independent vectors of R n {\displaystyle \mathbb {R} ^{n}} makes up a basis of R n {\displaystyle \mathbb {R} ^{n}} . The dimension of a vector space is unique, but the basis itself is not. Several bases can span the same space. Dependent vectors can still span a space, but the linear combinations of the latter are only suitable to a set of vectors lying on a straight line. == Inverse regression == Computing the inverse regression curve (IR) means instead of looking for E [ Y | X = x ] {\displaystyle \,E[Y|X=x]} , which is a curve in R p {\displaystyle \mathbb {R} ^{p}} it is actually E [ X | Y = y ] {\displaystyle \,E[X|Y=y]} , which is also a curve in R p {\displaystyle \mathbb {R} ^{p}} , but consisting of p {\displaystyle \,p} one-dimensional regressions. The center of the inverse regression curve is located at E [ E [ X | Y ] ] = E [ X ] {\displaystyle \,E[E[X|Y]]=E[X]} . Therefore, the centered inverse regression curve is E [ X | Y = y ] − E [ X ] {\displaystyle \,E[X|Y=y]-E[X]} which is a p {\displaystyle \,p} dimensional curve in R p {\displaystyle \mathbb {R} ^{p}} . == Inverse regression versus dimension reduction == The centered inverse regression curve lies on a k {\displaystyle \,k} -dimensional subspace spanned by Σ x x β i ′ s {\displaystyle \,\Sigma _{xx}\beta _{i}\,'s} . This is a connection between the model and inverse regression. Given this condition and ( 1 ) {\displaystyle \,(1)} , the centered inverse regression curve E [ X | Y = y ] − E [ X ] {\displaystyle \,E[X|Y=y]-E[X]} is contained in the linear subspace spanned by Σ x x β k ( k = 1 , … , K ) {\displaystyle \,\Sigma _{xx}\beta _{k}(k=1,\ldots ,K)} , where Σ x x = C o v ( X ) {\displaystyle \,\Sigma _{xx}=Cov(X)} . == Estimation of the EDR-directions == After having had a look at all the theoretical properties, the aim now is to estimate the EDR-directions. For that purpose, weighted principal component analyses are needed. If the sample means m ^ h ′ s {\displaystyle \,{\hat {m}}_{h}\,'s} , X {\displaystyle \,X} would have been standardized to Z = Σ x x − 1 / 2 { X − E ( X ) } {\displaystyle \,Z=\Sigma _{xx}^{-1/2}\{X-E(X)\}} . Corresponding to the theorem above, the IR-curve m 1 ( y ) = E [ Z | Y = y ] {\displaystyle \,m_{1}(y)=E[Z|Y=y]} lies in the space spanned by ( η 1 , … , η k ) {\displaystyle \,(\eta _{1},\ldots ,\eta _{k})} , where η i = Σ x x 1 / 2 β i {\displaystyle \,\eta _{i}=\Sigma _{xx}^{1/2}\beta _{i}} . As a consequence, the covariance matrix c o v [ E [ Z | Y ] ] {\displaystyle \,cov[E[Z|Y]]} is degenerate in any direction orthogonal to the η i ′ s {\displaystyle \,\eta _{i}\,'s} . Therefore, the eigenvectors η k ( k = 1 , … , K ) {\displaystyle \,\eta _{k}(k=1,\ldots ,K)} associated with the largest K {\displaystyle \,K} eigenvalues are the standardized EDR-directions. == Algorithm == === SIR algorithm === The algorithm from Li, K-C. (1991) to estimate the EDR-directions via SIR is as follows. 1. Let Σ x x {\displaystyle \,\Sigma _{xx}} be the covariance matrix of X {\displaystyle \,X} . Standardize X {\displaystyle \,X} to Z = Σ x x − 1 / 2 { X − E ( X ) } {\displaystyle \,Z=\Sigma _{xx}^{-1/2}\{X-E(X)\}} ( 1 ) {\displaystyle \,(1)} can also be rewritten as Y = f ( η 1 ⊤ Z , … , η k ⊤ Z , ε ) {\displaystyle Y=f(\eta _{1}^{\top }Z,\ldots ,\eta _{k}^{\top }Z,\varepsilon )} where η k = β k Σ x x 1 / 2 ∀ k {\displaystyle \,\eta _{k}=\beta _{k}\Sigma _{xx}^{1/2}\quad \forall \;k} .) 2. Divide the range of y i {\displaystyle \,y_{i}} into S {\displaystyle \,S} non-overlapping slices H s ( s = 1 , … , S ) . n s {\displaystyle \,H_{s}(s=1,\ldots ,S).\;n_{s}} is the number of observations within each slice and I H s {\displaystyle \,I_{H_{s}}} is the indicator function for the slice: n s = ∑ i = 1 n I H s ( y i ) {\displaystyle n_{s}=\sum _{i=1}^{n}I_{H_{s}}(y_{i})} 3. Compute the mean of z i {\displaystyle \,z_{i}} over all slices, which is a crude estimate m ^ 1 {\displaystyle \,{\hat {m}}_{1}} of the inverse regression curve m 1 {\displaystyle \,m_{1}} : z ¯ s = n s − 1 ∑ i = 1 n z i I H s ( y i ) {\displaystyle \,{\bar {z}}_{s}=n_{s}^{-1}\sum _{i=1}^{n}z_{i}I_{H_{s}}(y_{i})} 4. Calculate the estimate for C o v { m 1 ( y ) } {\displaystyle \,Cov\{m_{1}(y)\}} : V ^ = n − 1 ∑ i = 1 S n s z ¯ s z ¯ s ⊤ {\displaystyle \,{\hat {V}}=n^{-1}\sum _{i=1}^{S}n_{s}{\bar {z}}_{s}{\bar {z}}_{s}^{\top }} 5. Identify the eigenvalues λ ^ i {\displaystyle \,{\hat {\lambda }}_{i}} and the eigenvectors η ^ i {\displaystyle \,{\hat {\eta }}_{i}} of V ^ {\displaystyle \,{\hat {V}}} , which are the standardized EDR-directions. 6. Transform the standardized EDR-directions back to the original scale. The estimates for the EDR-directions are given by: β ^ i = Σ ^ x x − 1 / 2 η ^ i {\displaystyle \,{\hat {\beta }}_{i}={\hat {\Sigma }}_{xx}^{-1/2}{\hat {\eta }}_{i}} (which are not necessarily orthogonal.)

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  • FoundationDB

    FoundationDB

    FoundationDB is a free and open-source multi-model distributed NoSQL database owned by Apple Inc. with a shared-nothing architecture. The product was designed around a "core" database, with additional features supplied in "layers." The core database exposes an ordered key–value store with transactions. The transactions are able to read or write multiple keys stored on any machine in the cluster while fully supporting ACID properties. Transactions are used to implement a variety of data models via layers. The FoundationDB Alpha program began in January 2012 and concluded on March 4, 2013, with their public Beta release. Their 1.0 version was released for general availability on August 20, 2013. On March 24, 2015, it was reported that Apple has acquired the company. A notice on the FoundationDB web site indicated that the company has "evolved" its mission and would no longer offer downloads of the software. On April 19, 2018, Apple open sourced the software, releasing it under the Apache 2.0 license. == Main features == The main features of FoundationDB include the following: Ordered key–value store In addition to supporting standard key-based reads and writes, the ordering property enables range reads that can efficiently scan large swaths of data. Transactions Transaction processing employs multiversion concurrency control for reads and optimistic concurrency for writes. Transactions can span multiple keys stored on multiple machines. ACID properties FoundationDB guarantees serializable isolation and strong durability via redundant storage on disk before transactions are considered committed. Layers Layers map new data models, APIs, and query languages to the FoundationDB core. They employ FoundationDB's ability to update multiple data elements in a single transaction, ensuring consistency. An example is their SQL layer. Commodity clusters FoundationDB is designed for deployment on distributed clusters of commodity hardware running Linux. Replication FoundationDB stores each piece of data on multiple machines according to a configurable replication factor. Triple replication is the recommended mode for clusters of 5 or more machines. Scalability FoundationDB is designed to support horizontal scaling through the addition of machines to a cluster while automatically handling data replication and partitioning. Systems supported FoundationDB supports packages for Linux, Windows, and macOS. The Linux version supports production clusters, while the Windows and macOS versions support local operation for development purposes. Configurations on Amazon EC2 are also supported. Programming language bindings FoundationDB supports language bindings for Python, Go, Ruby, Node.js, Java, PHP, and C, all of which are made available with the product. == Design limitations == The design of FoundationDB results in several limitations: Long transactions FoundationDB does not support transactions running over five seconds. Large transactions Transaction size cannot exceed 10 MB of total written keys and values. Large keys and values Keys cannot exceed 10 kB in size. Values cannot exceed 100 kB in size. == History == FoundationDB, headquartered in Vienna, Virginia, was started in 2009 by Nick Lavezzo, Dave Rosenthal, and Dave Scherer, drawing on their experience in executive and technology roles at their previous company, Visual Sciences. In March 2015 the FoundationDB Community site was updated to state that the company had changed directions and would no longer be offering downloads of its product. The company was acquired by Apple Inc., which was confirmed March 25, 2015. On April 19, 2018, Apple open sourced the software, releasing it under the Apache 2.0 license.

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  • Genotypic and phenotypic repair

    Genotypic and phenotypic repair

    Genotypic and phenotypic repair are optional components of an evolutionary algorithm (EA). An EA reproduces essential elements of biological evolution as a computer algorithm in order to solve demanding optimization or planning tasks, at least approximately. A candidate solution is represented by a - usually linear - data structure that plays the role of an individual's chromosome. New solution candidates are generated by mutation and crossover operators following the example of biology. These offspring may be defective, which is corrected or compensated for by genotypic or phenotypic repair. == Description == Genotypic repair, also known as genetic repair, is the removal or correction of impermissible entries in the chromosome that violate restrictions. In phenotypic repair, the corrections are only made in the genotype-phenotype mapping and the chromosome remains unchanged. Michalewicz wrote about the importance of restrictions in real-world applications: "In general, constraints are an integral part of the formulation of any problem". Restriction violations are application-specific and therefore it depends on the current problem whether and which type of repair is useful. They can usually also be treated by a correspondingly extended evaluation and it depends on the problem which measures are possible and which is the most suitable. If a phenotypic repair is feasible, then it is usually the most efficient compared to the other measures. A survey on repair methods used as constraint handling techniques can be found in. Violations of the range limits of genes should be avoided as far as possible by the formulation of the genome. If this is not possible or if restrictions within the search space defined by the genome are involved, their violations are usually handled by the evaluation. This can be done, for example, by penalty functions that lower the fitness. Repair is often also required for combinatorial tasks. The application of a 1- or n-point crossover operator can, for example, lead to genes being missing in one of the child genomes that are present in duplicate in the other. In this case, a suitable genotypic repair measure is to move the surplus genes to the other genome in a positional manner. The use of the aforementioned operators in combinatorial tasks has also proven to be useful in combination with crossover types specially developed for permutations, at least for certain problems. Particularly in combinatorial problems, it has been observed that genotypic repair can promote premature convergence to a suboptimum, but can also significantly accelerate a successful search. Studies on various tasks have shown that this is application-dependent. An effective measure to avoid premature convergence is generally the use of structured populations instead of the usual panmictic ones. Sequence restrictions play a role in many scheduling tasks, for example when it comes to planning workflows. If, for example, it is specified that step A must be carried out before step B and the gene of step B is located before the gene of A in the chromosome, then there is an impermissible gene sequence. This is because the scheduling operation of step B requires the planned end of step A for correct scheduling, but this is not yet scheduled at the time gene B is processed. The problem can be solved in two ways: The scheduling operation of step B is postponed until the gene from step A has been processed. The genome remains unchanged and the repair only influences the genotype-phenotype mapping. Since only the phenotype is changed, this is referred to as phenotypic repair. If, on the other hand, the gene of step B is moved behind the gene of step A, this is a genotypic repair. The same applies to the alternative shift of gene A in front of gene B. In this case, genotypic repair has the disadvantage that it prevents a meaningful restructuring of the gene sequence in the chromosome if this requires several intermediate steps (mutations) that at least partially violate restrictions.

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  • T-distributed stochastic neighbor embedding

    T-distributed stochastic neighbor embedding

    t-distributed stochastic neighbor embedding (t-SNE) is a statistical method for visualizing high-dimensional data by giving each datapoint a location in a two or three-dimensional map. It is based on Stochastic Neighbor Embedding originally developed by Geoffrey Hinton and Sam Roweis, where Laurens van der Maaten and Hinton proposed the t-distributed variant. It is a nonlinear dimensionality reduction technique for embedding high-dimensional data for visualization in a low-dimensional space of two or three dimensions. Specifically, it models each high-dimensional object by a two- or three-dimensional point in such a way that similar objects are modeled by nearby points and dissimilar objects are modeled by distant points with high probability. The t-SNE algorithm comprises two main stages. First, t-SNE constructs a probability distribution over pairs of high-dimensional objects in such a way that similar objects are assigned a higher probability while dissimilar points are assigned a lower probability. Second, t-SNE defines a similar probability distribution over the points in the low-dimensional map, and it minimizes the Kullback–Leibler divergence (KL divergence) between the two distributions with respect to the locations of the points in the map. While the original algorithm uses the Euclidean distance between objects as the base of its similarity metric, this can be changed as appropriate. A Riemannian variant is UMAP. t-SNE has been used for visualization in a wide range of applications, including genomics, computer security research, natural language processing, music analysis, cancer research, bioinformatics, geological domain interpretation, and biomedical signal processing. For a data set with n {\displaystyle n} elements, t-SNE runs in O ( n 2 ) {\displaystyle O(n^{2})} time and requires O ( n 2 ) {\displaystyle O(n^{2})} space. == Details == Given a set of N {\displaystyle N} high-dimensional objects x 1 , … , x N {\displaystyle \mathbf {x} _{1},\dots ,\mathbf {x} _{N}} , t-SNE first computes probabilities p i j {\displaystyle p_{ij}} that are proportional to the similarity of objects x i {\displaystyle \mathbf {x} _{i}} and x j {\displaystyle \mathbf {x} _{j}} , as follows. For i ≠ j {\displaystyle i\neq j} , define p j ∣ i = exp ⁡ ( − ‖ x i − x j ‖ 2 / 2 σ i 2 ) ∑ k ≠ i exp ⁡ ( − ‖ x i − x k ‖ 2 / 2 σ i 2 ) {\displaystyle p_{j\mid i}={\frac {\exp(-\lVert \mathbf {x} _{i}-\mathbf {x} _{j}\rVert ^{2}/2\sigma _{i}^{2})}{\sum _{k\neq i}\exp(-\lVert \mathbf {x} _{i}-\mathbf {x} _{k}\rVert ^{2}/2\sigma _{i}^{2})}}} and set p i ∣ i = 0 {\displaystyle p_{i\mid i}=0} . Note the above denominator ensures ∑ j p j ∣ i = 1 {\displaystyle \sum _{j}p_{j\mid i}=1} for all i {\displaystyle i} . As van der Maaten and Hinton explained: "The similarity of datapoint x j {\displaystyle x_{j}} to datapoint x i {\displaystyle x_{i}} is the conditional probability, p j | i {\displaystyle p_{j|i}} , that x i {\displaystyle x_{i}} would pick x j {\displaystyle x_{j}} as its neighbor if neighbors were picked in proportion to their probability density under a Gaussian centered at x i {\displaystyle x_{i}} ." Now define p i j = p j ∣ i + p i ∣ j 2 N {\displaystyle p_{ij}={\frac {p_{j\mid i}+p_{i\mid j}}{2N}}} This is motivated because p i {\displaystyle p_{i}} and p j {\displaystyle p_{j}} from the N samples are estimated as 1/N, so the conditional probability can be written as p i ∣ j = N p i j {\displaystyle p_{i\mid j}=Np_{ij}} and p j ∣ i = N p j i {\displaystyle p_{j\mid i}=Np_{ji}} . Since p i j = p j i {\displaystyle p_{ij}=p_{ji}} , you can obtain previous formula. Also note that p i i = 0 {\displaystyle p_{ii}=0} and ∑ i , j p i j = 1 {\displaystyle \sum _{i,j}p_{ij}=1} . The bandwidth of the Gaussian kernels σ i {\displaystyle \sigma _{i}} is set in such a way that the entropy of the conditional distribution equals a predefined entropy using the bisection method. As a result, the bandwidth is adapted to the density of the data: smaller values of σ i {\displaystyle \sigma _{i}} are used in denser parts of the data space. The entropy increases with the perplexity of this distribution P i {\displaystyle P_{i}} ; this relation is seen as P e r p ( P i ) = 2 H ( P i ) {\displaystyle Perp(P_{i})=2^{H(P_{i})}} where H ( P i ) {\displaystyle H(P_{i})} is the Shannon entropy H ( P i ) = − ∑ j p j | i log 2 ⁡ p j | i . {\displaystyle H(P_{i})=-\sum _{j}p_{j|i}\log _{2}p_{j|i}.} The perplexity is a hand-chosen parameter of t-SNE, and as the authors state, "perplexity can be interpreted as a smooth measure of the effective number of neighbors. The performance of SNE is fairly robust to changes in the perplexity, and typical values are between 5 and 50.". Since the Gaussian kernel uses the Euclidean distance ‖ x i − x j ‖ {\displaystyle \lVert x_{i}-x_{j}\rVert } , it is affected by the curse of dimensionality, and in high dimensional data when distances lose the ability to discriminate, the p i j {\displaystyle p_{ij}} become too similar (asymptotically, they would converge to a constant). It has been proposed to adjust the distances with a power transform, based on the intrinsic dimension of each point, to alleviate this. t-SNE aims to learn a d {\displaystyle d} -dimensional map y 1 , … , y N {\displaystyle \mathbf {y} _{1},\dots ,\mathbf {y} _{N}} (with y i ∈ R d {\displaystyle \mathbf {y} _{i}\in \mathbb {R} ^{d}} and d {\displaystyle d} typically chosen as 2 or 3) that reflects the similarities p i j {\displaystyle p_{ij}} as well as possible. To this end, it measures similarities q i j {\displaystyle q_{ij}} between two points in the map y i {\displaystyle \mathbf {y} _{i}} and y j {\displaystyle \mathbf {y} _{j}} , using a very similar approach. Specifically, for i ≠ j {\displaystyle i\neq j} , define q i j {\displaystyle q_{ij}} as q i j = ( 1 + ‖ y i − y j ‖ 2 ) − 1 ∑ k ∑ l ≠ k ( 1 + ‖ y k − y l ‖ 2 ) − 1 {\displaystyle q_{ij}={\frac {(1+\lVert \mathbf {y} _{i}-\mathbf {y} _{j}\rVert ^{2})^{-1}}{\sum _{k}\sum _{l\neq k}(1+\lVert \mathbf {y} _{k}-\mathbf {y} _{l}\rVert ^{2})^{-1}}}} and set q i i = 0 {\displaystyle q_{ii}=0} . Herein a heavy-tailed Student t-distribution (with one-degree of freedom, which is the same as a Cauchy distribution) is used to measure similarities between low-dimensional points in order to allow dissimilar objects to be modeled far apart in the map. The locations of the points y i {\displaystyle \mathbf {y} _{i}} in the map are determined by minimizing the (non-symmetric) Kullback–Leibler divergence of the distribution P {\displaystyle P} from the distribution Q {\displaystyle Q} , that is: K L ( P ∥ Q ) = ∑ i ≠ j p i j log ⁡ p i j q i j {\displaystyle \mathrm {KL} \left(P\parallel Q\right)=\sum _{i\neq j}p_{ij}\log {\frac {p_{ij}}{q_{ij}}}} The minimization of the Kullback–Leibler divergence with respect to the points y i {\displaystyle \mathbf {y} _{i}} is performed using gradient descent. The result of this optimization is a map that reflects the similarities between the high-dimensional inputs. == Output == While t-SNE plots often seem to display clusters, the visual clusters can be strongly influenced by the chosen parameterization (especially the perplexity) and so a good understanding of the parameters for t-SNE is needed. Such "clusters" can be shown to even appear in structured data with no clear clustering, and so may be false findings. Similarly, the size of clusters produced by t-SNE is not informative, and neither is the distance between clusters. Thus, interactive exploration may be needed to choose parameters and validate results. It has been shown that t-SNE can often recover well-separated clusters, and with special parameter choices, approximates a simple form of spectral clustering. == Software == A C++ implementation of Barnes-Hut is available on the github account of one of the original authors. The R package Rtsne implements t-SNE in R. ELKI contains tSNE, also with Barnes-Hut approximation scikit-learn, a popular machine learning library in Python implements t-SNE with both exact solutions and the Barnes-Hut approximation. Tensorboard, the visualization kit associated with TensorFlow, also implements t-SNE (online version) The Julia package TSne implements t-SNE

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