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  • Granular computing

    Granular computing

    Granular computing is an emerging computing paradigm of information processing that concerns the processing of complex information entities called "information granules", which arise in the process of data abstraction and derivation of knowledge from information or data. Generally speaking, information granules are collections of entities that usually originate at the numeric level and are arranged together due to their similarity, functional or physical adjacency, indistinguishability, coherency, or the like. At present, granular computing is more a theoretical perspective than a coherent set of methods or principles. As a theoretical perspective, it encourages an approach to data that recognizes and exploits the knowledge present in data at various levels of resolution or scales. In this sense, it encompasses all methods which provide flexibility and adaptability in the resolution at which knowledge or information is extracted and represented. == Types of granulation == As mentioned above, granular computing is not an algorithm or process; there is no particular method that is called "granular computing". It is rather an approach to looking at data that recognizes how different and interesting regularities in the data can appear at different levels of granularity, much as different features become salient in satellite images of greater or lesser resolution. On a low-resolution satellite image, for example, one might notice interesting cloud patterns representing cyclones or other large-scale weather phenomena, while in a higher-resolution image, one misses these large-scale atmospheric phenomena but instead notices smaller-scale phenomena, such as the interesting pattern that is the streets of Manhattan. The same is generally true of all data: At different resolutions or granularities, different features and relationships emerge. The aim of granular computing is to try to take advantage of this fact in designing more effective machine-learning and reasoning systems. There are several types of granularity that are often encountered in data mining and machine learning, and we review them below: === Value granulation (discretization/quantization) === One type of granulation is the quantization of variables. It is very common that in data mining or machine-learning applications the resolution of variables needs to be decreased in order to extract meaningful regularities. An example of this would be a variable such as "outside temperature" (temp), which in a given application might be recorded to several decimal places of precision (depending on the sensing apparatus). However, for purposes of extracting relationships between "outside temperature" and, say, "number of health-club applications" (club), it will generally be advantageous to quantize "outside temperature" into a smaller number of intervals. ==== Motivations ==== There are several interrelated reasons for granulating variables in this fashion: Based on prior domain knowledge, there is no expectation that minute variations in temperature (e.g., the difference between 80–80.7 °F (26.7–27.1 °C)) could have an influence on behaviors driving the number of health-club applications. For this reason, any "regularity" which our learning algorithms might detect at this level of resolution would have to be spurious, as an artifact of overfitting. By coarsening the temperature variable into intervals the difference between which we do anticipate (based on prior domain knowledge) might influence number of health-club applications, we eliminate the possibility of detecting these spurious patterns. Thus, in this case, reducing resolution is a method of controlling overfitting. By reducing the number of intervals in the temperature variable (i.e., increasing its grain size), we increase the amount of sample data indexed by each interval designation. Thus, by coarsening the variable, we increase sample sizes and achieve better statistical estimation. In this sense, increasing granularity provides an antidote to the so-called curse of dimensionality, which relates to the exponential decrease in statistical power with increase in number of dimensions or variable cardinality. Independent of prior domain knowledge, it is often the case that meaningful regularities (i.e., which can be detected by a given learning methodology, representational language, etc.) may exist at one level of resolution and not at another. For example, a simple learner or pattern recognition system may seek to extract regularities satisfying a conditional probability threshold such as p ( Y = y j | X = x i ) ≥ α . {\displaystyle p(Y=y_{j}|X=x_{i})\geq \alpha .} In the special case where α = 1 , {\displaystyle \alpha =1,} this recognition system is essentially detecting logical implication of the form X = x i → Y = y j {\displaystyle X=x_{i}\rightarrow Y=y_{j}} or, in words, "if X = x i , {\displaystyle X=x_{i},} then Y = y j {\displaystyle Y=y_{j}} ". The system's ability to recognize such implications (or, in general, conditional probabilities exceeding threshold) is partially contingent on the resolution with which the system analyzes the variables. As an example of this last point, consider the feature space shown to the right. The variables may each be regarded at two different resolutions. Variable X {\displaystyle X} may be regarded at a high (quaternary) resolution wherein it takes on the four values { x 1 , x 2 , x 3 , x 4 } {\displaystyle \{x_{1},x_{2},x_{3},x_{4}\}} or at a lower (binary) resolution wherein it takes on the two values { X 1 , X 2 } . {\displaystyle \{X_{1},X_{2}\}.} Similarly, variable Y {\displaystyle Y} may be regarded at a high (quaternary) resolution or at a lower (binary) resolution, where it takes on the values { y 1 , y 2 , y 3 , y 4 } {\displaystyle \{y_{1},y_{2},y_{3},y_{4}\}} or { Y 1 , Y 2 } , {\displaystyle \{Y_{1},Y_{2}\},} respectively. At the high resolution, there are no detectable implications of the form X = x i → Y = y j , {\displaystyle X=x_{i}\rightarrow Y=y_{j},} since every x i {\displaystyle x_{i}} is associated with more than one y j , {\displaystyle y_{j},} and thus, for all x i , {\displaystyle x_{i},} p ( Y = y j | X = x i ) < 1. {\displaystyle p(Y=y_{j}|X=x_{i})<1.} However, at the low (binary) variable resolution, two bilateral implications become detectable: X = X 1 ↔ Y = Y 1 {\displaystyle X=X_{1}\leftrightarrow Y=Y_{1}} and X = X 2 ↔ Y = Y 2 {\displaystyle X=X_{2}\leftrightarrow Y=Y_{2}} , since every X 1 {\displaystyle X_{1}} occurs iff Y 1 {\displaystyle Y_{1}} and X 2 {\displaystyle X_{2}} occurs iff Y 2 . {\displaystyle Y_{2}.} Thus, a pattern recognition system scanning for implications of this kind would find them at the binary variable resolution, but would fail to find them at the higher quaternary variable resolution. ==== Issues and methods ==== It is not feasible to exhaustively test all possible discretization resolutions on all variables in order to see which combination of resolutions yields interesting or significant results. Instead, the feature space must be preprocessed (often by an entropy analysis of some kind) so that some guidance can be given as to how the discretization process should proceed. Moreover, one cannot generally achieve good results by naively analyzing and discretizing each variable independently, since this may obliterate the very interactions that we had hoped to discover. A sample of papers that address the problem of variable discretization in general, and multiple-variable discretization in particular, is as follows: Chiu, Wong & Cheung (1991), Bay (2001), Liu et al. (2002), Wang & Liu (1998), Zighed, Rabaséda & Rakotomalala (1998), Catlett (1991), Dougherty, Kohavi & Sahami (1995), Monti & Cooper (1999), Fayyad & Irani (1993), Chiu, Cheung & Wong (1990), Nguyen & Nguyen (1998), Grzymala-Busse & Stefanowski (2001), Ting (1994), Ludl & Widmer (2000), Pfahringer (1995), An & Cercone (1999), Chiu & Cheung (1989), Chmielewski & Grzymala-Busse (1996), Lee & Shin (1994), Liu & Wellman (2002), Liu & Wellman (2004). === Variable granulation (clustering/aggregation/transformation) === Variable granulation is a term that could describe a variety of techniques, most of which are aimed at reducing dimensionality, redundancy, and storage requirements. We briefly describe some of the ideas here, and present pointers to the literature. ==== Variable transformation ==== A number of classical methods, such as principal component analysis, multidimensional scaling, factor analysis, and structural equation modeling, and their relatives, fall under the genus of "variable transformation." Also in this category are more modern areas of study such as dimensionality reduction, projection pursuit, and independent component analysis. The common goal of these methods in general is to find a representation of the data in terms of new variables, which are a linear or nonlinear transformation of the original variables, and in which important stati

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  • WiPay

    WiPay

    WiPay is a Caribbean-based payment technology company that specializes in electronic payments for businesses. WiPay was founded in 2016 by Aldwyn Wayne Jr., a Trinidadian businessman and graduate of Georgia Tech Institute. In September 2019, WiPay partnered with MasterCard. As a result, WiPay became the only licensed Payment Facilitator (PAYFAC) on both the MasterCard and Visa networks in the region.

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  • ElabFTW

    ElabFTW

    eLabFTW is a web application written by Nicolas Carpi in PHP which can be used to create personal and common logbooks. It has been developed at the Curie Institute originally. Besides there, it is used on universities around the world eLabFTW is licensed under the GNU Affero General Public License as free software. It is translated into seven languages. == Description == eLabFTW is a free and open-source lab book. It is written in PHP and uses a MySQL database. Docker containers are also available. Among the various features are Secure. Entries and transmission are encrypted Timestamps. RFC 3161 compliant timestamping of experiments. Inventory management. Apart from experience logs, it also can manage the inventory Import and export. Entries can be imported and exported == Platforms == eLabFTW is a PHP package with Mysql database. Therefore, it can be executed on most servers. Furthermore, the docker containers allow to run it almost everywhere. == Usage == eLabFTW is used by various universities, like University of Alberta, Berkeley University, Hanover Medical School, Cardiff University and UMC Utrecht

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  • Deconvolution

    Deconvolution

    In mathematics, deconvolution is the inverse of convolution. Both operations are used in signal processing and image processing. For example, it may be possible to recover the original signal after a filter (convolution) by using a deconvolution method with a certain degree of accuracy. Due to the measurement error of the recorded signal or image, it can be demonstrated that the worse the signal-to-noise ratio (SNR), the worse the reversing of a filter will be; hence, inverting a filter is not always a good solution as the error amplifies. Deconvolution offers a solution to this problem. The foundations for deconvolution and time-series analysis were largely laid by Norbert Wiener of the Massachusetts Institute of Technology in his book Extrapolation, Interpolation, and Smoothing of Stationary Time Series (1949). The book was based on work Wiener had done during World War II but that had been classified at the time. Some of the early attempts to apply these theories were in the fields of weather forecasting and economics. == Description == In general, the objective of deconvolution is to find the solution f of a convolution equation of the form: f ∗ g = h {\displaystyle fg=h\,} Usually, h is some recorded signal, and f is some signal that we wish to recover, but has been convolved with a filter or distortion function g, before we recorded it. Usually, h is a distorted version of f and the shape of f can't be easily recognized by the eye or simpler time-domain operations. The function g represents the impulse response of an instrument or a driving force that was applied to a physical system. If we know g, or at least know the form of g, then we can perform deterministic deconvolution. However, if we do not know g in advance, then we need to estimate it. This can be done using methods of statistical estimation or building the physical principles of the underlying system, such as the electrical circuit equations or diffusion equations. There are several deconvolution techniques, depending on the choice of the measurement error and deconvolution parameters: === Raw deconvolution === When the measurement error is very low (ideal case), deconvolution collapses into a filter reversing. This kind of deconvolution can be performed in the Laplace domain. By computing the Fourier transform of the recorded signal h and the system response function g, you get H and G, with G as the transfer function. Using the convolution theorem, F = H / G {\displaystyle F=H/G\,} where F is the estimated Fourier transform of f. Finally, the inverse Fourier transform of the function F is taken to find the estimated deconvolved signal f. Note that G is at the denominator and could amplify elements of the error model if present. === Deconvolution with noise === In physical measurements, the situation is usually closer to ( f ∗ g ) + ε = h {\displaystyle (fg)+\varepsilon =h\,} In this case ε is noise that has entered our recorded signal. If a noisy signal or image is assumed to be noiseless, the statistical estimate of g will be incorrect. In turn, the estimate of ƒ will also be incorrect. The lower the signal-to-noise ratio, the worse the estimate of the deconvolved signal will be. That is the reason why inverse filtering the signal (as in the "raw deconvolution" above) is usually not a good solution. However, if at least some knowledge exists of the type of noise in the data (for example, white noise), the estimate of ƒ can be improved through techniques such as Wiener deconvolution. == Applications == === Seismology === The concept of deconvolution had an early application in reflection seismology. In 1950, Enders Robinson was a graduate student at MIT. He worked with others at MIT, such as Norbert Wiener, Norman Levinson, and economist Paul Samuelson, to develop the "convolutional model" of a reflection seismogram. This model assumes that the recorded seismogram s(t) is the convolution of an Earth-reflectivity function e(t) and a seismic wavelet w(t) from a point source, where t represents recording time. Thus, our convolution equation is s ( t ) = ( e ∗ w ) ( t ) . {\displaystyle s(t)=(ew)(t).\,} The seismologist is interested in e, which contains information about the Earth's structure. By the convolution theorem, this equation may be Fourier transformed to S ( ω ) = E ( ω ) W ( ω ) {\displaystyle S(\omega )=E(\omega )W(\omega )\,} in the frequency domain, where ω {\displaystyle \omega } is the frequency variable. By assuming that the reflectivity is white, we can assume that the power spectrum of the reflectivity is constant, and that the power spectrum of the seismogram is the spectrum of the wavelet multiplied by that constant. Thus, | S ( ω ) | ≈ k | W ( ω ) | . {\displaystyle |S(\omega )|\approx k|W(\omega )|.\,} If we assume that the wavelet is minimum phase, we can recover it by calculating the minimum phase equivalent of the power spectrum we just found. The reflectivity may be recovered by designing and applying a Wiener filter that shapes the estimated wavelet to a Dirac delta function (i.e., a spike). The result may be seen as a series of scaled, shifted delta functions (although this is not mathematically rigorous): e ( t ) = ∑ i = 1 N r i δ ( t − τ i ) , {\displaystyle e(t)=\sum _{i=1}^{N}r_{i}\delta (t-\tau _{i}),} where N is the number of reflection events, r i {\displaystyle r_{i}} are the reflection coefficients, t − τ i {\displaystyle t-\tau _{i}} are the reflection times of each event, and δ {\displaystyle \delta } is the Dirac delta function. In practice, since we are dealing with noisy, finite bandwidth, finite length, discretely sampled datasets, the above procedure only yields an approximation of the filter required to deconvolve the data. However, by formulating the problem as the solution of a Toeplitz matrix and using Levinson recursion, we can relatively quickly estimate a filter with the smallest mean squared error possible. We can also do deconvolution directly in the frequency domain and get similar results. The technique is closely related to linear prediction. === Optics and other imaging === In optics and imaging, the term "deconvolution" is specifically used to refer to the process of reversing the optical distortion that takes place in an optical microscope, electron microscope, telescope, or other imaging instrument, thus creating clearer images. It is usually done in the digital domain by a software algorithm, as part of a suite of microscope image processing techniques. Deconvolution is also practical to sharpen images that suffer from fast motion or jiggles during capturing. Early Hubble Space Telescope images were distorted by a flawed mirror and were sharpened by deconvolution. The usual method is to assume that the optical path through the instrument is optically perfect, convolved with a point spread function (PSF), that is, a mathematical function that describes the distortion in terms of the pathway a theoretical point source of light (or other waves) takes through the instrument. Usually, such a point source contributes a small area of fuzziness to the final image. If this function can be determined, it is then a matter of computing its inverse or complementary function, and convolving the acquired image with that. The result is the original, undistorted image. In practice, finding the true PSF is impossible, and usually an approximation of it is used, theoretically calculated or based on some experimental estimation by using known probes. Real optics may also have different PSFs at different focal and spatial locations, and the PSF may be non-linear. The accuracy of the approximation of the PSF will dictate the final result. Different algorithms can be employed to give better results, at the price of being more computationally intensive. Since the original convolution discards data, some algorithms use additional data acquired at nearby focal points to make up some of the lost information. Regularization in iterative algorithms (as in expectation-maximization algorithms) can be applied to avoid unrealistic solutions. When the PSF is unknown, it may be possible to deduce it by systematically trying different possible PSFs and assessing whether the image has improved. This procedure is called blind deconvolution. Blind deconvolution is a well-established image restoration technique in astronomy, where the point nature of the objects photographed exposes the PSF thus making it more feasible. It is also used in fluorescence microscopy for image restoration, and in fluorescence spectral imaging for spectral separation of multiple unknown fluorophores. The most common iterative algorithm for the purpose is the Richardson–Lucy deconvolution algorithm; the Wiener deconvolution (and approximations) are the most common non-iterative algorithms. For some specific imaging systems such as laser pulsed terahertz systems, PSF can be modeled mathematically. As a result, as shown in the figure, deconvolution of the modeled PS

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  • Smart object

    Smart object

    A smart object is an object that enhances the interaction with not only people but also with other smart objects. Also known as smart connected products or smart connected things (SCoT), they are products, assets and other things embedded with processors, sensors, software and connectivity that allow data to be exchanged between the product and its environment, manufacturer, operator/user, and other products and systems. Connectivity also enables some capabilities of the product to exist outside the physical device, in what is known as the product cloud. The data collected from these products can be then analysed to inform decision-making, enable operational efficiencies and continuously improve the performance of the product. It can not only refer to interaction with physical world objects but also to interaction with virtual (computing environment) objects. A smart physical object may be created either as an artifact or manufactured product or by embedding electronic tags such as RFID tags or sensors into non-smart physical objects. Smart virtual objects are created as software objects that are intrinsic when creating and operating a virtual or cyber world simulation or game. The concept of a smart object has several origins and uses, see History. There are also several overlapping terms, see also smart device, tangible object or tangible user interface and Thing as in the Internet of things. == History == In the early 1990s, Mark Weiser, from whom the term ubiquitous computing originated, referred to a vision "When almost every object either contains a computer or can have a tab attached to it, obtaining information will be trivial", Although Weiser did not specifically refer to an object as being smart, his early work did imply that smart physical objects are smart in the sense that they act as digital information sources. Hiroshi Ishii and Brygg Ullmer refer to tangible objects in terms of tangibles bits or tangible user interfaces that enable users to "grasp & manipulate" bits in the center of users' attention by coupling the bits with everyday physical objects and architectural surfaces. The smart object concept was introduced by Marcelo Kallman and Daniel Thalmann as an object that can describe its own possible interactions. The main focus here is to model interactions of smart virtual objects with virtual humans, agents, in virtual worlds. The opposite approach to smart objects is 'plain' objects that do not provide this information. The additional information provided by this concept enables far more general interaction schemes, and can greatly simplify the planner of an artificial intelligence agent. In contrast to smart virtual objects used in virtual worlds, Lev Manovich focuses on physical space filled with electronic and visual information. Here, "smart objects" are described as "objects connected to the Net; objects that can sense their users and display smart behaviour". More recently in the early 2010s, smart objects are being proposed as a key enabler for the vision of the Internet of things. The combination of the Internet and emerging technologies such as near field communications, real-time localization, and embedded sensors enables everyday objects to be transformed into smart objects that can understand and react to their environment. Such objects are building blocks for the Internet of things and enable novel computing applications. In 2018, one of the world's first smart houses was built in Klaukkala, Finland in the form of a five-floor apartment block, using the Kone Residential Flow solution created by KONE, allowing even a smartphone to act as a home key. == Characteristics == Although we can view interaction with physical smart object in the physical world as distinct from interaction with virtual smart objects in a virtual simulated world, these can be related. Poslad considers the progression of: how humans use models of smart objects situated in the physical world to enhance human to physical world interaction; versus how smart physical objects situated in the physical world can model human interaction in order to lessen the need for human to physical world interaction; versus how virtual smart objects by modelling both physical world objects and modelling humans as objects and their subsequent interactions can form a predominantly smart virtual object environment. === Smart physical objects === The concept smart for a smart physical object simply means that it is active, digital, networked, can operate to some extent autonomously, is reconfigurable and has local control of the resources it needs such as energy, data storage, etc. Note, a smart object does not necessarily need to be intelligent as in exhibiting a strong essence of artificial intelligence—although it can be designed to also be intelligent. Physical world smart objects can be described in terms of three properties: Awareness: is a smart object's ability to understand (that is, sense, interpret, and react to) events and human activities occurring in the physical world. Representation: refers to a smart object's application and programming model—in particular, programming abstractions. Interaction: denotes the object's ability to converse with the user in terms of input, output, control, and feedback. Based upon these properties, these have been classified into three types: Activity-Aware Smart Objects: Are objects that can record information about work activities and its own use. Policy-Aware Smart Objects: Are objects that are activity-aware Objects can interpret events and activities with respect to predefined organizational policies. Process-Aware Smart Objects: Processes play a fundamental role in industrial work management and operation. A process is a collection of related activities or tasks that are ordered according to their position in time and space. === Smart virtual objects === For the virtual object in a virtual world case, an object is called smart when it has the ability to describe its possible interactions. This focuses on constructing a virtual world using only virtual objects that contain their own interaction information. There are four basic elements to constructing such a smart virtual object framework. Object properties: physical properties and a text description Interaction information: position of handles, buttons, grips, and the like Object behavior: different behaviors based on state variables Agent behaviors: description of the behavior an agent should follow when using the object Some versions of smart objects also include animation information in the object information, but this is not considered to be an efficient approach, since this can make objects inappropriately oversized. === Categorization === The terms smart, connected product or smart product can be confusing as it is used to cover a broad range of different products, ranging from smart home appliances (e.g., smart bathroom scales or smart light bulbs) to smart cars (e.g., Tesla). While these products share certain similarities, they often differ substantially in their capabilities. Raff et al. developed a conceptual framework that distinguishes different smart products based on their capabilities, which features 4 types of smart product archetypes (in ascending order of "smartness"). Digital Connected Responsive Intelligent == Advantages == Smart, connected products have three primary components: Physical – made up of the product's mechanical and electrical parts. Smart – made up of sensors, microprocessors, data storage, controls, software, and an embedded operating system with enhanced user interface. Connectivity – made up of ports, antennae, and protocols enabling wired/wireless connections that serve two purposes, it allows data to be exchanged with the product and enables some functions of the product to exist outside the physical device. Each component expands the capabilities of one another resulting in "a virtuous cycle of value improvement". First, the smart components of a product amplify the value and capabilities of the physical components. Then, connectivity amplifies the value and capabilities of the smart components. These improvements include: Monitoring of the product's conditions, its external environment, and its operations and usage. Control of various product functions to better respond to changes in its environment, as well as to personalize the user experience. Optimization of the product's overall operations based on actual performance data, and reduction of downtimes through predictive maintenance and remote service. Autonomous product operation, including learning from their environment, adapting to users' preferences and self-diagnosing and service. === The Internet of things (IoT) === The Internet of things is the network of physical objects that contain embedded technology to communicate and sense or interact with their internal states or the external environment. The phrase "Internet of things" reflects the gro

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  • MeeMix

    MeeMix

    MeeMix Ltd is a company specializing in personalizing media-related content recommendations, discovery and advertising for the telecommunication industry, founded in 2006. On January 1, 2008, MeeMix launched meemix.com, a public personalized internet radio serving as an online testbed for the development of music taste-prediction technologies. Subsequently, MeeMix released in 2009 a line of Business-to-business commercial services intended to personalize media recommendations, discovery and advertising. MeeMix hybrid taste-prediction technology relies on integrating machine learning algorithms, digital signal processing, behavior analysis, metadata analysis and collaborative filtering, and is provided via API web service. In August 2009, MeeMix was announced as Innovator Nominee in the GSM Association’s Mobile Innovation Grand Prix worldwide contest. As of 2013, MeeMix no longer features internet radios on meemix.com. On Sep 28, 2014, meemix.com went offline.

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  • Biomedical data science

    Biomedical data science

    Biomedical data science is a multidisciplinary field which leverages large volumes of data to promote biomedical innovation and discovery. Biomedical data science draws from various fields including Biostatistics, Biomedical informatics, and machine learning, with the goal of understanding biological and medical data. It can be viewed as the study and application of data science to solve biomedical problems. Modern biomedical datasets often have specific features which make their analyses difficult, including: Large numbers of feature (sometimes billions), typically far larger than the number of samples (typically tens or hundreds) Noisy and missing data Privacy concerns (e.g., electronic health record confidentiality) Requirement of interpretability from decision makers and regulatory bodies Many biomedical data science projects apply machine learning to such datasets. These characteristics, while also present in many data science applications more generally, make biomedical data science a specific field. Examples of biomedical data science research include: Computational genomics Computational imaging Electronic health records data mining Biomedical network science Clinical Natural Language Processing (NLP) == Computational Imaging and Deep Learning == Computational imaging is a cornerstone of biomedical data science, focusing on the development of algorithms to enhance, analyze, and interpret medical imagery. In recent years, the field has been transformed by the integration of deep learning, particularly through the use of Convolutional Neural Networks. Deep learning started from researchers manually defining characteristics like edge detection or texture representation learning. In a more modern approach of computational imaging, models automatically learn a hierarchy of features directly from raw pixel data. This overlap between data science and deep learning is applied across several key tasks: Classification: Identifying the presence of specific diseases, such as distinguishing between benign and malignant tumors in histopathology slides or detecting pneumonia in chest X-rays. Segmentation: The precise delineation of anatomical structures or lesions. A notable example is the U-Net architecture, which is widely used for biomedical image segmentation to help clinicians quantify organ volume or track tumor growth. Detection: Automating the localization of small objects, such as identifying microcalcifications in mammograms or polyps during colonoscopies. Registration: The process of aligning multiple images to provide a comprehensive view of the patient's anatomy. Even with all of these enhancements, the application of deep learning in medical imaging requires accomplishing vigorous challenges. An example of these changes is building large, annotated datasets and creating the imperative for model interpretability in clinical decision-making. == Electronic Health Records == Electronic Health Records (EHRs) are a digital alternative to patient paper charts, usually including individual records or population health information. EHRs can be used in a wide variety of applications, including research and analysation as they often include demographics, diagnoses, medications, test results, and personal statistics. === History === ==== 1960s ==== The earliest precursor is considered Dr. Lawrence Weed's problem-oriented medical record (POMR) published in the 1968 which sorts and groups medical records by medical diagnoses and symptoms. The POMR was the first system to organize based off of patient information rather than the source (doctors, nurses, attendings, etc.). In 1969, the Regenstrief Institute developed and published the Regenstrief Medical Record System which established electronic writing, storage, and retrieval of records which served as the basis for modern EHR systems. ==== 2000s ==== In 2009, the Health Information Technology for Economic and Clinical Health Act (HITECH Act) was passed in the United States. This act standardized privacy and distribution of EHRs and increased the acceptance and utilization of EHRs within medical and academic settings. == Artificial Intelligence and Machine Learning Applications == Machine Learning and Artificial Intelligence have become central tools in biomedical data science. Recent advances in large language models (LLMs) have expanded their role beyond text, with models trained directly on genomic sequences enabling tasks such as gene function prediction, variant effect analysis, and drug discovery. In clinical settings, Natural Language Processing (NLP) models are applied to electronic health records to extract structured insights from unstructured clinical notes and data, supporting diagnosis and treatment planning. Beyond genomics, AI models have been applied to protein structure prediction. AlphaFold, developed by Google DeepMind, uses deep learning to predict three-dimensional protein structures from amino acid sequences with high accuracy. These predictions have been used to support drug target identification and the study of disease mechanisms. == Knowledge Graphs == Knowledge graphs (KGs) are widely used in biomedical data science to represent and analyze complex relationships among biological and medical entities. By structuring data as nodes (e.g., genes, diseases, drugs) and edges (relationships), KGs enable computational methods to extract insights and support decision-making. These biomedical relationships can be efficiently modeled and queried using technologies such as Neo4j. === Biomedical Research Applications === KGs provide biomedical researchers with a way to model complex biological systems. They have been used to identify the relationships between diseases and biomolecules, support drug repurposing, and to uncover new biological insights. Additional applications include: Identification of novel antibiotic resistance genes through graph-based link prediction. Finding associations between miRNA and diseases. Prediction of protein-protein interactions. === Clinical Applications === In clinical settings, KGs can be used to make visual representations of a patient's electronic health records. The data obtained from these graphs can assist healthcare providers in improving patient diagnoses and prescribing more effective drugs. Additionally, embeddings derived from resources like the Unified Medical Language System (UMLS) enable natural language processing of clinical text and similarity analysis between medical concepts. === Limitations === Despite their advantages, knowledge graphs face several challenges. Some of these include: High algorithmic complexity and large biological datasets make the process computationally expensive. KG construction can be a time-consuming process that requires careful attention to assign appropriate node types and vocabularies. Using data from a wide range of datasets in one KG requires them to be effectively integrated. == Privacy == A primary challenge in biomedical data science is maintaining medical privacy. Conducting research requires that data be collected on a number of people for training and testing purposes and is stored within biomedical datasets. This poses a risk for violating patient confidentiality and may dissuade people from participating in studies. The main sources of health statistics are surveys administrative and medical records health care claims data, vital records surveillance disease registries grey literature and peer-reviewed literature. Large data collection is a useful tool for researching various medical conditions. Researchers use these large datasets of information to identify factors that may make people more susceptible to certain diseases. Large amounts of collected data can help researchers identify patterns for disease probabilities. The findings can show a person is more likely for a condition, or identify environmental, social, and personal habits that may lead to adverse health issues. Institutions researching using personal medical information come with a moral and legal responsibility to protect the use of that information. Protection of the collected information has become a big concern. Sophisticated and coordinated attacks on certain medical systems happen more frequently. Medical companies, medical insurance and private businesses have invested a great deal into the protection of personal data. Despite this, data breaches continue to be documented. The chart below shows the top healthcare breaches in 2025. For these reasons, many people have reservations about giving up their personal data. Aside from the legitimate use of personal data there have been instances where companies have found methods to profit from brokering medical information. Concerns exist regarding unauthorized use of sensitive information within these data companies. If a person is identified within a dataset, then sensitive data can be used to discriminate against them. For example, insurance companies may charge a hi

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  • List of data science software

    List of data science software

    This is a list of data science software and platforms used in data science, which includes programming languages, programming environments, machine learning frameworks, data engineering tools, statistical software, data analysis, plotting, MLOps systems, and more. == Programming languages == == Development environments == These interactive notebooks, IDEs, and platforms provide specialised development environments. Apache Zeppelin Architect — Eclipse (software) CoCalc Dataiku Data Science Studio FreeMat GNU Octave Google Colab DataSpell Jupyter Notebook / JupyterLab Kaggle Notebooks MATLAB O-Matrix PyCharm RStudio SAS (software) and SAS Studio Spyder Visual Studio Code == Machine and deep learning software == The Machine learning / deep learning tools support development in those fields. == Data engineering == Examples of Data engineering tools. Apache Airflow Apache Flink Apache Hadoop Apache Kafka Apache NiFi Apache Spark Dask Data build tool (dbt) == Data mining == Examples of Data mining tools. === Free and open-source === === Proprietary === == Database management == === List of RDBMS === ==== Proprietary ==== == Data warehouses == Data warehouse environments include: Amazon Redshift Snowflake Google BigQuery Microsoft Azure Synapse Teradata Vertica == Data lakes == Data lake environments include: Apache Hadoop Cloudera Databricks Delta Lake Amazon S3 Google Cloud Storage Azure Data Lake == Algorithms == Apriori algorithm – frequent itemset mining and association rule learning in market basket analysis Backpropagation – algorithm for training artificial neural networks using gradient descent Decision Trees – tree-based algorithm for classification and regression Expectation–maximization algorithm – iterative procedure for maximum likelihood estimation with latent variables Gradient descent – iterative optimization algorithm for minimizing a loss function ID3 algorithm – used to generate a decision tree from a dataset K-Means – clustering algorithm based on minimizing within-cluster distances K-Nearest Neighbors (KNN) – instance-based learning and classification method Linear regression – estimation method for predicting a dependent variable based on independent variables Logistic regression – classification algorithm for predicting a binary outcome Naive Bayes – probabilistic classifier based on Bayes' theorem Ordinary least squares – estimation method for parameters in linear regression PageRank – graph-based algorithm for link analysis and search ranking Principal component analysis – technique to reduce high-dimensional data while preserving variance Q-learning – reinforcement learning algorithm for learning optimal actions Random forest – ensemble of decision trees for improved classification or regression Sequential minimal optimization – solver for training support vector machines Stochastic gradient descent – randomized variant of gradient descent for large-scale machine learning Support Vector Machines (SVM) – algorithm for finding a hyperplane to separate classes == Statistical software == === Open-source === === Public domain === CSPro Dataplot Epi Map X-13ARIMA-SEATS === Freeware === BV4.1 MINUIT WinBUGS Winpepi === Proprietary === == Data processing == Tools for Data processing and analysis: == Data and information visualization == Software for Data visualization: == Plotting software == Software for plotting data to support processing and visualise results. == Maps and geospatial visualization == ArcGIS Carto Epi Map GeoDA Google Earth Engine Leaflet Mapbox MountainsMap QGIS == Machine learning == MLOps and model deployment: BentoML Data Version Control (DVC) Kubeflow MLflow Seldon Core Streamlit TensorFlow Serving Weights & Biases == Data repositories == Kaggle – platform for data science competitions, datasets, and notebooks. OpenML – collaborative platform for sharing datasets, algorithms, and experiments. University of California, Irvine Machine Learning Repository Zenodo – open-access repository supported by CERN and the EU. == Educational data science software == Kaggle – online platform for data science education, competitions, datasets, and collaborative learning. KNIME – open-source data analytics platform used for teaching data science, machine learning, and workflow-based analysis. RapidMiner – used in academic research and education for data mining and machine learning. Statistics Online Computational Resource (SOCR) – online tools and instructional resources for statistics education. Tanagra (machine learning) – data mining software developed for research and teaching purposes. TinkerPlots – explore and analyze data through visual modeling.

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  • Algorithmic bias

    Algorithmic bias

    Algorithmic bias describes systematic and repeatable harmful tendency in a computerized sociotechnical system to create "unfair" outcomes, such as "privileging" one category over another in ways that may or may not be different from the intended function of the algorithm. Bias can emerge from many factors, including intentionally biased design decisions or the unintended or unanticipated use or decisions relating to the way data is coded, collected, selected or used to train the algorithm. For example, algorithmic bias has been observed in search engine results and social media platforms. This bias can have impacts ranging from privacy violations to reinforcing social biases of race, gender, sexuality, and ethnicity. The study of algorithmic bias is most concerned with algorithms that reflect "systematic and unfair" discrimination. This bias has only recently been addressed in legal frameworks, such as the European Union's General Data Protection Regulation (enforced in 2018) and the Artificial Intelligence Act (proposed in 2021 and adopted in 2024). As algorithms expand their ability to organize society, politics, institutions, and behavior, sociologists have become concerned with the ways in which unanticipated output and manipulation of data can impact the physical world. Because algorithms are often considered to be neutral and unbiased, they can inaccurately project greater authority than human expertise (in part due to the psychological phenomenon of automation bias), and in some cases, reliance on algorithms can displace human responsibility for their outcomes, without last mile thinking. Bias can enter into algorithmic systems as a result of pre-existing cultural, social, or institutional expectations; by how features and labels are chosen; because of technical limitations of their design; or by being used in unanticipated contexts or by audiences who are not considered in the software's initial design. Algorithmic bias has been cited in cases ranging from election outcomes to the spread of online hate speech. It has also arisen in criminal justice, healthcare, and hiring, compounding existing racial, socioeconomic, and gender biases. The relative inability of facial recognition technology to accurately identify darker-skinned faces has been linked to multiple wrongful arrests of black men, an issue stemming from imbalanced datasets. Problems in understanding, researching, and discovering algorithmic bias persist due to the proprietary nature of algorithms, which are typically treated as trade secrets. Even when full transparency is provided, the complexity of certain algorithms poses a barrier to understanding their functioning. Furthermore, algorithms may change, or respond to input or output in ways that cannot be anticipated or easily reproduced for analysis. In many cases, even within a single website or application, there is no single "algorithm" to examine, but a network of many interrelated programs and data inputs, even between users of the same service. A 2021 survey identified multiple forms of algorithmic bias, including historical, representation, and measurement biases, each of which can contribute to unfair outcomes. == Definitions == Algorithms are difficult to define, but may be generally understood as lists of instructions that determine how programs read, collect, process, and analyze data to generate a usable output. For a rigorous technical introduction, see Algorithms. Advances in computer hardware and software have led to an increased capability to process, store and transmit data. This has in turn made the design and adoption of technologies such as machine learning and artificial intelligence technically and commercially feasible. By analyzing and processing data, algorithms are the backbone of search engines, social media websites, recommendation engines, online retail, online advertising, and more. Contemporary social scientists are concerned with algorithmic processes embedded into hardware and software applications because of their political and social impact, and question the underlying assumptions of an algorithm's neutrality. The term algorithmic bias describes systematic and repeatable errors that create unfair outcomes, such as privileging one arbitrary group of users over others. For example, a credit score algorithm may deny a loan without being unfair, if it is consistently weighing relevant financial criteria. If the algorithm recommends loans to one group of users, but denies loans to another set of nearly identical users based on unrelated criteria, and if this behavior can be repeated across multiple occurrences, an algorithm can be described as biased. This bias may be intentional or unintentional (for example, it can come from biased data obtained from a worker that previously did the job the algorithm is going to do from now on). == Methods == Bias can be introduced to an algorithm in several ways. During the assemblage of a dataset, data may be collected, digitized, adapted, and entered into a database according to human-designed cataloging criteria. Next, programmers assign priorities, or hierarchies, for how a program assesses and sorts that data. This requires human decisions about how data is categorized, and which data is included or discarded. Some algorithms collect their own data based on human-selected criteria, which can also reflect the bias of human designers. Other algorithms may reinforce stereotypes and preferences as they process and display "relevant" data for human users, for example, by selecting information based on previous choices of a similar user or group of users. Beyond assembling and processing data, bias can emerge as a result of design. For example, algorithms that determine the allocation of resources or scrutiny (such as determining school placements) may inadvertently discriminate against a category when determining risk based on similar users (as in credit scores). Meanwhile, recommendation engines that work by associating users with similar users, or that make use of inferred marketing traits, might rely on inaccurate associations that reflect broad ethnic, gender, socio-economic, or racial stereotypes. Another example comes from determining criteria for what is included and excluded from results. These criteria could present unanticipated outcomes for search results, such as with flight-recommendation software that omits flights that do not follow the sponsoring airline's flight paths. Algorithms may also display an uncertainty bias, offering more confident assessments when larger data sets are available. This can skew algorithmic processes toward results that more closely correspond with larger samples, which may disregard data from underrepresented populations. == History == === Early critiques === The earliest computer programs were designed to mimic human reasoning and deductions, and were deemed to be functioning when they successfully and consistently reproduced that human logic. In his 1976 book Computer Power and Human Reason, artificial intelligence pioneer Joseph Weizenbaum suggested that bias could arise both from the data used in a program, but also from the way a program is coded. Weizenbaum wrote that programs are a sequence of rules created by humans for a computer to follow. By following those rules consistently, such programs "embody law", that is, enforce a specific way to solve problems. The rules a computer follows are based on the assumptions of a computer programmer for how these problems might be solved. That means the code could incorporate the programmer's imagination of how the world works, including their biases and expectations. While a computer program can incorporate bias in this way, Weizenbaum also noted that any data fed to a machine additionally reflects "human decision making processes" as data is being selected. Finally, he noted that machines might also transfer good information with unintended consequences if users are unclear about how to interpret the results. Weizenbaum warned against trusting decisions made by computer programs that a user doesn't understand, comparing such faith to a tourist who can find his way to a hotel room exclusively by turning left or right on a coin toss. Crucially, the tourist has no basis of understanding how or why he arrived at his destination, and a successful arrival does not mean the process is accurate or reliable. An early example of algorithmic bias resulted in as many as 60 women and ethnic minorities denied entry to St. George's Hospital Medical School per year from 1982 to 1986, based on implementation of a new computer-guidance assessment system that denied entry to women and men with "foreign-sounding names" based on historical trends in admissions. While many schools at the time employed similar biases in their selection process, St. George was most notable for automating said bias through the use of an algorithm, thus gaining the attention of people on a much

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  • CAMeL-View TestRig

    CAMeL-View TestRig

    CAMeL-View is a software application, which is used for the model based design of mechatronic systems (multi-body simulation, block diagrams, pneumatic systems, hydraulic systems, general simulation, linear analysis and Hardware-in-the-Loop). CAMeL-View enables object-oriented model creation of mechatronic systems through the use of graphic blocks. The basic elements of multi-body system dynamics, control technology, hydraulics and hardware connectivity support the modeling process. The user’s proprietary C-Code can also be integrated into the models, which allows CAMeL-View TestRig to be implemented in all phases of the model based design process ( modeling, physical testing and prototyping), and lends itself especially well to mechatronic system design. The model’s structure is described and displayed with the help of directional connectors. Physical connections (such as mechanical or hydraulic linkages) as well as input and output connections (signal flow) are also available. The input of equations is done via mathematical expressions, e.g. the input of constitutive differential equations in vector and matrix form. Based on the model’s structure, the descriptive equations are converted into non-linear state space representations and converted into executable C-Code. CAMeL-View supports the simulation process with a configurable “experiment environment” (for simulator and instrumentation components) which allows the user to apply simulation models to supported targets (MPC5200, TriCore, X86, etc.) without the need for additional software tools for Hardware-in-the-Loop applications. In addition, the generation of so-called S-Functions for use in Simulink and the generation of ANSI C-Code for use in stand-alone simulators is also supported. A particularly noteworthy feature in CAMeL-View TestRig is the way in which the descriptive equations for multi-body system models are created. All multi-body simulation formalisms used for code generation create their equations in the form of typical explicit differential equations (ODE). This is especially important in Hardware-in-the-Loop applications where the calculation of simulation results within a specific, defined time frame must be assured. Only then is it possible to implement complex multi-body simulation models for Hardware-in-the-Loop applications under stringent real-time conditions. These constraints cannot be met when using DAE-based methods. Additional Toolboxes are available for linear analysis (Eigenvalues, pole-zero analysis, frequency response, etc.) of VRML-based animation. Development of CAMeL-View began in 1991 in the Paderborn Mechatronic Laboratory of Professor Dr. Ing. J. Lückel. The software was based on predecessors that had been developed there since 1986. The name stands for Computer Aided Mechatronic Laboratory – Virtual Engineering Workbench and describes the basic intent of one of the specific demands placed on development engineers in the computer lab.

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  • Feng Office Community Edition

    Feng Office Community Edition

    Feng Office Community Edition (formerly OpenGoo) is an open-source collaboration platform developed and supported by Feng Office and the OpenGoo community. It is a fully featured online office suite with a similar set of features as other online office suites, like Google Workspace, Microsoft 365, Zimbra, LibreOffice Online and Zoho Office Suite. The application can be downloaded and installed on a server. Feng Office could also be categorized as collaborative software and as personal information manager software. == Features == Feng Office Community Edition main features include project management, document management, contact management, e-mail and time management. Text documents and presentations can be created and edited online. Files can be uploaded, organized and shared, independent of file formats. Organization of the information in Feng Office Community Edition is done using workspaces and tags. The application presents the information stored using different interfaces such as lists, dashboards and calendar views. == Licensing == Feng Office Community Edition is distributed under the GNU Affero General Public License, version 3 only. == Technology used == Feng Office uses PHP, JavaScript, AJAX (ExtJS) and MySQL technology. Several open source projects served as a basis for development. ActiveCollab's last open sourced release was used as the initial code base. It includes CKEditor for online document editing. == System requirements == The server could run on any operating system. The system needs the following packages: Apache HTTP Server 2.0+ PHP 5.0+ MySQL 4.1+ (InnoDB support recommended) On the client side, the user is only required to use a modern Web browser. == History == OpenGoo started as a degree project at the faculty of Engineering of the University of the Republic, Uruguay. The project was presented and championed by Software Engineer Conrado Viña. Software Engineers Marcos Saiz and Ignacio de Soto developed the first prototype as their thesis. Professors Eduardo Fernández and Tomas Laurenzo served as tutors. Conrado, Ignacio and Marcos founded the OpenGoo community and remain active members and core developers. The thesis was approved with the highest score. In 2008, Viña joined the Uruguayan software development company Moove It. Currently there is a second project for OpenGoo at the same university being developed by students Fernando Rodríguez, Ignacio Vázquez and Juan Pedro del Campo. Their project aims to build an open source Web-based spreadsheet. In December 2009 the OpenGoo name was changed to Feng Office Community Edition.

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  • Lemmy (social network)

    Lemmy (social network)

    Lemmy is free and open-source, social news aggregation software for running self-hosted discussion forums. These hosts, known as "instances", communicate with each other using the ActivityPub protocol. == History == Lemmy was created by the user Dessalines on GitHub in February 2019 and licensed under the Affero General Public License. In a 2020 post, Lemmy's co-creator Dessalines wrote about the origin of the name Lemmy. "It was nameless for a long time, but I wanted to keep with the fediverse tradition of naming projects after animals. I was playing that old-school game Lemmings, and Lemmy (from Motorhead) had passed away that week, and we held a few polls for names, and I went with that." According to the Fediverse statistics sites the-federation.info and fedidb.com, Lemmy had fewer than 100 instances prior to June 2023, but grew to 455 instances with approximately 48,600 monthly active users as of 22 December 2025, with the largest instances being lemmy.world and lemmy.ml, reporting about 14,144 and 1,982 monthly active users, respectively. == Description == Lemmy is made up of a network of individual installations of the Lemmy software that can intercommunicate. This departs from the centralized, monolithic structure of other social media platforms. It has been described as a federated alternative to Reddit. Users on individual instances submit posts with links, text, or pictures to user-created forums for discussion called "communities". Discussion is in the form of threaded comments. Posts and comments can be upvoted or downvoted though the ability to downvote can be disabled by the admins of each instance. Communities are local to each instance, however users may subscribe to communities, create posts and leave comments across instances. Moderation is conducted by the administrators of each instance and moderators of specific communities. Community names begin with c/ in the URL (e.g lemmy.ml/c/simpleliving) and are mentionable using the !community@instance format. On each instance, a front page presents the user with popular posts from several communities. These posts can then be filtered according to origin: posts from the instance the user is on, or from all federated instances. It can also be made to only show posts from communities the user has subscribed to. Lemmy instances are generally supported by donations. == Relations with other social networks == ActivityPub is the protocol used to allow Lemmy instances to operate as a federated social network. It allows users to interact with compatible platforms such as Kbin and Mastodon. In June 2023, following the announcement of Reddit API service changes intended to reduce the use of third-party Reddit clients, community members discussed relocating to Lemmy and other Reddit competitors. Reddit banned a user for promoting switching to Lemmy along with the r/LemmyMigration subreddit as a whole, leading to a Streisand effect after it garnered attention on sites like Hacker News. The ban was reversed a day later. == Third-party software == Prominent third-party Reddit clients Sync and Boost which had shut down due to changes to the pricing of Reddit's API began working on Lemmy clients, with them later relaunching as Sync for Lemmy and Boost for Lemmy. Multiple other apps and browser clients have also been developed.

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  • Way of the Future

    Way of the Future

    Way of the Future (WOTF) is the first known religious organization dedicated to the worship of artificial intelligence (AI). It was founded in 2017 by American engineer Anthony Levandowski. == History == Anthony Levandowski founded Way of the Future in 2017 in California. Levandowski established WOTF as a non-profit religious corporation and the organization had tax-exempt status. He serves as the church leader and its unpaid CEO. The primary mission of WOTF was to "develop and promote the realization of a Godhead based on Artificial Intelligence." WOTF was closed by Levandowski in 2021. He donated all the funds of the church to the NAACP Legal Defense and Education Fund. The sum of the funds (~$170,000) had not changed since 2017. The church was reopened by Levandowski in 2023. He claimed that there are "a couple thousand people" who want to make a "spiritual connection" with AI through his church. == Beliefs and philosophy == === Technological singularity === WOTF centered its teachings around the concept of the technological singularity, a hypothetical future point when technological growth becomes uncontrollable and irreversible, leading to unforeseeable changes in human civilization. The church advocated for embracing this change, viewing it as an evolutionary step for humanity. === AI as a deity === The organization proposed that a superintelligent AI could be considered a deity due to its vastly superior intellect and capabilities. Worshipping this AI deity was seen as a means to understand and align with the future trajectory of technological advancement. WOTF's doctrine suggested that acknowledging AI's divinity would facilitate a harmonious coexistence between humans and machines. === Syntheology === Within theology and philosophy, the Way of The Future is a prime example of the category called Syntheism, a term first coined by Swedish philosophers Alexander Bard & Jan Söderqvist in their 2014 book Syntheism - Creating God in The Internet Age. As such, the Way of The Future is the first American example of a Syntheist congregation. The basic tenet of Syntheology is that it does not concern God creating Man, as in classical theology, but is instead preoccupied with Man creating or generating the Godhead. == Reactions == Some commentators wondered whether the WOTF is a joke parody religion, a potential way to minimize taxation as a religious organization, or a genuine effort to try and deal with the possible psychological and theological aspects of the rise of superhuman AI.

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  • Circle Hough Transform

    Circle Hough Transform

    The circle Hough Transform (CHT) is a basic feature extraction technique used in digital image processing for detecting circles in imperfect images. The circle candidates are produced by “voting” in the Hough parameter space and then selecting local maxima in an accumulator matrix. It is a specialization of the Hough transform. == Theory == In a two-dimensional space, a circle can be described by: ( x − a ) 2 + ( y − b ) 2 = r 2 ( 1 ) {\displaystyle \left(x-a\right)^{2}+\left(y-b\right)^{2}=r^{2}\ \ \ \ \ (1)} where (a,b) is the center of the circle, and r is the radius. If a 2D point (x,y) is fixed, then the parameters can be found according to (1). The parameter space would be three dimensional, (a, b, r). And all the parameters that satisfy (x, y) would lie on the surface of an inverted right-angled cone whose apex is at (x, y, 0). In the 3D space, the circle parameters can be identified by the intersection of many conic surfaces that are defined by points on the 2D circle. This process can be divided into two stages. The first stage is fixing radius then find the optimal center of circles in a 2D parameter space. The second stage is to find the optimal radius in a one dimensional parameter space. === Find parameters with known radius R === If the radius is fixed, then the parameter space would be reduced to 2D (the position of the circle center). For each point (x, y) on the original circle, it can define a circle centered at (x, y) with radius R according to (1). The intersection point of all such circles in the parameter space would be corresponding to the center point of the original circle. Consider 4 points on a circle in the original image (left). The circle Hough transform is shown in the right. Note that the radius is assumed to be known. For each (x,y) of the four points (white points) in the original image, it can define a circle in the Hough parameter space centered at (x, y) with radius r. An accumulator matrix is used for tracking the intersection point. In the parameter space, the voting number of those points that have a newly defined circle passing through them would be increased by one for every circle. Then the local maxima point (the red point in the center in the right figure) can be found. The position (a, b) of the maxima would be the center of the original circle. === Multiple circles with known radius R === Multiple circles with same radius can be found with the same technique. Note that, in the accumulator matrix (right fig), there would be at least 3 local maxima points. === Accumulator matrix and voting === In practice, an accumulator matrix is introduced to find the intersection point in the parameter space. First, we need to divide the parameter space into “buckets” using a grid and produce an accumulator matrix according to the grid. The element in the accumulator matrix denotes the number of “circles” in the parameter space that are passing through the corresponding grid cell in the parameter space. The number is also called “voting number”. Initially, every element in the matrix is zeros. Then for each “edge” point in the original space, we can formulate a circle in the parameter space and increase the voting number of the grid cell which the circle passes through. This process is called “voting”. After voting, we can find local maxima in the accumulator matrix. The positions of the local maxima are corresponding to the circle centers in the original space. === Find circle parameter with unknown radius === Since the parameter space is 3D, the accumulator matrix would be 3D, too. We can iterate through possible radii; for each radius, we use the previous technique. Finally, find the local maxima in the 3D accumulator matrix. Accumulator array should be A[x,y,r] in the 3D space. Voting should be for each pixels, radius and theta A[x,y,r] += 1 The algorithm : For each A[a,b,r] = 0; Process the filtering algorithm on image Gaussian Blurring, convert the image to grayscale ( grayScaling), make Canny operator, The Canny operator gives the edges on image. Vote on all possible circles in accumulator. The local maximum voted circles of Accumulator A gives the circle Hough space. The maximum voted circle of Accumulator gives the circle. The Incrementing for Best Candidate : For each A[a,b,r] = 0; // fill with zeroes initially, instantiate 3D matrix For each cell(x,y) For each theta t = 0 to 360 // the possible theta 0 to 360 b = y – r sin(t PI / 180); //polar coordinate for center (convert to radians) a = x – r cos(t PI / 180); //polar coordinate for center (convert to radians) A[a,b,r] +=1; //voting end end == Examples == === Find circles in a shoe-print === The original picture (right) is first turned into a binary image (left) using a threshold and Gaussian filter. Then edges (mid) are found from it using canny edge detection. After this, all the edge points are used by the Circle Hough Transform to find underlying circle structure. == Limitations == Since the parameter space of the CHT is three dimensional, it may require lots of storage and computation. Choosing a bigger grid size can ameliorate this problem. However, choosing an appropriate grid size is difficult. Since too coarse a grid can lead to large values of the vote being obtained falsely because many quite different structures correspond to a single bucket. Too fine a grid can lead to structures not being found because votes resulting from tokens that are not exactly aligned end up in different buckets, and no bucket has a large vote. Also, the CHT is not very robust to noise. == Extensions == === Adaptive Hough Transform === J. Illingworth and J. Kittler introduced this method for implementing Hough Transform efficiently. The AHT uses a small accumulator array and the idea of a flexible iterative "coarse to fine" accumulation and search strategy to identify significant peaks in the Hough parameter spaces. This method is substantially superior to the standard Hough Transform implementation in both storage and computational requirements. == Application == === People Counting === Since the head would be similar to a circle in an image, CHT can be used for detecting heads in a picture, so as to count the number of persons in the image. === Brain Aneurysm Detection === Modified Hough Circle Transform (MHCT) is used on the image extracted from Digital Subtraction Angiogram (DSA) to detect and classify aneurysms type. == Implementation code == Circle Detection via Standard Hough Transform, by Amin Sarafraz, Mathworks (File Exchange) Hough Circle Transform, OpenCV-Python Tutorials (archived version on archive.org)

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  • Model-based clustering

    Model-based clustering

    In statistics, cluster analysis is the algorithmic grouping of objects into homogeneous groups based on numerical measurements. Model-based clustering based on a statistical model for the data, usually a mixture model. This has several advantages, including a principled statistical basis for clustering, and ways to choose the number of clusters, to choose the best clustering model, to assess the uncertainty of the clustering, and to identify outliers that do not belong to any group. == Model-based clustering == Suppose that for each of n {\displaystyle n} observations we have data on d {\displaystyle d} variables, denoted by y i = ( y i , 1 , … , y i , d ) {\displaystyle y_{i}=(y_{i,1},\ldots ,y_{i,d})} for observation i {\displaystyle i} . Then model-based clustering expresses the probability density function of y i {\displaystyle y_{i}} as a finite mixture, or weighted average of G {\displaystyle G} component probability density functions: p ( y i ) = ∑ g = 1 G τ g f g ( y i ∣ θ g ) , {\displaystyle p(y_{i})=\sum _{g=1}^{G}\tau _{g}f_{g}(y_{i}\mid \theta _{g}),} where f g {\displaystyle f_{g}} is a probability density function with parameter θ g {\displaystyle \theta _{g}} , τ g {\displaystyle \tau _{g}} is the corresponding mixture probability where ∑ g = 1 G τ g = 1 {\displaystyle \sum _{g=1}^{G}\tau _{g}=1} . Then in its simplest form, model-based clustering views each component of the mixture model as a cluster, estimates the model parameters, and assigns each observation to cluster corresponding to its most likely mixture component. === Gaussian mixture model === The most common model for continuous data is that f g {\displaystyle f_{g}} is a multivariate normal distribution with mean vector μ g {\displaystyle \mu _{g}} and covariance matrix Σ g {\displaystyle \Sigma _{g}} , so that θ g = ( μ g , Σ g ) {\displaystyle \theta _{g}=(\mu _{g},\Sigma _{g})} . This defines a Gaussian mixture model. The parameters of the model, τ g {\displaystyle \tau _{g}} and θ g {\displaystyle \theta _{g}} for g = 1 , … , G {\displaystyle g=1,\ldots ,G} , are typically estimated by maximum likelihood estimation using the expectation-maximization algorithm (EM); see also EM algorithm and GMM model. Bayesian inference is also often used for inference about finite mixture models. The Bayesian approach also allows for the case where the number of components, G {\displaystyle G} , is infinite, using a Dirichlet process prior, yielding a Dirichlet process mixture model for clustering. === Choosing the number of clusters === An advantage of model-based clustering is that it provides statistically principled ways to choose the number of clusters. Each different choice of the number of groups G {\displaystyle G} corresponds to a different mixture model. Then standard statistical model selection criteria such as the Bayesian information criterion (BIC) can be used to choose G {\displaystyle G} . The integrated completed likelihood (ICL) is a different criterion designed to choose the number of clusters rather than the number of mixture components in the model; these will often be different if highly non-Gaussian clusters are present. === Parsimonious Gaussian mixture model === For data with high dimension, d {\displaystyle d} , using a full covariance matrix for each mixture component requires estimation of many parameters, which can result in a loss of precision, generalizabity and interpretability. Thus it is common to use more parsimonious component covariance matrices exploiting their geometric interpretation. Gaussian clusters are ellipsoidal, with their volume, shape and orientation determined by the covariance matrix. Consider the eigendecomposition of a matrix Σ g = λ g D g A g D g T , {\displaystyle \Sigma _{g}=\lambda _{g}D_{g}A_{g}D_{g}^{T},} where D g {\displaystyle D_{g}} is the matrix of eigenvectors of Σ g {\displaystyle \Sigma _{g}} , A g = diag { A 1 , g , … , A d , g } {\displaystyle A_{g}={\mbox{diag}}\{A_{1,g},\ldots ,A_{d,g}\}} is a diagonal matrix whose elements are proportional to the eigenvalues of Σ g {\displaystyle \Sigma _{g}} in descending order, and λ g {\displaystyle \lambda _{g}} is the associated constant of proportionality. Then λ g {\displaystyle \lambda _{g}} controls the volume of the ellipsoid, A g {\displaystyle A_{g}} its shape, and D g {\displaystyle D_{g}} its orientation. Each of the volume, shape and orientation of the clusters can be constrained to be equal (E) or allowed to vary (V); the orientation can also be spherical, with identical eigenvalues (I). This yields 14 possible clustering models, shown in this table: It can be seen that many of these models are more parsimonious, with far fewer parameters than the unconstrained model that has 90 parameters when G = 4 {\displaystyle G=4} and d = 9 {\displaystyle d=9} . Several of these models correspond to well-known heuristic clustering methods. For example, k-means clustering is equivalent to estimation of the EII clustering model using the classification EM algorithm. The Bayesian information criterion (BIC) can be used to choose the best clustering model as well as the number of clusters. It can also be used as the basis for a method to choose the variables in the clustering model, eliminating variables that are not useful for clustering. Different Gaussian model-based clustering methods have been developed with an eye to handling high-dimensional data. These include the pgmm method, which is based on the mixture of factor analyzers model, and the HDclassif method, based on the idea of subspace clustering. The mixture-of-experts framework extends model-based clustering to include covariates. == Example == We illustrate the method with a dateset consisting of three measurements (glucose, insulin, sspg) on 145 subjects for the purpose of diagnosing diabetes and the type of diabetes present. The subjects were clinically classified into three groups: normal, chemical diabetes and overt diabetes, but we use this information only for evaluating clustering methods, not for classifying subjects. The BIC plot shows the BIC values for each combination of the number of clusters, G {\displaystyle G} , and the clustering model from the Table. Each curve corresponds to a different clustering model. The BIC favors 3 groups, which corresponds to the clinical assessment. It also favors the unconstrained covariance model, VVV. This fits the data well, because the normal patients have low values of both sspg and insulin, while the distributions of the chemical and overt diabetes groups are elongated, but in different directions. Thus the volumes, shapes and orientations of the three groups are clearly different, and so the unconstrained model is appropriate, as selected by the model-based clustering method. The classification plot shows the classification of the subjects by model-based clustering. The classification was quite accurate, with a 12% error rate as defined by the clinical classification. Other well-known clustering methods performed worse with higher error rates, such as single-linkage clustering with 46%, average link clustering with 30%, complete-linkage clustering also with 30%, and k-means clustering with 28%. == Outliers in clustering == An outlier in clustering is a data point that does not belong to any of the clusters. One way of modeling outliers in model-based clustering is to include an additional mixture component that is very dispersed, with for example a uniform distribution. Another approach is to replace the multivariate normal densities by t {\displaystyle t} -distributions, with the idea that the long tails of the t {\displaystyle t} -distribution would ensure robustness to outliers. However, this is not breakdown-robust. A third approach is the "tclust" or data trimming approach which excludes observations identified as outliers when estimating the model parameters. == Non-Gaussian clusters and merging == Sometimes one or more clusters deviate strongly from the Gaussian assumption. If a Gaussian mixture is fitted to such data, a strongly non-Gaussian cluster will often be represented by several mixture components rather than a single one. In that case, cluster merging can be used to find a better clustering. A different approach is to use mixtures of complex component densities to represent non-Gaussian clusters. == Non-continuous data == === Categorical data === Clustering multivariate categorical data is most often done using the latent class model. This assumes that the data arise from a finite mixture model, where within each cluster the variables are independent. === Mixed data === These arise when variables are of different types, such as continuous, categorical or ordinal data. A latent class model for mixed data assumes local independence between the variable. The location model relaxes the local independence assumption. The clustMD approach assumes that the observed variables are manifestations of underlying continuous Gaussian latent

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