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  • Region Based Convolutional Neural Networks

    Region Based Convolutional Neural Networks

    Region-based Convolutional Neural Networks (R-CNN) are a family of machine learning models for computer vision, and specifically object detection and localization. The original goal of R-CNN was to take an input image and produce a set of bounding boxes as output, where each bounding box contains an object and also the category (e.g. car or pedestrian) of the object. In general, R-CNN architectures perform selective search over feature maps outputted by a CNN. R-CNN has been extended to perform other computer vision tasks, such as: tracking objects from a drone-mounted camera, locating text in an image, and enabling object detection in Google Lens. Mask R-CNN is also one of seven tasks in the MLPerf Training Benchmark, which is a competition to speed up the training of neural networks. == History == The following covers some of the versions of R-CNN that have been developed. November 2013: R-CNN. April 2015: Fast R-CNN. June 2015: Faster R-CNN. March 2017: Mask R-CNN. December 2017: Cascade R-CNN is trained with increasing Intersection over Union (IoU, also known as the Jaccard index) thresholds, making each stage more selective against nearby false positives. June 2019: Mesh R-CNN adds the ability to generate a 3D mesh from a 2D image. == Architecture == For review articles see. === Selective search === Given an image (or an image-like feature map), selective search (also called Hierarchical Grouping) first segments the image by the algorithm in (Felzenszwalb and Huttenlocher, 2004), then performs the following: Input: (colour) image Output: Set of object location hypotheses L Segment image into initial regions R = {r1, ..., rn} using Felzenszwalb and Huttenlocher (2004) Initialise similarity set S = ∅ foreach Neighbouring region pair (ri, rj) do Calculate similarity s(ri, rj) S = S ∪ s(ri, rj) while S ≠ ∅ do Get highest similarity s(ri, rj) = max(S) Merge corresponding regions rt = ri ∪ rj Remove similarities regarding ri: S = S \ s(ri, r∗) Remove similarities regarding rj: S = S \ s(r∗, rj) Calculate similarity set St between rt and its neighbours S = S ∪ St R = R ∪ rt Extract object location boxes L from all regions in R === R-CNN === With R-CNN, prediction follows a two-step process. A preprocessing selective search step generates a large set of candidate objects (typically as many as 2000), known as regions of interest (ROI). These are forwarded to a CNN, which predicts an object class score and bounding box estimate, independently for each ROI. Importantly, the ROIs are heavily filtered to remove excess candidates. This is achieved using two mechanism. Filtering begins by removing ROIs assigned to the background category. This is a specialized category, which is scored by the CNN alongside other categories. An unfortunate reality is that remaining ROIs typically suffer from heavy duplication. Namely, multiple ROIs that cover same objects in the image are all assigned non-background categories. This is resolved by a heuristic non-maximum suppression (NMS) step. === Fast R-CNN === While the original R-CNN independently computed the neural network features on each of as many as two thousand regions of interest, Fast R-CNN runs the neural network once on the whole image. At the end of the network is a ROIPooling module, which slices out each ROI from the network's output tensor, reshapes it, and classifies it. As in the original R-CNN, the Fast R-CNN uses selective search to generate its region proposals. === Faster R-CNN === While Fast R-CNN used selective search to generate ROIs, Faster R-CNN integrates the ROI generation into the neural network itself. === Mask R-CNN === While previous versions of R-CNN focused on object detections, Mask R-CNN adds instance segmentation. Mask R-CNN also replaced ROIPooling with a new method called ROIAlign, which can represent fractions of a pixel.

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  • Wolfram Mathematica

    Wolfram Mathematica

    Wolfram Mathematica (also known as Mathematica) is a software system with built-in libraries for several areas of technical computing that allows machine learning, statistics, symbolic computation, data manipulation, network analysis, time series analysis, NLP, optimization, plotting functions and various types of data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other programming languages. It was conceived by Stephen Wolfram, and is developed by Wolfram Research of Champaign, Illinois. The Wolfram Language is the programming language used in Mathematica. Mathematica 1.0 was released on June 23, 1988 in Champaign, Illinois and Santa Clara, California. Mathematica's Wolfram Language is fundamentally based on Lisp; for example, the Mathematica command Most is identically equal to the Lisp command butlast. == Notebook interface == Mathematica is split into two parts: the kernel and the front end. The kernel interprets expressions (Wolfram Language code) and returns result expressions, which can then be displayed by the front end. The original front end, designed by Theodore Gray in 1988, consists of a notebook interface and allows the creation and editing of notebook documents that can contain code, plaintext, images, and graphics. Code development is also supported through support in a range of standard integrated development environment (IDE) including Eclipse, IntelliJ IDEA, Atom, Vim, Visual Studio Code and Git. The Mathematica Kernel also includes a command line front end. Other interfaces include JMath, based on GNU Readline and WolframScript which runs self-contained Mathematica programs (with arguments) from the UNIX command line. == High-performance computing == Capabilities for high-performance computing were extended with the introduction of packed arrays in version 4 (1999) and sparse matrices (version 5, 2003), and by adopting the GNU Multiple Precision Arithmetic Library to evaluate high-precision arithmetic. Version 5.2 (2005) added automatic multi-threading when computations are performed on multi-core computers. This release included CPU-specific optimized libraries. In addition Mathematica is supported by third party specialist acceleration hardware such as ClearSpeed. In 2002, gridMathematica was introduced to allow user level parallel programming on heterogeneous clusters and multiprocessor systems and in 2008 parallel computing technology was included in all Mathematica licenses including support for grid technology such as Windows HPC Server 2008, Microsoft Compute Cluster Server and Sun Grid. Support for CUDA and OpenCL GPU hardware was added in 2010. == Extensions == As of Version 14, there are 6,602 built-in functions and symbols in the Wolfram Language. Stephen Wolfram announced the launch of the Wolfram Function Repository in June 2019 as a way for the public Wolfram community to contribute functionality to the Wolfram Language. There are currently more than 3000 functions contributed as Resource Functions. In addition to the Wolfram Function Repository, there is a Wolfram Data Repository with computable data and the Wolfram Neural Net Repository for machine learning. Wolfram Mathematica is the basis of the Combinatorica package, which adds discrete mathematics functionality in combinatorics and graph theory to the program. == Connections to other applications, programming languages, and services == Communication with other applications can be done using a protocol called Wolfram Symbolic Transfer Protocol (WSTP). It allows communication between the Wolfram Mathematica kernel and the front end and provides a general interface between the kernel and other applications. Wolfram Research freely distributes a developer kit for linking applications written in the programming language C to the Mathematica kernel through WSTP using J/Link., a Java program that can ask Mathematica to perform computations. Similar functionality is achieved with .NET /Link, but with .NET programs instead of Java programs. Other languages that connect to Mathematica include Haskell, AppleScript, Racket, Visual Basic, Python, and Clojure. Mathematica supports the generation and execution of Modelica models for systems modeling and connects with Wolfram System Modeler. Links are also available to many third-party software packages and APIs. Mathematica can also capture real-time data from a variety of sources and can read and write to public blockchains (Bitcoin, Ethereum, and ARK). It supports import and export of over 220 data, image, video, sound, computer-aided design (CAD), geographic information systems (GIS), document, and biomedical formats. In 2019, support was added for compiling Wolfram Language code to LLVM. Version 12.3 of the Wolfram Language added support for Arduino. == Computable data == Mathematica is also integrated with Wolfram Alpha, an online answer engine that provides additional data, some of which is kept updated in real time, for users who use Mathematica with an internet connection. Some of the data sets include astronomical, chemical, geopolitical, language, biomedical, airplane, and weather data, in addition to mathematical data (such as knots and polyhedra). == Reception == BYTE in 1989 listed Mathematica as among the "Distinction" winners of the BYTE Awards, stating that it "is another breakthrough Macintosh application ... it could enable you to absorb the algebra and calculus that seemed impossible to comprehend from a textbook". Mathematica has been criticized for being closed source. Wolfram Research claims keeping Mathematica closed source is central to its business model and the continuity of the software.

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  • Vanishing gradient problem

    Vanishing gradient problem

    In machine learning, the vanishing gradient problem is the problem of greatly diverging gradient magnitudes between earlier and later layers encountered when training neural networks with backpropagation. In such methods, neural network weights are updated proportional to their partial derivative of the loss function. As the number of forward propagation steps in a network increases, for instance due to greater network depth, the gradients of earlier weights are calculated with increasingly many multiplications. These multiplications shrink the gradient magnitude. Consequently, the gradients of earlier weights will be exponentially smaller than the gradients of later weights. This difference in gradient magnitude might introduce instability in the training process, slow it, or halt it entirely. For instance, consider the hyperbolic tangent activation function. The gradients of this function are in range [0,1]. The product of repeated multiplication with such gradients decreases exponentially. The inverse problem, when weight gradients at earlier layers get exponentially larger, is called the exploding gradient problem. Backpropagation allowed researchers to train supervised deep artificial neural networks from scratch, initially with little success. Hochreiter's diplom thesis of 1991 formally identified the reason for this failure in the "vanishing gradient problem", which not only affects many-layered feedforward networks, but also recurrent networks. The latter are trained by unfolding them into very deep feedforward networks, where a new layer is created for each time-step of an input sequence processed by the network (the combination of unfolding and backpropagation is termed backpropagation through time). == Prototypical models == This section is based on the paper On the difficulty of training Recurrent Neural Networks by Pascanu, Mikolov, and Bengio. === Recurrent network model === A generic recurrent network has hidden states h 1 , h 2 , … {\displaystyle h_{1},h_{2},\dots } , inputs u 1 , u 2 , … {\displaystyle u_{1},u_{2},\dots } , and outputs x 1 , x 2 , … {\displaystyle x_{1},x_{2},\dots } . Let it be parameterized by θ {\displaystyle \theta } , so that the system evolves as ( h t , x t ) = F ( h t − 1 , u t , θ ) {\displaystyle (h_{t},x_{t})=F(h_{t-1},u_{t},\theta )} Often, the output x t {\displaystyle x_{t}} is a function of h t {\displaystyle h_{t}} , as some x t = G ( h t ) {\displaystyle x_{t}=G(h_{t})} . The vanishing gradient problem already presents itself clearly when x t = h t {\displaystyle x_{t}=h_{t}} , so we simplify our notation to the special case with: x t = F ( x t − 1 , u t , θ ) {\displaystyle x_{t}=F(x_{t-1},u_{t},\theta )} Now, take its differential: d x t = ∇ θ F ( x t − 1 , u t , θ ) d θ + ∇ x F ( x t − 1 , u t , θ ) d x t − 1 = ∇ θ F ( x t − 1 , u t , θ ) d θ + ∇ x F ( x t − 1 , u t , θ ) [ ∇ θ F ( x t − 2 , u t − 1 , θ ) d θ + ∇ x F ( x t − 2 , u t − 1 , θ ) d x t − 2 ] ⋮ = [ ∇ θ F ( x t − 1 , u t , θ ) + ∇ x F ( x t − 1 , u t , θ ) ∇ θ F ( x t − 2 , u t − 1 , θ ) + ⋯ ] d θ {\displaystyle {\begin{aligned}dx_{t}&=\nabla _{\theta }F(x_{t-1},u_{t},\theta )d\theta +\nabla _{x}F(x_{t-1},u_{t},\theta )dx_{t-1}\\&=\nabla _{\theta }F(x_{t-1},u_{t},\theta )d\theta +\nabla _{x}F(x_{t-1},u_{t},\theta )\left[\nabla _{\theta }F(x_{t-2},u_{t-1},\theta )d\theta +\nabla _{x}F(x_{t-2},u_{t-1},\theta )dx_{t-2}\right]\\&\;\;\vdots \\&=\left[\nabla _{\theta }F(x_{t-1},u_{t},\theta )+\nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{\theta }F(x_{t-2},u_{t-1},\theta )+\cdots \right]d\theta \end{aligned}}} Training the network requires us to define a loss function to be minimized. Let it be L ( x T , u 1 , … , u T ) {\displaystyle L(x_{T},u_{1},\dots ,u_{T})} , then minimizing it by gradient descent gives Δ θ = − η ⋅ [ ∇ x L ( x T ) ( ∇ θ F ( x t − 1 , u t , θ ) + ∇ x F ( x t − 1 , u t , θ ) ∇ θ F ( x t − 2 , u t − 1 , θ ) + ⋯ ) ] T {\displaystyle \Delta \theta =-\eta \cdot \left[\nabla _{x}L(x_{T})\left(\nabla _{\theta }F(x_{t-1},u_{t},\theta )+\nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{\theta }F(x_{t-2},u_{t-1},\theta )+\cdots \right)\right]^{T}} where η {\displaystyle \eta } is the learning rate. The vanishing/exploding gradient problem appears because there are repeated multiplications, of the form ∇ x F ( x t − 1 , u t , θ ) ∇ x F ( x t − 2 , u t − 1 , θ ) ∇ x F ( x t − 3 , u t − 2 , θ ) ⋯ {\displaystyle \nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{x}F(x_{t-2},u_{t-1},\theta )\nabla _{x}F(x_{t-3},u_{t-2},\theta )\cdots } ==== Example: recurrent network with sigmoid activation ==== For a concrete example, consider a typical recurrent network defined by x t = F ( x t − 1 , u t , θ ) = W rec σ ( x t − 1 ) + W in u t + b {\displaystyle x_{t}=F(x_{t-1},u_{t},\theta )=W_{\text{rec}}\sigma (x_{t-1})+W_{\text{in}}u_{t}+b} where θ = ( W rec , W in ) {\displaystyle \theta =(W_{\text{rec}},W_{\text{in}})} is the network parameter, σ {\displaystyle \sigma } is the sigmoid activation function, applied to each vector coordinate separately, and b {\displaystyle b} is the bias vector. Then, ∇ x F ( x t − 1 , u t , θ ) = W rec diag ⁡ ( σ ′ ( x t − 1 ) ) {\displaystyle \nabla _{x}F(x_{t-1},u_{t},\theta )=W_{\text{rec}}\operatorname {diag} (\sigma '(x_{t-1}))} , and so ∇ x F ( x t − 1 , u t , θ ) ∇ x F ( x t − 2 , u t − 1 , θ ) ⋯ ∇ x F ( x t − k , u t − k + 1 , θ ) = W rec diag ⁡ ( σ ′ ( x t − 1 ) ) W rec diag ⁡ ( σ ′ ( x t − 2 ) ) ⋯ W rec diag ⁡ ( σ ′ ( x t − k ) ) {\displaystyle {\begin{aligned}&\nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{x}F(x_{t-2},u_{t-1},\theta )\cdots \nabla _{x}F(x_{t-k},u_{t-k+1},\theta )\\&=W_{\text{rec}}\operatorname {diag} (\sigma '(x_{t-1}))W_{\text{rec}}\operatorname {diag} (\sigma '(x_{t-2}))\cdots W_{\text{rec}}\operatorname {diag} (\sigma '(x_{t-k}))\end{aligned}}} Since | σ ′ | ≤ 1 {\displaystyle \left|\sigma '\right|\leq 1} , the operator norm of the above multiplication is bounded above by ‖ W rec ‖ k {\displaystyle \left\|W_{\text{rec}}\right\|^{k}} . So if the spectral radius of W rec {\displaystyle W_{\text{rec}}} is γ < 1 {\displaystyle \gamma <1} , then at large k {\displaystyle k} , the above multiplication has operator norm bounded above by γ k → 0 {\displaystyle \gamma ^{k}\to 0} . This is the prototypical vanishing gradient problem. The effect of a vanishing gradient is that the network cannot learn long-range effects. Recall Equation (loss differential): ∇ θ L = ∇ x L ( x T , u 1 , … , u T ) [ ∇ θ F ( x t − 1 , u t , θ ) + ∇ x F ( x t − 1 , u t , θ ) ∇ θ F ( x t − 2 , u t − 1 , θ ) + ⋯ ] {\displaystyle \nabla _{\theta }L=\nabla _{x}L(x_{T},u_{1},\dots ,u_{T})\left[\nabla _{\theta }F(x_{t-1},u_{t},\theta )+\nabla _{x}F(x_{t-1},u_{t},\theta )\nabla _{\theta }F(x_{t-2},u_{t-1},\theta )+\cdots \right]} The components of ∇ θ F ( x , u , θ ) {\displaystyle \nabla _{\theta }F(x,u,\theta )} are just components of σ ( x ) {\displaystyle \sigma (x)} and u {\displaystyle u} , so if u t , u t − 1 , … {\displaystyle u_{t},u_{t-1},\dots } are bounded, then ‖ ∇ θ F ( x t − k − 1 , u t − k , θ ) ‖ {\displaystyle \left\|\nabla _{\theta }F(x_{t-k-1},u_{t-k},\theta )\right\|} is also bounded by some M > 0 {\displaystyle M>0} , and so the terms in ∇ θ L {\displaystyle \nabla _{\theta }L} decay as M γ k {\displaystyle M\gamma ^{k}} . This means that, effectively, ∇ θ L {\displaystyle \nabla _{\theta }L} is affected only by the first O ( γ − 1 ) {\displaystyle O(\gamma ^{-1})} terms in the sum. If γ ≥ 1 {\displaystyle \gamma \geq 1} , the above analysis does not quite work. For the prototypical exploding gradient problem, the next model is clearer. === Dynamical systems model === Following (Doya, 1993), consider this one-neuron recurrent network with sigmoid activation: x t + 1 = ( 1 − ε ) x t + ε σ ( w x t + b ) + ε w ′ u t {\displaystyle x_{t+1}=(1-\varepsilon )x_{t}+\varepsilon \sigma (wx_{t}+b)+\varepsilon w'u_{t}} At the small ε {\displaystyle \varepsilon } limit, the dynamics of the network becomes d x d t = − x ( t ) + σ ( w x ( t ) + b ) + w ′ u ( t ) {\displaystyle {\frac {dx}{dt}}=-x(t)+\sigma (wx(t)+b)+w'u(t)} Consider first the autonomous case, with u = 0 {\displaystyle u=0} . Set w = 5.0 {\displaystyle w=5.0} , and vary b {\displaystyle b} in [ − 3 , − 2 ] {\displaystyle [-3,-2]} . As b {\displaystyle b} decreases, the system has 1 stable point, then has 2 stable points and 1 unstable point, and finally has 1 stable point again. Explicitly, the stable points are ( x , b ) = ( x , ln ⁡ ( x 1 − x ) − 5 x ) {\displaystyle (x,b)=\left(x,\ln \left({\frac {x}{1-x}}\right)-5x\right)} . Now consider Δ x ( T ) Δ x ( 0 ) {\displaystyle {\frac {\Delta x(T)}{\Delta x(0)}}} and Δ x ( T ) Δ b {\displaystyle {\frac {\Delta x(T)}{\Delta b}}} , where T {\displaystyle T} is large enough that the system has settled into one of the stable points. If ( x ( 0 ) , b ) {\displaystyle (x(0),b)} puts the system very close to an unstable point, then a tiny variation in x ( 0 ) {\displaystyle x(0)} or b {\displaystyle b} wo

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  • Tucker decomposition

    Tucker decomposition

    In mathematics, Tucker decomposition decomposes a tensor into a set of matrices and one small core tensor. It is named after Ledyard R. Tucker although it goes back to Hitchcock in 1927. Initially described as a three-mode extension of factor analysis and principal component analysis it may actually be generalized to higher mode analysis, which is also called higher-order singular value decomposition (HOSVD) or the M-mode SVD. The algorithm to which the literature typically refers when discussing the Tucker decomposition or the HOSVD is the M-mode SVD algorithm introduced by Vasilescu and Terzopoulos, but misattributed to Tucker or De Lathauwer etal. It may be regarded as a more flexible PARAFAC (parallel factor analysis) model. In PARAFAC the core tensor is restricted to be "diagonal". In practice, Tucker decomposition is used as a modelling tool. For instance, it is used to model three-way (or higher way) data by means of relatively small numbers of components for each of the three or more modes, and the components are linked to each other by a three- (or higher-) way core array. The model parameters are estimated in such a way that, given fixed numbers of components, the modelled data optimally resemble the actual data in the least squares sense. The model gives a summary of the information in the data, in the same way as principal components analysis does for two-way data. For a 3rd-order tensor T ∈ F n 1 × n 2 × n 3 {\displaystyle T\in F^{n_{1}\times n_{2}\times n_{3}}} , where F {\displaystyle F} is either R {\displaystyle \mathbb {R} } or C {\displaystyle \mathbb {C} } , Tucker Decomposition can be denoted as follows, T = T × 1 U ( 1 ) × 2 U ( 2 ) × 3 U ( 3 ) {\displaystyle T={\mathcal {T}}\times _{1}U^{(1)}\times _{2}U^{(2)}\times _{3}U^{(3)}} where T ∈ F d 1 × d 2 × d 3 {\displaystyle {\mathcal {T}}\in F^{d_{1}\times d_{2}\times d_{3}}} is the core tensor, a 3rd-order tensor that contains the 1-mode, 2-mode and 3-mode singular values of T {\displaystyle T} , which are defined as the Frobenius norm of the 1-mode, 2-mode and 3-mode slices of tensor T {\displaystyle {\mathcal {T}}} respectively. U ( 1 ) , U ( 2 ) , U ( 3 ) {\displaystyle U^{(1)},U^{(2)},U^{(3)}} are unitary matrices in F d 1 × n 1 , F d 2 × n 2 , F d 3 × n 3 {\displaystyle F^{d_{1}\times n_{1}},F^{d_{2}\times n_{2}},F^{d_{3}\times n_{3}}} respectively. The k-mode product (k = 1, 2, 3) of T {\displaystyle {\mathcal {T}}} by U ( k ) {\displaystyle U^{(k)}} is denoted as T × U ( k ) {\displaystyle {\mathcal {T}}\times U^{(k)}} with entries as ( T × 1 U ( 1 ) ) ( i 1 , j 2 , j 3 ) = ∑ j 1 = 1 d 1 T ( j 1 , j 2 , j 3 ) U ( 1 ) ( j 1 , i 1 ) ( T × 2 U ( 2 ) ) ( j 1 , i 2 , j 3 ) = ∑ j 2 = 1 d 2 T ( j 1 , j 2 , j 3 ) U ( 2 ) ( j 2 , i 2 ) ( T × 3 U ( 3 ) ) ( j 1 , j 2 , i 3 ) = ∑ j 3 = 1 d 3 T ( j 1 , j 2 , j 3 ) U ( 3 ) ( j 3 , i 3 ) {\displaystyle {\begin{aligned}({\mathcal {T}}\times _{1}U^{(1)})(i_{1},j_{2},j_{3})&=\sum _{j_{1}=1}^{d_{1}}{\mathcal {T}}(j_{1},j_{2},j_{3})U^{(1)}(j_{1},i_{1})\\({\mathcal {T}}\times _{2}U^{(2)})(j_{1},i_{2},j_{3})&=\sum _{j_{2}=1}^{d_{2}}{\mathcal {T}}(j_{1},j_{2},j_{3})U^{(2)}(j_{2},i_{2})\\({\mathcal {T}}\times _{3}U^{(3)})(j_{1},j_{2},i_{3})&=\sum _{j_{3}=1}^{d_{3}}{\mathcal {T}}(j_{1},j_{2},j_{3})U^{(3)}(j_{3},i_{3})\end{aligned}}} Altogether, the decomposition may also be written more directly as T ( i 1 , i 2 , i 3 ) = ∑ j 1 = 1 d 1 ∑ j 2 = 1 d 2 ∑ j 3 = 1 d 3 T ( j 1 , j 2 , j 3 ) U ( 1 ) ( j 1 , i 1 ) U ( 2 ) ( j 2 , i 2 ) U ( 3 ) ( j 3 , i 3 ) {\displaystyle T(i_{1},i_{2},i_{3})=\sum _{j_{1}=1}^{d_{1}}\sum _{j_{2}=1}^{d_{2}}\sum _{j_{3}=1}^{d_{3}}{\mathcal {T}}(j_{1},j_{2},j_{3})U^{(1)}(j_{1},i_{1})U^{(2)}(j_{2},i_{2})U^{(3)}(j_{3},i_{3})} Taking d i = n i {\displaystyle d_{i}=n_{i}} for all i {\displaystyle i} is always sufficient to represent T {\displaystyle T} exactly, but often T {\displaystyle T} can be compressed or efficiently approximately by choosing d i < n i {\displaystyle d_{i} Read more →

  • Web container

    Web container

    A web container (also known as a servlet container; and compare "webcontainer") is the component of a web server that interacts with Jakarta Servlets. A web container is responsible for managing the lifecycle of servlets, mapping a URL to a particular servlet and ensuring that the URL requester has the correct access-rights. A web container handles requests to servlets, Jakarta Server Pages (JSP) files, and other types of files that include server-side code. The Web container creates servlet instances, loads and unloads servlets, creates and manages request and response objects, and performs other servlet-management tasks. A web container implements the web component contract of the Jakarta EE architecture. This architecture specifies a runtime environment for additional web components, including security, concurrency, lifecycle management, transaction, deployment, and other services. == List of Servlet containers == The following is a list of notable applications which implement the Jakarta Servlet specification from Eclipse Foundation, divided depending on whether they are directly sold or not. === Open source Web containers === Apache Tomcat (formerly Jakarta Tomcat) is an open source web container available under the Apache Software License. Apache Tomcat 6 and above are operable as general application container (prior versions were web containers only) Apache Geronimo is a full Java EE 6 implementation by Apache Software Foundation. Enhydra, from Lutris Technologies. GlassFish from Eclipse Foundation (an application server, but includes a web container). Jetty, from the Eclipse Foundation. Also supports SPDY and WebSocket protocols. Open Liberty, from IBM, is a fully compliant Jakarta EE server Virgo from Eclipse Foundation provides modular, OSGi based web containers implemented using embedded Tomcat and Jetty. Virgo is available under the Eclipse Public License. WildFly (formerly JBoss Application Server) is a full Java EE implementation by Red Hat, division JBoss. === Commercial Web containers === iPlanet Web Server, from Oracle. JBoss Enterprise Application Platform from Red Hat, division JBoss is subscription-based/open-source Jakarta EE-based application server. WebLogic Application Server, from Oracle Corporation (formerly developed by BEA Systems). Orion Application Server, from IronFlare. Resin Pro, from Caucho Technology. IBM WebSphere Application Server. SAP NetWeaver.

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  • Radial basis function kernel

    Radial basis function kernel

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

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  • Stress majorization

    Stress majorization

    Stress majorization is an optimization strategy used in multidimensional scaling (MDS) where, for a set of n {\displaystyle n} m {\displaystyle m} -dimensional data items, a configuration X {\displaystyle X} of n {\displaystyle n} points in r {\displaystyle r} ( ≪ m ) {\displaystyle (\ll m)} -dimensional space is sought that minimizes the so-called stress function σ ( X ) {\displaystyle \sigma (X)} . Usually r {\displaystyle r} is 2 {\displaystyle 2} or 3 {\displaystyle 3} , i.e. the ( n × r ) {\displaystyle (n\times r)} matrix X {\displaystyle X} lists points in 2 − {\displaystyle 2-} or 3 − {\displaystyle 3-} dimensional Euclidean space so that the result may be visualised (i.e. an MDS plot). The function σ {\displaystyle \sigma } is a cost or loss function that measures the squared differences between ideal ( m {\displaystyle m} -dimensional) distances and actual distances in r-dimensional space. It is defined as: σ ( X ) = ∑ i < j ≤ n w i j ( d i j ( X ) − δ i j ) 2 {\displaystyle \sigma (X)=\sum _{i Read more →

  • Gaussian process emulator

    Gaussian process emulator

    In statistics, Gaussian process emulator is one name for a general type of statistical model that has been used in contexts where the problem is to make maximum use of the outputs of a complicated (often non-random) computer-based simulation model. Each run of the simulation model is computationally expensive and each run is based on many different controlling inputs. The variation of the outputs of the simulation model is expected to vary reasonably smoothly with the inputs, but in an unknown way. The overall analysis involves two models: the simulation model, or "simulator", and the statistical model, or "emulator", which notionally emulates the unknown outputs from the simulator. The Gaussian process emulator model treats the problem from the viewpoint of Bayesian statistics. In this approach, even though the output of the simulation model is fixed for any given set of inputs, the actual outputs are unknown unless the computer model is run and hence can be made the subject of a Bayesian analysis. The main element of the Gaussian process emulator model is that it models the outputs as a Gaussian process on a space that is defined by the model inputs. The model includes a description of the correlation or covariance of the outputs, which enables the model to encompass the idea that differences in the output will be small if there are only small differences in the inputs.

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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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  • Curriculum learning

    Curriculum learning

    Curriculum learning is a technique in machine learning in which a model is trained on examples of increasing difficulty, where the definition of "difficulty" may be provided externally or discovered as part of the training process. This is intended to attain good performance more quickly, or to converge to a better local optimum if the global optimum is not found. == Approach == Most generally, curriculum learning is the technique of successively increasing the difficulty of examples in the training set that is presented to a model over multiple training iterations. This can produce better results than exposing the model to the full training set immediately under some circumstances; most typically, when the model is able to learn general principles from easier examples, and then gradually incorporate more complex and nuanced information as harder examples are introduced, such as edge cases. This has been shown to work in many domains, most likely as a form of regularization. There are several major variations in how the technique is applied: A concept of "difficulty" must be defined. This may come from human annotation or an external heuristic; for example in language modeling, shorter sentences might be classified as easier than longer ones. Another approach is to use the performance of another model, with examples accurately predicted by that model being classified as easier (providing a connection to boosting). Difficulty can be increased steadily or in distinct epochs, and in a deterministic schedule or according to a probability distribution. This may also be moderated by a requirement for diversity at each stage, in cases where easier examples are likely to be disproportionately similar to each other. Applications must also decide the schedule for increasing the difficulty. Simple approaches may use a fixed schedule, such as training on easy examples for half of the available iterations and then all examples for the second half. Other approaches use self-paced learning to increase the difficulty in proportion to the performance of the model on the current set. Since curriculum learning only concerns the selection and ordering of training data, it can be combined with many other techniques in machine learning. The success of the method assumes that a model trained for an easier version of the problem can generalize to harder versions, so it can be seen as a form of transfer learning. Some authors also consider curriculum learning to include other forms of progressively increasing complexity, such as increasing the number of model parameters. It is frequently combined with reinforcement learning, such as learning a simplified version of a game first. Some domains have shown success with anti-curriculum learning: training on the most difficult examples first. One example is the ACCAN method for speech recognition, which trains on the examples with the lowest signal-to-noise ratio first. == History == The term "curriculum learning" was introduced by Yoshua Bengio et al in 2009, with reference to the psychological technique of shaping in animals and structured education for humans: beginning with the simplest concepts and then building on them. The authors also note that the application of this technique in machine learning has its roots in the early study of neural networks such as Jeffrey Elman's 1993 paper Learning and development in neural networks: the importance of starting small. Bengio et al showed good results for problems in image classification, such as identifying geometric shapes with progressively more complex forms, and language modeling, such as training with a gradually expanding vocabulary. They conclude that, for curriculum strategies, "their beneficial effect is most pronounced on the test set", suggesting good generalization. The technique has since been applied to many other domains: Natural language processing: Part-of-speech tagging Intent detection Sentiment analysis Machine translation Speech recognition Language model pre-training Image recognition: Facial recognition Object detection Reinforcement learning: Game-playing Graph learning Matrix factorization

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  • Genetic representation

    Genetic representation

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

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  • Triplet loss

    Triplet loss

    Triplet loss is a machine learning loss function widely used in one-shot learning, a setting where models are trained to generalize effectively from limited examples. It was conceived by Google researchers for their prominent FaceNet algorithm for face detection. Triplet loss is designed to support metric learning. Namely, to assist training models to learn an embedding (mapping to a feature space) where similar data points are closer together and dissimilar ones are farther apart, enabling robust discrimination across varied conditions. In the context of face detection, data points correspond to images. == Definition == The loss function is defined using triplets of training points of the form ( A , P , N ) {\displaystyle (A,P,N)} . In each triplet, A {\displaystyle A} (called an "anchor point") denotes a reference point of a particular identity, P {\displaystyle P} (called a "positive point") denotes another point of the same identity in point A {\displaystyle A} , and N {\displaystyle N} (called a "negative point") denotes a point of an identity different from the identity in point A {\displaystyle A} and P {\displaystyle P} . Let x {\displaystyle x} be some point and let f ( x ) {\displaystyle f(x)} be the embedding of x {\displaystyle x} in the finite-dimensional Euclidean space. It shall be assumed that the L2-norm of f ( x ) {\displaystyle f(x)} is unity (the L2 norm of a vector X {\displaystyle X} in a finite dimensional Euclidean space is denoted by ‖ X ‖ {\displaystyle \Vert X\Vert } .) We assemble m {\displaystyle m} triplets of points from the training dataset. The goal of training here is to ensure that, after learning, the following condition (called the "triplet constraint") is satisfied by all triplets ( A ( i ) , P ( i ) , N ( i ) ) {\displaystyle (A^{(i)},P^{(i)},N^{(i)})} in the training data set: ‖ f ( A ( i ) ) − f ( P ( i ) ) ‖ 2 2 + α < ‖ f ( A ( i ) ) − f ( N ( i ) ) ‖ 2 2 {\displaystyle \Vert f(A^{(i)})-f(P^{(i)})\Vert _{2}^{2}+\alpha <\Vert f(A^{(i)})-f(N^{(i)})\Vert _{2}^{2}} The variable α {\displaystyle \alpha } is a hyperparameter called the margin, and its value must be set manually. In the FaceNet system, its value was set as 0.2. Thus, the full form of the function to be minimized is the following: L = ∑ i = 1 m max ( ‖ f ( A ( i ) ) − f ( P ( i ) ) ‖ 2 2 − ‖ f ( A ( i ) ) − f ( N ( i ) ) ‖ 2 2 + α , 0 ) {\displaystyle L=\sum _{i=1}^{m}\max {\Big (}\Vert f(A^{(i)})-f(P^{(i)})\Vert _{2}^{2}-\Vert f(A^{(i)})-f(N^{(i)})\Vert _{2}^{2}+\alpha ,0{\Big )}} == Intuition == A baseline for understanding the effectiveness of triplet loss is the contrastive loss, which operates on pairs of samples (rather than triplets). Training with the contrastive loss pulls embeddings of similar pairs closer together, and pushes dissimilar pairs apart. Its pairwise approach is greedy, as it considers each pair in isolation. Triplet loss innovates by considering relative distances. Its goal is that the embedding of an anchor (query) point be closer to positive points than to negative points (also accounting for the margin). It does not try to further optimize the distances once this requirement is met. This is approximated by simultaneously considering two pairs (anchor-positive and anchor-negative), rather than each pair in isolation. == Triplet "mining" == One crucial implementation detail when training with triplet loss is triplet "mining", which focuses on the smart selection of triplets for optimization. This process adds an additional layer of complexity compared to contrastive loss. A naive approach to preparing training data for the triplet loss involves randomly selecting triplets from the dataset. In general, the set of valid triplets of the form ( A ( i ) , P ( i ) , N ( i ) ) {\displaystyle (A^{(i)},P^{(i)},N^{(i)})} is very large. To speed-up training convergence, it is essential to focus on challenging triplets. In the FaceNet paper, several options were explored, eventually arriving at the following. For each anchor-positive pair, the algorithm considers only semi-hard negatives. These are negatives that violate the triplet requirement (i.e, are "hard"), but lie farther from the anchor than the positive (not too hard). Restated, for each A ( i ) {\displaystyle A^{(i)}} and P ( i ) {\displaystyle P^{(i)}} , they seek N ( i ) {\displaystyle N^{(i)}} such that: The rationale for this design choice is heuristic. It may appear puzzling that the mining process neglects "very hard" negatives (i.e., closer to the anchor than the positive). Experiments conducted by the FaceNet designers found that this often leads to a convergence to degenerate local minima. Triplet mining is performed at each training step, from within the sample points contained in the training batch (this is known as online mining), after embeddings were computed for all points in the batch. While ideally the entire dataset could be used, this is impractical in general. To support a large search space for triplets, the FaceNet authors used very large batches (1800 samples). Batches are constructed by selecting a large number of same-category sample points (40), and randomly selected negatives for them. == Extensions == Triplet loss has been extended to simultaneously maintain a series of distance orders by optimizing a continuous relevance degree with a chain (i.e., ladder) of distance inequalities. This leads to the Ladder Loss, which has been demonstrated to offer performance enhancements of visual-semantic embedding in learning to rank tasks. In Natural Language Processing, triplet loss is one of the loss functions considered for BERT fine-tuning in the SBERT architecture. Other extensions involve specifying multiple negatives (multiple negatives ranking loss).

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  • Server.com

    Server.com

    Server.com is a domain name that was owned by software as a service (SaaS) company Server Corporation. They offered a suite of services from 1996 until 2007. It was the first SaaS site to offer a variety of services and the first to use the term WebApp to describe its services. It was selected as an Incredibly Useful Site by Yahoo! Internet Life magazine. net magazine listed Server.com among the 100 most influential websites of all time. Server.com launched in 1996 offering the first online personal information manager. In 1997, they rolled out the first threaded message board service; the first web based mailing list manager; one of the first online calendar services; and one of the first online form builders. In 2000, Server.com partnered with NBCi and became server.snap.com until 2001. In 2001, Server.com was serving 100 million monthly pageviews. Media Life declared it one of the 20 biggest ad domains on the Web. In 2002, Server.com developed one of the first web-based RSS aggregators. In 2007, all services were moved to YourWebApps.com. The domain name Server.com was sold in 2009 for $770,000.

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  • VIGRA

    VIGRA

    VIGRA is the abbreviation for "Vision with Generic Algorithms". It is a free open-source computer vision library which focuses on customizable algorithms and data structures. VIGRA component can be easily adapted to specific needs of target application without compromising execution speed, by using template techniques similar to those in the C++ Standard Template Library. == Features == VIGRA is cross-platform, with working builds on Microsoft Windows, Mac OS X, Linux, and OpenBSD. Since version 1.7.1, VIGRA provides Python bindings based on numpy framework. == History == VIGRA was originally designed and implemented by scientists at University of Hamburg faculty of computer science; its core maintainers are now working at Heidelberg Collaboratory for Image Processing (HCI) University of Heidelberg. In the meantime, many developers have contributed to the project. == Application == CellCognition and ilastik uses VIGRA computer vision library. OpenOffice.org uses VIGRA as part of its headless software rendering backend; LibreOffice does so until version 5.2.

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  • Prescription monitoring program

    Prescription monitoring program

    In the United States, prescription monitoring programs (PMPs) or prescription drug monitoring programs (PDMPs) are state-run programs which collect and distribute data about the prescription and dispensation of federally controlled substances and, depending on state requirements, other potentially abusable prescription drugs. PMPs are meant to help prevent adverse drug-related events such as opioid overdoses, drug diversion, and substance abuse by decreasing the amount and/or frequency of opioid prescribing, and by identifying those patients who are obtaining prescriptions from multiple providers (i.e., "doctor shopping") or those physicians overprescribing opioids. Most US health care workers support the idea of PMPs, which intend to assist physicians, physician assistants, nurse practitioners, dentists and other prescribers, the pharmacists, chemists and support staff of dispensing establishments. The database, whose use is required by State law, typically requires prescribers and pharmacies dispensing controlled substances to register with their respective state PMPs and (for pharmacies and providers who dispense from their offices) to report the dispensation of such prescriptions to an electronic online database. The majority of PMPs are authorized to notify law enforcement agencies or licensing boards or physicians when a prescriber, or patients receiving prescriptions, exceed thresholds established by the state or prescription recipient exceeds thresholds established by the State. All states have implemented PDMPs, although evidence for the effectiveness of these programs is mixed. While prescription of opioids has decreased with PMP use, overdose deaths in many states have actually increased, with those states sharing data with neighboring jurisdictions or requiring reporting of more drugs experiencing highest increases in deaths. This may be because those declined opioid prescriptions turn to street drugs, whose potency and contaminants carry greater overdose risk. == History == Prescription drug monitoring programs, or PDMPs, are an example of one initiative proposed to alleviate effects of the opioid crisis. The programs are designed to restrict prescription drug abuse by limiting a patient's ability to obtain similar prescriptions from multiple providers (i.e. “doctor shopping”) and reducing diversion of controlled substances. This is meant to reduce risk of fatal overdose caused by high doses of opioids or interactions between opioids and benzodiazepenes, and to enable better decision making on the part of healthcare providers who may be unaware of a patient's prescription drug use, history or other prescriptions. PDMPs have been implemented in state legislations since 1939 in California, a time before electronic medical records, though implementation rose alongside increased awareness of overprescribing of opioids and overdose. A later New York state program was struck down by the U.S. Supreme Court in Whalen v. Roe. But, by 2019, 49 states, the District of Columbia, and Guam had enacted PDMP legislation. In 2021 Missouri, the last State to not use a PMP, adopted legislation to create one. PMPs are constantly being updated to increase speed of data collection, sharing of data across States, and ease of interpretation. This is being done by integrating PDMP reports with other health information technologies such as health information exchanges (HIE), electronic health record (EHR) systems, and/ or pharmacy dispensing software systems. One program that has been implemented in nine states is called the PDMP Electronic Health Records Integration and Interoperability Expansion, also known as PEHRIIE. Another software, marketed by Bamboo Health and integrated with PMPs in 43 states, uses an algorithm to track factors thought to increase risk of diversion, abuse or overdose, and assigns patients a three digit score based on presumed indicators of risk. While some studies have suggested that PDMP-HIT integration and sharing of interstate data brings benefits such as reduced opioid-related inpatient morbidity, others have found no or negative impact on mortality compared to states without PMP data sharing. Patient and media reports suggest need for testing and evaluation of algorithmic software used to score risk, with some patients reporting denial of prescriptions without c explanation or clarity of data. == Goals == Most health care workers support PMPs which intend to assist physicians, physician assistants, nurse practitioners, dentists and other prescribers, the pharmacists, chemists and support staff of dispensing establishments, as well as law-enforcement agencies. The collaboration supports the legitimate medical use of controlled substances while limiting their abuse and diversion. Pharmacies dispensing controlled substances and prescribers typically must register with their respective state PMPs and (for pharmacies and providers who dispense controlled substances from their offices) report the dispensation to an electronic online database. Some pharmacy software can submit these reports automatically to multiple states. == Usage == === List of programs by state === === Software systems === NarxCare is a prescription drug monitoring program (PDMP) run by Bamboo Health. Bamboo Health was formerly known as Appriss. It is widely used across the United States by pharmacies including Rite Aid as well as those at Walmart and Sam’s Club. The NarxCare software allows doctors to view data about a patient, combining data from the prescription registries of various U.S. states to make the registries interoperable nationally. It also uses machine learning to generate an "Overdose Risk Score" that potentially includes EMS and criminal justice data; these scores have been criticized by researchers and patient advocates for the lack of transparency in the process as well as the potential for disparate treatment of women and minority groups. Advertised as an "analytics tool and care management platform", the NarxCare software allows doctors to view data about a patient including how many pharmacies they have visited and the combinations of medication they are prescribed. It combines data from the prescription registries of various U.S. states, making the registries interoperable nationally. It additionally uses machine learning to generate various three-digit "risk scores" and an overall "Overdose Risk Score", collectively referred to as Narx Scores, in a process that potentially includes EMS and criminal justice data as well as court records. == Controversy == Many doctors and researchers support the idea of PDMPs as a tool in combatting the opioid epidemic. Opioid prescribing, opioid diversion and supply, opioid misuse, and opioid-related morbidity and mortality are common elements in data entered into PDMPs. Prescription Monitoring Programs are purported to offer economic benefits for the states who implement them by decreasing overall health care costs, lost productivity, and investigation times. However, there are many studies that conclude the impact of PDMPs is unclear. While use of PMPs has been accompanied by decrease in opioid prescribing, few analyses consider corresponding use of street opioids, extramedical use, or diversion, which might provide a more holistic method for evaluation of PMP intent and efficacy. Evidence for PDMP impact on fatal overdoses is decidedly mixed, with multiple studies finding increased overdose rates in some states, decreases in others, or no clear impact. Interestingly, an increase in heroin overdoses after PDMP implementation has been commonly reported, presumably as denial of prescription opioids sends patients in search of street drugs. Narx Scores have been criticized by researchers and patient advocates for the lack of transparency in the generation process as well as the potential for disparate treatment of women and minority groups. Writing in Duke Law Journal, Jennifer Oliva stated that "black-box algorithms" are used to generate the scores.

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