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Framebuffer

A framebuffer (frame buffer, or sometimes framestore) is a portion of random-access memory (RAM) containing a bitmap that drives a video display. It is a memory buffer containing data representing all the pixels in a complete video frame. Modern video cards contain framebuffer circuitry in their cores. This circuitry converts an in-memory bitmap into a video signal that can be displayed on a computer monitor. In computing, a screen buffer is a part of computer memory used by a computer application for the representation of the content to be shown on the computer display. The screen buffer may also be called the video buffer, the regeneration buffer, or regen buffer for short. The phrase "screen buffer” refers to a logical function, while video memory refers to a hardware storage location. In particular, the screen buffer may be placed in the main RAM, the video memory, or some other hardware location. To reduce latency and avoid screen tearing, multiple frames can be buffered, and this technique is called multiple buffering. When this is so, at any time, only one frame would be visible, and the others would not be. The currently invisible frames are located in the off-screen buffer. The information in the buffer typically consists of color values for every pixel to be shown on the display. Color values are commonly stored in 1-bit binary (monochrome), 4-bit palettized, 8-bit palettized, 16-bit high color and 24-bit true color formats. An additional alpha channel is sometimes used to retain information about pixel transparency. The total amount of memory required for the framebuffer depends on the resolution of the output signal, and on the color depth or palette size. == History == Computer researchers had long discussed the theoretical advantages of a framebuffer but were unable to produce a machine with sufficient memory at an economically practicable cost. In 1947, the Manchester Baby computer used a Williams tube, later the Williams-Kilburn tube, to store 1024 bits on a cathode-ray tube (CRT) memory and displayed on a second CRT. Other research labs were exploring these techniques with MIT Lincoln Laboratory achieving a 4096 display in 1950. A color-scanned display was implemented in the late 1960s, called the Brookhaven RAster Display (BRAD), which used a drum memory and a television monitor. In 1969, A. Michael Noll of Bell Telephone Laboratories, Inc. implemented a scanned display with a frame buffer, using magnetic-core memory. A year or so later, the Bell Labs system was expanded to display an image with a color depth of three bits on a standard color TV monitor. The vector graphics used in the computer had to be converted for the scanned graphics of a TV display. In the early 1970s, the development of MOS memory (metal–oxide–semiconductor memory) integrated-circuit chips, particularly high-density DRAM (dynamic random-access memory) chips with at least 1 kb memory, made it practical to create, for the first time, a digital memory system with framebuffers capable of holding a standard video image. This led to the development of the SuperPaint system by Richard Shoup at Xerox PARC in 1972. Shoup was able to use the SuperPaint framebuffer to create an early digital video-capture system. By synchronizing the output signal to the input signal, Shoup was able to overwrite each pixel of data as it shifted in. Shoup also experimented with modifying the output signal using color tables. These color tables allowed the SuperPaint system to produce a wide variety of colors outside the range of the limited 8-bit data it contained. This scheme would later become commonplace in computer framebuffers. In 1974, Evans & Sutherland released the first commercial framebuffer, the Picture System, costing about $15,000. It was capable of producing resolutions of up to 512 by 512 pixels in 8-bit grayscale, and became a boon for graphics researchers who did not have the resources to build their own framebuffer. The New York Institute of Technology would later create the first 24-bit color system using three of the Evans & Sutherland framebuffers. Each framebuffer was connected to an RGB color output (one for red, one for green and one for blue), with a Digital Equipment Corporation PDP 11/04 minicomputer controlling the three devices as one. In 1975, the UK company Quantel produced the first commercial full-color broadcast framebuffer, the Quantel DFS 3000. It was first used in TV coverage of the 1976 Montreal Olympics to generate a picture-in-picture inset of the Olympic flaming torch while the rest of the picture featured the runner entering the stadium. The rapid improvement of integrated-circuit technology made it possible for many of the home computers of the late 1970s to contain low-color-depth framebuffers. Today, nearly all computers with graphical capabilities utilize a framebuffer for generating the video signal. Amiga computers, created in the 1980s, featured special design attention to graphics performance and included a unique Hold-And-Modify framebuffer capable of displaying 4096 colors. Framebuffers also became popular in high-end workstations and arcade system boards throughout the 1980s. SGI, Sun Microsystems, HP, DEC and IBM all released framebuffers for their workstation computers in this period. These framebuffers were usually of a much higher quality than could be found in most home computers, and were regularly used in television, printing, computer modeling and 3D graphics. Framebuffers were also used by Sega for its high-end arcade boards, which were also of a higher quality than on home computers. == Display modes == Framebuffers used in personal and home computing often had sets of defined modes under which the framebuffer can operate. These modes reconfigure the hardware to output different resolutions, color depths, memory layouts and refresh rate timings. In the world of Unix machines and operating systems, such conveniences were usually eschewed in favor of directly manipulating the hardware settings. This manipulation was far more flexible in that any resolution, color depth and refresh rate was attainable – limited only by the memory available to the framebuffer. An unfortunate side-effect of this method was that the display device could be driven beyond its capabilities. In some cases, this resulted in hardware damage to the display. More commonly, it simply produced garbled and unusable output. Modern CRT monitors fix this problem through the introduction of protection circuitry. When the display mode is changed, the monitor attempts to obtain a signal lock on the new refresh frequency. If the monitor is unable to obtain a signal lock or if the signal is outside the range of its design limitations, the monitor will ignore the framebuffer signal and possibly present the user with an error message. LCD monitors tend to contain similar protection circuitry, but for different reasons. Since the LCD must digitally sample the display signal (thereby emulating an electron beam), any signal that is out of range cannot be physically displayed on the monitor. == Color palette == Framebuffers have traditionally supported a wide variety of color modes. Due to the expense of memory, most early framebuffers used 1-bit (2 colors per pixel), 2-bit (4 colors), 4-bit (16 colors) or 8-bit (256 colors) color depths. The problem with such small color depths is that a full range of colors cannot be produced. The solution to this problem was indexed color, which adds a lookup table to the framebuffer. Each color stored in framebuffer memory acts as a color index. The lookup table serves as a palette with a limited number of different colors, while the rest is used as an index table. Here is a typical indexed 256-color image and its own palette (shown as a rectangle of swatches): In some designs, it was also possible to write data to the lookup table (or switch between existing palettes) on the fly, allowing dividing the picture into horizontal bars with their own palette and thus rendering an image that had a far wider palette. For example, viewing an outdoor shot photograph, the picture could be divided into four bars: the top one with emphasis on sky tones, the next with foliage tones, the next with skin and clothing tones, and the bottom one with ground colors. This required each palette to have overlapping colors, but, carefully done, allowed great flexibility. == Memory access == While framebuffers are commonly accessed via a memory mapping directly to the CPU memory space, this is not the only method by which they may be accessed. Framebuffers have varied widely in the methods used to access memory. Some of the most common are: Mapping the entire framebuffer to a given memory range. Port commands to set each pixel, range of pixels or palette entry. Mapping a memory range smaller than the framebuffer memory, then bank switching as necessary. The framebuffer organization may be packed pixel or planar. The framebuffer may be all
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LIBSVM

LIBSVM and LIBLINEAR are two popular open source machine learning libraries, both developed at the National Taiwan University and both written in C++ though with a C API. LIBSVM implements the sequential minimal optimization (SMO) algorithm for kernelized support vector machines (SVMs), supporting classification and regression. LIBLINEAR implements linear SVMs and logistic regression models trained using a coordinate descent algorithm. The SVM learning code from both libraries is often reused in other open source machine learning toolkits, including GATE, KNIME, Orange and scikit-learn. Bindings and ports exist for programming languages such as Java, MATLAB, R, Julia, and Python. It is available in e1071 library in R and scikit-learn in Python. Both libraries are free software released under the 3-clause BSD license.
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Distribution learning theory

The distributional learning theory or learning of probability distribution is a framework in computational learning theory. It has been proposed from Michael Kearns, Yishay Mansour, Dana Ron, Ronitt Rubinfeld, Robert Schapire and Linda Sellie in 1994 and it was inspired from the PAC-framework introduced by Leslie Valiant. In this framework the input is a number of samples drawn from a distribution that belongs to a specific class of distributions. The goal is to find an efficient algorithm that, based on these samples, determines with high probability the distribution from which the samples have been drawn. Because of its generality, this framework has been used in a large variety of different fields like machine learning, approximation algorithms, applied probability and statistics. This article explains the basic definitions, tools and results in this framework from the theory of computation point of view. == Definitions == Let X {\displaystyle \textstyle X} be the support of the distributions of interest. As in the original work of Kearns et al. if X {\displaystyle \textstyle X} is finite it can be assumed without loss of generality that X = { 0 , 1 } n {\displaystyle \textstyle X=\{0,1\}^{n}} where n {\displaystyle \textstyle n} is the number of bits that have to be used in order to represent any y ∈ X {\displaystyle \textstyle y\in X} . We focus in probability distributions over X {\displaystyle \textstyle X} . There are two possible representations of a probability distribution D {\displaystyle \textstyle D} over X {\displaystyle \textstyle X} . probability distribution function (or evaluator) an evaluator E D {\displaystyle \textstyle E_{D}} for D {\displaystyle \textstyle D} takes as input any y ∈ X {\displaystyle \textstyle y\in X} and outputs a real number E D [ y ] {\displaystyle \textstyle E_{D}[y]} which denotes the probability that of y {\displaystyle \textstyle y} according to D {\displaystyle \textstyle D} , i.e. E D [ y ] = Pr [ Y = y ] {\displaystyle \textstyle E_{D}[y]=\Pr[Y=y]} if Y ∼ D {\displaystyle \textstyle Y\sim D} . generator a generator G D {\displaystyle \textstyle G_{D}} for D {\displaystyle \textstyle D} takes as input a string of truly random bits y {\displaystyle \textstyle y} and outputs G D [ y ] ∈ X {\displaystyle \textstyle G_{D}[y]\in X} according to the distribution D {\displaystyle \textstyle D} . Generator can be interpreted as a routine that simulates sampling from the distribution D {\displaystyle \textstyle D} given a sequence of fair coin tosses. A distribution D {\displaystyle \textstyle D} is called to have a polynomial generator (respectively evaluator) if its generator (respectively evaluator) exists and can be computed in polynomial time. Let C X {\displaystyle \textstyle C_{X}} a class of distribution over X, that is C X {\displaystyle \textstyle C_{X}} is a set such that every D ∈ C X {\displaystyle \textstyle D\in C_{X}} is a probability distribution with support X {\displaystyle \textstyle X} . The C X {\displaystyle \textstyle C_{X}} can also be written as C {\displaystyle \textstyle C} for simplicity. In order to evaluate learnability, it is necessary to have a way to measure how well an approximated distribution D ′ {\displaystyle \textstyle D'} fits the sampled distribution D {\displaystyle \textstyle D} . There are several ways to measure the divergence between two distributions. Three common possibilities are Kullback–Leibler divergence Total variation distance of probability measures Kolmogorov distance Total variation and Kolmogorov distance are true metrics, while KL divergence is not (it lacks symmetry). These measures are ordered by convergence strength: closeness in KL divergence implies closeness in total variation (via Pinsker's inequality), which in turn implies closeness in Kolmogorov distance. Therefore, a learnability result proven under KL divergence automatically holds under the weaker measures, but not vice versa. Since certain measures may be more appropriate in specific applications, we will use d ( D , D ′ ) {\displaystyle \textstyle d(D,D')} to denote a selected divergence between the distribution D {\displaystyle \textstyle D} and the distribution D ′ {\displaystyle \textstyle D'} . The basic input that we use in order to learn a distribution is a number of samples drawn by this distribution. For the computational point of view the assumption is that such a sample is given in a constant amount of time. So it's like having access to an oracle G E N ( D ) {\displaystyle \textstyle GEN(D)} that returns a sample from the distribution D {\displaystyle \textstyle D} . Sometimes the interest is, apart from measuring the time complexity, to measure the number of samples that have to be used in order to learn a specific distribution D {\displaystyle \textstyle D} in class of distributions C {\displaystyle \textstyle C} . This quantity is called sample complexity of the learning algorithm. In order for the problem of distribution learning to be more clear consider the problem of supervised learning as defined in. In this framework of statistical learning theory a training set S = { ( x 1 , y 1 ) , … , ( x n , y n ) } {\displaystyle \textstyle S=\{(x_{1},y_{1}),\dots ,(x_{n},y_{n})\}} and the goal is to find a target function f : X → Y {\displaystyle \textstyle f:X\rightarrow Y} that minimizes some loss function, e.g. the square loss function. More formally f = arg ⁡ min g ∫ V ( y , g ( x ) ) d ρ ( x , y ) {\displaystyle f=\arg \min _{g}\int V(y,g(x))d\rho (x,y)} , where V ( ⋅ , ⋅ ) {\displaystyle V(\cdot ,\cdot )} is the loss function, e.g. V ( y , z ) = ( y − z ) 2 {\displaystyle V(y,z)=(y-z)^{2}} and ρ ( x , y ) {\displaystyle \rho (x,y)} the probability distribution according to which the elements of the training set are sampled. If the conditional probability distribution ρ x ( y ) {\displaystyle \rho _{x}(y)} is known then the target function has the closed form f ( x ) = ∫ y y d ρ x ( y ) {\displaystyle f(x)=\int _{y}yd\rho _{x}(y)} . So the set S {\displaystyle S} is a set of samples from the probability distribution ρ ( x , y ) {\displaystyle \rho (x,y)} . Now the goal of distributional learning theory if to find ρ {\displaystyle \rho } given S {\displaystyle S} which can be used to find the target function f {\displaystyle f} . Definition of learnability A class of distributions C {\displaystyle \textstyle C} is called efficiently learnable if for every ϵ > 0 {\displaystyle \textstyle \epsilon >0} and 0 < δ ≤ 1 {\displaystyle \textstyle 0<\delta \leq 1} given access to G E N ( D ) {\displaystyle \textstyle GEN(D)} for an unknown distribution D ∈ C {\displaystyle \textstyle D\in C} , there exists a polynomial time algorithm A {\displaystyle \textstyle A} , called learning algorithm of C {\displaystyle \textstyle C} , that outputs a generator or an evaluator of a distribution D ′ {\displaystyle \textstyle D'} such that Pr [ d ( D , D ′ ) ≤ ϵ ] ≥ 1 − δ {\displaystyle \Pr[d(D,D')\leq \epsilon ]\geq 1-\delta } If we know that D ′ ∈ C {\displaystyle \textstyle D'\in C} then A {\displaystyle \textstyle A} is called proper learning algorithm, otherwise is called improper learning algorithm. In some settings the class of distributions C {\displaystyle \textstyle C} is a class with well known distributions which can be described by a set of parameters. For instance C {\displaystyle \textstyle C} could be the class of all the Gaussian distributions N ( μ , σ 2 ) {\displaystyle \textstyle N(\mu ,\sigma ^{2})} . In this case the algorithm A {\displaystyle \textstyle A} should be able to estimate the parameters μ , σ {\displaystyle \textstyle \mu ,\sigma } . In this case A {\displaystyle \textstyle A} is called parameter learning algorithm. Obviously the parameter learning for simple distributions is a very well studied field that is called statistical estimation and there is a very long bibliography on different estimators for different kinds of simple known distributions. But distributions learning theory deals with learning class of distributions that have more complicated description. == First results == In their seminal work, Kearns et al. deal with the case where A {\displaystyle \textstyle A} is described in term of a finite polynomial sized circuit and they proved the following for some specific classes of distribution. O R {\displaystyle \textstyle OR} gate distributions for this kind of distributions there is no polynomial-sized evaluator, unless # P ⊆ P / poly {\displaystyle \textstyle \#P\subseteq P/{\text{poly}}} . On the other hand, this class is efficiently learnable with generator. Parity gate distributions this class is efficiently learnable with both generator and evaluator. Mixtures of Hamming Balls this class is efficiently learnable with both generator and evaluator. Probabilistic Finite Automata this class is not efficiently learnable with evaluator under the Noisy Parity Assumption which is an impossibility assumption in the PAC learning fram
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Information gain (decision tree)

In the context of decision trees in information theory and machine learning, information gain refers to the conditional expected value of the Kullback–Leibler divergence of the univariate probability distribution of one variable from the conditional distribution of this variable given the other one. (In broader contexts, information gain can also be used as a synonym for either Kullback–Leibler divergence or mutual information, but the focus of this article is on the more narrow meaning below.) Explicitly, the information gain of a random variable X {\displaystyle X} obtained from an observation of a random variable A {\displaystyle A} taking value a {\displaystyle a} is defined as: I G ( X , a ) = D KL ( P X ∣ a ∥ P X ) {\displaystyle {\mathit {IG}}(X,a)=D_{\text{KL}}{\bigl (}P_{X\mid a}\parallel P_{X}{\bigr )}} In other words, it is the Kullback–Leibler divergence of P X ( x ) {\displaystyle P_{X}(x)} (the prior distribution for X {\displaystyle X} ) from P X ∣ a ( x ) {\displaystyle P_{X\mid a}(x)} (the posterior distribution for X {\displaystyle X} given A = a {\displaystyle A=a} ). The expected value of the information gain is the mutual information I ( X ; A ) {\displaystyle I(X;A)} : E A ⁡ [ I G ( X , A ) ] = I ( X ; A ) {\displaystyle \operatorname {E} _{A}[{\mathit {IG}}(X,A)]=I(X;A)} i.e. the reduction in the entropy of X {\displaystyle X} achieved by learning the state of the random variable A {\displaystyle A} . In machine learning, this concept can be used to define a preferred sequence of attributes to investigate to most rapidly narrow down the state of X. Such a sequence (which depends on the outcome of the investigation of previous attributes at each stage) is called a decision tree, and when applied in the area of machine learning is known as decision tree learning. Usually an attribute with high mutual information should be preferred to other attributes. == General definition == In general terms, the expected information gain is the reduction in information entropy Η from a prior state to a state that takes some information as given: I G ( T , a ) = H ( T ) − H ( T | a ) , {\displaystyle IG(T,a)=\mathrm {H} {(T)}-\mathrm {H} {(T|a)},} where H ( T | a ) {\displaystyle \mathrm {H} {(T|a)}} is the conditional entropy of T {\displaystyle T} given the value of attribute a {\displaystyle a} . This is intuitively plausible when interpreting entropy Η as a measure of uncertainty of a random variable T {\displaystyle T} : by learning (or assuming) a {\displaystyle a} about T {\displaystyle T} , our uncertainty about T {\displaystyle T} is reduced (i.e. I G ( T , a ) {\displaystyle IG(T,a)} is positive), unless of course T {\displaystyle T} is independent of a {\displaystyle a} , in which case H ( T | a ) = H ( T ) {\displaystyle \mathrm {H} (T|a)=\mathrm {H} (T)} , meaning I G ( T , a ) = 0 {\displaystyle IG(T,a)=0} . == Formal definition == Let T denote a set of training examples, each of the form ( x , y ) = ( x 1 , x 2 , x 3 , . . . , x k , y ) {\displaystyle ({\textbf {x}},y)=(x_{1},x_{2},x_{3},...,x_{k},y)} where x a ∈ v a l s ( a ) {\displaystyle x_{a}\in \mathrm {vals} (a)} is the value of the a th {\displaystyle a^{\text{th}}} attribute or feature of example x {\displaystyle {\textbf {x}}} and y is the corresponding class label. The information gain for an attribute a is defined in terms of Shannon entropy H ( − ) {\displaystyle \mathrm {H} (-)} as follows. For a value v taken by attribute a, let S a ( v ) = { x ∈ T | x a = v } {\displaystyle S_{a}{(v)}=\{{\textbf {x}}\in T|x_{a}=v\}} be defined as the set of training inputs of T for which attribute a is equal to v. Then the information gain of T for attribute a is the difference between the a priori Shannon entropy H ( T ) {\displaystyle \mathrm {H} (T)} of the training set and the conditional entropy H ( T | a ) {\displaystyle \mathrm {H} {(T|a)}} . H ( T | a ) = ∑ v ∈ v a l s ( a ) | S a ( v ) | | T | ⋅ H ( S a ( v ) ) . {\displaystyle \mathrm {H} (T|a)=\sum _{v\in \mathrm {vals} (a)}{{\frac {|S_{a}{(v)}|}{|T|}}\cdot \mathrm {H} \left(S_{a}{\left(v\right)}\right)}.} I G ( T , a ) = H ( T ) − H ( T | a ) {\displaystyle IG(T,a)=\mathrm {H} (T)-\mathrm {H} (T|a)} The mutual information is equal to the total entropy for an attribute if for each of the attribute values a unique classification can be made for the result attribute. In this case, the relative entropies subtracted from the total entropy are 0. In particular, the values v ∈ v a l s ( a ) {\displaystyle v\in vals(a)} defines a partition of the training set data T into mutually exclusive and all-inclusive subsets, inducing a categorical probability distribution P a ( v ) {\textstyle P_{a}{(v)}} on the values v ∈ v a l s ( a ) {\textstyle v\in vals(a)} of attribute a. The distribution is given P a ( v ) := | S a ( v ) | | T | {\textstyle P_{a}{(v)}:={\frac {|S_{a}{(v)}|}{|T|}}} . In this representation, the information gain of T given a can be defined as the difference between the unconditional Shannon entropy of T and the expected entropy of T conditioned on a, where the expectation value is taken with respect to the induced distribution on the values of a. I G ( T , a ) = H ( T ) − ∑ v ∈ v a l s ( a ) P a ( v ) H ( S a ( v ) ) = H ( T ) − E P a [ H ( S a ( v ) ) ] = H ( T ) − H ( T | a ) . {\displaystyle {\begin{alignedat}{2}IG(T,a)&=\mathrm {H} (T)-\sum _{v\in \mathrm {vals} (a)}{P_{a}{(v)}\mathrm {H} \left(S_{a}{(v)}\right)}\\&=\mathrm {H} (T)-\mathbb {E} _{P_{a}}{\left[\mathrm {H} {(S_{a}{(v)})}\right]}\\&=\mathrm {H} (T)-\mathrm {H} {(T|a)}.\end{alignedat}}} == Example == In engineering applications, information is analogous to signal, and entropy is analogous to noise. It determines how a decision tree chooses to split data. The leftmost figure below is very impure and has high entropy corresponding to higher disorder and lower information value. As we go to the right, the entropy decreases, and the information value increases. Now, it is clear that information gain is the measure of how much information a feature provides about a class. Let's visualize information gain in a decision tree as shown in the right: The node t is the parent node, and the sub-nodes tL and tR are child nodes. In this case, the parent node t has a collection of cancer and non-cancer samples denoted as C and NC respectively. We can use information gain to determine how good the splitting of nodes is in a decision tree. In terms of entropy, information gain is defined as: To understand this idea, let's start by an example in which we create a simple dataset and want to see if gene mutations could be related to patients with cancer. Given four different gene mutations, as well as seven samples, the training set for a decision can be created as follows: In this dataset, a 1 means the sample has the mutation (True), while a 0 means the sample does not (False). A sample with C denotes that it has been confirmed to be cancerous, while NC means it is non-cancerous. Using this data, a decision tree can be created with information gain used to determine the candidate splits for each node. For the next step, the entropy at parent node t of the above simple decision tree is computed as:H(t) = −[pC,t log2(pC,t) + pNC,t log2(pNC,t)] where, probability of selecting a class ‘C’ sample at node t, pC,t = n(t, C) / n(t), probability of selecting a class ‘NC’ sample at node t, pNC,t = n(t, NC) / n(t), n(t), n(t, C), and n(t, NC) are the number of total samples, ‘C’ samples and ‘NC’ samples at node t respectively.Using this with the example training set, the process for finding information gain beginning with H ( t ) {\displaystyle \mathrm {H} {(t)}} for Mutation 1 is as follows: pC, t = 4/7 pNC, t = 3/7 H ( t ) {\displaystyle \mathrm {H} {(t)}} = −(4/7 × log2(4/7) + 3/7 × log2(3/7)) = 0.985 Note: H ( t ) {\displaystyle \mathrm {H} {(t)}} will be the same for all mutations at the root. The relatively high value of entropy H ( t ) = 0.985 {\displaystyle \mathrm {H} {(t)}=0.985} (1 is the optimal value) suggests that the root node is highly impure and the constituents of the input at the root node would look like the leftmost figure in the above Entropy Diagram. However, such a set of data is good for learning the attributes of the mutations used to split the node. At a certain node, when the homogeneity of the constituents of the input occurs (as shown in the rightmost figure in the above Entropy Diagram), the dataset would no longer be good for learning. Moving on, the entropy at left and right child nodes of the above decision tree is computed using the formulae:H(tL) = −[pC,L log2(pC,L) + pNC,L log2(pNC,L)]H(tR) = −[pC,R log2(pC,R) + pNC,R log2(pNC,R)]where, probability of selecting a class ‘C’ sample at the left child node, pC,L = n(tL, C) / n(tL), probability of selecting a class ‘NC’ sample at the left child node, pNC,L = n(tL, NC) / n(tL), probability of selecting a class ‘C’ sample at the right child node, pC,R = n(tR, C) / n(tR), prob
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Mobile Passport Control

Mobile Passport Control (MPC) is a mobile app that enables eligible travelers entering the United States to submit their passport information and customs declaration form to Customs and Border Protection via smartphone or tablet and go through the inspections process using an expedited lane. It is available to "U.S. citizens, U.S. lawful permanent residents, Canadian B1/B2 citizen visitors and returning Visa Waiver Program travelers with approved ESTA". The app is available on iOS and Android devices and is operational at 34 US airports, 14 international airports offering preclearance facilities, and 4 seaports. The use of Mobile Passport Control operations have increased threefold from 2016 to 2017. == History == Mobile Passport Control operations were launched in Atlanta at the Hartsfield-Jackson International Airport in 2016 and is now available at 34 U.S. airports, 14 international airports that offer preclearance and 4 U.S. cruise ports. The Mobile Passport app is authorized by CBP and sponsored by the Airports Council International-North America, Boeing, and the Port of Everglades. Airside Mobile, Inc. secured a Series A funding of $6 million in the fall of 2017. == How it works == During the customs process at the Federal Inspection Service (FIS) area of a U.S. airport, travelers arriving from international locations typically wait in long lines before presenting passports and paperwork and verbally answering questions made by CBP officials. Eligible travelers who have downloaded the Mobile Passport app can expedite this process by submitting information regarding their passport and trip details, and a newly-taken selfie, via their mobile device to CBP officials, then access an expedited line. Mobile Passport Control users will be required to show their physical passport(s) and briefly talk to a CBP officer. == Locations == === US airports === Atlanta (ATL) Baltimore (BWI) Boston (BOS) Charlotte (CLT) Chicago (ORD) Dallas/Ft Worth (DFW) Denver (DEN) Detroit (DTW) as of 7/2024 Ft. Lauderdale (FLL) Honolulu (HNL) Houston (HOU and IAH) Kansas City (MCI) Las Vegas (LAS) Los Angeles (LAX) Miami (MIA) Minneapolis (MSP) New York (JFK) Newark (EWR) Oakland (OAK) Orlando (MCO) Palm Beach (PBI) Philadelphia (PHL) Phoenix (PHX) Pittsburgh (PIT) Portland (PDX) Sacramento (SMF) San Diego (SAN) San Francisco (SFO) San Jose (SJC) San Juan (SJU) Seattle (SEA) Tampa (TPA) Washington Dulles (IAD) === International Preclearance locations === Abu Dhabi (AUH) Aruba (AUA) Bermuda (BDA) Calgary (YYC) Dublin (DUB) Edmonton (YEG) Halifax (YHZ) Montreal (YUL) Nassau (NAS) Ottawa (YOW) Shannon (SNN) Toronto (YYZ) Vancouver (YVR) Winnipeg (YWG) Sepinggan (BPN) === Seaports === Fort Lauderdale (PEV) Miami (MSE) San Juan (PUE) West Palm Beach (WPB)
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Radial basis function

In mathematics a radial basis function (RBF) is a real-valued function φ {\textstyle \varphi } whose value depends only on the distance between the input and some fixed point, either the origin, so that φ ( x ) = φ ^ ( ‖ x ‖ ) {\textstyle \varphi (\mathbf {x} )={\hat {\varphi }}(\left\|\mathbf {x} \right\|)} , or some other fixed point c {\textstyle \mathbf {c} } , called a center, so that φ ( x ) = φ ^ ( ‖ x − c ‖ ) {\textstyle \varphi (\mathbf {x} )={\hat {\varphi }}(\left\|\mathbf {x} -\mathbf {c} \right\|)} . Any function φ {\textstyle \varphi } that satisfies the property φ ( x ) = φ ^ ( ‖ x ‖ ) {\textstyle \varphi (\mathbf {x} )={\hat {\varphi }}(\left\|\mathbf {x} \right\|)} is a radial function. The distance is usually Euclidean distance, although other metrics are sometimes used. They are often used as a collection { φ k } k {\displaystyle \{\varphi _{k}\}_{k}} which forms a basis for some function space of interest, hence the name. Sums of radial basis functions are typically used to approximate given functions. This approximation process can also be interpreted as a simple kind of neural network; this was the context in which they were originally applied to machine learning, in work by David Broomhead and David Lowe in 1988, which stemmed from Michael J. D. Powell's seminal research from 1977. RBFs are also used as a kernel in support vector classification. The technique has proven effective and flexible enough that radial basis functions are now applied in a variety of engineering applications. == Definition == A radial function is a function φ : [ 0 , ∞ ) → R {\textstyle \varphi :[0,\infty )\to \mathbb {R} } . When paired with a norm ‖ ⋅ ‖ : V → [ 0 , ∞ ) {\textstyle \|\cdot \|:V\to [0,\infty )} on a vector space, a function of the form φ c = φ ( ‖ x − c ‖ ) {\textstyle \varphi _{\mathbf {c} }=\varphi (\|\mathbf {x} -\mathbf {c} \|)} is said to be a radial kernel centered at c ∈ V {\textstyle \mathbf {c} \in V} . A radial function and the associated radial kernels are said to be radial basis functions if, for any finite set of nodes { x k } k = 1 n ⊆ V {\displaystyle \{\mathbf {x} _{k}\}_{k=1}^{n}\subseteq V} , all of the following conditions are true: === Examples === Commonly used types of radial basis functions include (writing r = ‖ x − x i ‖ {\textstyle r=\left\|\mathbf {x} -\mathbf {x} _{i}\right\|} and using ε {\textstyle \varepsilon } to indicate a shape parameter that can be used to scale the input of the radial kernel): == Approximation == Radial basis functions are typically used to build up function approximations of the form where the approximating function y ( x ) {\textstyle y(\mathbf {x} )} is represented as a sum of N {\displaystyle N} radial basis functions, each associated with a different center x i {\textstyle \mathbf {x} _{i}} , and weighted by an appropriate coefficient w i . {\textstyle w_{i}.} The weights w i {\textstyle w_{i}} can be estimated using the matrix methods of linear least squares, because the approximating function is linear in the weights w i {\textstyle w_{i}} . Approximation schemes of this kind have been particularly used in time series prediction and control of nonlinear systems exhibiting sufficiently simple chaotic behaviour and 3D reconstruction in computer graphics (for example, hierarchical RBF and Pose Space Deformation). == RBF Network == The sum can also be interpreted as a rather simple single-layer type of artificial neural network called a radial basis function network, with the radial basis functions taking on the role of the activation functions of the network. It can be shown that any continuous function on a compact interval can in principle be interpolated with arbitrary accuracy by a sum of this form, if a sufficiently large number N {\textstyle N} of radial basis functions is used. The approximant y ( x ) {\textstyle y(\mathbf {x} )} is differentiable with respect to the weights w i {\textstyle w_{i}} . The weights could thus be learned using any of the standard iterative methods for neural networks. Using radial basis functions in this manner yields a reasonable interpolation approach provided that the fitting set has been chosen such that it covers the entire range systematically (equidistant data points are ideal). However, without a polynomial term that is orthogonal to the radial basis functions, estimates outside the fitting set tend to perform poorly. == RBFs for PDEs == Radial basis functions are used to approximate functions and so can be used to discretize and numerically solve Partial Differential Equations (PDEs). This was first done in 1990 by E. J. Kansa who developed the first RBF based numerical method. It is called the Kansa method and was used to solve the elliptic Poisson equation and the linear advection-diffusion equation. The function values at points x {\displaystyle \mathbf {x} } in the domain are approximated by the linear combination of RBFs: The derivatives are approximated as such: where N {\displaystyle N} are the number of points in the discretized domain, d {\displaystyle d} the dimension of the domain and λ {\displaystyle \lambda } the scalar coefficients that are unchanged by the differential operator. Different numerical methods based on Radial Basis Functions were developed thereafter. Some methods are the RBF-FD method, the RBF-QR method and the RBF-PUM method.
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Dynamic Bayesian network

A dynamic Bayesian network (DBN) is a Bayesian network (BN) which relates variables to each other over adjacent time steps. == History == A dynamic Bayesian network (DBN) is often called a "two-timeslice" BN (2TBN) because it says that at any point in time T, the value of a variable can be calculated from the internal regressors and the immediate prior value (time T-1). DBNs were developed by Paul Dagum in the early 1990s at Stanford University's Section on Medical Informatics. Dagum developed DBNs to unify and extend traditional linear state-space models such as Kalman filters, linear and normal forecasting models such as ARMA and simple dependency models such as hidden Markov models into a general probabilistic representation and inference mechanism for arbitrary nonlinear and non-normal time-dependent domains. Today, DBNs are common in robotics, and have shown potential for a wide range of data mining applications. For example, they have been used in speech recognition, digital forensics, protein sequencing, and bioinformatics. DBN is a generalization of hidden Markov models and Kalman filters. DBNs are conceptually related to probabilistic Boolean networks and can, similarly, be used to model dynamical systems at steady-state.
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Prototype methods

Prototype methods are machine learning methods that use data prototypes. A data prototype is a data value that reflects other values in its class, e.g., the centroid in a K-means clustering problem. == Methods == The following are some prototype methods K-means clustering Learning vector quantization (LVQ) Gaussian mixtures == Related Methods == While K-nearest neighbor's does not use prototypes, it is similar to prototype methods like K-means clustering.
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Foodsi

Foodsi is a Polish mobile application that connects customers with restaurants, convenience stores, bakeries and cafes that have a surplus of food, allowing its users to buy the surplus at a reduced price. The service launched in 2019 in Warsaw and has expanded to other major cities in Poland. In 2023, a new feature was introduced in the app, allowing users to buy packages not only with self-pickup but also with delivery. The products range has also been expanded to include unsold magazines, cosmetics or plants. == History == The company was created in 2019 in Poland by Mateusz Kowalczyk and Jakub Fryszczyn. During studies in their home country and abroad, when they made a living working in restaurants and bakeries, they recognized the problem and the scale of food waste. They launched the application by themselves, having previously raised PLN 100,000 on their own for the purpose. Initially, Foodsi was an Android-only app, but over time, an IOS version was developed. In 2022, the startup raised PLN 6 million in a seed round from VC companies including CofounderZone and Status Starter, as well as private investors such as founders of Pyszne.pl. As of December 2023, it claimed more than 5000 businesses, serving over 1,5 million users, have saved nearly 3 million bags of food. == Purpose == Foodsi aims to significantly reduce food waste, which contributes to the Sustainable Development Goals. The application bridges the gap between the customers who are looking for shopping deals and the companies that want to reduce surplus products but are unable to sell them at a normal price. This allows the customers to buy unsold products for as little as 30% of the normal price. The company claims that every 4 out of 5 packages are sold on average. As of 2019 Foodsi employed more than 30 people. By 2024 it was more than 50. For now, Foodsi operates in major Polish cities such as Warsaw, Kraków, Trójmiasto, Wrocław, Poznań etc. However, in the upcoming years, Foodsi plans to expand to other countries. == Use == To start selling surplus, a company must leave Foodsi its contact information to register in the system. Registration in the app is completely free of charge. Then, companies offer available packages anticipating what won’t be sold and post them in the app along with the price so that users can buy them and pick them up. Companies can put their packages in the app at any time during the day. Users can pick up packages from bakeries, grocery stores, restaurants, but also florists and beauty stores. Foodsi charges a small commission on each package from the cooperating companies. If a user wants to start ordering packages from Foodsi, he or she needs to install the app on their mobile phone (Android or IOS) and register an account. The app displays a list of restaurants and other venues available in a specific region set by the user's location. Customers can see the price, address, distance and time range for package pickup. Packages are usually in the form of so-called 'surprise-packages', meaning that customers do not know specifically what kind of food/product will be inside. Some restaurants offer a choice of different package sizes. Prices are up to 70% lower than those of the original products. Customers have to show up at the restaurant to pick up the package using their phone at a time specified in the app. == Awards == Auler All-Stars 2025 - 3rd place Deloitte Technology Fast 50 - 2025 Central Europe Executive Club - Innowacja Roku: Żywność i Rolnictwo - Wyróżnienie (2025) Stena Circular Economy Award - Lider Gospodarki Obiegu Zamkniętego (2025) - wyróżnienie w kategorii start-up wdrażający GOZ na rynku polskim 255th place in the international poll FoodTech 500 2025 Finalist for the EY Entrepreneur Of The Year™ 2025 Wpływowi 2024 - Laureat w kategorii “Zrównoważony rozwój” Supplier of the Year 2024 - XXII Food & Business Forum Supplier of the Year 2024 - VII Sweets & Coffee Forum Innovative Leader 2024 - Leader in Food / Food-Tech Category - Executive Summit “Orzeł Innowacji - Start-up z potencjałem Polska-Świat” (Rzeczpospolita, 2024) 102nd place in the international poll FoodTech 500 2024 Auler 2023 Startup of the Year 2023 according to money.pl Start(up) w zrównoważoną przyszłość Kongresu Kompas ESG 2023 Marka Godna Zaufania according to My Company Polska 2023 184th place in the international poll FoodTech 500 2023 In 2023, Foodsi co-founder Mateusz Kowalczyk was recognized by Forbes magazine and included in its "30 before 30" list.
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Abess

abess (Adaptive Best Subset Selection, also ABESS) is a machine learning method designed to address the problem of best subset selection. It aims to determine which features or variables are crucial for optimal model performance when provided with a dataset and a prediction task. abess was introduced by Zhu in 2020 and it dynamically selects the appropriate model size adaptively, eliminating the need for selecting regularization parameters. abess is applicable in various statistical and machine learning tasks, including linear regression, the Single-index model, and other common predictive models. abess can also be applied in biostatistics. == Basic Form == The basic form of abess is employed to address the optimal subset selection problem in general linear regression. abess is an l 0 {\displaystyle l_{0}} method, it is characterized by its polynomial time complexity and the property of providing both unbiased and consistent estimates. In the context of linear regression, assuming we have knowledge of n {\displaystyle n} independent samples ( x i , y i ) , i = 1 , … , n {\displaystyle (x_{i},y_{i}),i=1,\ldots ,n} , where x i ∈ R p × 1 {\displaystyle x_{i}\in \mathbb {R} ^{p\times 1}} and y i ∈ R {\displaystyle y_{i}\in \mathbb {R} } , we define X = ( x 1 , … , x n ) ⊤ {\displaystyle X=(x_{1},\ldots ,x_{n})^{\top }} and y = ( y 1 , … , y n ) ⊤ {\displaystyle y=(y_{1},\ldots ,y_{n})^{\top }} . The following equation represents the general linear regression model: y = X β + ε . {\displaystyle y=X\beta +\varepsilon .} To obtain appropriate parameters β {\displaystyle \beta } , one can consider the loss function for linear regression: L n LR ( β ; X , y ) = 1 2 n ‖ y − X β ‖ 2 2 . {\displaystyle {\mathcal {L}}_{n}^{\text{LR}}(\beta ;X,y)={\frac {1}{2n}}\|y-X\beta \|_{2}^{2}.} In abess, the initial focus is on optimizing the loss function under the l 0 {\displaystyle l_{0}} constraint. That is, we consider the following problem: min β ∈ R p × 1 L n LR ( β ; X , y ) , subject to ‖ β ‖ 0 ≤ s , {\displaystyle \min _{\beta \in \mathbb {R} ^{p\times 1}}{\mathcal {L}}_{n}^{\text{LR}}(\beta ;X,y),{\text{ subject to }}\|\beta \|_{0}\leq s,} where s {\displaystyle s} represents the desired size of the support set, and ‖ β ‖ 0 = ∑ i = 1 p I ( β i ≠ 0 ) {\displaystyle \|\beta \|_{0}=\sum _{i=1}^{p}{\mathcal {I}}_{(\beta _{i}\neq 0)}} is the l 0 {\displaystyle l_{0}} norm of the vector. To address the optimization problem described above, abess iteratively exchanges an equal number of variables between the active set and the inactive set. In each iteration, the concept of sacrifice is introduced as follows: For j in the active set ( j ∈ A ^ {\displaystyle j\in {\hat {\mathcal {A}}}} ): ξ j = L n LR ( β ^ A ∖ { j } ) − L n LR ( β ^ A ) = X j ⊤ X j 2 n ( β ^ j ) 2 {\displaystyle \xi _{j}={\mathcal {L}}_{n}^{\text{LR}}\left({\hat {\boldsymbol {\beta }}}^{{\mathcal {A}}\backslash \{j\}}\right)-{\mathcal {L}}_{n}^{\text{LR}}\left({\hat {\boldsymbol {\beta }}}^{\mathcal {A}}\right)={\frac {{\boldsymbol {X}}_{j}^{\top }{\boldsymbol {X}}_{j}}{2n}}\left({\hat {\beta }}_{j}\right)^{2}} For j in the inactive set ( j ∉ A ^ {\displaystyle j\notin {\hat {\mathcal {A}}}} ): ξ j = L n LR ( β ^ A ) − L n LR ( β ^ A + t ^ { j } ) = X j ⊤ X j 2 n ( d ^ j X j ⊤ X j / n ) 2 {\displaystyle \xi _{j}={\mathcal {L}}_{n}^{\text{LR}}\left({\hat {\boldsymbol {\beta }}}^{\mathcal {A}}\right)-{\mathcal {L}}_{n}^{\text{LR}}\left({\hat {\boldsymbol {\beta }}}^{\mathcal {A}}+{\hat {\boldsymbol {t}}}^{\{j\}}\right)={\frac {{\boldsymbol {X}}_{j}^{\top }{\boldsymbol {X}}_{j}}{2n}}\left({\frac {{\hat {\mathrm {d} }}_{j}}{{\boldsymbol {X}}_{j}^{\top }{\boldsymbol {X}}_{j}/n}}\right)^{2}} Here are the key elements in the above equations: β ^ A {\displaystyle {\hat {\beta }}^{\mathcal {A}}} : This represents the estimate of β {\displaystyle \beta } obtained in the previous iteration. A ^ {\displaystyle {\hat {\mathcal {A}}}} : It denotes the estimated active set from the previous iteration. β ^ A ∖ { j } {\displaystyle {\hat {\boldsymbol {\beta }}}^{{\mathcal {A}}\backslash \{j\}}} : This is a vector where the j-th element is set to 0, while the other elements are the same as β ^ A {\displaystyle {\hat {\beta }}^{\mathcal {A}}} . t ^ { j } = arg ⁡ min t L n LR ( β ^ A + t { j } ) {\displaystyle {\hat {\boldsymbol {t}}}^{\{j\}}=\arg \min _{t}{\mathcal {L}}_{n}^{\text{LR}}\left({\hat {\boldsymbol {\beta }}}^{\mathcal {A}}+{\boldsymbol {t}}^{\{j\}}\right)} : Here, t { j } {\displaystyle t^{\{j\}}} represents a vector where all elements are 0 except the j-th element. d ^ j = X j ⊤ ( y − X β ^ ) / n {\displaystyle {\hat {d}}_{j}={\boldsymbol {X}}_{j}^{\top }({\boldsymbol {y}}-{\boldsymbol {X}}{\hat {\boldsymbol {\beta }}})/n} : This is calculated based on the equation mentioned. The iterative process involves exchanging variables, with the aim of minimizing the sacrifices in the active set while maximizing the sacrifices in the inactive set during each iteration. This approach allows abess to efficiently search for the optimal feature subset. In abess, select an appropriate s max {\displaystyle s_{\max }} and optimize the above problem for active sets size s = 1 , … , s max {\displaystyle s=1,\ldots ,s_{\max }} using the information criterion GIC = n log ⁡ L n LR + s log ⁡ p log ⁡ log ⁡ n , {\displaystyle {\text{GIC}}=n\log {\mathcal {L}}_{n}^{\text{LR}}+s\log p\log \log n,} to adaptively choose the appropriate active set size s {\displaystyle s} and obtain its corresponding abess estimator. == Generalizations == The splicing algorithm in abess can be employed for subset selection in other models. === Distribution-Free Location-Scale Regression === In 2023, Siegfried extends abess to the case of Distribution-Free and Location-Scale. Specifically, it considers the optimization problem max ϑ ∈ R P , β ∈ R J , γ ∈ R J ∑ i = 1 N ℓ i ( ϑ , x i ⊤ β , exp ⁡ ( x i ⊤ γ ) − 1 ) , {\displaystyle \max _{{\boldsymbol {\vartheta }}\in \mathbb {R} ^{P},{\boldsymbol {\beta }}\in \mathbb {R} ^{J},{\boldsymbol {\gamma }}\in \mathbb {R} ^{J}}\sum _{i=1}^{N}\ell _{i}\left({\boldsymbol {\vartheta }},{\boldsymbol {x}}_{i}^{\top }{\boldsymbol {\beta }},{\sqrt {\exp \left({\boldsymbol {x}}_{i}^{\top }{\boldsymbol {\gamma }}\right)}}^{-1}\right),} subject to ‖ ( β ⊤ , γ ⊤ ) ⊤ ‖ 0 ≤ s , {\displaystyle \left\|\left({\boldsymbol {\beta }}^{\top },{\boldsymbol {\gamma }}^{\top }\right)^{\top }\right\|_{0}\leq s,} where ℓ i {\displaystyle \ell _{i}} is a loss function, ϑ {\displaystyle {\boldsymbol {\vartheta }}} is a parameter vector, β {\displaystyle {\boldsymbol {\beta }}} and γ {\displaystyle {\boldsymbol {\gamma }}} are vectors, and x i {\displaystyle {\boldsymbol {x}}_{i}} is a data vector. This approach, demonstrated across various applications, enables parsimonious regression modeling for arbitrary outcomes while maintaining interpretability through innovative subset selection procedures. === Groups Selection === In 2023, Zhang applied the splicing algorithm to group selection, optimizing the following model: min β ∈ R p L n LR ( β ; X , y ) subject to ∑ j = 1 J I ( ‖ β G j ‖ 2 ≠ 0 ) ≤ s {\displaystyle \min _{{\boldsymbol {\beta }}\in \mathbb {R} ^{p}}{\mathcal {L}}_{n}^{\text{LR}}(\beta ;X,y){\text{ subject to }}\sum _{j=1}^{J}I\left(\|{\boldsymbol {\beta }}_{G_{j}}\|_{2}\neq 0\right)\leq s} Here are the symbols involved: J {\displaystyle J} : Total number of feature groups, representing the existence of J {\displaystyle J} non-overlapping feature groups in the dataset. G j {\displaystyle G_{j}} : Index set for the j {\displaystyle j} -th feature group, where j {\displaystyle j} ranges from 1 to J {\displaystyle J} , representing the feature grouping structure in the data. s {\displaystyle s} : Model size, a positive integer determined from the data, limiting the number of selected feature groups. === Regression with Corrupted Data === Zhang applied the splicing algorithm to handle corrupted data. Corrupted data refers to information that has been disrupted or contains errors during the data collection or recording process. This interference may include sensor inaccuracies, recording errors, communication issues, or other external disturbances, leading to inaccurate or distorted observations within the dataset. === Single Index Models === In 2023, Tang applied the splicing algorithm to optimal subset selection in the Single-index model. The form of the Single Index Model (SIM) is given by y i = g ( b ⊤ x i , e i ) , i = 1 , … , n , {\displaystyle y_{i}=g({\boldsymbol {b}}^{\top }{\boldsymbol {x}}_{i},e_{i}),\quad i=1,\ldots ,n,} where b {\displaystyle {\boldsymbol {b}}} is the parameter vector, e i {\displaystyle e_{i}} is the error term. The corresponding loss function is defined as l n ( β ) = ∑ i = 1 n ( r i n − 1 2 − x i ⊤ β ) 2 , {\displaystyle l_{n}({\boldsymbol {\beta }})=\sum _{i=1}^{n}\left({\frac {r_{i}}{n}}-{\frac {1}{2}}-{\boldsymbol {x}}_{i}^{\top }{\boldsymbol {\beta }}\right)^{2},} where r {\disp
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Jpred

Jpred v.4 is the latest version of the JPred Protein Secondary Structure Prediction Server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction, that has existed since 1998 in different versions. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 134 000 jobs per month and has carried out over 2 million predictions in total for users in 179 countries. == JPred 2 == The static HTML pages of JPred 2 are still available for reference. == JPred 3 == The JPred v3 followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References). This release added new functionality and fixed many bugs. The highlights are: New, friendlier user interface Retrained and optimised version of Jnet (v2) - mean secondary structure prediction accuracy of >81% Batch submission of jobs Better error checking of input sequences/alignments Predictions now (optionally) returned via e-mail Users may provide their own query names for each submission JPred now makes a prediction even when there are no PSI-BLAST hits to the query PS/PDF output now incorporates all the predictions == JPred 4 == The current version of JPred (v4) has the following improvements and updates incorporated: Retrained on the latest UniRef90 and SCOPe/ASTRAL version of Jnet (v2.3.1) - mean secondary structure prediction accuracy of >82%. Upgraded the Web Server to the latest technologies (Bootstrap framework, JavaScript) and updating the web pages – improving the design and usability through implementing responsive technologies. Added RESTful API and mass-submission and results retrieval scripts - resulting in peak throughput above 20,000 predictions per day. Added prediction jobs monitoring tools. Upgraded the results reporting – both, on the web-site, and through the optional email summary reports: improved batch submission, added results summary preview through Jalview results visualization summary in SVG and adding full multiple sequence alignments into the reports. Improved help-pages, incorporating tool-tips, and adding one-page step-by-step tutorials. Sequence residues are categorised or assigned to one of the secondary structure elements, such as alpha-helix, beta-sheet and coiled-coil. Jnet uses two neural networks for its prediction. The first network is fed with a window of 17 residues over each amino acid in the alignment plus a conservation number. It uses a hidden layer of nine nodes and has three output nodes, one for each secondary structure element. The second network is fed with a window of 19 residues (the result of first network) plus the conservation number. It has a hidden layer with nine nodes and has three output nodes.
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Ensemble learning

In statistics and machine learning, ensemble methods use multiple learning algorithms to obtain better predictive performance than could be obtained from any of the constituent learning algorithms alone. Unlike a statistical ensemble in statistical mechanics, which is usually infinite, a machine learning ensemble consists of only a concrete finite set of alternative models, but typically allows for much more flexible structure to exist among those alternatives. == Overview == Supervised learning algorithms search through a hypothesis space to find a suitable hypothesis that will make good predictions with a particular problem. Even if this space contains hypotheses that are very well-suited for a particular problem, it may be very difficult to find a good one. Ensembles combine multiple hypotheses to form one which should be theoretically better. Ensemble learning trains two or more machine learning algorithms on a specific classification or regression task. The algorithms within the ensemble model are generally referred as "base models", "base learners", or "weak learners" in literature. These base models can be constructed using a single modelling algorithm, or several different algorithms. The idea is to train a diverse set of weak models on the same modelling task, such that the outputs of each weak learner have poor predictive ability (i.e., high bias), and among all weak learners, the outcome and error values exhibit high variance. Fundamentally, an ensemble learning model trains at least two high-bias (weak) and high-variance (diverse) models to be combined into a better-performing model. The set of weak models — which would not produce satisfactory predictive results individually — are combined or averaged to produce a single, high performing, accurate, and low-variance model to fit the task as required. Ensemble learning typically refers to bagging (bootstrap aggregating), boosting or stacking/blending techniques to induce high variance among the base models. Bagging creates diversity by generating random samples from the training observations and fitting the same model to each different sample — also known as homogeneous parallel ensembles. Boosting follows an iterative process by sequentially training each base model on the up-weighted errors of the previous base model, producing an additive model to reduce the final model errors — also known as sequential ensemble learning. Stacking or blending consists of different base models, each trained independently (i.e. diverse/high variance) to be combined into the ensemble model — producing a heterogeneous parallel ensemble. Common applications of ensemble learning include random forests (an extension of bagging), Boosted Tree models, and Gradient Boosted Tree Models. Models in applications of stacking are generally more task-specific — such as combining clustering techniques with other parametric and/or non-parametric techniques. Evaluating the prediction of an ensemble typically requires more computation than evaluating the prediction of a single model. In one sense, ensemble learning may be thought of as a way to compensate for poor learning algorithms by performing a lot of extra computation. On the other hand, the alternative is to do a lot more learning with one non-ensemble model. An ensemble may be more efficient at improving overall accuracy for the same increase in compute, storage, or communication resources by using that increase on two or more methods, than would have been improved by increasing resource use for a single method. Fast algorithms such as decision trees are commonly used in ensemble methods (e.g., random forests), although slower algorithms can benefit from ensemble techniques as well. By analogy, ensemble techniques have been used also in unsupervised learning scenarios, for example in consensus clustering or in anomaly detection. == Ensemble theory == Empirically, ensembles tend to yield better results when there is a significant diversity among the models. Many ensemble methods, therefore, seek to promote diversity among the models they combine. Although perhaps non-intuitive, more random algorithms (like random decision trees) can be used to produce a stronger ensemble than very deliberate algorithms (like entropy-reducing decision trees). Using a variety of strong learning algorithms, however, has been shown to be more effective than using techniques that attempt to dumb-down the models in order to promote diversity. It is possible to increase diversity in the training stage of the model using correlation for regression tasks or using information measures such as cross entropy for classification tasks. Theoretically, one can justify the diversity concept because the lower bound of the error rate of an ensemble system can be decomposed into accuracy, diversity, and the other term. === The geometric framework === Ensemble learning, including both regression and classification tasks, can be explained using a geometric framework. Within this framework, the output of each individual classifier or regressor for the entire dataset can be viewed as a point in a multi-dimensional space. Additionally, the target result is also represented as a point in this space, referred to as the "ideal point." The Euclidean distance is used as the metric to measure both the performance of a single classifier or regressor (the distance between its point and the ideal point) and the dissimilarity between two classifiers or regressors (the distance between their respective points). This perspective transforms ensemble learning into a deterministic problem. For example, within this geometric framework, it can be proved that the averaging of the outputs (scores) of all base classifiers or regressors can lead to equal or better results than the average of all the individual models. It can also be proved that if the optimal weighting scheme is used, then a weighted averaging approach can outperform any of the individual classifiers or regressors that make up the ensemble or as good as the best performer at least. == Ensemble size == While the number of component classifiers of an ensemble has a great impact on the accuracy of prediction, there is a limited number of studies addressing this problem. A priori determining of ensemble size and the volume and velocity of big data streams make this even more crucial for online ensemble classifiers. Mostly statistical tests were used for determining the proper number of components. More recently, a theoretical framework suggested that there is an ideal number of component classifiers for an ensemble such that having more or less than this number of classifiers would deteriorate the accuracy. It is called "the law of diminishing returns in ensemble construction." Their theoretical framework shows that using the same number of independent component classifiers as class labels gives the highest accuracy. == Common types of ensembles == === Bayes optimal classifier === The Bayes optimal classifier is a classification technique. It is an ensemble of all the hypotheses in the hypothesis space. On average, no other ensemble can outperform it. The Naive Bayes classifier is a version of this that assumes that the data is conditionally independent on the class and makes the computation more feasible. Each hypothesis is given a vote proportional to the likelihood that the training dataset would be sampled from a system if that hypothesis were true. To facilitate training data of finite size, the vote of each hypothesis is also multiplied by the prior probability of that hypothesis. The Bayes optimal classifier can be expressed with the following equation: y = a r g m a x c j ∈ C ∑ h i ∈ H P ( c j | h i ) P ( T | h i ) P ( h i ) {\displaystyle y={\underset {c_{j}\in C}{\mathrm {argmax} }}\sum _{h_{i}\in H}{P(c_{j}|h_{i})P(T|h_{i})P(h_{i})}} where y {\displaystyle y} is the predicted class, C {\displaystyle C} is the set of all possible classes, H {\displaystyle H} is the hypothesis space, P {\displaystyle P} refers to a probability, and T {\displaystyle T} is the training data. As an ensemble, the Bayes optimal classifier represents a hypothesis that is not necessarily in H {\displaystyle H} . The hypothesis represented by the Bayes optimal classifier, however, is the optimal hypothesis in ensemble space (the space of all possible ensembles consisting only of hypotheses in H {\displaystyle H} ). This formula can be restated using Bayes' theorem, which says that the posterior is proportional to the likelihood times the prior: P ( h i | T ) ∝ P ( T | h i ) P ( h i ) {\displaystyle P(h_{i}|T)\propto P(T|h_{i})P(h_{i})} hence, y = a r g m a x c j ∈ C ∑ h i ∈ H P ( c j | h i ) P ( h i | T ) {\displaystyle y={\underset {c_{j}\in C}{\mathrm {argmax} }}\sum _{h_{i}\in H}{P(c_{j}|h_{i})P(h_{i}|T)}} === Bootstrap aggregating (bagging) === Bootstrap aggregation (bagging) involves training an ensemble on bootstrapped data sets. A bootstrapped set is cr
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Aldus PhotoStyler

Aldus PhotoStyler was a graphics software program developed by the Taiwanese company Ulead. Released in June 1991 as the first 24 bit image editor for Windows, it was bought the same year by the Aldus Prepress group. Its main competition was Adobe Photoshop. Version 2.0 (late 1993) introduced a new user interface and improved color calibration. PhotoStyler SE - lacking some features of the version 2.0 - was bundled with scanners like HP ScanJet. The product disappeared from the Adobe product line after Adobe acquired Aldus in 1994.
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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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Margin-infused relaxed algorithm

Margin-infused relaxed algorithm (MIRA) is a machine learning and online algorithm for multiclass classification problems. It is designed to learn a set of parameters (vector or matrix) by processing all the given training examples one-by-one and updating the parameters according to each training example, so that the current training example is classified correctly with a margin against incorrect classifications at least as large as their loss. The change of the parameters is kept as small as possible. A two-class version called binary MIRA simplifies the algorithm by not requiring the solution of a quadratic programming problem (see below). When used in a one-vs-all configuration, binary MIRA can be extended to a multiclass learner that approximates full MIRA, but may be faster to train. The flow of the algorithm looks as follows: The update step is then formalized as a quadratic programming problem: Find m i n ‖ w ( i + 1 ) − w ( i ) ‖ {\displaystyle min\|w^{(i+1)}-w^{(i)}\|} , so that s c o r e ( x t , y t ) − s c o r e ( x t , y ′ ) ≥ L ( y t , y ′ ) ∀ y ′ {\displaystyle score(x_{t},y_{t})-score(x_{t},y')\geq L(y_{t},y')\ \forall y'} , i.e. the score of the current correct training y {\displaystyle y} must be greater than the score of any other possible y ′ {\displaystyle y'} by at least the loss (number of errors) of that y ′ {\displaystyle y'} in comparison to y {\displaystyle y} .
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