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  • WriterDuet

    WriterDuet

    WriterDuet is a screenwriting software for writing and editing screenplays and other forms of mass media. == History == WriterDuet was founded in 2013 by Guy Goldstein. In April 2015, WriterDuet acquired the domain for Scripped.com after they closed, citing a serious technical failure. In August 2016, WriterDuet released a localized version of its software in China. In May 2018, WriterDuet included Bechdel test analysis functions to address issues of gender diversity in the screenwriting industry. In 2018, WriterDuet published WriterSolo, an offline version of their app that runs on the browser and opens/saves files on the computer, Dropbox, Google Drive, and iCloud. In July 2019, WriterDuet made the WriterSolo browser app and desktop app available as pay-what-you-want under the web address FreeScreenwriting.com. == Features == WriterDuet is primarily used to outline, write, and format screenplays to the standards recommended by the AMPAS. It also supports formats for theater, novels, and video games. The software is powered by Firebase allowing users to write together in real-time from multiple devices. WriterDuet's main competitors in the screenwriting industry are Final Draft, Celtx, and Movie Magic Screenwriter.

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  • Correlation clustering

    Correlation clustering

    Clustering is the problem of partitioning data points into groups based on similarity or dissimilarity. Correlation clustering is a clustering framework in which a set of objects is partitioned into clusters based on pairwise similarity and dissimilarity information, without requiring the number of clusters to be specified in advance. == Description of the problem == In machine learning, correlation clustering (also known as cluster editing) considers settings in which pairwise similarity or dissimilarity relationships between objects are known. A standard formulation models the input as an unweighted complete graph G = ( V , E ) {\displaystyle G=(V,E)} , where each edge is labeled either + {\displaystyle +} or − {\displaystyle -} (that is, the graph is a signed graph), indicating whether the corresponding endpoints are similar or dissimilar. The goal is to find a clustering (that is, a partition of V {\displaystyle V} ) that either maximizes the number of agreements—the sum of positive edges whose endpoints lie in the same cluster and negative edges whose endpoints lie in different clusters—or minimizes the number of disagreements—the sum of positive edges whose endpoints are separated and negative edges whose endpoints lie in the same cluster. Unlike other clustering methods such as k-means, correlation clustering does not require choosing the number of clusters k {\displaystyle k} in advance. It is not always possible to find a clustering with zero disagreements. For example, consider a triangle graph containing two positive edges and one negative edge. In this case, every clustering incurs at least one disagreement. Such configurations are referred to in the literature as bad triangles. From a computational perspective, optimizing the correlation clustering objective is challenging. The (decision version of the) problem is NP-complete. A large body of subsequent work has developed approximation algorithms for correlation clustering under various assumptions, including complete or general graphs and unweighted or weighted graphs, for both minimization and maximization objectives. This problem is considered one of the fundamental combinatorial optimization problems, and many algorithmic techniques have been developed to address it. The problem has also been studied extensively across multiple disciplines. A comprehensive literature review of early correlation clustering research is provided by Wahid and Hassini. == Formal Definitions == Let G = ( V , E ) {\displaystyle G=(V,E)} be a graph with nodes V {\displaystyle V} and edges E {\displaystyle E} . A clustering of G {\displaystyle G} is a partition of its node set Π = { π 1 , … , π k } {\displaystyle \Pi =\{\pi _{1},\dots ,\pi _{k}\}} with V = π 1 ∪ ⋯ ∪ π k {\displaystyle V=\pi _{1}\cup \dots \cup \pi _{k}} and π i ∩ π j = ∅ {\displaystyle \pi _{i}\cap \pi _{j}=\emptyset } for i ≠ j {\displaystyle i\neq j} . For a given clustering Π {\displaystyle \Pi } , let δ ( Π ) = { { u , v } ∈ E ∣ { u , v } ⊈ π ∀ π ∈ Π } {\displaystyle \delta (\Pi )=\{\{u,v\}\in E\mid \{u,v\}\not \subseteq \pi \;\forall \pi \in \Pi \}} denote the subset of edges of G {\displaystyle G} whose endpoints are in different subsets of the clustering Π {\displaystyle \Pi } . Now, let w : E → R ≥ 0 {\displaystyle w\colon E\to \mathbb {R} _{\geq 0}} be a function that assigns a non-negative weight to each edge of the graph and let E = E + ∪ E − {\displaystyle E=E^{+}\cup E^{-}} be a partition of the edges into attractive ( E + {\displaystyle E^{+}} ) and repulsive ( E − {\displaystyle E^{-}} ) edges; that is, the edges are signed. The minimum disagreement correlation clustering problem is the following optimization problem: minimize Π ∑ e ∈ E + ∩ δ ( Π ) w e + ∑ e ∈ E − ∖ δ ( Π ) w e . {\displaystyle {\begin{aligned}&{\underset {\Pi }{\operatorname {minimize} }}&&\sum _{e\in E^{+}\cap \delta (\Pi )}w_{e}+\sum _{e\in E^{-}\setminus \delta (\Pi )}w_{e}\;.\end{aligned}}} Here, the set E + ∩ δ ( Π ) {\displaystyle E^{+}\cap \delta (\Pi )} contains the attractive edges whose endpoints are in different components with respect to the clustering Π {\displaystyle \Pi } and the set E − ∖ δ ( Π ) {\displaystyle E^{-}\setminus \delta (\Pi )} contains the repulsive edges whose endpoints are in the same component with respect to the clustering Π {\displaystyle \Pi } . Together these two sets contain all edges that disagree with the clustering Π {\displaystyle \Pi } . Similarly to the minimum disagreement correlation clustering problem, the maximum agreement correlation clustering problem is defined as maximize Π ∑ e ∈ E + ∖ δ ( Π ) w e + ∑ e ∈ E − ∩ δ ( Π ) w e . {\displaystyle {\begin{aligned}&{\underset {\Pi }{\operatorname {maximize} }}&&\sum _{e\in E^{+}\setminus \delta (\Pi )}w_{e}+\sum _{e\in E^{-}\cap \delta (\Pi )}w_{e}\;.\end{aligned}}} Here, the set E + ∖ δ ( Π ) {\displaystyle E^{+}\setminus \delta (\Pi )} contains the attractive edges whose endpoints are in the same component with respect to the clustering Π {\displaystyle \Pi } and the set E − ∩ δ ( Π ) {\displaystyle E^{-}\cap \delta (\Pi )} contains the repulsive edges whose endpoints are in different components with respect to the clustering Π {\displaystyle \Pi } . Together these two sets contain all edges that agree with the clustering Π {\displaystyle \Pi } . Instead of formulating the correlation clustering problem in terms of non-negative edge weights and a partition of the edges into attractive and repulsive edges the problem is also formulated in terms of positive and negative edge costs without partitioning the set of edges explicitly. For given weights w : E → R ≥ 0 {\displaystyle w\colon E\to \mathbb {R} _{\geq 0}} and a given partition E = E + ∪ E − {\displaystyle E=E^{+}\cup E^{-}} of the edges into attractive and repulsive edges, the edge costs can be defined by c e = { w e if e ∈ E + − w e if e ∈ E − {\displaystyle {\begin{aligned}c_{e}={\begin{cases}\;\;w_{e}&{\text{if }}e\in E^{+}\\-w_{e}&{\text{if }}e\in E^{-}\end{cases}}\end{aligned}}} for all e ∈ E {\displaystyle e\in E} . An edge whose endpoints are in different clusters is said to be cut. The set δ ( Π ) {\displaystyle \delta (\Pi )} of all edges that are cut is often called a multicut of G {\displaystyle G} . The minimum cost multicut problem is the problem of finding a clustering Π {\displaystyle \Pi } of G {\displaystyle G} such that the sum of the costs of the edges whose endpoints are in different clusters is minimal: minimize Π ∑ e ∈ δ ( Π ) c e . {\displaystyle {\begin{aligned}&{\underset {\Pi }{\operatorname {minimize} }}&&\sum _{e\in \delta (\Pi )}c_{e}\;.\end{aligned}}} Similar to the minimum cost multicut problem, coalition structure generation in weighted graph games is the problem of finding a clustering such that the sum of the costs of the edges that are not cut is maximal: maximize Π ∑ e ∈ E ∖ δ ( Π ) c e . {\displaystyle {\begin{aligned}&{\underset {\Pi }{\operatorname {maximize} }}&&\sum _{e\in E\setminus \delta (\Pi )}c_{e}\;.\end{aligned}}} This formulation is also known as the clique partitioning problem. It can be shown that all four problems that are formulated above are equivalent. This means that a clustering that is optimal with respect to any of the four objectives is optimal for all of the four objectives. == Algorithms == If the graph admits a clustering with zero disagreements, then deleting all negative edges and computing the connected components of the remaining graph yields an optimal clustering. A necessary and sufficient condition for the existence of such a clustering was given by Davis: no cycle in the graph may contain exactly one negative edge. Bansal et al. discuss the NP-completeness proof and also present both a constant factor approximation algorithm and polynomial-time approximation scheme to find the clusters in this setting. Ailon et al. propose a randomized 3-approximation algorithm for the same problem. CC-Pivot(G=(V,E+,E−)) Pick random pivot i ∈ V Set C = { i } {\displaystyle C=\{i\}} , V'=Ø For all j ∈ V, j ≠ i; If (i,j) ∈ E+ then Add j to C Else (If (i,j) ∈ E−) Add j to V' Let G' be the subgraph induced by V' Return clustering C,CC-Pivot(G') The authors show that the above algorithm is a 3-approximation algorithm for correlation clustering. The best polynomial-time approximation algorithm known at the moment for this problem achieves a ~2.06 approximation by rounding a linear program, as shown by Chawla, Makarychev, Schramm, and Yaroslavtsev. Karpinski and Schudy proved existence of a polynomial time approximation scheme (PTAS) for that problem on complete graphs and fixed number of clusters. == Optimal number of clusters == In 2011, it was shown by Bagon and Galun that the optimization of the correlation clustering functional is closely related to well known discrete optimization methods. In their work they proposed a probabilistic analysis of the underlying implicit model that allows the correlation clustering functional to estimate the

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  • Softplus

    Softplus

    In mathematics and machine learning, the softplus function is f ( x ) = ln ⁡ ( 1 + e x ) . {\displaystyle f(x)=\ln(1+e^{x}).} It is a smooth approximation (in fact, an analytic function) to the ramp function, which is known as the rectifier or ReLU (rectified linear unit) in machine learning. For large negative x {\displaystyle x} it is ln ⁡ ( 1 + e x ) = ln ⁡ ( 1 + ϵ ) ⪆ ln ⁡ 1 = 0 {\displaystyle \ln(1+e^{x})=\ln(1+\epsilon )\gtrapprox \ln 1=0} , so just above 0, while for large positive x {\displaystyle x} it is ln ⁡ ( 1 + e x ) ⪆ ln ⁡ ( e x ) = x {\displaystyle \ln(1+e^{x})\gtrapprox \ln(e^{x})=x} , so just above x {\displaystyle x} . The names softplus and SmoothReLU are used in machine learning. The name "softplus" (2000), by analogy with the earlier softmax (1989) is presumably because it is a smooth (soft) approximation of the positive part of x, which is sometimes denoted with a superscript plus, x + := max ( 0 , x ) {\displaystyle x^{+}:=\max(0,x)} . == Alternative forms == This function can be approximated as: ln ⁡ ( 1 + e x ) ≈ { ln ⁡ 2 , x = 0 , x 1 − e − x / ln ⁡ 2 , x ≠ 0 {\displaystyle \ln \left(1+e^{x}\right)\approx {\begin{cases}\ln 2,&x=0,\\[6pt]{\frac {x}{1-e^{-x/\ln 2}}},&x\neq 0\end{cases}}} By making the change of variables x = y ln ⁡ ( 2 ) {\displaystyle x=y\ln(2)} , this is equivalent to log 2 ⁡ ( 1 + 2 y ) ≈ { 1 , y = 0 , y 1 − e − y , y ≠ 0. {\displaystyle \log _{2}(1+2^{y})\approx {\begin{cases}1,&y=0,\\[6pt]{\frac {y}{1-e^{-y}}},&y\neq 0.\end{cases}}} A sharpness parameter k {\displaystyle k} may be included: f ( x ) = ln ⁡ ( 1 + e k x ) k , f ′ ( x ) = e k x 1 + e k x = 1 1 + e − k x . {\displaystyle f(x)={\frac {\ln(1+e^{kx})}{k}},\qquad \qquad f'(x)={\frac {e^{kx}}{1+e^{kx}}}={\frac {1}{1+e^{-kx}}}.} Additionally, the softplus function is equivalent to the log of the sigmoid function in the following way: − ln ⁡ ( sigmoid ( − x ) ) = − ln ⁡ ( 1 1 + e x ) = ln ⁡ ( 1 + e x ) = softplus ( x ) {\displaystyle -\ln({\text{sigmoid}}(-x))=-\ln \left({\frac {1}{1+e^{x}}}\right)=\ln \left(1+e^{x}\right)={\text{softplus}}(x)} == Related functions == The derivative of softplus is the standard logistic function: f ′ ( x ) = e x 1 + e x = 1 1 + e − x {\displaystyle f'(x)={\frac {e^{x}}{1+e^{x}}}={\frac {1}{1+e^{-x}}}} The logistic function or the sigmoid function is a smooth approximation of the rectifier, the Heaviside step function. === LogSumExp === The multivariable generalization of single-variable softplus is the LogSumExp with the first argument set to zero: L S E 0 + ⁡ ( x 1 , … , x n ) := LSE ⁡ ( 0 , x 1 , … , x n ) = ln ⁡ ( 1 + e x 1 + ⋯ + e x n ) . {\displaystyle \operatorname {LSE_{0}} ^{+}(x_{1},\dots ,x_{n}):=\operatorname {LSE} (0,x_{1},\dots ,x_{n})=\ln(1+e^{x_{1}}+\cdots +e^{x_{n}}).} The LogSumExp function is LSE ⁡ ( x 1 , … , x n ) = ln ⁡ ( e x 1 + ⋯ + e x n ) , {\displaystyle \operatorname {LSE} (x_{1},\dots ,x_{n})=\ln(e^{x_{1}}+\cdots +e^{x_{n}}),} and its gradient is the softmax; the softmax with the first argument set to zero is the multivariable generalization of the logistic function. Both LogSumExp and softmax are used in machine learning. === Convex conjugate === The convex conjugate (specifically, the Legendre transformation) of the softplus function is the negative binary entropy function (with base e). This is because (following the definition of the Legendre transformation: the derivatives are inverse functions) the derivative of softplus is the logistic function, whose inverse function is the logit, which is the derivative of negative binary entropy. Softplus can be interpreted as logistic loss (as a positive number), so, by duality, minimizing logistic loss corresponds to maximizing entropy. This justifies the principle of maximum entropy as loss minimization.

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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 →

  • CineAsset

    CineAsset

    CineAsset was a complete mastering software suite by Doremi Labs that could create and playback encrypted (Pro version) and unencrypted DCI compliant packages from virtually any source. CineAsset included a separate "Editor" application for generating Digital Cinema Packages (DCPs). CineAsset Pro added the ability to generate encrypted DCPs and Key Delivery Messages (KDMs) for any encrypted content in the database. It has since been discontinued, along with CineAsset Player. == Features == == Supported formats == === Input === Source: ==== Containers ==== AVI MOV MXF MPG TS WMV M2TS MTS MP4 MKV ==== Video Codecs ==== JPEG2000 ProRes 422 DNxHD® YUV Uncompressed 8-10 bits DIVX® XVID® MPEG4 AVC / H-264 VC-1 MPEG2 ==== Image Sequences ==== BMP TIFF TGA DPX JPG J2C ==== Audio Files ==== WAV MP3 WMA MP2 === Output === Source: ==== JPEG2000 ==== 2D and 3D at up to 4K resolution Bit Rate: 50–250 Mbit/s (500 Mbit/s for frame rates above 30 fps) Speed: Faster than real-time processing when using optional render nodes ==== MPEG2 ==== I-Only or Long GOP 1080p up to 80 Mbit/s ==== H264 ==== 1080p up to 50 Mbit/s ==== VC1 ==== DCP wrapping only (no transcode)

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  • Bayesian network

    Bayesian network

    A Bayesian network (also known as a Bayes network, Bayes net, belief network, or decision network) is a probabilistic graphical model that represents a set of variables and their conditional dependencies via a directed acyclic graph (DAG). While it is one of several forms of causal notation, causal networks are special cases of Bayesian networks. Bayesian networks are ideal for taking an event that occurred and predicting the likelihood that any one of several possible known causes was the contributing factor. For example, a Bayesian network could represent the probabilistic relationships between diseases and symptoms. Given symptoms, the network can be used to compute the probabilities of the presence of various diseases. Efficient algorithms can perform inference and learning in Bayesian networks. Bayesian networks that model sequences of variables (e.g. speech signals or protein sequences) are called dynamic Bayesian networks. Generalizations of Bayesian networks that can represent and solve decision problems under uncertainty are called influence diagrams. == Graphical model == Formally, Bayesian networks are directed acyclic graphs (DAGs) whose nodes represent variables in the Bayesian sense: they may be observable quantities, latent variables, unknown parameters or hypotheses. Each edge represents a direct conditional dependency. Any pair of nodes that are not connected (i.e. no path connects one node to the other) represent variables that are conditionally independent of each other. Each node is associated with a probability function that takes, as input, a particular set of values for the node's parent variables, and gives (as output) the probability (or probability distribution, if applicable) of the variable represented by the node. For example, if m {\displaystyle m} parent nodes represent m {\displaystyle m} Boolean variables, then the probability function could be represented by a table of 2 m {\displaystyle 2^{m}} entries, one entry for each of the 2 m {\displaystyle 2^{m}} possible parent combinations. Similar ideas may be applied to undirected, and possibly cyclic, graphs such as Markov networks. == Example == Suppose we want to model the dependencies between three variables: the sprinkler (or more appropriately, its state - whether it is on or not), the presence or absence of rain and whether the grass is wet or not. Observe that two events can cause the grass to become wet: an active sprinkler or rain. Rain has a direct effect on the use of the sprinkler (namely that when it rains, the sprinkler usually is not active). This situation can be modeled with a Bayesian network (shown to the right). Each variable has two possible values, T (for true) and F (for false). The joint probability function is, by the chain rule of probability, Pr ( G , S , R ) = Pr ( G ∣ S , R ) Pr ( S ∣ R ) Pr ( R ) {\displaystyle \Pr(G,S,R)=\Pr(G\mid S,R)\Pr(S\mid R)\Pr(R)} where G = "Grass wet (true/false)", S = "Sprinkler turned on (true/false)", and R = "Raining (true/false)". The model can answer questions about the presence of a cause given the presence of an effect (so-called inverse probability) like "What is the probability that it is raining, given the grass is wet?" by using the conditional probability formula and summing over all nuisance variables: Pr ( R = T ∣ G = T ) = Pr ( G = T , R = T ) Pr ( G = T ) = ∑ x ∈ { T , F } Pr ( G = T , S = x , R = T ) ∑ x , y ∈ { T , F } Pr ( G = T , S = x , R = y ) {\displaystyle \Pr(R=T\mid G=T)={\frac {\Pr(G=T,R=T)}{\Pr(G=T)}}={\frac {\sum _{x\in \{T,F\}}\Pr(G=T,S=x,R=T)}{\sum _{x,y\in \{T,F\}}\Pr(G=T,S=x,R=y)}}} Using the expansion for the joint probability function Pr ( G , S , R ) {\displaystyle \Pr(G,S,R)} and the conditional probabilities from the conditional probability tables (CPTs) stated in the diagram, one can evaluate each term in the sums in the numerator and denominator. For example, Pr ( G = T , S = T , R = T ) = Pr ( G = T ∣ S = T , R = T ) Pr ( S = T ∣ R = T ) Pr ( R = T ) = 0.99 × 0.01 × 0.2 = 0.00198. {\displaystyle {\begin{aligned}\Pr(G=T,S=T,R=T)&=\Pr(G=T\mid S=T,R=T)\Pr(S=T\mid R=T)\Pr(R=T)\\&=0.99\times 0.01\times 0.2\\&=0.00198.\end{aligned}}} Then the numerical results (subscripted by the associated variable values) are Pr ( R = T ∣ G = T ) = 0.00198 T T T + 0.1584 T F T 0.00198 T T T + 0.288 T T F + 0.1584 T F T + 0.0 T F F = 891 2491 ≈ 35.77 % . {\displaystyle \Pr(R=T\mid G=T)={\frac {0.00198_{TTT}+0.1584_{TFT}}{0.00198_{TTT}+0.288_{TTF}+0.1584_{TFT}+0.0_{TFF}}}={\frac {891}{2491}}\approx 35.77\%.} To answer an interventional question, such as "What is the probability that it would rain, given that we wet the grass?" the answer is governed by the post-intervention joint distribution function Pr ( S , R ∣ do ( G = T ) ) = Pr ( S ∣ R ) Pr ( R ) {\displaystyle \Pr(S,R\mid {\text{do}}(G=T))=\Pr(S\mid R)\Pr(R)} obtained by removing the factor Pr ( G ∣ S , R ) {\displaystyle \Pr(G\mid S,R)} from the pre-intervention distribution. The do operator forces the value of G to be true. The probability of rain is unaffected by the action: Pr ( R ∣ do ( G = T ) ) = Pr ( R ) . {\displaystyle \Pr(R\mid {\text{do}}(G=T))=\Pr(R).} To predict the impact of turning the sprinkler on: Pr ( R , G ∣ do ( S = T ) ) = Pr ( R ) Pr ( G ∣ R , S = T ) {\displaystyle \Pr(R,G\mid {\text{do}}(S=T))=\Pr(R)\Pr(G\mid R,S=T)} with the term Pr ( S = T ∣ R ) {\displaystyle \Pr(S=T\mid R)} removed, showing that the action affects the grass but not the rain. These predictions may not be feasible given unobserved variables, as in most policy evaluation problems. The effect of the action do ( x ) {\displaystyle {\text{do}}(x)} can still be predicted, however, whenever the back-door criterion is satisfied. It states that, if a set Z of nodes can be observed that d-separates (or blocks) all back-door paths from X to Y then Pr ( Y , Z ∣ do ( x ) ) = Pr ( Y , Z , X = x ) Pr ( X = x ∣ Z ) . {\displaystyle \Pr(Y,Z\mid {\text{do}}(x))={\frac {\Pr(Y,Z,X=x)}{\Pr(X=x\mid Z)}}.} A back-door path is one that ends with an arrow into X. Sets that satisfy the back-door criterion are called "sufficient" or "admissible." For example, the set Z = R is admissible for predicting the effect of S = T on G, because R d-separates the (only) back-door path S ← R → G. However, if S is not observed, no other set d-separates this path and the effect of turning the sprinkler on (S = T) on the grass (G) cannot be predicted from passive observations. In that case P(G | do(S = T)) is not "identified". This reflects the fact that, lacking interventional data, the observed dependence between S and G is due to a causal connection or is spurious (apparent dependence arising from a common cause, R). (see Simpson's paradox) To determine whether a causal relation is identified from an arbitrary Bayesian network with unobserved variables, one can use the three rules of "do-calculus" and test whether all do terms can be removed from the expression of that relation, thus confirming that the desired quantity is estimable from frequency data. Using a Bayesian network can save considerable amounts of memory over exhaustive probability tables, if the dependencies in the joint distribution are sparse. For example, a naive way of storing the conditional probabilities of 10 two-valued variables as a table requires storage space for 2 10 = 1024 {\displaystyle 2^{10}=1024} values. If no variable's local distribution depends on more than three parent variables, the Bayesian network representation stores at most 10 ⋅ 2 3 = 80 {\displaystyle 10\cdot 2^{3}=80} values. One advantage of Bayesian networks is that it is intuitively easier for a human to understand (a sparse set of) direct dependencies and local distributions than complete joint distributions. == Inference and learning == Bayesian networks perform three main inference tasks: Inferring unobserved variables Parameter learning for the probability distributions of each node in the network Structure learning of the graphical network === Inferring unobserved variables === Because a Bayesian network is a complete model for its variables and their relationships, it can be used to answer probabilistic queries about them. For example, the network can be used to update knowledge of the state of a subset of variables when other variables (the evidence variables) are observed. This process of computing the posterior distribution of variables given evidence is called probabilistic inference. The posterior gives a universal sufficient statistic for detection applications, when choosing values for the variable subset that minimize some expected loss function, for instance the probability of decision error. A Bayesian network can thus be considered a mechanism for automatically applying Bayes' theorem to complex problems. The most common exact inference methods are: variable elimination, which eliminates (by integration or summation) the non-observed non-query variables one by one by distributing the sum over the prod

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  • Spatial Analysis of Principal Components

    Spatial Analysis of Principal Components

    Spatial Principal Component Analysis (sPCA) is a multivariate statistical technique that complements the traditional Principal Component Analysis (PCA) by incorporating spatial information into the analysis of genetic variation. While traditional PCA can be used to find spatial patterns, it focuses on reducing data dimensionality by identifying uncorrelated principal components that capture maximum variance, thus often lacking power to identify non-trivial spatial genetic patterns. By accounting for spatial autocorrelation, sPCA is able to uncover spatial patterns in the data and find the spatial structure of datasets where observations are either geographically or topologically linked. This statistical power improvement allows the investigation of cryptic spatial patterns of genetic variability otherwise overlooked. sPCA has been applied in various fields, including geography, ecology and genetics. == History == sPCA was introduced in 2008 by Thibaut Jombart, Sébastien Devillard, Anne-Béatrice Dufour, and D. Pontier as a spatially explicit method to investigate the spatial pattern of genetic variation among individuals or populations. In 2017, Valeria Montano and Thibaut Jombart published an alternative non-parametric test to evaluate the significance of global and local spatial genetic patterns with improved statistical power. == Details == sPCA modifies the PCA framework by integrating spatial weights, typically in the form of connectivity matrices or spatial adjacency graphs. It identifies principal components (PCs) that maximize both genentic variance and spatial autocorreation, as measured by Moran's I. These weights represent relationships between observations based on geographic distance or other spatial criteria. The method decomposes variance into two components: Global structures, correspond to positive autocorrelation, that is, reflect broad-scale spatial patterns where similar values cluster over large regions. Local structures, correspond to negative autocorrelation, that is, capture fine-scale spatial variations or localized patterns. The core of sPCA relies on the eigenanalysis of a spatially weighted covariance or correlation matrix. The spatial weight matrix can be constructed using techniques such as Delaunay triangulation, nearest-neighbor graphs, or distance-based criteria. Applications of sPCA should be used only as an explorative tool. == Applications == sPCA has been widely used in many fields, including: Ecology: To find spatial patterns in species distributions and environmental gradients. Genetics: Population structure and gene flow analysis while allowing for spatial autocorrelation considerations. Biogeography: To identify historical dispersal routes, and barriers to gene flow, providing insights into species distribution patterns and evolutionary history. == Software/Source Code == sPCA implementations are available in R in adegenet and ntbox . These tools facilitate the application of sPCA by providing functions for constructing spatial weight matrices, performing eigenanalysis, and obtaining spatial principal components in an easy-to-read form.

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  • Multiclass classification

    Multiclass classification

    In machine learning and statistical classification, multiclass classification or multinomial classification is the problem of classifying instances into one of three or more classes (classifying instances into one of two classes is called binary classification). For example, deciding on whether an image is showing a banana, peach, orange, or an apple is a multiclass classification problem, with four possible classes (banana, peach, orange, apple), while deciding on whether an image contains an apple or not is a binary classification problem (with the two possible classes being: apple, no apple). While many classification algorithms (e.g., decision trees, k-NN, neural networks and multinomial logistic regression) naturally permit the use of more than two classes, some are by nature binary algorithms (e.g., classical binary support vector machine) and require decomposition strategies such as one-vs-all, one-vs-one, or ECOC to solve multiclass problems. Multiclass classification should not be confused with multi-label classification, where multiple labels are to be predicted for each instance (e.g., predicting that an image contains both an apple and an orange, in the previous example). == Better-than-random multiclass models == From the confusion matrix of a multiclass model, we can determine whether a model does better than chance. Let K ≥ 3 {\displaystyle K\geq 3} be the number of classes, O {\displaystyle {\mathcal {O}}} a set of observations, y ^ : O → { 1 , . . . , K } {\displaystyle {\hat {y}}:{\mathcal {O}}\to \{1,...,K\}} a model of the target variable y : O → { 1 , . . . , K } {\displaystyle y:{\mathcal {O}}\to \{1,...,K\}} and n i , j {\displaystyle n_{i,j}} be the number of observations in the set { y = i } ∩ { y ^ = j } {\displaystyle \{y=i\}\cap \{{\hat {y}}=j\}} . We note n i . = ∑ j n i , j {\displaystyle n_{i.}=\sum _{j}n_{i,j}} , n . j = ∑ i n i , j {\displaystyle n_{.j}=\sum _{i}n_{i,j}} , n = ∑ j n . j = ∑ i n i . {\displaystyle n=\sum _{j}n_{.j}=\sum _{i}n_{i.}} , λ i = n i . n {\displaystyle \lambda _{i}={\frac {n_{i.}}{n}}} and μ j = n . j n {\displaystyle \mu _{j}={\frac {n_{.j}}{n}}} . It is assumed that the confusion matrix ( n i , j ) i , j {\displaystyle (n_{i,j})_{i,j}} contains at least one non-zero entry in each row, that is λ i > 0 {\displaystyle \lambda _{i}>0} for any i {\displaystyle i} . Finally we call "normalized confusion matrix" the matrix of conditional probabilities ( P ( y ^ = j ∣ y = i ) ) i , j = ( n i , j n i . ) i , j {\displaystyle (\mathbb {P} ({\hat {y}}=j\mid y=i))_{i,j}=\left({\frac {n_{i,j}}{n_{i.}}}\right)_{i,j}} . === Intuitive explanation === The lift is a way of measuring the deviation from independence of two events A {\displaystyle A} and B {\displaystyle B} : L i f t ( A , B ) = P ( A ∩ B ) P ( A ) P ( B ) = P ( A ∣ B ) P ( A ) = P ( B ∣ A ) P ( B ) {\displaystyle \mathrm {Lift} (A,B)={\frac {\mathbb {P} (A\cap B)}{\mathbb {P} (A)\mathbb {P} (B)}}={\frac {\mathbb {P} (A\mid B)}{\mathbb {P} (A)}}={\frac {\mathbb {P} (B\mid A)}{\mathbb {P} (B)}}} We have L i f t ( A , B ) > 1 {\displaystyle \mathrm {Lift} (A,B)>1} if and only if events A {\displaystyle A} and B {\displaystyle B} occur simultaneously with a greater probability than if they were independent. In other words, if one of the two events occurs, the probability of observing the other event increases. A first condition to satisfy is to have L i f t ( y = i , y ^ = i ) ≥ 1 {\displaystyle \mathrm {Lift} (y=i,{\hat {y}}=i)\geq 1} for any i {\displaystyle i} . And the quality of a model (better or worse than chance) does not change if we over- or undersample the dataset, that is if we multiply each row R i {\displaystyle R_{i}} of the confusion matrix by a constant c i {\displaystyle c_{i}} . Thus the second condition is that the necessary and sufficient conditions for doing better than chance need only depend on the normalized confusion matrix. The condition on lifts can be reformulated with One versus Rest binary models : for any i {\displaystyle i} , we define the binary target variable y i {\displaystyle y_{i}} which is the indicator of event { y = i } {\displaystyle \{y=i\}} , and the binary model y ^ i {\displaystyle {\hat {y}}_{i}} of y i {\displaystyle y_{i}} which is the indicator of event { y ^ = i } {\displaystyle \{{\hat {y}}=i\}} . Each of the y ^ i {\displaystyle {\hat {y}}_{i}} models is a "One versus Rest" model. L i f t ( y = i , y ^ = i ) {\displaystyle \mathrm {Lift} (y=i,{\hat {y}}=i)} only depends on the events { y = i } {\displaystyle \{y=i\}} and { y ^ = i } {\displaystyle \{{\hat {y}}=i\}} , so merging or not merging the other classes doesn't change its value. We therefore have L i f t ( y = i , y ^ = i ) = L i f t ( y i = 1 , y ^ i = 1 ) {\displaystyle \mathrm {Lift} (y=i,{\hat {y}}=i)=\mathrm {Lift} (y_{i}=1,{\hat {y}}_{i}=1)} and the first condition is that all binary One versus Rest models are better than chance. ==== Example ==== If K = 2 {\displaystyle K=2} and 2 is the class of interest , the normalized confusion matrix is ( s p e c i f i c i t y 1 − s p e c i f i c i t y 1 − s e n s i t i v i t y s e n s i t i v i t y ) {\displaystyle {\begin{pmatrix}\mathrm {specificity} &1-\mathrm {specificity} \\1-\mathrm {sensitivity} &\mathrm {sensitivity} \end{pmatrix}}} and we have L i f t ( y = 1 , y ^ = 1 ) − 1 = P ( y = y ^ = 1 ) λ 1 μ 1 − 1 = n 1 , 1 n n 1. n .1 − 1 {\displaystyle \mathrm {Lift} (y=1,{\hat {y}}=1)-1={\frac {\mathbb {P} (y={\hat {y}}=1)}{\lambda _{1}\mu _{1}}}-1={\frac {n_{1,1}n}{n_{1.}n_{.1}}}-1} = n 1 , 1 ( n 1 , 1 + n 1 , 2 + n 2 , 1 + n 2 , 2 ) − ( n 1 , 1 + n 1 , 2 ) ( n 1 , 1 + n 2 , 1 ) n 1. n .1 = n 1 , 1 n 2 , 2 − n 1 , 2 n 2 , 1 n 1. n .1 {\displaystyle ={\frac {n_{1,1}(n_{1,1}+n_{1,2}+n_{2,1}+n_{2,2})-(n_{1,1}+n_{1,2})(n_{1,1}+n_{2,1})}{n_{1.}n_{.1}}}={\frac {n_{1,1}n_{2,2}-n_{1,2}n_{2,1}}{n_{1.}n_{.1}}}} . Thus L i f t ( y = 1 , y ^ = 1 ) ≥ 1 ⟺ n 1 , 1 n 2 , 2 − n 1 , 2 n 2 , 1 ≥ 0 {\displaystyle \mathrm {Lift} (y=1,{\hat {y}}=1)\geq 1\iff n_{1,1}n_{2,2}-n_{1,2}n_{2,1}\geq 0} . Similarly, by swapping the roles of 1 and 2, we find that L i f t ( y = 2 , y ^ = 2 ) ≥ 1 ⟺ n 1 , 1 n 2 , 2 − n 1 , 2 n 2 , 1 ≥ 0 {\displaystyle \mathrm {Lift} (y=2,{\hat {y}}=2)\geq 1\iff n_{1,1}n_{2,2}-n_{1,2}n_{2,1}\geq 0} . Dividing by n 1. n 2. {\displaystyle n_{1.}n_{2.}} we find that the necessary and sufficient condition on the normalized confusion matrix is s e n s i t i v i t y s p e c i f i c i t y − ( 1 − s e n s i t i v i t y ) ( 1 − s p e c i f i c i t y ) ≥ 0 ⟺ s e n s i t i v i t y + s p e c i f i c i t y − 1 ≥ 0 ⟺ J ≥ 0 {\displaystyle \mathrm {sensitivity} \ \mathrm {specificity} -(1-\mathrm {sensitivity} )(1-\mathrm {specificity} )\geq 0\iff \mathrm {sensitivity} +\mathrm {specificity} -1\geq 0\iff J\geq 0} . This brings us back to the classical binary condition: Youden's J must be positive (or zero for random models). === Random models === A random model is a model that is independent of the target variable. This property is easily reformulated with the confusion matrix. This proposition shows that the model y ^ {\displaystyle {\hat {y}}} of y {\displaystyle y} is uninformative if and only if there are two families of numbers ( α i ) i {\displaystyle (\alpha _{i})_{i}} and ( β j ) j {\displaystyle (\beta _{j})_{j}} such that P ( { y = i } ∩ { y ^ = j } ) = α i β j {\displaystyle \mathbb {P} (\{y=i\}\cap \{{\hat {y}}=j\})=\alpha _{i}\beta _{j}} for any i {\displaystyle i} and j {\displaystyle j} . === Multiclass likelihood ratios and diagnostic odds ratios === We define generalized likelihood ratios calculated from the normalized confusion matrix: for any i {\displaystyle i} and j ≠ i {\displaystyle j\not =i} , let L R i , j = P ( y ^ = j ∣ y = j ) P ( y ^ = j ∣ y = i ) {\displaystyle \mathrm {LR} _{i,j}={\frac {\mathbb {P} ({\hat {y}}=j\mid y=j)}{\mathbb {P} ({\hat {y}}=j\mid y=i)}}} . When K = 2 {\displaystyle K=2} , if 2 is the class of interest,, we find the classical likelihood ratios L R 1 , 2 = L R + {\displaystyle \mathrm {LR} _{1,2}=\mathrm {LR} _{+}} and L R 2 , 1 = 1 L R − {\displaystyle \mathrm {LR} _{2,1}={\frac {1}{\mathrm {LR} _{-}}}} . Multiclass diagnostic odds ratios can also be defined using the formula D O R i , j = D O R j , i = L R i , j L R j , i = n i , i n j , j n i , j n j , i = P ( y ^ = j ∣ y = j ) / P ( y ^ = i ∣ y = j ) P ( y ^ = j ∣ y = i ) / P ( y ^ = i ∣ y = i ) {\displaystyle \mathrm {DOR} _{i,j}=\mathrm {DOR} _{j,i}=\mathrm {LR} _{i,j}\mathrm {LR} _{j,i}={\frac {n_{i,i}n_{j,j}}{n_{i,j}n_{j,i}}}={\frac {\mathbb {P} ({\hat {y}}=j\mid y=j)/\mathbb {P} ({\hat {y}}=i\mid y=j)}{\mathbb {P} ({\hat {y}}=j\mid y=i)/\mathbb {P} ({\hat {y}}=i\mid y=i)}}} We saw above that a better-than-chance model (or a random model) must verify L i f t ( y = i , y ^ = i ) ≥ 1 {\displaystyle \mathrm {Lift} (y=i,{\hat {y}}=i)\geq 1} for any i {\displaystyle i} and λ i {\displaystyle \lambda _{i}} . According to the previous corollary, likelihood ratios are thus greater

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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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  • Q-learning

    Q-learning

    Q-learning is a reinforcement learning algorithm that trains an agent to assign values to its possible actions based on its current state, without requiring a model of the environment (model-free). It can handle problems with stochastic transitions and rewards without requiring adaptations. For example, in a grid maze, an agent learns to reach an exit worth 10 points. At a junction, Q-learning might assign a higher value to moving right than left if right gets to the exit faster, improving this choice by trying both directions over time. For any finite Markov decision process, Q-learning finds an optimal policy in the sense of maximizing the expected value of the total reward over any and all successive steps, starting from the current state. Q-learning can identify an optimal action-selection policy for any given finite Markov decision process, given infinite exploration time and a partly random policy. "Q" refers to the function that the algorithm computes: the expected reward—that is, the quality—of an action taken in a given state. == Reinforcement learning == Reinforcement learning involves an agent, a set of states S {\displaystyle {\mathcal {S}}} , and a set A {\displaystyle {\mathcal {A}}} of actions per state. By performing an action a ∈ A {\displaystyle a\in {\mathcal {A}}} , the agent transitions from state to state. Executing an action in a specific state provides the agent with a reward (a numerical score). The goal of the agent is to maximize its total reward. It does this by adding the maximum reward attainable from future states to the reward for achieving its current state, effectively influencing the current action by the potential future reward. This potential reward is a weighted sum of expected values of the rewards of all future steps starting from the current state. As an example, consider the process of boarding a train, in which the reward is measured by the negative of the total time spent boarding (alternatively, the cost of boarding the train is equal to the boarding time). One strategy is to enter the train door as soon as they open, minimizing the initial wait time for yourself. If the train is crowded, however, then you will have a slow entry after the initial action of entering the door as people are fighting you to depart the train as you attempt to board. The total boarding time, or cost, is then: 0 seconds wait time + 15 seconds fight time On the next day, by random chance (exploration), you decide to wait and let other people depart first. This initially results in a longer wait time. However, less time is spent fighting the departing passengers. Overall, this path has a higher reward than that of the previous day, since the total boarding time is now: 5 second wait time + 0 second fight time Through exploration, despite the initial (patient) action resulting in a larger cost (or negative reward) than in the forceful strategy, the overall cost is lower, thus revealing a more rewarding strategy. == Algorithm == After Δ t {\displaystyle \Delta t} steps into the future the agent will decide some next step. The weight for this step is calculated as γ Δ t {\displaystyle \gamma ^{\Delta t}} , where γ {\displaystyle \gamma } (the discount factor) is a number between 0 and 1 ( 0 ≤ γ ≤ 1 {\displaystyle 0\leq \gamma \leq 1} ). Assuming γ < 1 {\displaystyle \gamma <1} , it has the effect of valuing rewards received earlier higher than those received later (reflecting the value of a "good start"). γ {\displaystyle \gamma } may also be interpreted as the probability to succeed (or survive) at every step Δ t {\displaystyle \Delta t} . The algorithm, therefore, has a function that calculates the quality of a state–action combination: Q : S × A → R {\displaystyle Q:{\mathcal {S}}\times {\mathcal {A}}\to \mathbb {R} } . Before learning begins, ⁠ Q {\displaystyle Q} ⁠ is initialized to a possibly arbitrary fixed value (chosen by the programmer). Then, at each time t {\displaystyle t} the agent selects an action A t {\displaystyle A_{t}} , observes a reward R t + 1 {\displaystyle R_{t+1}} , enters a new state S t + 1 {\displaystyle S_{t+1}} (that may depend on both the previous state S t {\displaystyle S_{t}} and the selected action), and Q {\displaystyle Q} is updated. The core of the algorithm is a Bellman equation as a simple value iteration update, using the weighted average of the current value and the new information: Q n e w ( S t , A t ) ← ( 1 − α ⏟ learning rate ) ⋅ Q ( S t , A t ) ⏟ current value + α ⏟ learning rate ⋅ ( R t + 1 ⏟ reward + γ ⏟ discount factor ⋅ max a Q ( S t + 1 , a ) ⏟ estimate of optimal future value ⏟ new value (temporal difference target) ) {\displaystyle Q^{new}(S_{t},A_{t})\leftarrow (1-\underbrace {\alpha } _{\text{learning rate}})\cdot \underbrace {Q(S_{t},A_{t})} _{\text{current value}}+\underbrace {\alpha } _{\text{learning rate}}\cdot {\bigg (}\underbrace {\underbrace {R_{t+1}} _{\text{reward}}+\underbrace {\gamma } _{\text{discount factor}}\cdot \underbrace {\max _{a}Q(S_{t+1},a)} _{\text{estimate of optimal future value}}} _{\text{new value (temporal difference target)}}{\bigg )}} where R t + 1 {\displaystyle R_{t+1}} is the reward received when moving from the state S t {\displaystyle S_{t}} to the state S t + 1 {\displaystyle S_{t+1}} , and α {\displaystyle \alpha } is the learning rate ( 0 < α ≤ 1 ) {\displaystyle (0<\alpha \leq 1)} . Note that Q n e w ( S t , A t ) {\displaystyle Q^{new}(S_{t},A_{t})} is the sum of three terms: ( 1 − α ) Q ( S t , A t ) {\displaystyle (1-\alpha )Q(S_{t},A_{t})} : the current value (weighted by one minus the learning rate) α R t + 1 {\displaystyle \alpha \,R_{t+1}} : the reward R t + 1 {\displaystyle R_{t+1}} to obtain if action A t {\displaystyle A_{t}} is taken when in state S t {\displaystyle S_{t}} (weighted by learning rate) α γ max a Q ( S t + 1 , a ) {\displaystyle \alpha \gamma \max _{a}Q(S_{t+1},a)} : the maximum reward that can be obtained from state S t + 1 {\displaystyle S_{t+1}} (weighted by learning rate and discount factor) An episode of the algorithm ends when state S t + 1 {\displaystyle S_{t+1}} is a final or terminal state. However, Q-learning can also learn in non-episodic tasks (as a result of the property of convergent infinite series). If the discount factor is lower than 1, the action values are finite even if the problem can contain infinite loops or paths. For all final states s f {\displaystyle s_{f}} , Q ( s f , a ) {\displaystyle Q(s_{f},a)} is never updated, but is set to the reward value r {\displaystyle r} observed for state s f {\displaystyle s_{f}} . In most cases, Q ( s f , a ) {\displaystyle Q(s_{f},a)} can be taken to equal zero. == Influence of variables == === Learning rate === The learning rate or step size determines to what extent newly acquired information overrides old information. A factor of 0 makes the agent learn nothing (exclusively exploiting prior knowledge), while a factor of 1 makes the agent consider only the most recent information (ignoring prior knowledge to explore possibilities). In fully deterministic environments, a learning rate of α t = 1 {\displaystyle \alpha _{t}=1} is optimal. When the problem is stochastic, the algorithm converges under some technical conditions on the learning rate that require it to decrease to zero. In practice, often a constant learning rate is used, such as α t = 0.1 {\displaystyle \alpha _{t}=0.1} for all t {\displaystyle t} . === Discount factor === The discount factor ⁠ γ {\displaystyle \gamma } ⁠ determines the importance of future rewards. A factor of 0 will make the agent "myopic" (or short-sighted) by only considering current rewards, i.e. r t {\displaystyle r_{t}} (in the update rule above), while a factor approaching 1 will make it strive for a long-term high reward. If the discount factor meets or exceeds 1, the action values may diverge. For ⁠ γ = 1 {\displaystyle \gamma =1} ⁠, without a terminal state, or if the agent never reaches one, all environment histories become infinitely long, and utilities with additive, undiscounted rewards generally become infinite. Even with a discount factor only slightly lower than 1, Q-function learning leads to propagation of errors and instabilities when the value function is approximated with an artificial neural network. In that case, starting with a lower discount factor and increasing it towards its final value accelerates learning. === Initial conditions (Q0) === Since Q-learning is an iterative algorithm, it implicitly assumes an initial condition before the first update occurs. High initial values, also known as "optimistic initial conditions", can encourage exploration: no matter what action is selected, the update rule will cause it to have lower values than the other alternative, thus increasing their choice probability. The first reward r {\displaystyle r} can be used to reset the initial conditions. According to this idea, the first time an action is taken the reward is used to set the value

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  • Log-linear model

    Log-linear model

    A log-linear model is a mathematical model that takes the form of a function whose logarithm equals a linear combination of the parameters of the model, which makes it possible to apply (possibly multivariate) linear regression. That is, it has the general form exp ⁡ ( c + ∑ i w i f i ( X ) ) {\displaystyle \exp \left(c+\sum _{i}w_{i}f_{i}(X)\right)} , in which the fi(X) are quantities that are functions of the variable X, in general a vector of values, while c and the wi stand for the model parameters. The term may specifically be used for: A log-linear plot or graph, which is a type of semi-log plot. Poisson regression for contingency tables, a type of generalized linear model. The specific applications of log-linear models are where the output quantity lies in the range 0 to ∞, for values of the independent variables X, or more immediately, the transformed quantities fi(X) in the range −∞ to +∞. This may be contrasted to logistic models, similar to the logistic function, for which the output quantity lies in the range 0 to 1. Thus the contexts where these models are useful or realistic often depends on the range of the values being modelled.

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  • Hinge loss

    Hinge loss

    In machine learning, the hinge loss is a loss function used for training classifiers. The hinge loss is used for "maximum-margin" classification, most notably for support vector machines (SVMs). For an intended output t = ±1 and a classifier score y, the hinge loss of the prediction y is defined as ℓ ( y ) = max ( 0 , 1 − t ⋅ y ) {\displaystyle \ell (y)=\max(0,1-t\cdot y)} Note that y {\displaystyle y} should be the "raw" output of the classifier's decision function, not the predicted class label. For instance, in linear SVMs, y = w ⋅ x + b {\displaystyle y=\mathbf {w} \cdot \mathbf {x} +b} , where ( w , b ) {\displaystyle (\mathbf {w} ,b)} are the parameters of the hyperplane and x {\displaystyle \mathbf {x} } is the input variable(s). When t and y have the same sign (meaning y predicts the right class) and | y | ≥ 1 {\displaystyle |y|\geq 1} , the hinge loss ℓ ( y ) = 0 {\displaystyle \ell (y)=0} . When they have opposite signs, ℓ ( y ) {\displaystyle \ell (y)} increases linearly with y, and similarly if | y | < 1 {\displaystyle |y|<1} , even if it has the same sign (correct prediction, but not by enough margin). The Hinge loss is not a proper scoring rule. == Extensions == While binary SVMs are commonly extended to multiclass classification in a one-vs.-all or one-vs.-one fashion, it is also possible to extend the hinge loss itself for such an end. Several different variations of multiclass hinge loss have been proposed. For example, Crammer and Singer defined it for a linear classifier as ℓ ( y ) = max ( 0 , 1 + max y ≠ t w y x − w t x ) {\displaystyle \ell (y)=\max(0,1+\max _{y\neq t}\mathbf {w} _{y}\mathbf {x} -\mathbf {w} _{t}\mathbf {x} )} , where t {\displaystyle t} is the target label, w t {\displaystyle \mathbf {w} _{t}} and w y {\displaystyle \mathbf {w} _{y}} are the model parameters. Weston and Watkins provided a similar definition, but with a sum rather than a max: ℓ ( y ) = ∑ y ≠ t max ( 0 , 1 + w y x − w t x ) {\displaystyle \ell (y)=\sum _{y\neq t}\max(0,1+\mathbf {w} _{y}\mathbf {x} -\mathbf {w} _{t}\mathbf {x} )} . In structured prediction, the hinge loss can be further extended to structured output spaces. Structured SVMs with margin rescaling use the following variant, where w denotes the SVM's parameters, y the SVM's predictions, φ the joint feature function, and Δ the Hamming loss: ℓ ( y ) = max ( 0 , Δ ( y , t ) + ⟨ w , ϕ ( x , y ) ⟩ − ⟨ w , ϕ ( x , t ) ⟩ ) = max ( 0 , max y ∈ Y ( Δ ( y , t ) + ⟨ w , ϕ ( x , y ) ⟩ ) − ⟨ w , ϕ ( x , t ) ⟩ ) {\displaystyle {\begin{aligned}\ell (\mathbf {y} )&=\max(0,\Delta (\mathbf {y} ,\mathbf {t} )+\langle \mathbf {w} ,\phi (\mathbf {x} ,\mathbf {y} )\rangle -\langle \mathbf {w} ,\phi (\mathbf {x} ,\mathbf {t} )\rangle )\\&=\max(0,\max _{y\in {\mathcal {Y}}}\left(\Delta (\mathbf {y} ,\mathbf {t} )+\langle \mathbf {w} ,\phi (\mathbf {x} ,\mathbf {y} )\rangle \right)-\langle \mathbf {w} ,\phi (\mathbf {x} ,\mathbf {t} )\rangle )\end{aligned}}} . == Optimization == The hinge loss is a convex function, so many of the usual convex optimizers used in machine learning can work with it. It is not differentiable, but has a subgradient with respect to model parameters w of a linear SVM with score function y = w ⋅ x {\displaystyle y=\mathbf {w} \cdot \mathbf {x} } that is given by ∂ ℓ ∂ w i = { − t ⋅ x i if t ⋅ y < 1 , 0 otherwise . {\displaystyle {\frac {\partial \ell }{\partial w_{i}}}={\begin{cases}-t\cdot x_{i}&{\text{if }}t\cdot y<1,\\0&{\text{otherwise}}.\end{cases}}} However, since the derivative of the hinge loss at t y = 1 {\displaystyle ty=1} is undefined, smoothed versions may be preferred for optimization, such as Rennie and Srebro's ℓ ( y ) = { 1 2 − t y if t y ≤ 0 , 1 2 ( 1 − t y ) 2 if 0 < t y < 1 , 0 if 1 ≤ t y {\displaystyle \ell (y)={\begin{cases}{\frac {1}{2}}-ty&{\text{if}}~~ty\leq 0,\\{\frac {1}{2}}(1-ty)^{2}&{\text{if}}~~0 Read more →

  • Naked Objects for .NET

    Naked Objects for .NET

    Naked Objects for .NET or Naked Objects MVC is a software framework that builds upon the ASP.NET MVC framework. As the name suggests, the framework synthesizes two architectural patterns: naked objects and model–view–controller (MVC). These two patterns have been considered as antithetical. However, Trygve Reenskaug (the inventor of the MVC pattern) has made it clear that he does not see it that way, in his foreword to Richard Pawson's PhD thesis on the Naked Objects pattern. The Naked Objects MVC framework will take a domain model (written as Plain Old CLR Objects) and render it as a complete HTML application without the need for writing any user interface code - by means of a small set of generic View and Controller classes. The framework uses reflection rather than code generation. The developer may then choose to create customised Views and/or Controllers, using standard ASP.NET MVC patterns, for use where the generic user interface is not suitable.

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  • Sparse PCA

    Sparse PCA

    Sparse principal component analysis (SPCA or sparse PCA) is a technique used in statistical analysis and, in particular, in the analysis of multivariate data sets. It extends the classic method of principal component analysis (PCA) for the reduction of dimensionality of data by introducing sparsity structures to the input variables. A particular disadvantage of ordinary PCA is that the principal components are usually linear combinations of all input variables. SPCA overcomes this disadvantage by finding components that are linear combinations of just a few input variables (SPCs). This means that some of the coefficients of the linear combinations defining the SPCs, called loadings, are equal to zero. The number of nonzero loadings is called the cardinality of the SPC. == Mathematical formulation == Consider a data matrix, X {\displaystyle X} , where each of the p {\displaystyle p} columns represent an input variable, and each of the n {\displaystyle n} rows represents an independent sample from data population. One assumes each column of X {\displaystyle X} has mean zero, otherwise one can subtract column-wise mean from each element of X {\displaystyle X} . Let Σ = 1 n − 1 X ⊤ X {\displaystyle \Sigma ={\frac {1}{n-1}}X^{\top }X} be the empirical covariance matrix of X {\displaystyle X} , which has dimension p × p {\displaystyle p\times p} . Given an integer k {\displaystyle k} with 1 ≤ k ≤ p {\displaystyle 1\leq k\leq p} , the sparse PCA problem can be formulated as maximizing the variance along a direction represented by vector v ∈ R p {\displaystyle v\in \mathbb {R} ^{p}} while constraining its cardinality: max v T Σ v subject to ‖ v ‖ 2 = 1 ‖ v ‖ 0 ≤ k . {\displaystyle {\begin{aligned}\max \quad &v^{T}\Sigma v\\{\text{subject to}}\quad &\left\Vert v\right\Vert _{2}=1\\&\left\Vert v\right\Vert _{0}\leq k.\end{aligned}}} Eq. 1 The first constraint specifies that v is a unit vector. In the second constraint, ‖ v ‖ 0 {\displaystyle \left\Vert v\right\Vert _{0}} represents the ℓ 0 {\displaystyle \ell _{0}} pseudo-norm of v, which is defined as the number of its non-zero components. So the second constraint specifies that the number of non-zero components in v is less than or equal to k, which is typically an integer that is much smaller than dimension p. The optimal value of Eq. 1 is known as the k-sparse largest eigenvalue. If one takes k=p, the problem reduces to the ordinary PCA, and the optimal value becomes the largest eigenvalue of covariance matrix Σ. After finding the optimal solution v, one deflates Σ to obtain a new matrix Σ 1 = Σ − ( v T Σ v ) v v T , {\displaystyle \Sigma _{1}=\Sigma -(v^{T}\Sigma v)vv^{T},} and iterate this process to obtain further principal components. However, unlike PCA, sparse PCA cannot guarantee that different principal components are orthogonal. In order to achieve orthogonality, additional constraints must be enforced. The following equivalent definition is in matrix form. Let V {\displaystyle V} be a p×p symmetric matrix, one can rewrite the sparse PCA problem as max T r ( Σ V ) subject to T r ( V ) = 1 ‖ V ‖ 0 ≤ k 2 R a n k ( V ) = 1 , V ⪰ 0. {\displaystyle {\begin{aligned}\max \quad &Tr(\Sigma V)\\{\text{subject to}}\quad &Tr(V)=1\\&\Vert V\Vert _{0}\leq k^{2}\\&Rank(V)=1,V\succeq 0.\end{aligned}}} Eq. 2 Tr is the matrix trace, and ‖ V ‖ 0 {\displaystyle \Vert V\Vert _{0}} represents the non-zero elements in matrix V. The last line specifies that V has matrix rank one and is positive semidefinite. The last line means that one has V = v v T {\displaystyle V=vv^{T}} , so Eq. 2 is equivalent to Eq. 1. Moreover, the rank constraint in this formulation is actually redundant, and therefore sparse PCA can be cast as the following mixed-integer semidefinite program max T r ( Σ V ) subject to T r ( V ) = 1 | V i , i | ≤ z i , ∀ i ∈ { 1 , . . . , p } , | V i , j | ≤ 1 2 z i , ∀ i , j ∈ { 1 , . . . , p } : i ≠ j , V ⪰ 0 , z ∈ { 0 , 1 } p , ∑ i z i ≤ k {\displaystyle {\begin{aligned}\max \quad &Tr(\Sigma V)\\{\text{subject to}}\quad &Tr(V)=1\\&\vert V_{i,i}\vert \leq z_{i},\forall i\in \{1,...,p\},\vert V_{i,j}\vert \leq {\frac {1}{2}}z_{i},\forall i,j\in \{1,...,p\}:i\neq j,\\&V\succeq 0,z\in \{0,1\}^{p},\sum _{i}z_{i}\leq k\end{aligned}}} Eq. 3 Because of the cardinality constraint, the maximization problem is hard to solve exactly, especially when dimension p is high. In fact, the sparse PCA problem in Eq. 1 is NP-hard in the strong sense. == Computational considerations == As most sparse problems, variable selection in SPCA is a computationally intractable non-convex NP-hard problem, therefore greedy sub-optimal algorithms are often employed to find solutions. Note also that SPCA introduces hyperparameters quantifying in what capacity large parameter values are penalized. These might need tuning to achieve satisfactory performance, thereby adding to the total computational cost. == Algorithms for SPCA == Several alternative approaches (of Eq. 1) have been proposed, including a regression framework, a penalized matrix decomposition framework, a convex relaxation/semidefinite programming framework, a generalized power method framework an alternating maximization framework forward-backward greedy search and exact methods using branch-and-bound techniques, a certifiably optimal branch-and-bound approach Bayesian formulation framework. A certifiably optimal mixed-integer semidefinite branch-and-cut approach The methodological and theoretical developments of Sparse PCA as well as its applications in scientific studies are recently reviewed in a survey paper. === Notes on Semidefinite Programming Relaxation === It has been proposed that sparse PCA can be approximated by semidefinite programming (SDP). If one drops the rank constraint and relaxes the cardinality constraint by a 1-norm convex constraint, one gets a semidefinite programming relaxation, which can be solved efficiently in polynomial time: max T r ( Σ V ) subject to T r ( V ) = 1 1 T | V | 1 ≤ k V ⪰ 0. {\displaystyle {\begin{aligned}\max \quad &Tr(\Sigma V)\\{\text{subject to}}\quad &Tr(V)=1\\&\mathbf {1} ^{T}|V|\mathbf {1} \leq k\\&V\succeq 0.\end{aligned}}} Eq. 3 In the second constraint, 1 {\displaystyle \mathbf {1} } is a p×1 vector of ones, and |V| is the matrix whose elements are the absolute values of the elements of V. The optimal solution V {\displaystyle V} to the relaxed problem Eq. 3 is not guaranteed to have rank one. In that case, V {\displaystyle V} can be truncated to retain only the dominant eigenvector. While the semidefinite program does not scale beyond n=300 covariates, it has been shown that a second-order cone relaxation of the semidefinite relaxation is almost as tight and successfully solves problems with n=1000s of covariates == Applications == === Financial Data Analysis === Suppose ordinary PCA is applied to a dataset where each input variable represents a different asset, it may generate principal components that are weighted combination of all the assets. In contrast, sparse PCA would produce principal components that are weighted combination of only a few input assets, so one can easily interpret its meaning. Furthermore, if one uses a trading strategy based on these principal components, fewer assets imply less transaction costs. === Biology === Consider a dataset where each input variable corresponds to a specific gene. Sparse PCA can produce a principal component that involves only a few genes, so researchers can focus on these specific genes for further analysis. === High-dimensional Hypothesis Testing === Contemporary datasets often have the number of input variables ( p {\displaystyle p} ) comparable with or even much larger than the number of samples ( n {\displaystyle n} ). It has been shown that if p / n {\displaystyle p/n} does not converge to zero, the classical PCA is not consistent. In other words, if we let k = p {\displaystyle k=p} in Eq. 1, then the optimal value does not converge to the largest eigenvalue of data population when the sample size n → ∞ {\displaystyle n\rightarrow \infty } , and the optimal solution does not converge to the direction of maximum variance. But sparse PCA can retain consistency even if p ≫ n . {\displaystyle p\gg n.} The k-sparse largest eigenvalue (the optimal value of Eq. 1) can be used to discriminate an isometric model, where every direction has the same variance, from a spiked covariance model in high-dimensional setting. Consider a hypothesis test where the null hypothesis specifies that data X {\displaystyle X} are generated from a multivariate normal distribution with mean 0 and covariance equal to an identity matrix, and the alternative hypothesis specifies that data X {\displaystyle X} is generated from a spiked model with signal strength θ {\displaystyle \theta } : H 0 : X ∼ N ( 0 , I p ) , H 1 : X ∼ N ( 0 , I p + θ v v T ) , {\displaystyle H_{0}:X\sim N(0,I_{p}),\quad H_{1}:X\sim N(0,I_{p}+\theta vv^{T}),} where v ∈ R p {\displaystyle v\in \mathbb {R} ^{p}

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  • Polynomial kernel

    Polynomial kernel

    In machine learning, the polynomial kernel is a kernel function commonly used with support vector machines (SVMs) and other kernelized models, that represents the similarity of vectors (training samples) in a feature space over polynomials of the original variables, allowing learning of non-linear models. Intuitively, the polynomial kernel looks not only at the given features of input samples to determine their similarity, but also combinations of these. In the context of regression analysis, such combinations are known as interaction features. The (implicit) feature space of a polynomial kernel is equivalent to that of polynomial regression, but without the combinatorial blowup in the number of parameters to be learned. When the input features are binary-valued (booleans), then the features correspond to logical conjunctions of input features. == Definition == For degree-d polynomials, the polynomial kernel is defined as K ( x , y ) = ( x T y + c ) d {\displaystyle K(\mathbf {x} ,\mathbf {y} )=(\mathbf {x} ^{\mathsf {T}}\mathbf {y} +c)^{d}} where x and y are vectors of size n in the input space, i.e. vectors of features computed from training or test samples and c ≥ 0 is a free parameter trading off the influence of higher-order versus lower-order terms in the polynomial. When c = 0, the kernel is called homogeneous. (A further generalized polykernel divides xTy by a user-specified scalar parameter a.) As a kernel, K corresponds to an inner product in a feature space based on some mapping φ: K ( x , y ) = ⟨ φ ( x ) , φ ( y ) ⟩ {\displaystyle K(\mathbf {x} ,\mathbf {y} )=\langle \varphi (\mathbf {x} ),\varphi (\mathbf {y} )\rangle } The nature of φ can be seen from an example. Let d = 2, so we get the special case of the quadratic kernel. After using the multinomial theorem (twice—the outermost application is the binomial theorem) and regrouping, K ( x , y ) = ( ∑ i = 1 n x i y i + c ) 2 = ∑ i = 1 n ( x i 2 ) ( y i 2 ) + ∑ i = 2 n ∑ j = 1 i − 1 ( 2 x i x j ) ( 2 y i y j ) + ∑ i = 1 n ( 2 c x i ) ( 2 c y i ) + c 2 {\displaystyle K(\mathbf {x} ,\mathbf {y} )=\left(\sum _{i=1}^{n}x_{i}y_{i}+c\right)^{2}=\sum _{i=1}^{n}\left(x_{i}^{2}\right)\left(y_{i}^{2}\right)+\sum _{i=2}^{n}\sum _{j=1}^{i-1}\left({\sqrt {2}}x_{i}x_{j}\right)\left({\sqrt {2}}y_{i}y_{j}\right)+\sum _{i=1}^{n}\left({\sqrt {2c}}x_{i}\right)\left({\sqrt {2c}}y_{i}\right)+c^{2}} From this it follows that the feature map is given by: φ ( x ) = ( x n 2 , … , x 1 2 , 2 x n x n − 1 , … , 2 x n x 1 , 2 x n − 1 x n − 2 , … , 2 x n − 1 x 1 , … , 2 x 2 x 1 , 2 c x n , … , 2 c x 1 , c ) {\displaystyle \varphi (x)=\left(x_{n}^{2},\ldots ,x_{1}^{2},{\sqrt {2}}x_{n}x_{n-1},\ldots ,{\sqrt {2}}x_{n}x_{1},{\sqrt {2}}x_{n-1}x_{n-2},\ldots ,{\sqrt {2}}x_{n-1}x_{1},\ldots ,{\sqrt {2}}x_{2}x_{1},{\sqrt {2c}}x_{n},\ldots ,{\sqrt {2c}}x_{1},c\right)} generalizing for ( x T y + c ) d {\displaystyle \left(\mathbf {x} ^{T}\mathbf {y} +c\right)^{d}} , where x ∈ R n {\displaystyle \mathbf {x} \in \mathbb {R} ^{n}} , y ∈ R n {\displaystyle \mathbf {y} \in \mathbb {R} ^{n}} and applying the multinomial theorem: ( x T y + c ) d = ∑ j 1 + j 2 + ⋯ + j n + 1 = d d ! j 1 ! ⋯ j n ! j n + 1 ! x 1 j 1 ⋯ x n j n c j n + 1 d ! j 1 ! ⋯ j n ! j n + 1 ! y 1 j 1 ⋯ y n j n c j n + 1 = φ ( x ) T φ ( y ) {\displaystyle {\begin{alignedat}{2}\left(\mathbf {x} ^{T}\mathbf {y} +c\right)^{d}&=\sum _{j_{1}+j_{2}+\dots +j_{n+1}=d}{\frac {\sqrt {d!}}{\sqrt {j_{1}!\cdots j_{n}!j_{n+1}!}}}x_{1}^{j_{1}}\cdots x_{n}^{j_{n}}{\sqrt {c}}^{j_{n+1}}{\frac {\sqrt {d!}}{\sqrt {j_{1}!\cdots j_{n}!j_{n+1}!}}}y_{1}^{j_{1}}\cdots y_{n}^{j_{n}}{\sqrt {c}}^{j_{n+1}}\\&=\varphi (\mathbf {x} )^{T}\varphi (\mathbf {y} )\end{alignedat}}} The last summation has l d = ( n + d d ) {\displaystyle l_{d}={\tbinom {n+d}{d}}} elements, so that: φ ( x ) = ( a 1 , … , a l , … , a l d ) {\displaystyle \varphi (\mathbf {x} )=\left(a_{1},\dots ,a_{l},\dots ,a_{l_{d}}\right)} where l = ( j 1 , j 2 , . . . , j n , j n + 1 ) {\displaystyle l=(j_{1},j_{2},...,j_{n},j_{n+1})} and a l = d ! j 1 ! ⋯ j n ! j n + 1 ! x 1 j 1 ⋯ x n j n c j n + 1 | j 1 + j 2 + ⋯ + j n + j n + 1 = d {\displaystyle a_{l}={\frac {\sqrt {d!}}{\sqrt {j_{1}!\cdots j_{n}!j_{n+1}!}}}x_{1}^{j_{1}}\cdots x_{n}^{j_{n}}{\sqrt {c}}^{j_{n+1}}\quad |\quad j_{1}+j_{2}+\dots +j_{n}+j_{n+1}=d} == Practical use == Although the RBF kernel is more popular in SVM classification than the polynomial kernel, the latter is quite popular in natural language processing (NLP). The most common degree is d = 2 (quadratic), since larger degrees tend to overfit on NLP problems. Various ways of computing the polynomial kernel (both exact and approximate) have been devised as alternatives to the usual non-linear SVM training algorithms, including: full expansion of the kernel prior to training/testing with a linear SVM, i.e. full computation of the mapping φ as in polynomial regression; basket mining (using a variant of the apriori algorithm) for the most commonly occurring feature conjunctions in a training set to produce an approximate expansion; inverted indexing of support vectors. One problem with the polynomial kernel is that it may suffer from numerical instability: when xTy + c < 1, K(x, y) = (xTy + c)d tends to zero with increasing d, whereas when xTy + c > 1, K(x, y) tends to infinity.

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