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  • Image moment

    Image moment

    In image processing, computer vision and related fields, an image moment is a certain particular weighted average (moment) of the image pixels' intensities, or a function of such moments, usually chosen to have some attractive property or interpretation. Image moments are useful to describe objects after segmentation. Simple properties of the image which are found via image moments include area (or total intensity), its centroid, and information about its orientation. == Raw moments == For a 2D continuous function f(x,y) the moment (sometimes called "raw moment") of order (p + q) is defined as M p q = ∫ − ∞ ∞ ∫ − ∞ ∞ x p y q f ( x , y ) d x d y {\displaystyle M_{pq}=\int \limits _{-\infty }^{\infty }\int \limits _{-\infty }^{\infty }x^{p}y^{q}f(x,y)\,dx\,dy} for p,q = 0,1,2,... Adapting this to scalar (grayscale) image with pixel intensities I(x,y), raw image moments Mij are calculated by M i j = ∑ x ∑ y x i y j I ( x , y ) {\displaystyle M_{ij}=\sum _{x}\sum _{y}x^{i}y^{j}I(x,y)\,\!} In some cases, this may be calculated by considering the image as a probability density function, i.e., by dividing the above by ∑ x ∑ y I ( x , y ) {\displaystyle \sum _{x}\sum _{y}I(x,y)\,\!} A uniqueness theorem states that if f(x,y) is piecewise continuous and has nonzero values only in a finite part of the xy plane, moments of all orders exist, and the moment sequence (Mpq) is uniquely determined by f(x,y). Conversely, (Mpq) uniquely determines f(x,y). In practice, the image is summarized with functions of a few lower order moments. === Examples === Simple image properties derived via raw moments include: Area (for binary images) or sum of grey level (for greytone images): M 00 {\displaystyle M_{00}} Centroid: { x ¯ , y ¯ } = { M 10 M 00 , M 01 M 00 } {\displaystyle \{{\bar {x}},\ {\bar {y}}\}=\left\{{\frac {M_{10}}{M_{00}}},{\frac {M_{01}}{M_{00}}}\right\}} == Central moments == Central moments are defined as μ p q = ∫ − ∞ ∞ ∫ − ∞ ∞ ( x − x ¯ ) p ( y − y ¯ ) q f ( x , y ) d x d y {\displaystyle \mu _{pq}=\int \limits _{-\infty }^{\infty }\int \limits _{-\infty }^{\infty }(x-{\bar {x}})^{p}(y-{\bar {y}})^{q}f(x,y)\,dx\,dy} where x ¯ = M 10 M 00 {\displaystyle {\bar {x}}={\frac {M_{10}}{M_{00}}}} and y ¯ = M 01 M 00 {\displaystyle {\bar {y}}={\frac {M_{01}}{M_{00}}}} are the components of the centroid. If ƒ(x, y) is a digital image, then the previous equation becomes μ p q = ∑ x ∑ y ( x − x ¯ ) p ( y − y ¯ ) q f ( x , y ) {\displaystyle \mu _{pq}=\sum _{x}\sum _{y}(x-{\bar {x}})^{p}(y-{\bar {y}})^{q}f(x,y)} The central moments of order up to 3 are: μ 00 = M 00 , μ 01 = 0 , μ 10 = 0 , μ 11 = M 11 − x ¯ M 01 = M 11 − y ¯ M 10 , μ 20 = M 20 − x ¯ M 10 , μ 02 = M 02 − y ¯ M 01 , μ 21 = M 21 − 2 x ¯ M 11 − y ¯ M 20 + 2 x ¯ 2 M 01 , μ 12 = M 12 − 2 y ¯ M 11 − x ¯ M 02 + 2 y ¯ 2 M 10 , μ 30 = M 30 − 3 x ¯ M 20 + 2 x ¯ 2 M 10 , μ 03 = M 03 − 3 y ¯ M 02 + 2 y ¯ 2 M 01 . {\displaystyle {\begin{aligned}\mu _{00}&=M_{00},&\mu _{01}&=0,\\\mu _{10}&=0,&\mu _{11}&=M_{11}-{\bar {x}}M_{01}=M_{11}-{\bar {y}}M_{10},\\\mu _{20}&=M_{20}-{\bar {x}}M_{10},&\mu _{02}&=M_{02}-{\bar {y}}M_{01},\\\mu _{21}&=M_{21}-2{\bar {x}}M_{11}-{\bar {y}}M_{20}+2{\bar {x}}^{2}M_{01},&\mu _{12}&=M_{12}-2{\bar {y}}M_{11}-{\bar {x}}M_{02}+2{\bar {y}}^{2}M_{10},\\\mu _{30}&=M_{30}-3{\bar {x}}M_{20}+2{\bar {x}}^{2}M_{10},&\mu _{03}&=M_{03}-3{\bar {y}}M_{02}+2{\bar {y}}^{2}M_{01}.\end{aligned}}} It can be shown that: μ p q = ∑ m p ∑ n q ( p m ) ( q n ) ( − x ¯ ) ( p − m ) ( − y ¯ ) ( q − n ) M m n {\displaystyle \mu _{pq}=\sum _{m}^{p}\sum _{n}^{q}{p \choose m}{q \choose n}(-{\bar {x}})^{(p-m)}(-{\bar {y}})^{(q-n)}M_{mn}} Central moments are translational invariant. === Examples === Information about image orientation can be derived by first using the second order central moments to construct a covariance matrix. μ 20 ′ = μ 20 / μ 00 = M 20 / M 00 − x ¯ 2 μ 02 ′ = μ 02 / μ 00 = M 02 / M 00 − y ¯ 2 μ 11 ′ = μ 11 / μ 00 = M 11 / M 00 − x ¯ y ¯ {\displaystyle {\begin{aligned}\mu '_{20}&=\mu _{20}/\mu _{00}=M_{20}/M_{00}-{\bar {x}}^{2}\\\mu '_{02}&=\mu _{02}/\mu _{00}=M_{02}/M_{00}-{\bar {y}}^{2}\\\mu '_{11}&=\mu _{11}/\mu _{00}=M_{11}/M_{00}-{\bar {x}}{\bar {y}}\end{aligned}}} The covariance matrix of the image I ( x , y ) {\displaystyle I(x,y)} is now cov ⁡ [ I ( x , y ) ] = [ μ 20 ′ μ 11 ′ μ 11 ′ μ 02 ′ ] . {\displaystyle \operatorname {cov} [I(x,y)]={\begin{bmatrix}\mu '_{20}&\mu '_{11}\\\mu '_{11}&\mu '_{02}\end{bmatrix}}.} The eigenvectors of this matrix correspond to the major and minor axes of the image intensity, so the orientation can thus be extracted from the angle of the eigenvector associated with the largest eigenvalue towards the axis closest to this eigenvector. It can be shown that this angle Θ is given by the following formula: Θ = 1 2 arctan ⁡ ( 2 μ 11 ′ μ 20 ′ − μ 02 ′ ) {\displaystyle \Theta ={\frac {1}{2}}\arctan \left({\frac {2\mu '_{11}}{\mu '_{20}-\mu '_{02}}}\right)} The above formula holds as long as: μ 20 ′ − μ 02 ′ ≠ 0 {\displaystyle \mu '_{20}-\mu '_{02}\neq 0} The eigenvalues of the covariance matrix can easily be shown to be λ i = μ 20 ′ + μ 02 ′ 2 ± 4 μ ′ 11 2 + ( μ ′ 20 − μ ′ 02 ) 2 2 , {\displaystyle \lambda _{i}={\frac {\mu '_{20}+\mu '_{02}}{2}}\pm {\frac {\sqrt {4{\mu '}_{11}^{2}+({\mu '}_{20}-{\mu '}_{02})^{2}}}{2}},} and are proportional to the squared length of the eigenvector axes. The relative difference in magnitude of the eigenvalues are thus an indication of the eccentricity of the image, or how elongated it is. The eccentricity is 1 − λ 2 λ 1 . {\displaystyle {\sqrt {1-{\frac {\lambda _{2}}{\lambda _{1}}}}}.} == Moment invariants == Moments are well-known for their application in image analysis, since they can be used to derive invariants with respect to specific transformation classes. The term invariant moments is often abused in this context. However, while moment invariants are invariants that are formed from moments, the only moments that are invariants themselves are the central moments. Note that the invariants detailed below are exactly invariant only in the continuous domain. In a discrete domain, neither scaling nor rotation are well defined: a discrete image transformed in such a way is generally an approximation, and the transformation is not reversible. These invariants therefore are only approximately invariant when describing a shape in a discrete image. === Translation invariants === The central moments μi j of any order are, by construction, invariant with respect to translations. === Scale invariants === Invariants ηi j with respect to both translation and scale can be constructed from central moments by dividing through a properly scaled zero-th central moment: η i j = μ i j μ 00 ( 1 + i + j 2 ) {\displaystyle \eta _{ij}={\frac {\mu _{ij}}{\mu _{00}^{\left(1+{\frac {i+j}{2}}\right)}}}\,\!} where i + j ≥ 2. Note that translational invariance directly follows by only using central moments. === Rotation invariants === As shown in the work of Hu, invariants with respect to translation, scale, and rotation can be constructed: I 1 = η 20 + η 02 {\displaystyle I_{1}=\eta _{20}+\eta _{02}} I 2 = ( η 20 − η 02 ) 2 + 4 η 11 2 {\displaystyle I_{2}=(\eta _{20}-\eta _{02})^{2}+4\eta _{11}^{2}} I 3 = ( η 30 − 3 η 12 ) 2 + ( 3 η 21 − η 03 ) 2 {\displaystyle I_{3}=(\eta _{30}-3\eta _{12})^{2}+(3\eta _{21}-\eta _{03})^{2}} I 4 = ( η 30 + η 12 ) 2 + ( η 21 + η 03 ) 2 {\displaystyle I_{4}=(\eta _{30}+\eta _{12})^{2}+(\eta _{21}+\eta _{03})^{2}} I 5 = ( η 30 − 3 η 12 ) ( η 30 + η 12 ) [ ( η 30 + η 12 ) 2 − 3 ( η 21 + η 03 ) 2 ] + ( 3 η 21 − η 03 ) ( η 21 + η 03 ) [ 3 ( η 30 + η 12 ) 2 − ( η 21 + η 03 ) 2 ] {\displaystyle I_{5}=(\eta _{30}-3\eta _{12})(\eta _{30}+\eta _{12})[(\eta _{30}+\eta _{12})^{2}-3(\eta _{21}+\eta _{03})^{2}]+(3\eta _{21}-\eta _{03})(\eta _{21}+\eta _{03})[3(\eta _{30}+\eta _{12})^{2}-(\eta _{21}+\eta _{03})^{2}]} I 6 = ( η 20 − η 02 ) [ ( η 30 + η 12 ) 2 − ( η 21 + η 03 ) 2 ] + 4 η 11 ( η 30 + η 12 ) ( η 21 + η 03 ) {\displaystyle I_{6}=(\eta _{20}-\eta _{02})[(\eta _{30}+\eta _{12})^{2}-(\eta _{21}+\eta _{03})^{2}]+4\eta _{11}(\eta _{30}+\eta _{12})(\eta _{21}+\eta _{03})} I 7 = ( 3 η 21 − η 03 ) ( η 30 + η 12 ) [ ( η 30 + η 12 ) 2 − 3 ( η 21 + η 03 ) 2 ] − ( η 30 − 3 η 12 ) ( η 21 + η 03 ) [ 3 ( η 30 + η 12 ) 2 − ( η 21 + η 03 ) 2 ] . {\displaystyle I_{7}=(3\eta _{21}-\eta _{03})(\eta _{30}+\eta _{12})[(\eta _{30}+\eta _{12})^{2}-3(\eta _{21}+\eta _{03})^{2}]-(\eta _{30}-3\eta _{12})(\eta _{21}+\eta _{03})[3(\eta _{30}+\eta _{12})^{2}-(\eta _{21}+\eta _{03})^{2}].} These are well-known as Hu moment invariants. The first one, I1, is analogous to the moment of inertia around the image's centroid, where the pixels' intensities are analogous to physical density. The first six, I1 ... I6, are reflection symmetric, i.e. they are unchanged if the image is changed to a mirror image. The last one, I7, is reflection antisymmetric (changes sign under reflection), which enables it to distinguish mirror images of otherwise identical im

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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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  • One-shot learning (computer vision)

    One-shot learning (computer vision)

    One-shot learning is an object categorization problem, found mostly in computer vision. Whereas most machine learning-based object categorization algorithms require training on hundreds or thousands of examples, one-shot learning aims to classify objects from one, or only a few, examples. The term few-shot learning is also used for these problems, especially when more than one example is needed. == Motivation == The ability to learn object categories from few examples, and at a rapid pace, has been demonstrated in humans. It is estimated that a child learns almost all of the 10 ~ 30 thousand object categories in the world by age six. This is due not only to the human mind's computational power, but also to its ability to synthesize and learn new object categories from existing information about different, previously learned categories. Given two examples from two object categories: one, an unknown object composed of familiar shapes, the second, an unknown, amorphous shape; it is much easier for humans to recognize the former than the latter, suggesting that humans make use of previously learned categories when learning new ones. The key motivation for solving one-shot learning is that systems, like humans, can use knowledge about object categories to classify new objects. == Background == As with most classification schemes, one-shot learning involves three main challenges: Representation: How should objects and categories be described? Learning: How can such descriptions be created? Recognition: How can a known object be filtered from enveloping clutter, irrespective of occlusion, viewpoint, and lighting? One-shot learning differs from single object recognition and standard category recognition algorithms in its emphasis on knowledge transfer, which makes use of previously learned categories. Model parameters: Reuses model parameters, based on the similarity between old and new categories. Categories are first learned on numerous training examples, then new categories are learned using transformations of model parameters from those initial categories or selecting relevant parameters for a classifier. Feature sharing: Shares parts or features of objects across categories. One algorithm extracts "diagnostic information" in patches from already learned categories by maximizing the patches' mutual information, and then applies these features to the learning of a new category. A dog category, for example, may be learned in one shot from previous knowledge of horse and cow categories, because dog objects may contain similar distinguishing patches. Contextual information: Appeals to global knowledge of the scene in which the object appears. Such global information can be used as frequency distributions in a conditional random field framework to recognize objects. Alternatively context can consider camera height and scene geometry. Algorithms of this type have two advantages. First, they learn object categories that are relatively dissimilar; and second, they perform well in ad hoc situations where an image has not been hand-cropped and aligned. == Theory == The Bayesian one-shot learning algorithm represents the foreground and background of images as parametrized by a mixture of constellation models. During the learning phase, the parameters of these models are learned using a conjugate density parameter posterior and variational Bayesian expectation–maximization (VBEM). In this stage the previously learned object categories inform the choice of model parameters via transfer by contextual information. For object recognition on new images, the posterior obtained during the learning phase is used in a Bayesian decision framework to estimate the ratio of p(object | test, train) to p(background clutter | test, train) where p is the probability of the outcome. === Bayesian framework === Given the task of finding a particular object in a query image, the overall objective of the Bayesian one-shot learning algorithm is to compare the probability that object is present vs the probability that only background clutter is present. If the former probability is higher, the algorithm reports the object's presence, otherwise the algorithm reports its absence. To compute these probabilities, the object class must be modeled from a set of (1 ~ 5) training images containing examples. To formalize these ideas, let I {\displaystyle I} be the query image, which contains either an example of the foreground category O f g {\displaystyle O_{fg}} or only background clutter of a generic background category O b g {\displaystyle O_{bg}} . Also let I t {\displaystyle I_{t}} be the set of training images used as the foreground category. The decision of whether I {\displaystyle I} contains an object from the foreground category, or only clutter from the background category is: R = p ( O f g | I , I t ) p ( O b g | I , I t ) = p ( I | I t , O f g ) p ( O f g ) p ( I | I t , O b g ) p ( O b g ) , {\displaystyle R={\frac {p(O_{fg}|I,I_{t})}{p(O_{bg}|I,I_{t})}}={\frac {p(I|I_{t},O_{fg})p(O_{fg})}{p(I|I_{t},O_{bg})p(O_{bg})}},} where the class posteriors p ( O f g | I , I t ) {\displaystyle p(O_{fg}|I,I_{t})} and p ( O b g | I , I t ) {\displaystyle p(O_{bg}|I,I_{t})} have been expanded by Bayes' theorem, yielding a ratio of likelihoods and a ratio of object category priors. We decide that the image I {\displaystyle I} contains an object from the foreground class if R {\displaystyle R} exceeds a certain threshold T {\displaystyle T} . We next introduce parametric models for the foreground and background categories with parameters θ {\displaystyle \theta } and θ b g {\displaystyle \theta _{bg}} respectively. This foreground parametric model is learned during the learning stage from I t {\displaystyle I_{t}} , as well as prior information of learned categories. The background model we assume to be uniform across images. Omitting the constant ratio of category priors, p ( O f g ) p ( O b g ) {\displaystyle {\frac {p(O_{fg})}{p(O_{bg})}}} , and parametrizing over θ {\displaystyle \theta } and θ b g {\displaystyle \theta _{bg}} yields R ∝ ∫ p ( I | θ , O f g ) p ( θ | I t , O f g ) d θ ∫ p ( I | θ b g , O b g ) p ( θ b g | I t , O b g ) d θ b g = ∫ p ( I | θ ) p ( θ | I t , O f g ) d θ ∫ p ( I | θ b g ) p ( θ b g | I t , O b g ) d θ b g {\displaystyle R\propto {\frac {\int {p(I|\theta ,O_{fg})p(\theta |I_{t},O_{fg})}d\theta }{\int {p(I|\theta _{bg},O_{bg})p(\theta _{bg}|I_{t},O_{bg})}d\theta _{bg}}}={\frac {\int {p(I|\theta )p(\theta |I_{t},O_{fg})}d\theta }{\int {p(I|\theta _{bg})p(\theta _{bg}|I_{t},O_{bg})}d\theta _{bg}}}} , having simplified p ( I | θ , O f g ) {\displaystyle p(I|\theta ,O_{fg})} and p ( I | θ , O b g ) {\displaystyle p(I|\theta ,O_{bg})} to p ( I | θ f g ) {\displaystyle p(I|\theta _{fg})} and p ( I | θ b g ) . {\displaystyle p(I|\theta _{bg}).} The posterior distribution of model parameters given the training images, p ( θ | I t , O f g ) {\displaystyle p(\theta |I_{t},O_{fg})} is estimated in the learning phase. In this estimation, one-shot learning differs sharply from more traditional Bayesian estimation models that approximate the integral as δ ( θ M L ) {\displaystyle \delta (\theta ^{ML})} . Instead, it uses a variational approach using prior information from previously learned categories. However, the traditional maximum likelihood estimation of the model parameters is used for the background model and the categories learned in advance through training. === Object category model === For each query image I {\displaystyle I} and training images I t {\displaystyle I_{t}} , a constellation model is used for representation. To obtain this model for a given image I {\displaystyle I} , first a set of N interesting regions is detected in the image using the Kadir–Brady saliency detector. Each region selected is represented by a location in the image, X i {\displaystyle X_{i}} and a description of its appearance, A i {\displaystyle A_{i}} . Letting X = ∑ i = 1 N X i , A = ∑ i = 1 N A i {\displaystyle X=\sum _{i=1}^{N}X_{i},A=\sum _{i=1}^{N}A_{i}} and X t {\displaystyle X_{t}} and A t {\displaystyle A_{t}} the analogous representations for training images, the expression for R becomes: R ∝ ∫ p ( X , A | θ , O f g ) p ( θ | X t , A t , O f g ) d θ ∫ p ( X , A | θ b g , O b g ) p ( θ b g | X t , A t , O b g ) d θ b g = ∫ p ( X , A | θ ) p ( θ | X t , A t , O f g ) d θ ∫ p ( X , A | θ b g ) p ( θ b g | X t , A t , O b g ) d θ b g {\displaystyle R\propto {\frac {\int {p(X,A|\theta ,O_{fg})p(\theta |X_{t},A_{t},O_{fg})}d\theta }{\int {p(X,A|\theta _{bg},O_{bg})p(\theta _{bg}|X_{t},A_{t},O_{bg})}d\theta _{bg}}}={\frac {\int {p(X,A|\theta )p(\theta |X_{t},A_{t},O_{fg})}d\theta }{\int {p(X,A|\theta _{bg})p(\theta _{bg}|X_{t},A_{t},O_{bg})}\,d\theta _{bg}}}} The likelihoods p ( X , A | θ ) {\displaystyle p(X,A|\theta )} and p ( X , A | θ b g ) {\displaystyle p(X,A|\theta _{bg})} are represented as mixtures of constellation models. A typical constellation model has

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  • ARKA descriptors in QSAR

    ARKA descriptors in QSAR

    In computational chemistry and cheminformatics, ARKA descriptors in QSAR are a class of molecular descriptors used in quantitative structure–activity relationship (QSAR) modeling (or related approaches such as QSPR and QSTR), a computational method for predicting the biological activity or toxicity of chemical compounds based on their molecular structure. Molecular descriptors are numerical values that summarize information about a molecule's structure, topology, geometry, or physicochemical properties in a form suitable for machine learning or statistical modeling. ARKA (Arithmetic Residuals in K-Groups Analysis) descriptors differ from traditional descriptors by encoding atomic-level information through recursive autoregression techniques, which aim to capture subtle structural patterns and improve predictive accuracy. They are designed to be both interpretable and well-suited to modeling nonlinear relationships in QSAR studies. == Comparisons == While QSAR is essentially a similarity-based approach, the occurrence of activity/property cliffs may greatly reduce the predictive accuracy of the developed models. The novel Arithmetic Residuals in K-groups Analysis (ARKA) approach is a supervised dimensionality reduction technique developed by the DTC Laboratory, Jadavpur University that can easily identify activity cliffs in a data set. Activity cliffs are similar in their structures but differ considerably in their activity. The basic idea of the ARKA descriptors is to group the conventional QSAR descriptors based on a predefined criterion and then assign weightage to each descriptor in each group. ARKA descriptors have also been used to develop classification-based and regression-based QSAR models with acceptable quality statistics. The ARKA descriptors have been used for the identification of activity cliffs in QSAR studies and/or model development by multiple researchers. A tutorial presentation on the ARKA descriptors is available. Recently a multi-class ARKA framework has been proposed for improved q-RASAR model generation.

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  • FoundationDB

    FoundationDB

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

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  • Genetic programming

    Genetic programming

    Genetic programming (GP) is an evolutionary algorithm, an artificial intelligence technique mimicking natural evolution, which operates on a population of programs. It applies the genetic operators selection according to a predefined fitness measure, mutation and crossover. The crossover operation involves swapping specified parts of selected pairs (parents) to produce new and different offspring that become part of the new generation of programs. Some programs not selected for reproduction are copied from the current generation to the new generation. Mutation involves substitution of some random part of a program with some other random part of a program. Then the selection and other operations are recursively applied to the new generation of programs. Typically, members of each new generation are on average more fit than the members of the previous generation, and the best-of-generation program is often better than the best-of-generation programs from previous generations. Termination of the evolution usually occurs when some individual program reaches a predefined proficiency or fitness level. It may and often does happen that a particular run of the algorithm results in premature convergence to some local maximum that is not a globally optimal or even good solution. Multiple runs (dozens to hundreds) are usually necessary to produce a very good result. It may also be necessary to have a large starting population size and variability of the individuals to avoid pathologies. == History == The first record of the proposal to evolve programs is probably that of Alan Turing in 1950 in "Computing Machinery and Intelligence". There was a gap of 25 years before the publication of John Holland's 'Adaptation in Natural and Artificial Systems' laid out the theoretical and empirical foundations of the science. In 1981, Richard Forsyth demonstrated the successful evolution of small programs, represented as trees, to perform classification of crime scene evidence for the UK Home Office. Although the idea of evolving programs, initially in the computer language Lisp, was current amongst John Holland's students, it was not until they organised the first Genetic Algorithms (GA) conference in Pittsburgh that Nichael Cramer published evolved programs in two specially designed languages, which included the first statement of modern "tree-based" genetic programming (that is, procedural languages organized in tree-based structures and operated on by suitably defined GA-operators). In 1988, John Koza (also a PhD student of John Holland) patented his invention of a GA for program evolution. This was followed by publication in the International Joint Conference on Artificial Intelligence IJCAI-89. Koza followed this with 205 publications on "genetic programming", a term coined by David Goldberg, also a PhD student of John Holland. However, it is the series of 4 books by Koza, starting in 1992 with accompanying videos, that really established GP. Subsequently, there was an enormous expansion of the number of publications with the Genetic Programming Bibliography, surpassing 10,000 entries. In 2010, Koza listed 77 results where genetic programming was human competitive. The departure of GP from the rigid, fixed-length representations typical of early GA models was not entirely without precedent. Early work on variable-length representations laid the groundwork. One notable example is messy genetic algorithms, which introduced irregular, variable-length chromosomes to address building block disruption and positional bias in standard GAs. Another precursor was robot trajectory programming, where genome representations encoded program instructions for robotic movements—structures inherently variable in length. Even earlier, unfixed-length representations were proposed in a doctoral dissertation by Cavicchio, who explored adaptive search using simulated evolution. His work provided foundational ideas for flexible program structures. In 1996, Koza started the annual Genetic Programming conference, which was followed in 1998 by the annual EuroGP conference, and the first book in a GP series edited by Koza. 1998 also saw the first GP textbook. GP continued to flourish, leading to the first specialist GP journal and three years later (2003) the annual Genetic Programming Theory and Practice (GPTP) workshop was established by Rick Riolo. Genetic programming papers continue to be published at a diversity of conferences and associated journals. Today there are nineteen GP books including several for students. === Foundational work in GP === Early work that set the stage for current genetic programming research topics and applications is diverse, and includes software synthesis and repair, predictive modeling, data mining, financial modeling, soft sensors, design, and image processing. Applications in some areas, such as design, often make use of intermediate representations, such as Fred Gruau's cellular encoding. Industrial uptake has been significant in several areas including finance, the chemical industry, bioinformatics and the steel industry. == Methods == === Program representation === GP evolves computer programs, traditionally represented in memory as tree structures. Trees can be easily evaluated in a recursive manner. Every internal node has an operator function and every terminal node has an operand, making mathematical expressions easy to evolve and evaluate. Thus traditionally GP favors the use of programming languages that naturally embody tree structures (for example, Lisp; other functional programming languages are also suitable). Non-tree representations have been suggested and successfully implemented, such as linear genetic programming, which perhaps suits the more traditional imperative languages. The commercial GP software Discipulus uses automatic induction of binary machine code ("AIM") to achieve better performance. μGP uses directed multigraphs to generate programs that fully exploit the syntax of a given assembly language. Multi expression programming uses three-address code for encoding solutions. Other program representations on which significant research and development have been conducted include programs for stack-based virtual machines, and sequences of integers that are mapped to arbitrary programming languages via grammars. Cartesian genetic programming is another form of GP, which uses a graph representation instead of the usual tree based representation to encode computer programs. Most representations have structurally noneffective code (introns). Such non-coding genes may seem to be useless because they have no effect on the performance of any one individual. However, they alter the probabilities of generating different offspring under the variation operators, and thus alter the individual's variational properties. Experiments seem to show faster convergence when using program representations that allow such non-coding genes, compared to program representations that do not have any non-coding genes. Instantiations may have both trees with introns and those without; the latter are called canonical trees. Special canonical crossover operators are introduced that maintain the canonical structure of parents in their children. === Initialisation === The methods for creation of the initial population include: Grow creates the individuals sequentially. Every GP tree is created starting from the root, creating functional nodes with children as well as terminal nodes up to a certain depth. Full is similar to the Grow. The difference is that all brunches in a tree are of same predetermined depth. Ramped half-and-half creates a population consisting of m d − 1 {\displaystyle md-1} parts and a maximum depth of m d {\displaystyle md} for its trees. The first part has a maximum depth of 2, second of 3 and so on up to the m d − 1 {\displaystyle md-1} -th part with maximum depth m d {\displaystyle md} . Half of every part is created by Grow, while the other part is created by Full. === Selection === Selection is a process whereby certain individuals are selected from the current generation that would serve as parents for the next generation. The individuals are selected probabilistically such that the better performing individuals have a higher chance of getting selected. The most commonly used selection method in GP is tournament selection, although other methods such as fitness proportionate selection, lexicase selection, and others have been demonstrated to perform better for many GP problems. Elitism, which involves seeding the next generation with the best individual (or best n individuals) from the current generation, is a technique sometimes employed to avoid regression. === Crossover === In genetic programming two fit individuals are chosen from the population to be parents for one or two children. In tree genetic programming, these parents are represented as inverted lisp like trees, with their root nodes at the top. In subtree cro

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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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  • World Programming System

    World Programming System

    The World Programming System, also known as WPS Analytics or WPS, is a software product developed by a company called World Programming (acquired by Altair Engineering). WPS Analytics supports users of mixed ability to access and process data and to perform data science tasks. It has interactive visual programming tools using data workflows, and it has coding tools supporting the use of the SAS language mixed with Python, R and SQL. == About == WPS can use programs written in the language of SAS without the need for translating them into any other language. In this regard WPS is compatible with the SAS system. WPS has a built-in language interpreter able to process the language of SAS and produce similar results. WPS is available to run on z/OS, Windows, macOS, Linux (x86, Armv8 64-bit, IBM Power LE, IBM Z), and AIX. On all supported platforms, programs written in the language of SAS can be executed from a WPS command line interface, often referred to as running in batch mode. WPS can also be used from a graphical user interface known as the WPS Workbench for managing, editing and running programs written in the language of SAS. The WPS Workbench user interface is based on Eclipse. WPS version 4 (released in March 2018) introduced a drag-and-drop workflow canvas providing interactive blocks for data retrieval, blending and preparation, data discovery and profiling, predictive modelling powered by machine learning algorithms, model performance validation and scorecards. WPS version 3 (released in February 2012) provided a new client/server architecture that allows the WPS Workbench GUI to execute SAS programs on remote server installations of WPS in a network or cloud. The resulting output, data sets, logs, etc., can then all be viewed and manipulated from inside the Workbench as if the workloads had been executed locally. SAS programs do not require any special language statements to use this feature. == Summary of main features == Runs on Windows, macOS, z/OS, Linux (x86, Armv8 64-bit, IBM Power LE, IBM Z), and AIX An integrated development environment based on Eclipse for Linux, macOS and Windows. Support for language of SAS elements. Support for the language of SAS Macros. Matrix Programming support using PROC IML. Support for generating band plots, bar charts, box plots, bubble plots, contour plots, dendrogram plots, ellipse plots, fringe plots, heat maps, high-low plots, histograms, loess plots, needle plots, pie charts, penalised b-spline, radar charts, reference lines, scatter plots, series plots, step plots, regression plots and vector plots. Support for statistical procedures ACECLUS, ASSOCRULES, ANOVA, BIN, BOXPLOT, CANCORR, CANDISC, CLUSTER, CORRESP, DISCRIM, DISTANCE, FACTOR, FASTCLUS, FREQ, GAM, GANNO, GENMOD, GLIMMIX, GLM, GLMMOD, GLMSELECT, ICLIFETEST, KDE, LIFEREG, LIFETEST, LOESS, LOGISTIC, MDS, MEANS, MI, MIANALYSE, MIXED, MODECLUS, NESTED, NLIN, NPAR1WAY, PHREG, PLAN, PLS, POWER, PRINCOMP, PROBIT, QUANTREG, RBF, REG, ROBUSTREG, RSREG, SCORE, SEGMENT, SIMNORMAL, STANDARD, STDSIZE, STDRATE, STEPDISC, SUMMARY, SURVEYMEANS, SURVEYSELECT, TPSPLINE, TRANSREG, TREE, TTEST, UNIVARIATE, VARCLUS, VARCOMP Support for time series procedures ARIMA, AUTOREG, ESM, EXPAND, FORECAST, LOAN, SEVERITY, SPECTRA, TIMESERIES, X12 Support for machine learning procedures DECISIONFOREST, DECISIONTREE, GMM, MLP, OPTIMALBIN, SEGMENT, SVM Support for ODS. Reads and writes SAS datasets (compressed or uncompressed). Access: Actian Matrix (previously known as ParAccel), DASD, DB2, Excel, Greenplum, Hadoop, Informix, Kognitio Archived 2012-08-24 at the Wayback Machine, MariaDB, MySQL, Netezza, ODBC, OLEDB, Oracle, PostgreSQL, SAND, Snowflake, SPSS/PSPP, SQL Server, Sybase, Sybase IQ, Teradata, VSAM, Vertica and XML. Support for SAS Tape Format. Direct output of reports to CSV, PDF and HTML. Support to connect WPS systems programmatically, remote submit parts of a program to execute on connected remote servers, upload and download data between the connected systems. Support for Hadoop Support for R Support for Python == Industry recognition == Gartner recognized World Programming in their Cool Vendors in Data Science, 2014 Report. == Lawsuit == In 2010 World Programming defended its use of the language of SAS in the High Court of England and Wales in SAS Institute Inc. v World Programming Ltd. The software was the subject of a lawsuit by SAS Institute. The EU Court of Justice ruled in favor of World Programming, stating that the copyright protection does not extend to the software functionality, the programming language used and the format of the data files used by the program. It stated that there is no copyright infringement when a company which does not have access to the source code of a program studies, observes and tests that program to create another program with the same functionality.

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  • Phase stretch transform

    Phase stretch transform

    Phase stretch transform (PST) is a computational approach to signal and image processing. One of its utilities is for feature detection and classification. PST is related to time stretch dispersive Fourier transform. It transforms the image by emulating propagation through a diffractive medium with engineered 3D dispersive property (refractive index). The operation relies on symmetry of the dispersion profile and can be understood in terms of dispersive eigenfunctions or stretch modes. PST performs similar functionality as phase-contrast microscopy, but on digital images. PST can be applied to digital images and temporal (time series) data. It is a physics-based feature engineering algorithm. == Operation principle == Here the principle is described in the context of feature enhancement in digital images. The image is first filtered with a spatial kernel followed by application of a nonlinear frequency-dependent phase. The output of the transform is the phase in the spatial domain. The main step is the 2-D phase function which is typically applied in the frequency domain. The amount of phase applied to the image is frequency dependent, with higher amount of phase applied to higher frequency features of the image. Since sharp transitions, such as edges and corners, contain higher frequencies, PST emphasizes the edge information. Features can be further enhanced by applying thresholding and morphological operations. PST is a pure phase operation whereas conventional edge detection algorithms operate on amplitude. == Physical and mathematical foundations of phase stretch transform == Photonic time stretch technique can be understood by considering the propagation of an optical pulse through a dispersive fiber. By disregarding the loss and non-linearity in fiber, the non-linear Schrödinger equation governing the optical pulse propagation in fiber upon integration reduces to: E o ( z , t ) = 1 2 π ∫ − ∞ ∞ E ~ i ( 0 , ω ) ⋅ e − i β 2 z ω 2 2 ⋅ e i ω t d ω {\displaystyle E_{o}(z,t)={\frac {1}{2\pi }}\int _{-\infty }^{\infty }{\tilde {E}}_{i}(0,\omega )\cdot e^{\frac {-i\beta _{2}z\omega ^{2}}{2}}\cdot e^{i\omega {t}}\,d\omega } (1) where β 2 {\displaystyle \beta _{2}} = GVD parameter, z is propagation distance, E o ( z , t ) {\displaystyle E_{o}(z,t)} is the reshaped output pulse at distance z and time t. The response of this dispersive element in the time-stretch system can be approximated as a phase propagator as presented in H ( ω ) = e i φ ( ω ) = e i ∑ m = 0 ∞ φ m ( ω ) = ∏ m = 0 ∞ H m ( ω ) {\displaystyle H(\omega )=e^{i\varphi (\omega )}=e^{i\sum _{m=0}^{\infty }\varphi _{m}(\omega )}=\prod _{m=0}^{\infty }H_{m}(\omega )} (2) Therefore, Eq. 1 can be written as following for a pulse that propagates through the time-stretch system and is reshaped into a temporal signal with a complex envelope given by E o ( t ) = 1 2 π ∫ − ∞ ∞ E ~ i ( ω ) ⋅ H ( ω ) ⋅ e i ω t d ω {\displaystyle E_{o}(t)={\frac {1}{2\pi }}\int _{-\infty }^{\infty }{\tilde {E}}_{i}(\omega )\cdot H(\omega )\cdot e^{i\omega t}\,d\omega } (3) The time stretch operation is formulated as generalized phase and amplitude operations, S { E i ( t ) } = ∫ − ∞ + ∞ F { E i ( t ) } ⋅ e i φ ( ω ) ⋅ L ~ ( ω ) ⋅ e i ω t d ω {\displaystyle \mathbb {S} \{E_{i}(t)\}=\int _{-\infty }^{+\infty }{\mathcal {F}}\{E_{i}(t)\}\cdot e^{i\varphi (\omega )}\cdot {\tilde {L}}(\omega )\cdot e^{i\omega {t}}d\omega } (4) where e i φ ( ω ) {\displaystyle e^{i\varphi (\omega )}} is the phase filter and L ~ ( ω ) {\displaystyle {\tilde {L}}(\omega )} is the amplitude filter. Next the operator is converted to discrete domain, S { E i [ n ] } = 1 N ∑ u = 0 N − 1 F F T { E i ( n ) } ⋅ K ~ ( u ) ⋅ L ~ ( u ) ⋅ e i 2 π N u n {\displaystyle \mathbb {S} \{E_{i}[n]\}={\frac {1}{N}}\sum _{u=0}^{N-1}FFT\{E_{i}(n)\}\cdot {\tilde {K}}(u)\cdot {\tilde {L}}(u)\cdot e^{i{\frac {2\pi }{N}}un}} (5) where u {\displaystyle u} is the discrete frequency, K ~ ( u ) {\displaystyle {\tilde {K}}(u)} is the phase filter, L ~ ( u ) {\displaystyle {\tilde {L}}(u)} is the amplitude filter and FFT is fast Fourier transform. The stretch operator S { } {\displaystyle \mathbb {S} \{\}} for a digital image is then S { E i [ n , m ] } = 1 M N ∑ v = 0 N − 1 ∑ u = 0 M − 1 F F T 2 { E i ( n , m ) } ⋅ K ~ ( u , v ) ⋅ L ~ ( u , v ) ⋅ e i 2 π M u m ⋅ e i 2 π N v n {\displaystyle \mathbb {S} \{E_{i}[n,m]\}={\frac {1}{MN}}\sum _{v=0}^{N-1}\sum _{u=0}^{M-1}FFT^{2}\{E_{i}(n,m)\}\cdot {\tilde {K}}(u,v)\cdot {\tilde {L}}(u,v)\cdot e^{i{\frac {2\pi }{M}}um}\cdot e^{i{\frac {2\pi }{N}}vn}} (6) In the above equations, E i [ n , m ] {\displaystyle E_{i}[n,m]} is the input image, n {\displaystyle n} and m {\displaystyle m} are the spatial variables, F F T 2 {\displaystyle FFT^{2}} is the two-dimensional fast Fourier transform, and u {\displaystyle u} and v {\displaystyle v} are spatial frequency variables. The function K ~ ( u , v ) {\displaystyle {\tilde {K}}(u,v)} is the warped phase kernel and the function L ~ ( u , v ) {\displaystyle {\tilde {L}}(u,v)} is a localization kernel implemented in frequency domain. PST operator is defined as the phase of the Warped Stretch Transform output as follows P S T { E i [ n , m ] } ≜ ∡ { S { E i [ x , y ] } } {\displaystyle PST\{E_{i}[n,m]\}\triangleq \measuredangle \{\mathbb {S} \{E_{i}[x,y]\}\}} (7) where ∡ { } {\displaystyle \measuredangle \{\}} is the angle operator. == PST kernel implementation == The warped phase kernel K ~ ( u , v ) {\displaystyle {\tilde {K}}(u,v)} can be described by a nonlinear frequency dependent phase K ~ ( u , v ) = e i φ ( u , v ) {\displaystyle {\tilde {K}}(u,v)=e^{i\varphi (u,v)}} While arbitrary phase kernels can be considered for PST operation, here we study the phase kernels for which the kernel phase derivative is a linear or sublinear function with respect to frequency variables. A simple example for such phase derivative profiles is the inverse tangent function. Consider the phase profile in the polar coordinate system φ ( u , v ) = φ polar ( r , θ ) = φ polar ( r ) {\displaystyle \varphi (u,v)=\varphi _{\text{polar}}(r,\theta )=\varphi _{\text{polar}}(r)} From d φ ( r ) d r = tan − 1 ⁡ ( r ) {\displaystyle {\frac {d\varphi (r)}{dr}}=\tan ^{-1}(r)} we have φ ( r ) = r tan − 1 ⁡ ( r ) − 1 2 log ⁡ ( r 2 + 1 ) {\displaystyle \varphi (r)=r\tan ^{-1}(r)-{\frac {1}{2}}\log(r^{2}+1)} Therefore, the PST kernel is implemented as φ ( r ) = S ⋅ ( W r ) ⋅ tan − 1 ⁡ ( W r ) − 1 2 log ⁡ ( 1 + ( W r ) 2 ) ( W r max ) ⋅ tan − 1 ⁡ ( W r max ) − 1 2 log ⁡ ( 1 + ( W r max ) 2 ) {\displaystyle \varphi (r)=S\cdot {\frac {(Wr)\cdot \tan ^{-1}(Wr)-{\frac {1}{2}}\log(1+(Wr)^{2})}{(Wr_{\max })\cdot \tan ^{-1}(Wr_{\max })-{\frac {1}{2}}\log(1+(Wr_{\max })^{2})}}} where S {\displaystyle S} and W {\displaystyle W} are real-valued numbers related to the strength and warp of the phase profile == Applications == PST has been used for edge detection in biological and biomedical images as well as synthetic-aperture radar (SAR) image processing, as well as detail and feature enhancement for digital images. PST has also been applied to improve the point spread function for single molecule imaging in order to achieve super-resolution. The transform exhibits intrinsic superior properties compared to conventional edge detectors for feature detection in low contrast visually impaired images. The PST function can also be performed on 1-D temporal waveforms in the analog domain to reveal transitions and anomalies in real time. == Open source code release == On February 9, 2016, a UCLA Engineering research group has made public the computer code for PST algorithm that helps computers process images at high speeds and "see" them in ways that human eyes cannot. The researchers say the code could eventually be used in face, fingerprint, and iris recognition systems for high-tech security, as well as in self-driving cars' navigation systems or for inspecting industrial products. The Matlab implementation for PST can also be downloaded from Matlab Files Exchange. However, it is provided for research purposes only, and a license must be obtained for any commercial applications. The software is protected under a US patent. The code was then significantly refactored and improved to support GPU acceleration. In May 2022, it became one algorithm in PhyCV: the first physics-inspired computer vision library.

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  • Robust principal component analysis

    Robust principal component analysis

    Robust Principal Component Analysis (RPCA) is a modification of the widely used statistical procedure of principal component analysis (PCA) which works well with respect to grossly corrupted observations. A number of different approaches exist for Robust PCA, including an idealized version of Robust PCA, which aims to recover a low-rank matrix L0 from highly corrupted measurements M = L0 +S0. This decomposition in low-rank and sparse matrices can be achieved by techniques such as Principal Component Pursuit method (PCP), Stable PCP, Quantized PCP, Block based PCP, and Local PCP. Then, optimization methods are used such as the Augmented Lagrange Multiplier Method (ALM), Alternating Direction Method (ADM), Fast Alternating Minimization (FAM), Iteratively Reweighted Least Squares (IRLS ) or alternating projections (AP). == Algorithms == === Non-convex method === The 2014 guaranteed algorithm for the robust PCA problem (with the input matrix being M = L + S {\displaystyle M=L+S} ) is an alternating minimization type algorithm. The computational complexity is O ( m n r 2 log ⁡ 1 ϵ ) {\displaystyle O\left(mnr^{2}\log {\frac {1}{\epsilon }}\right)} where the input is the superposition of a low-rank (of rank r {\displaystyle r} ) and a sparse matrix of dimension m × n {\displaystyle m\times n} and ϵ {\displaystyle \epsilon } is the desired accuracy of the recovered solution, i.e., ‖ L ^ − L ‖ F ≤ ϵ {\displaystyle \|{\widehat {L}}-L\|_{F}\leq \epsilon } where L {\displaystyle L} is the true low-rank component and L ^ {\displaystyle {\widehat {L}}} is the estimated or recovered low-rank component. Intuitively, this algorithm performs projections of the residual onto the set of low-rank matrices (via the SVD operation) and sparse matrices (via entry-wise hard thresholding) in an alternating manner - that is, low-rank projection of the difference the input matrix and the sparse matrix obtained at a given iteration followed by sparse projection of the difference of the input matrix and the low-rank matrix obtained in the previous step, and iterating the two steps until convergence. This alternating projections algorithm is later improved by an accelerated version, coined AccAltProj. The acceleration is achieved by applying a tangent space projection before projecting the residue onto the set of low-rank matrices. This trick improves the computational complexity to O ( m n r log ⁡ 1 ϵ ) {\displaystyle O\left(mnr\log {\frac {1}{\epsilon }}\right)} with a much smaller constant in front while it maintains the theoretically guaranteed linear convergence. Another fast version of accelerated alternating projections algorithm is IRCUR. It uses the structure of CUR decomposition in alternating projections framework to dramatically reduces the computational complexity of RPCA to O ( max { m , n } r 2 log ⁡ ( m ) log ⁡ ( n ) log ⁡ 1 ϵ ) {\displaystyle O\left(\max\{m,n\}r^{2}\log(m)\log(n)\log {\frac {1}{\epsilon }}\right)} === Convex relaxation === This method consists of relaxing the rank constraint r a n k ( L ) {\displaystyle rank(L)} in the optimization problem to the nuclear norm ‖ L ‖ ∗ {\displaystyle \|L\|_{}} and the sparsity constraint ‖ S ‖ 0 {\displaystyle \|S\|_{0}} to ℓ 1 {\displaystyle \ell _{1}} -norm ‖ S ‖ 1 {\displaystyle \|S\|_{1}} . The resulting program can be solved using methods such as the method of Augmented Lagrange Multipliers. === Deep-learning augmented method === Some recent works propose RPCA algorithms with learnable/training parameters. Such a learnable/trainable algorithm can be unfolded as a deep neural network whose parameters can be learned via machine learning techniques from a given dataset or problem distribution. The learned algorithm will have superior performance on the corresponding problem distribution. == Applications == RPCA has many real life important applications particularly when the data under study can naturally be modeled as a low-rank plus a sparse contribution. Following examples are inspired by contemporary challenges in computer science, and depending on the applications, either the low-rank component or the sparse component could be the object of interest: === Video surveillance === Given a sequence of surveillance video frames, it is often required to identify the activities that stand out from the background. If we stack the video frames as columns of a matrix M, then the low-rank component L0 naturally corresponds to the stationary background and the sparse component S0 captures the moving objects in the foreground. === Face recognition === Images of a convex, Lambertian surface under varying illuminations span a low-dimensional subspace. This is one of the reasons for effectiveness of low-dimensional models for imagery data. In particular, it is easy to approximate images of a human's face by a low-dimensional subspace. To be able to correctly retrieve this subspace is crucial in many applications such as face recognition and alignment. It turns out that RPCA can be applied successfully to this problem to exactly recover the face.

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  • Bondy's theorem

    Bondy's theorem

    In mathematics, Bondy's theorem is a bound on the number of elements needed to distinguish the sets in a family of sets from each other. It belongs to the field of combinatorics, and is named after John Adrian Bondy, who published it in 1972. == Statement == The theorem is as follows: Let X be a set with n elements and let A1, A2, ..., An be distinct subsets of X. Then there exists a subset S of X with n − 1 elements such that the sets Ai ∩ S are all distinct. In other words, if we have a 0-1 matrix with n rows and n columns such that each row is distinct, we can remove one column such that the rows of the resulting n × (n − 1) matrix are distinct. == Example == Consider the 4 × 4 matrix [ 1 1 0 1 0 1 0 1 0 0 1 1 0 1 1 0 ] {\displaystyle {\begin{bmatrix}1&1&0&1\\0&1&0&1\\0&0&1&1\\0&1&1&0\end{bmatrix}}} where all rows are pairwise distinct. If we delete, for example, the first column, the resulting matrix [ 1 0 1 1 0 1 0 1 1 1 1 0 ] {\displaystyle {\begin{bmatrix}1&0&1\\1&0&1\\0&1&1\\1&1&0\end{bmatrix}}} no longer has this property: the first row is identical to the second row. Nevertheless, by Bondy's theorem we know that we can always find a column that can be deleted without introducing any identical rows. In this case, we can delete the third column: all rows of the 3 × 4 matrix [ 1 1 1 0 1 1 0 0 1 0 1 0 ] {\displaystyle {\begin{bmatrix}1&1&1\\0&1&1\\0&0&1\\0&1&0\end{bmatrix}}} are distinct. Another possibility would have been deleting the fourth column. == Learning theory application == From the perspective of computational learning theory, Bondy's theorem can be rephrased as follows: Let C be a concept class over a finite domain X. Then there exists a subset S of X with the size at most |C| − 1 such that S is a witness set for every concept in C. This implies that every finite concept class C has its teaching dimension bounded by |C| − 1.

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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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  • Residual neural network

    Residual neural network

    A residual neural network (also referred to as a residual network or ResNet) is a deep learning architecture in which the layers learn residual functions with reference to the layer inputs. It was developed in 2015 for image recognition, and won the ImageNet Large Scale Visual Recognition Challenge (ILSVRC) of that year. As a point of terminology, "residual connection" refers to the specific architectural motif of x ↦ f ( x ) + x {\displaystyle x\mapsto f(x)+x} , where f {\displaystyle f} is an arbitrary neural network module. The motif had been used previously (see §History for details). However, the publication of ResNet made it widely popular for feedforward networks, appearing in neural networks that are seemingly unrelated to ResNet. The residual connection stabilizes the training and convergence of deep neural networks with hundreds of layers, and is a common motif in deep neural networks, such as transformer models (e.g., BERT, and GPT models such as ChatGPT), the AlphaGo Zero system, the AlphaStar system, and the AlphaFold system. == Mathematics == === Residual connection === In a multilayer neural network model, consider a (non-residual) subnetwork with a certain number of stacked layers (e.g., 2 or 3). Let H ( x ; α ) {\displaystyle H(x;\alpha )} denote the subnetwork. Suppose H ∗ {\displaystyle H^{}} is the desired optimal output of this subnetwork. Residual learning simply adds x {\displaystyle x} directly to the output, such that the optimal learned output now becomes be H ∗ − x {\displaystyle H^{}-x} , which is interpreted as a "residual" with respect to x {\displaystyle x} . The operation of "adding x {\displaystyle x} " is implemented via a "skip connection" that performs an identity mapping to connect the input of the subnetwork with its output. This connection is referred to as a "residual connection" in later work. Let F ( x ; α ) = H ( x ; a ) + x {\displaystyle F(x;\alpha )=H(x;a)+x} . The function F {\displaystyle F} is often represented by matrix multiplication interlaced with activation functions and normalization operations (e.g., batch normalization or layer normalization). As a whole, one of these subnetworks is referred to as a "residual block". A deep residual network is constructed by simply stacking these blocks. Long short-term memory (LSTM) has a memory mechanism that serves as a residual connection. In an LSTM without a forget gate, an input x t {\displaystyle x_{t}} is processed by a function F {\displaystyle F} and added to a memory cell c t {\displaystyle c_{t}} , resulting in c t + 1 = c t + F ( x t ) {\displaystyle c_{t+1}=c_{t}+F(x_{t})} . An LSTM with a forget gate essentially functions as a highway network. To stabilize the variance of the layers' inputs, it is recommended to replace the residual connections x + f ( x ) {\displaystyle x+f(x)} with x / L + f ( x ) {\displaystyle x/L+f(x)} , where L {\displaystyle L} is the total number of residual layers. === Projection connection === If the function F {\displaystyle F} is of type F : R n → R m {\displaystyle F:\mathbb {R} ^{n}\to \mathbb {R} ^{m}} where n ≠ m {\displaystyle n\neq m} , then F ( x ) + x {\displaystyle F(x)+x} is undefined. To handle this special case, a projection connection is used: y = F ( x ) + P ( x ) {\displaystyle y=F(x)+P(x)} where P {\displaystyle P} is typically a linear projection, defined by P ( x ) = M x {\displaystyle P(x)=Mx} where M {\displaystyle M} is a m × n {\displaystyle m\times n} matrix. The matrix is trained via backpropagation, as is any other parameter of the model. === Signal propagation === The introduction of identity mappings facilitates signal propagation in both forward and backward paths. ==== Forward propagation ==== If the output of the ℓ {\displaystyle \ell } -th residual block is the input to the ( ℓ + 1 ) {\displaystyle (\ell +1)} -th residual block (assuming no activation function between blocks), then the ( ℓ + 1 ) {\displaystyle (\ell +1)} -th input is: x ℓ + 1 = F ( x ℓ ) + x ℓ {\displaystyle x_{\ell +1}=F(x_{\ell })+x_{\ell }} Applying this formulation recursively, e.g.: x ℓ + 2 = F ( x ℓ + 1 ) + x ℓ + 1 = F ( x ℓ + 1 ) + F ( x ℓ ) + x ℓ {\displaystyle {\begin{aligned}x_{\ell +2}&=F(x_{\ell +1})+x_{\ell +1}\\&=F(x_{\ell +1})+F(x_{\ell })+x_{\ell }\end{aligned}}} yields the general relationship: x L = x ℓ + ∑ i = ℓ L − 1 F ( x i ) {\displaystyle x_{L}=x_{\ell }+\sum _{i=\ell }^{L-1}F(x_{i})} where L {\textstyle L} is the index of a residual block and ℓ {\textstyle \ell } is the index of some earlier block. This formulation suggests that there is always a signal that is directly sent from a shallower block ℓ {\textstyle \ell } to a deeper block L {\textstyle L} . ==== Backward propagation ==== The residual learning formulation provides the added benefit of mitigating the vanishing gradient problem to some extent. However, it is crucial to acknowledge that the vanishing gradient issue is not the root cause of the degradation problem, which is tackled through the use of normalization. To observe the effect of residual blocks on backpropagation, consider the partial derivative of a loss function E {\displaystyle {\mathcal {E}}} with respect to some residual block input x ℓ {\displaystyle x_{\ell }} . Using the equation above from forward propagation for a later residual block L > ℓ {\displaystyle L>\ell } : ∂ E ∂ x ℓ = ∂ E ∂ x L ∂ x L ∂ x ℓ = ∂ E ∂ x L ( 1 + ∂ ∂ x ℓ ∑ i = ℓ L − 1 F ( x i ) ) = ∂ E ∂ x L + ∂ E ∂ x L ∂ ∂ x ℓ ∑ i = ℓ L − 1 F ( x i ) {\displaystyle {\begin{aligned}{\frac {\partial {\mathcal {E}}}{\partial x_{\ell }}}&={\frac {\partial {\mathcal {E}}}{\partial x_{L}}}{\frac {\partial x_{L}}{\partial x_{\ell }}}\\&={\frac {\partial {\mathcal {E}}}{\partial x_{L}}}\left(1+{\frac {\partial }{\partial x_{\ell }}}\sum _{i=\ell }^{L-1}F(x_{i})\right)\\&={\frac {\partial {\mathcal {E}}}{\partial x_{L}}}+{\frac {\partial {\mathcal {E}}}{\partial x_{L}}}{\frac {\partial }{\partial x_{\ell }}}\sum _{i=\ell }^{L-1}F(x_{i})\end{aligned}}} This formulation suggests that the gradient computation of a shallower layer, ∂ E ∂ x ℓ {\textstyle {\frac {\partial {\mathcal {E}}}{\partial x_{\ell }}}} , always has a later term ∂ E ∂ x L {\textstyle {\frac {\partial {\mathcal {E}}}{\partial x_{L}}}} that is directly added. Even if the gradients of the F ( x i ) {\displaystyle F(x_{i})} terms are small, the total gradient ∂ E ∂ x ℓ {\textstyle {\frac {\partial {\mathcal {E}}}{\partial x_{\ell }}}} resists vanishing due to the added term ∂ E ∂ x L {\textstyle {\frac {\partial {\mathcal {E}}}{\partial x_{L}}}} . == Variants of residual blocks == === Basic block === A basic block is the simplest building block studied in the original ResNet. This block consists of two sequential 3x3 convolutional layers and a residual connection. The input and output dimensions of both layers are equal. === Bottleneck block === A bottleneck block consists of three sequential convolutional layers and a residual connection. The first layer in this block is a 1×1 convolution for dimension reduction (e.g., to 1/2 of the input dimension); the second layer performs a 3×3 convolution; the last layer is another 1×1 convolution for dimension restoration. The models of ResNet-50, ResNet-101, and ResNet-152 are all based on bottleneck blocks. === Pre-activation block === The pre-activation residual block applies activation functions before applying the residual function F {\displaystyle F} . Formally, the computation of a pre-activation residual block can be written as: x ℓ + 1 = F ( ϕ ( x ℓ ) ) + x ℓ {\displaystyle x_{\ell +1}=F(\phi (x_{\ell }))+x_{\ell }} where ϕ {\displaystyle \phi } can be any activation (e.g. ReLU) or normalization (e.g. LayerNorm) operation. This design reduces the number of non-identity mappings between residual blocks, and allows an identity mapping directly from the input to the output. This design was used to train models with 200 to over 1000 layers, and was found to consistently outperform variants where the residual path is not an identity function. The pre-activation ResNet with 200 layers took 3 weeks to train for ImageNet on 8 GPUs in 2016. Since GPT-2, transformer blocks have been mostly implemented as pre-activation blocks. This is often referred to as "pre-normalization" in the literature of transformer models. == Applications == Originally, ResNet was designed for computer vision. All transformer architectures include residual connections. Indeed, very deep transformers cannot be trained without them. The original ResNet paper made no claim on being inspired by biological systems. However, later research has related ResNet to biologically-plausible algorithms. A study published in Science in 2023 disclosed the complete connectome of an insect brain (specifically that of a fruit fly larva). This study discovered "multilayer shortcuts" that resemble the skip connections in artificial neural networks, including ResNets. == History == === Previous work === Residual connections were noticed in neu

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  • Relation network

    Relation network

    A relation network (RN) is an artificial neural network component with a structure that can reason about relations among objects. An example category of such relations is spatial relations (above, below, left, right, in front of, behind). RNs can infer relations, they are data efficient, and they operate on a set of objects without regard to the objects' order. == History == In June 2017, DeepMind announced the first relation network. It claimed that the technology had achieved "superhuman" performance on multiple question-answering problem sets. == Design == RNs constrain the functional form of a neural network to capture the common properties of relational reasoning. These properties are explicitly added to the system, rather than established by learning just as the capacity to reason about spatial, translation-invariant properties is explicitly part of convolutional neural networks (CNN). The data to be considered can be presented as a simple list or as a directed graph whose nodes are objects and whose edges are the pairs of objects whose relationships are to be considered. The RN is a composite function: R N ( O ) = f ϕ ( ∑ i , j g θ ( o i , o j , q ) ) , {\displaystyle RN\left(O\right)=f_{\phi }\left(\sum _{i,j}g_{\theta }\left(o_{i},o_{j},q\right)\right),} where the input is a set of "objects" O = { o 1 , o 2 , . . . , o n } , o i ∈ R m {\displaystyle O=\left\lbrace o_{1},o_{2},...,o_{n}\right\rbrace ,o_{i}\in \mathbb {R} ^{m}} is the ith object, and fφ and gθ are functions with parameters φ and θ, respectively and q is the question. fφ and gθ are multilayer perceptrons, while the 2 parameters are learnable synaptic weights. RNs are differentiable. The output of gθ is a "relation"; therefore, the role of gθ is to infer any ways in which two objects are related. Image (128x128 pixel) processing is done with a 4-layer CNN. Outputs from the CNN are treated as the objects for relation analysis, without regard for what those "objects" explicitly represent. Questions were processed with a long short-term memory network.

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  • ARKA descriptors in QSAR

    ARKA descriptors in QSAR

    In computational chemistry and cheminformatics, ARKA descriptors in QSAR are a class of molecular descriptors used in quantitative structure–activity relationship (QSAR) modeling (or related approaches such as QSPR and QSTR), a computational method for predicting the biological activity or toxicity of chemical compounds based on their molecular structure. Molecular descriptors are numerical values that summarize information about a molecule's structure, topology, geometry, or physicochemical properties in a form suitable for machine learning or statistical modeling. ARKA (Arithmetic Residuals in K-Groups Analysis) descriptors differ from traditional descriptors by encoding atomic-level information through recursive autoregression techniques, which aim to capture subtle structural patterns and improve predictive accuracy. They are designed to be both interpretable and well-suited to modeling nonlinear relationships in QSAR studies. == Comparisons == While QSAR is essentially a similarity-based approach, the occurrence of activity/property cliffs may greatly reduce the predictive accuracy of the developed models. The novel Arithmetic Residuals in K-groups Analysis (ARKA) approach is a supervised dimensionality reduction technique developed by the DTC Laboratory, Jadavpur University that can easily identify activity cliffs in a data set. Activity cliffs are similar in their structures but differ considerably in their activity. The basic idea of the ARKA descriptors is to group the conventional QSAR descriptors based on a predefined criterion and then assign weightage to each descriptor in each group. ARKA descriptors have also been used to develop classification-based and regression-based QSAR models with acceptable quality statistics. The ARKA descriptors have been used for the identification of activity cliffs in QSAR studies and/or model development by multiple researchers. A tutorial presentation on the ARKA descriptors is available. Recently a multi-class ARKA framework has been proposed for improved q-RASAR model generation.

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