In computer science theory – particularly formal language theory – Glushkov's construction algorithm, invented by Victor Mikhailovich Glushkov, transforms a given regular expression into an equivalent nondeterministic finite automaton (NFA). Thus, it forms a bridge between regular expressions and nondeterministic finite automata: two abstract representations of the same class of formal languages. A regular expression may be used to conveniently describe an advanced search pattern in a "find and replace"–like operation of a text processing utility. Glushkov's algorithm can be used to transform it into an NFA, which furthermore is small by nature, as the number of its states equals the number of symbols of the regular expression, plus one. Subsequently, the NFA can be made deterministic by the powerset construction and then be minimized to get an optimal automaton corresponding to the given regular expression. The latter format is best suited for execution on a computer. From another, more theoretical point of view, Glushkov's algorithm is a part of the proof that NFA and regular expressions both accept exactly the same languages; that is, the regular languages. The converse of Glushkov's algorithm is Kleene's algorithm, which transforms a finite automaton into a regular expression. The automaton obtained by Glushkov's construction is the same as the one obtained by Thompson's construction algorithm, once its ε-transitions are removed. Glushkov's construction algorithm is also called The algorithm of Berry-Sethi, named after Gérard Berry and Ravi Sethi who worked on this construction. == Construction == Given a regular expression e, the Glushkov Construction Algorithm creates a non-deterministic automaton that accepts the language L ( e ) {\displaystyle L(e)} accepted by e. The construction uses four steps: === Step 1 === Linearisation of the expression. Each letter of the alphabet appearing in the expression e is renamed, so that each letter occurs at most once in the new expression e ′ {\displaystyle e'} . Glushkov's construction essentially relies on the fact that e ′ {\displaystyle e'} represents a local language L ( e ′ ) {\displaystyle L(e')} . Let A be the old alphabet and let B be the new one. === Step 2a === Computation of the sets P ( e ′ ) {\displaystyle P(e')} , D ( e ′ ) {\displaystyle D(e')} , and F ( e ′ ) {\displaystyle F(e')} . The first, P ( e ′ ) {\displaystyle P(e')} , is the set of letters which occurs as first letter of a word of L ( e ′ ) {\displaystyle L(e')} . The second, D ( e ′ ) {\displaystyle D(e')} , is the set of letters that can end a word of L ( e ′ ) {\displaystyle L(e')} . The last one, F ( e ′ ) {\displaystyle F(e')} , is the set of letter pairs that can occur in words of L ( e ′ ) {\displaystyle L(e')} , i.e. it is the set of factors of length two of the words of L ( e ′ ) {\displaystyle L(e')} . Those sets are mathematically defined by P ( e ′ ) = { x ∈ B ∣ x B ∗ ∩ L ( e ′ ) ≠ ∅ } {\displaystyle P(e')=\{x\in B\mid xB^{}\cap L(e')\neq \emptyset \}} , D ( e ′ ) = { y ∈ B ∣ B ∗ y ∩ L ( e ′ ) ≠ ∅ } {\displaystyle D(e')=\{y\in B\mid B^{}y\cap L(e')\neq \emptyset \}} , F ( e ′ ) = { u ∈ B 2 ∣ B ∗ u B ∗ ∩ L ( e ′ ) ≠ ∅ } {\displaystyle F(e')=\{u\in B^{2}\mid B^{}uB^{}\cap L(e')\neq \emptyset \}} . They are computed by induction over the structure of the expression, as explained below. === Step 2b === Computation of the set Λ ( e ′ ) {\displaystyle \Lambda (e')} which contains the empty word ε {\displaystyle \varepsilon } if this word belongs to L ( e ′ ) {\displaystyle L(e')} , and is the empty set otherwise. Formally, this is Λ ( e ′ ) = { ε } ∩ L ( e ′ ) {\displaystyle \Lambda (e')=\{\varepsilon \}\cap L(e')} . === Step 3 === Computation of automaton recognizing the local language, as defined by P ( e ′ ) {\displaystyle P(e')} , D ( e ′ ) {\displaystyle D(e')} , F ( e ′ ) {\displaystyle F(e')} , and Λ ( e ′ ) {\displaystyle \Lambda (e')} . By definition, the local language defined by the sets P, D, and F is the set of words which begin with a letter of P, end by a letter of D, and whose factors of length 2 belong to F, optionally also including the empty word; that is, it is the language: L ′ = ( P B ∗ ∩ B ∗ D ) ∖ B ∗ ( B 2 ∖ F ) B ∗ ∪ Λ ( e ′ ) {\displaystyle L'=(PB^{}\cap B^{}D)\setminus B^{}(B^{2}\setminus F)B^{}\cup \Lambda (e')} . Strictly speaking, it is the computation of the automaton for the local language denoted by this linearised expression that is Glushkov's construction. === Step 4 === Remove the linearisation, replacing each indexed letter B by the original letter of A. == Example == Consider the regular expression e = ( a ( a b ) ∗ ) ∗ + ( b a ) ∗ {\displaystyle e=(a(ab)^{})^{}+(ba)^{}} . == Computation of the set of letters == The computation of the sets P, D, F, and Λ is done inductively over the regular expression e ′ {\displaystyle e'} . One must give the values for ∅, ε (the symbols for the empty language and the singleton language containing the empty word), the letters, and the results of the operations + , ⋅ , ∗ {\displaystyle +,\cdot ,^{}} . The most costly operations are the cartesian products of sets for the computation of F. == Properties == The obtained automaton is non-deterministic, and it has as many states as the number of letters of the regular expression, plus one. It has been proven that every Thompson's automaton can be transformed into Glushkov's automaton via a ε-transitions elimination method. == Applications and deterministic expressions == The computation of the automaton by the expression occurs often; it has been systematically used in search functions, in particular by the Unix grep command. Similarly, XML's specification also uses such constructions; for more efficiency, regular expressions of a certain kind, called deterministic expressions, have been studied.
Clipping (computer graphics)
Clipping, in the context of computer graphics, is a method to selectively enable or disable rendering operations within a defined region of interest. Mathematically, clipping can be described using the terminology of constructive geometry. A rendering algorithm only draws pixels in the intersection between the clip region and the scene model. Lines and surfaces outside the view volume (aka. frustum) are removed. Clip regions are commonly specified to improve render performance. Pixels that will be drawn are said to be within the clip region. Pixels that will not be drawn are outside the clip region. More informally, pixels that will not be drawn are said to be "clipped." == In 2D graphics == In two-dimensional graphics, a clip region may be defined so that pixels are only drawn within the boundaries of a window or frame. Clip regions can also be used to selectively control pixel rendering for aesthetic or artistic purposes. In many implementations, the final clip region is the composite (or intersection) of one or more application-defined shapes, as well as any system hardware constraints In one example application, consider an image editing program. A user application may render the image into a viewport. As the user zooms and scrolls to view a smaller portion of the image, the application can set a clip boundary so that pixels outside the viewport are not rendered. In addition, GUI widgets, overlays, and other windows or frames may obscure some pixels from the original image. In this sense, the clip region is the composite of the application-defined "user clip" and the "device clip" enforced by the system's software and hardware implementation. Application software can take advantage of this clip information to save computation time, energy, and memory, avoiding work related to pixels that aren't visible. == In 3D graphics == In three-dimensional graphics, the terminology of clipping can be used to describe many related features. Typically, "clipping" refers to operations in the plane that work with rectangular shapes, and "culling" refers to more general methods to selectively process scene model elements. This terminology is not rigid, and exact usage varies among many sources. Scene model elements include geometric primitives: points or vertices; line segments or edges; polygons or faces; and more abstract model objects such as curves, splines, surfaces, and even text. In complicated scene models, individual elements may be selectively disabled (clipped) for reasons including visibility within the viewport (frustum culling); orientation (backface culling), obscuration by other scene or model elements (occlusion culling, depth- or "z" clipping). Sophisticated algorithms exist to efficiently detect and perform such clipping. Many optimized clipping methods rely on specific hardware acceleration logic provided by a graphics processing unit (GPU). The concept of clipping can be extended to higher dimensionality using methods of abstract algebraic geometry. === Near clipping === Beyond projection of vertices & 2D clipping, near clipping is required to correctly rasterise 3D primitives; this is because vertices may have been projected behind the eye. Near clipping ensures that all the vertices used have valid 2D coordinates. Together with far-clipping it also helps prevent overflow of depth-buffer values. Some early texture mapping hardware (using forward texture mapping) in video games suffered from complications associated with near clipping and UV coordinates. === Occlusion clipping (Z- or depth clipping) === In 3D computer graphics, "Z" often refers to the depth axis in the system of coordinates centered at the viewport origin: "Z" is used interchangeably with "depth", and conceptually corresponds to the distance "into the virtual screen." In this coordinate system, "X" and "Y" therefore refer to a conventional cartesian coordinate system laid out on the user's screen or viewport. This viewport is defined by the geometry of the viewing frustum, and parameterizes the field of view. Z-clipping, or depth clipping, refers to techniques that selectively render certain scene objects based on their depth relative to the screen. Most graphics toolkits allow the programmer to specify a "near" and "far" clip depth, and only portions of objects between those two planes are displayed. A creative application programmer can use this method to render visualizations of the interior of a 3D object in the scene. For example, a medical imaging application could use this technique to render the organs inside a human body. A video game programmer can use clipping information to accelerate game logic. For example, a tall wall or building that occludes other game entities can save GPU time that would otherwise be spent transforming and texturing items in the rear areas of the scene; and a tightly integrated software program can use this same information to save CPU time by optimizing out game logic for objects that aren't seen by the player. == Algorithms == Line clipping algorithms: Cohen–Sutherland Liang–Barsky Fast-clipping Cyrus–Beck Nicholl–Lee–Nicholl Skala O(lg N) algorithm Polygon clipping algorithms: Greiner–Hormann Sutherland–Hodgman Weiler–Atherton Vatti Rendering methodologies Painter's algorithm
Triplet loss
Triplet loss is a machine learning loss function widely used in one-shot learning, a setting where models are trained to generalize effectively from limited examples. It was conceived by Google researchers for their prominent FaceNet algorithm for face detection. Triplet loss is designed to support metric learning. Namely, to assist training models to learn an embedding (mapping to a feature space) where similar data points are closer together and dissimilar ones are farther apart, enabling robust discrimination across varied conditions. In the context of face detection, data points correspond to images. == Definition == The loss function is defined using triplets of training points of the form ( A , P , N ) {\displaystyle (A,P,N)} . In each triplet, A {\displaystyle A} (called an "anchor point") denotes a reference point of a particular identity, P {\displaystyle P} (called a "positive point") denotes another point of the same identity in point A {\displaystyle A} , and N {\displaystyle N} (called a "negative point") denotes a point of an identity different from the identity in point A {\displaystyle A} and P {\displaystyle P} . Let x {\displaystyle x} be some point and let f ( x ) {\displaystyle f(x)} be the embedding of x {\displaystyle x} in the finite-dimensional Euclidean space. It shall be assumed that the L2-norm of f ( x ) {\displaystyle f(x)} is unity (the L2 norm of a vector X {\displaystyle X} in a finite dimensional Euclidean space is denoted by ‖ X ‖ {\displaystyle \Vert X\Vert } .) We assemble m {\displaystyle m} triplets of points from the training dataset. The goal of training here is to ensure that, after learning, the following condition (called the "triplet constraint") is satisfied by all triplets ( A ( i ) , P ( i ) , N ( i ) ) {\displaystyle (A^{(i)},P^{(i)},N^{(i)})} in the training data set: ‖ f ( A ( i ) ) − f ( P ( i ) ) ‖ 2 2 + α < ‖ f ( A ( i ) ) − f ( N ( i ) ) ‖ 2 2 {\displaystyle \Vert f(A^{(i)})-f(P^{(i)})\Vert _{2}^{2}+\alpha <\Vert f(A^{(i)})-f(N^{(i)})\Vert _{2}^{2}} The variable α {\displaystyle \alpha } is a hyperparameter called the margin, and its value must be set manually. In the FaceNet system, its value was set as 0.2. Thus, the full form of the function to be minimized is the following: L = ∑ i = 1 m max ( ‖ f ( A ( i ) ) − f ( P ( i ) ) ‖ 2 2 − ‖ f ( A ( i ) ) − f ( N ( i ) ) ‖ 2 2 + α , 0 ) {\displaystyle L=\sum _{i=1}^{m}\max {\Big (}\Vert f(A^{(i)})-f(P^{(i)})\Vert _{2}^{2}-\Vert f(A^{(i)})-f(N^{(i)})\Vert _{2}^{2}+\alpha ,0{\Big )}} == Intuition == A baseline for understanding the effectiveness of triplet loss is the contrastive loss, which operates on pairs of samples (rather than triplets). Training with the contrastive loss pulls embeddings of similar pairs closer together, and pushes dissimilar pairs apart. Its pairwise approach is greedy, as it considers each pair in isolation. Triplet loss innovates by considering relative distances. Its goal is that the embedding of an anchor (query) point be closer to positive points than to negative points (also accounting for the margin). It does not try to further optimize the distances once this requirement is met. This is approximated by simultaneously considering two pairs (anchor-positive and anchor-negative), rather than each pair in isolation. == Triplet "mining" == One crucial implementation detail when training with triplet loss is triplet "mining", which focuses on the smart selection of triplets for optimization. This process adds an additional layer of complexity compared to contrastive loss. A naive approach to preparing training data for the triplet loss involves randomly selecting triplets from the dataset. In general, the set of valid triplets of the form ( A ( i ) , P ( i ) , N ( i ) ) {\displaystyle (A^{(i)},P^{(i)},N^{(i)})} is very large. To speed-up training convergence, it is essential to focus on challenging triplets. In the FaceNet paper, several options were explored, eventually arriving at the following. For each anchor-positive pair, the algorithm considers only semi-hard negatives. These are negatives that violate the triplet requirement (i.e, are "hard"), but lie farther from the anchor than the positive (not too hard). Restated, for each A ( i ) {\displaystyle A^{(i)}} and P ( i ) {\displaystyle P^{(i)}} , they seek N ( i ) {\displaystyle N^{(i)}} such that: The rationale for this design choice is heuristic. It may appear puzzling that the mining process neglects "very hard" negatives (i.e., closer to the anchor than the positive). Experiments conducted by the FaceNet designers found that this often leads to a convergence to degenerate local minima. Triplet mining is performed at each training step, from within the sample points contained in the training batch (this is known as online mining), after embeddings were computed for all points in the batch. While ideally the entire dataset could be used, this is impractical in general. To support a large search space for triplets, the FaceNet authors used very large batches (1800 samples). Batches are constructed by selecting a large number of same-category sample points (40), and randomly selected negatives for them. == Extensions == Triplet loss has been extended to simultaneously maintain a series of distance orders by optimizing a continuous relevance degree with a chain (i.e., ladder) of distance inequalities. This leads to the Ladder Loss, which has been demonstrated to offer performance enhancements of visual-semantic embedding in learning to rank tasks. In Natural Language Processing, triplet loss is one of the loss functions considered for BERT fine-tuning in the SBERT architecture. Other extensions involve specifying multiple negatives (multiple negatives ranking loss).
Modern Hopfield network
Modern Hopfield networks (also known as Dense Associative Memories) are generalizations of the classical Hopfield networks that break the linear scaling relationship between the number of input features and the number of stored memories. This is achieved by introducing stronger non-linearities (either in the energy function or neurons’ activation functions) leading to super-linear (even an exponential) memory storage capacity as a function of the number of feature neurons. The network still requires a sufficient number of hidden neurons. The key theoretical idea behind the modern Hopfield networks is to use an energy function and an update rule that is more sharply peaked around the stored memories in the space of neuron’s configurations compared to the classical Hopfield network. == Classical Hopfield networks == Hopfield networks are recurrent neural networks with dynamical trajectories converging to fixed point attractor states and described by an energy function. The state of each model neuron i {\textstyle i} is defined by a time-dependent variable V i {\displaystyle V_{i}} , which can be chosen to be either discrete or continuous. A complete model describes the mathematics of how the future state of activity of each neuron depends on the known present or previous activity of all the neurons. In the original Hopfield model of associative memory, the variables were binary, and the dynamics were described by a one-at-a-time update of the state of the neurons. An energy function quadratic in the V i {\displaystyle V_{i}} was defined, and the dynamics consisted of changing the activity of each single neuron i {\displaystyle i} only if doing so would lower the total energy of the system. This same idea was extended to the case of V i {\displaystyle V_{i}} being a continuous variable representing the output of neuron i {\displaystyle i} , and V i {\displaystyle V_{i}} being a monotonic function of an input current. The dynamics became expressed as a set of first-order differential equations for which the "energy" of the system always decreased. The energy in the continuous case has one term which is quadratic in the V i {\displaystyle V_{i}} (as in the binary model), and a second term which depends on the gain function (neuron's activation function). While having many desirable properties of associative memory, both of these classical systems suffer from a small memory storage capacity, which scales linearly with the number of input features. == Discrete variables == A simple example of the Modern Hopfield network can be written in terms of binary variables V i {\displaystyle V_{i}} that represent the active V i = + 1 {\displaystyle V_{i}=+1} and inactive V i = − 1 {\displaystyle V_{i}=-1} state of the model neuron i {\displaystyle i} . E = − ∑ μ = 1 N mem F ( ∑ i = 1 N f ξ μ i V i ) {\displaystyle E=-\sum \limits _{\mu =1}^{N_{\text{mem}}}F{\Big (}\sum \limits _{i=1}^{N_{f}}\xi _{\mu i}V_{i}{\Big )}} In this formula the weights ξ μ i {\textstyle \xi _{\mu i}} represent the matrix of memory vectors (index μ = 1... N mem {\displaystyle \mu =1...N_{\text{mem}}} enumerates different memories, and index i = 1... N f {\displaystyle i=1...N_{f}} enumerates the content of each memory corresponding to the i {\displaystyle i} -th feature neuron), and the function F ( x ) {\displaystyle F(x)} is a rapidly growing non-linear function. The update rule for individual neurons (in the asynchronous case) can be written in the following form V i ( t + 1 ) = sign [ ∑ μ = 1 N mem ( F ( ξ μ i + ∑ j ≠ i ξ μ j V j ( t ) ) − F ( − ξ μ i + ∑ j ≠ i ξ μ j V j ( t ) ) ) ] {\displaystyle V_{i}^{(t+1)}=\operatorname {sign} {\bigg [}\sum \limits _{\mu =1}^{N_{\text{mem}}}{\bigg (}F{\Big (}\xi _{\mu i}+\sum \limits _{j\neq i}\xi _{\mu j}V_{j}^{(t)}{\Big )}-F{\Big (}-\xi _{\mu i}+\sum \limits _{j\neq i}\xi _{\mu j}V_{j}^{(t)}{\Big )}{\bigg )}{\bigg ]}} which states that in order to calculate the updated state of the i {\textstyle i} -th neuron the network compares two energies: the energy of the network with the i {\displaystyle i} -th neuron in the ON state and the energy of the network with the i {\displaystyle i} -th neuron in the OFF state, given the states of the remaining neuron. The updated state of the i {\displaystyle i} -th neuron selects the state that has the lowest of the two energies. In the limiting case when the non-linear energy function is quadratic F ( x ) = x 2 {\displaystyle F(x)=x^{2}} these equations reduce to the familiar energy function and the update rule for the classical binary Hopfield network. The memory storage capacity of these networks can be calculated for random binary patterns. For the power energy function F ( x ) = x n {\displaystyle F(x)=x^{n}} the maximal number of memories that can be stored and retrieved from this network without errors is given by N mem max ≈ 1 2 ( 2 n − 3 ) ! ! N f n − 1 ln ( N f ) {\displaystyle N_{\text{mem}}^{\max }\approx {\frac {1}{2(2n-3)!!}}{\frac {N_{f}^{n-1}}{\ln(N_{f})}}} For an exponential energy function F ( x ) = e x {\textstyle F(x)=e^{x}} the memory storage capacity is exponential in the number of feature neurons N mem max ≈ 2 N f / 2 {\displaystyle N_{\text{mem}}^{\max }\approx 2^{N_{f}/2}} == Continuous variables == Modern Hopfield networks or Dense Associative Memories can be best understood in continuous variables and continuous time. Consider the network architecture, shown in Fig.1, and the equations for the neurons' state evolutionwhere the currents of the feature neurons are denoted by x i {\textstyle x_{i}} , and the currents of the memory neurons are denoted by h μ {\displaystyle h_{\mu }} ( h {\displaystyle h} stands for hidden neurons). There are no synaptic connections among the feature neurons or the memory neurons. A matrix ξ μ i {\displaystyle \xi _{\mu i}} denotes the strength of synapses from a feature neuron i {\displaystyle i} to the memory neuron μ {\displaystyle \mu } . The synapses are assumed to be symmetric, so that the same value characterizes a different physical synapse from the memory neuron μ {\displaystyle \mu } to the feature neuron i {\displaystyle i} . The outputs of the memory neurons and the feature neurons are denoted by f μ {\displaystyle f_{\mu }} and g i {\displaystyle g_{i}} , which are non-linear functions of the corresponding currents. In general these outputs can depend on the currents of all the neurons in that layer so that f μ = f ( { h μ } ) {\displaystyle f_{\mu }=f(\{h_{\mu }\})} and g i = g ( { x i } ) {\textstyle g_{i}=g(\{x_{i}\})} . It is convenient to define these activation function as derivatives of the Lagrangian functions for the two groups of neuronsThis way the specific form of the equations for neuron's states is completely defined once the Lagrangian functions are specified. Finally, the time constants for the two groups of neurons are denoted by τ f {\displaystyle \tau _{f}} and τ h {\displaystyle \tau _{h}} , I i {\displaystyle I_{i}} is the input current to the network that can be driven by the presented data. General systems of non-linear differential equations can have many complicated behaviors that can depend on the choice of the non-linearities and the initial conditions. For Hopfield networks, however, this is not the case - the dynamical trajectories always converge to a fixed point attractor state. This property is achieved because these equations are specifically engineered so that they have an underlying energy function The terms grouped into square brackets represent a Legendre transform of the Lagrangian function with respect to the states of the neurons. If the Hessian matrices of the Lagrangian functions are positive semi-definite, the energy function is guaranteed to decrease on the dynamical trajectory This property makes it possible to prove that the system of dynamical equations describing temporal evolution of neurons' activities will eventually reach a fixed point attractor state. In certain situations one can assume that the dynamics of hidden neurons equilibrates at a much faster time scale compared to the feature neurons, τ h ≪ τ f {\textstyle \tau _{h}\ll \tau _{f}} . In this case the steady state solution of the second equation in the system (1) can be used to express the currents of the hidden units through the outputs of the feature neurons. This makes it possible to reduce the general theory (1) to an effective theory for feature neurons only. The resulting effective update rules and the energies for various common choices of the Lagrangian functions are shown in Fig.2. In the case of log-sum-exponential Lagrangian function the update rule (if applied once) for the states of the feature neurons is the attention mechanism commonly used in many modern AI systems (see Ref. for the derivation of this result from the continuous time formulation). == Relationship to classical Hopfield network with continuous variables == Classical formulation of continuous Hopfield networks can be understood as a
Diffusion map
Diffusion maps is a dimensionality reduction or feature extraction algorithm introduced by Coifman and Lafon which computes a family of embeddings of a data set into Euclidean space (often low-dimensional) whose coordinates can be computed from the eigenvectors and eigenvalues of a diffusion operator on the data. The Euclidean distance between points in the embedded space is equal to the "diffusion distance" between probability distributions centered at those points. Different from linear dimensionality reduction methods such as principal component analysis (PCA), diffusion maps are part of the family of nonlinear dimensionality reduction methods which focus on discovering the underlying manifold that the data has been sampled from. By integrating local similarities at different scales, diffusion maps give a global description of the data-set. Compared with other methods, the diffusion map algorithm is robust to noise perturbation and computationally inexpensive. == Definition of diffusion maps == Following and , diffusion maps can be defined in four steps. === Connectivity === Diffusion maps exploit the relationship between heat diffusion and random walk Markov chain. The basic observation is that if we take a random walk on the data, walking to a nearby data-point is more likely than walking to another that is far away. Let ( X , A , μ ) {\displaystyle (X,{\mathcal {A}},\mu )} be a measure space, where X {\displaystyle X} is the data set and μ {\displaystyle \mu } represents the distribution of the points on X {\displaystyle X} . Based on this, the connectivity k {\displaystyle k} between two data points, x {\displaystyle x} and y {\displaystyle y} , can be defined as the probability of walking from x {\displaystyle x} to y {\displaystyle y} in one step of the random walk. Usually, this probability is specified in terms of a kernel function of the two points: k : X × X → R {\displaystyle k:X\times X\rightarrow \mathbb {R} } . For example, the popular Gaussian kernel: k ( x , y ) = exp ( − | | x − y | | 2 ϵ ) {\displaystyle k(x,y)=\exp \left(-{\frac {||x-y||^{2}}{\epsilon }}\right)} More generally, the kernel function has the following properties k ( x , y ) = k ( y , x ) {\displaystyle k(x,y)=k(y,x)} ( k {\displaystyle k} is symmetric) k ( x , y ) ≥ 0 ∀ x , y {\displaystyle k(x,y)\geq 0\,\,\forall x,y} ( k {\displaystyle k} is positivity preserving). The kernel constitutes the prior definition of the local geometry of the data-set. Since a given kernel will capture a specific feature of the data set, its choice should be guided by the application that one has in mind. This is a major difference with methods such as principal component analysis, where correlations between all data points are taken into account at once. Given ( X , k ) {\displaystyle (X,k)} , we can then construct a reversible discrete-time Markov chain on X {\displaystyle X} (a process known as the normalized graph Laplacian construction): d ( x ) = ∫ X k ( x , y ) d μ ( y ) {\displaystyle d(x)=\int _{X}k(x,y)d\mu (y)} and define: p ( x , y ) = k ( x , y ) d ( x ) {\displaystyle p(x,y)={\frac {k(x,y)}{d(x)}}} Although the new normalized kernel does not inherit the symmetric property, it does inherit the positivity-preserving property and gains a conservation property: ∫ X p ( x , y ) d μ ( y ) = 1 {\displaystyle \int _{X}p(x,y)d\mu (y)=1} === Diffusion process === From p ( x , y ) {\displaystyle p(x,y)} we can construct a transition matrix of a Markov chain ( M {\displaystyle M} ) on X {\displaystyle X} . In other words, p ( x , y ) {\displaystyle p(x,y)} represents the one-step transition probability from x {\displaystyle x} to y {\displaystyle y} , and M t {\displaystyle M^{t}} gives the t-step transition matrix. We define the diffusion matrix L {\displaystyle L} (it is also a version of graph Laplacian matrix) L i , j = k ( x i , x j ) {\displaystyle L_{i,j}=k(x_{i},x_{j})\,} We then define the new kernel L i , j ( α ) = k ( α ) ( x i , x j ) = L i , j ( d ( x i ) d ( x j ) ) α {\displaystyle L_{i,j}^{(\alpha )}=k^{(\alpha )}(x_{i},x_{j})={\frac {L_{i,j}}{(d(x_{i})d(x_{j}))^{\alpha }}}\,} or equivalently, L ( α ) = D − α L D − α {\displaystyle L^{(\alpha )}=D^{-\alpha }LD^{-\alpha }\,} where D is a diagonal matrix and D i , i = ∑ j L i , j . {\displaystyle D_{i,i}=\sum _{j}L_{i,j}.} We apply the graph Laplacian normalization to this new kernel: M = ( D ( α ) ) − 1 L ( α ) , {\displaystyle M=({D}^{(\alpha )})^{-1}L^{(\alpha )},\,} where D ( α ) {\displaystyle D^{(\alpha )}} is a diagonal matrix and D i , i ( α ) = ∑ j L i , j ( α ) . {\displaystyle {D}_{i,i}^{(\alpha )}=\sum _{j}L_{i,j}^{(\alpha )}.} p ( x j , t | x i ) = M i , j t {\displaystyle p(x_{j},t|x_{i})=M_{i,j}^{t}\,} One of the main ideas of the diffusion framework is that running the chain forward in time (taking larger and larger powers of M {\displaystyle M} ) reveals the geometric structure of X {\displaystyle X} at larger and larger scales (the diffusion process). Specifically, the notion of a cluster in the data set is quantified as a region in which the probability of escaping this region is low (within a certain time t). Therefore, t not only serves as a time parameter, but it also has the dual role of scale parameter. The eigendecomposition of the matrix M t {\displaystyle M^{t}} yields M i , j t = ∑ l λ l t ψ l ( x i ) ϕ l ( x j ) {\displaystyle M_{i,j}^{t}=\sum _{l}\lambda _{l}^{t}\psi _{l}(x_{i})\phi _{l}(x_{j})\,} where { λ l } {\displaystyle \{\lambda _{l}\}} is the sequence of eigenvalues of M {\displaystyle M} and { ψ l } {\displaystyle \{\psi _{l}\}} and { ϕ l } {\displaystyle \{\phi _{l}\}} are the biorthogonal left and right eigenvectors respectively. Due to the spectrum decay of the eigenvalues, only a few terms are necessary to achieve a given relative accuracy in this sum. ==== Parameter α and the diffusion operator ==== The reason to introduce the normalization step involving α {\displaystyle \alpha } is to tune the influence of the data point density on the infinitesimal transition of the diffusion. In some applications, the sampling of the data is generally not related to the geometry of the manifold we are interested in describing. In this case, we can set α = 1 {\displaystyle \alpha =1} and the diffusion operator approximates the Laplace–Beltrami operator. We then recover the Riemannian geometry of the data set regardless of the distribution of the points. To describe the long-term behavior of the point distribution of a system of stochastic differential equations, we can use α = 0.5 {\displaystyle \alpha =0.5} and the resulting Markov chain approximates the Fokker–Planck diffusion. With α = 0 {\displaystyle \alpha =0} , it reduces to the classical graph Laplacian normalization. === Diffusion distance === The diffusion distance at time t {\displaystyle t} between two points can be measured as the similarity of two points in the observation space with the connectivity between them. It is given by D t ( x i , x j ) 2 = ∑ y ( p ( y , t | x i ) − p ( y , t | x j ) ) 2 ϕ 0 ( y ) {\displaystyle D_{t}(x_{i},x_{j})^{2}=\sum _{y}{\frac {(p(y,t|x_{i})-p(y,t|x_{j}))^{2}}{\phi _{0}(y)}}} where ϕ 0 ( y ) {\displaystyle \phi _{0}(y)} is the stationary distribution of the Markov chain, given by the first left eigenvector of M {\displaystyle M} . Explicitly: ϕ 0 ( y ) = d ( y ) ∑ z ∈ X d ( z ) {\displaystyle \phi _{0}(y)={\frac {d(y)}{\sum _{z\in X}d(z)}}} Intuitively, D t ( x i , x j ) {\displaystyle D_{t}(x_{i},x_{j})} is small if there is a large number of short paths connecting x i {\displaystyle x_{i}} and x j {\displaystyle x_{j}} . There are several interesting features associated with the diffusion distance, based on our previous discussion that t {\displaystyle t} also serves as a scale parameter: Points are closer at a given scale (as specified by D t ( x i , x j ) {\displaystyle D_{t}(x_{i},x_{j})} ) if they are highly connected in the graph, therefore emphasizing the concept of a cluster. This distance is robust to noise, since the distance between two points depends on all possible paths of length t {\displaystyle t} between the points. From a machine learning point of view, the distance takes into account all evidences linking x i {\displaystyle x_{i}} to x j {\displaystyle x_{j}} , allowing us to conclude that this distance is appropriate for the design of inference algorithms based on the majority of preponderance. === Diffusion process and low-dimensional embedding === The diffusion distance can be calculated using the eigenvectors by D t ( x i , x j ) 2 = ∑ l λ l 2 t ( ψ l ( x i ) − ψ l ( x j ) ) 2 {\displaystyle D_{t}(x_{i},x_{j})^{2}=\sum _{l}\lambda _{l}^{2t}(\psi _{l}(x_{i})-\psi _{l}(x_{j}))^{2}\,} So the eigenvectors can be used as a new set of coordinates for the data. The diffusion map is defined as: Ψ t ( x ) = ( λ 1 t ψ 1 ( x ) , λ 2 t ψ 2 ( x ) , … , λ k t ψ k ( x ) ) {\displaystyle \Psi _{t}(x)=(\lambda _{1}^{t}\psi _{1}(x),\lambda _{2}^{t}\psi _{2}(x),\ld
Space partitioning
In geometry, space partitioning is the process of dividing an entire space (usually a Euclidean space) into two or more disjoint subsets (see also partition of a set). In other words, space partitioning divides a space into non-overlapping regions. Any point in the space can then be identified to lie in exactly one of the regions. == Overview == Space-partitioning systems are often hierarchical, meaning that a space (or a region of space) is divided into several regions, and then the same space-partitioning system is recursively applied to each of the regions thus created. The regions can be organized into a tree, called a space-partitioning tree. Most space-partitioning systems use planes (or, in higher dimensions, hyperplanes) to divide space: points on one side of the plane form one region, and points on the other side form another. Points exactly on the plane are usually arbitrarily assigned to one or the other side. Recursively partitioning space using planes in this way produces a BSP tree, one of the most common forms of space partitioning. == Uses == === In computer graphics === Space partitioning is particularly important in computer graphics, especially heavily used in ray tracing, where it is frequently used to organize the objects in a virtual scene. A typical scene may contain millions of polygons. Performing a ray/polygon intersection test with each would be a very computationally expensive task. Storing objects in a space-partitioning data structure (k-d tree or BSP tree for example) makes it easy and fast to perform certain kinds of geometry queries—for example in determining whether a ray intersects an object, space partitioning can reduce the number of intersection test to just a few per primary ray, yielding a logarithmic time complexity with respect to the number of polygons. Space partitioning is also often used in scanline algorithms to eliminate the polygons out of the camera's viewing frustum, limiting the number of polygons processed by the pipeline. There is also a usage in collision detection: determining whether two objects are close to each other can be much faster using space partitioning. === In integrated circuit design === In integrated circuit design, an important step is design rule check. This step ensures that the completed design is manufacturable. The check involves rules that specify widths and spacings and other geometry patterns. A modern design can have billions of polygons that represent wires and transistors. Efficient checking relies heavily on geometry query. For example, a rule may specify that any polygon must be at least n nanometers from any other polygon. This is converted into a geometry query by enlarging a polygon by n/2 at all sides and query to find all intersecting polygons. === In probability and statistical learning theory === The number of components in a space partition plays a central role in some results in probability theory. See Growth function for more details. === In geography and GIS === There are many studies and applications where Geographical Spatial Reality is partitioned by hydrological criteria, administrative criteria, mathematical criteria or many others. In the context of cartography and GIS - Geographic Information System, is common to identify cells of the partition by standard codes. For example the for HUC code identifying hydrographical basins and sub-basins, ISO 3166-2 codes identifying countries and its subdivisions, or arbitrary DGGs - discrete global grids identifying quadrants or locations. == Data structures == Common space-partitioning systems include: BSP trees Quadtrees Octrees k-d trees Bins == Number of components == Suppose the n-dimensional Euclidean space is partitioned by r {\displaystyle r} hyperplanes that are ( n − 1 ) {\displaystyle (n-1)} -dimensional. What is the number of components in the partition? The largest number of components is attained when the hyperplanes are in general position, i.e, no two are parallel and no three have the same intersection. Denote this maximum number of components by C o m p ( n , r ) {\displaystyle Comp(n,r)} . Then, the following recurrence relation holds: C o m p ( n , r ) = C o m p ( n , r − 1 ) + C o m p ( n − 1 , r − 1 ) {\displaystyle Comp(n,r)=Comp(n,r-1)+Comp(n-1,r-1)} C o m p ( 0 , r ) = 1 {\displaystyle Comp(0,r)=1} - when there are no dimensions, there is a single point. C o m p ( n , 0 ) = 1 {\displaystyle Comp(n,0)=1} - when there are no hyperplanes, all the space is a single component. And its solution is: C o m p ( n , r ) = ∑ k = 0 n ( r k ) {\displaystyle Comp(n,r)=\sum _{k=0}^{n}{r \choose k}} if r ≥ n {\displaystyle r\geq n} C o m p ( n , r ) = 2 r {\displaystyle Comp(n,r)=2^{r}} if r ≤ n {\displaystyle r\leq n} (consider e.g. r {\displaystyle r} perpendicular hyperplanes; each additional hyperplane divides each existing component to 2). which is upper-bounded as: C o m p ( n , r ) ≤ r n + 1 {\displaystyle Comp(n,r)\leq r^{n}+1}
Ordination (statistics)
Ordination or gradient analysis, in multivariate analysis, is a method complementary to data clustering, and used mainly in exploratory data analysis (rather than in hypothesis testing). In contrast to cluster analysis, ordination orders quantities in a (usually lower-dimensional) latent space. In the ordination space, quantities that are near each other share attributes (i.e., are similar to some degree), and dissimilar objects are farther from each other. Such relationships between the objects, on each of several axes or latent variables, are then characterized numerically and/or graphically in a biplot. The first ordination method, principal components analysis, was suggested by Karl Pearson in 1901. == Methods == Ordination methods can broadly be categorized in eigenvector-, algorithm-, or model-based methods. Many classical ordination techniques, including principal components analysis, correspondence analysis (CA) and its derivatives (detrended correspondence analysis, canonical correspondence analysis, and redundancy analysis, belong to the first group). The second group includes some distance-based methods such as non-metric multidimensional scaling, and machine learning methods such as T-distributed stochastic neighbor embedding and nonlinear dimensionality reduction. The third group includes model-based ordination methods, which can be considered as multivariate extensions of Generalized Linear Models. Model-based ordination methods are more flexible in their application than classical ordination methods, so that it is for example possible to include random-effects. Unlike in the aforementioned two groups, there is no (implicit or explicit) distance measure in the ordination. Instead, a distribution needs to be specified for the responses as is typical for statistical models. These and other assumptions, such as the assumed mean-variance relationship, can be validated with the use of residual diagnostics, unlike in other ordination methods. == Applications == Ordination can be used on the analysis of any set of multivariate objects. It is frequently used in several environmental or ecological sciences, particularly plant community ecology. It is also used in genetics and systems biology for microarray data analysis and in psychometrics.