AI Email Message Generator

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  Cozi

  Cozi is a family organization website and mobile app designed to streamline household management. It offers shared calendars, to-do lists, shopping lists, and messaging tools, allowing multiple users to coordinate under one account. Founded in 2005 by former Microsoft employees, Cozi has evolved through acquisitions and now operates under OurFamilyWizard. The app is available in both free and premium versions on iOS, Android, and desktop platforms. == History == Cozi was founded in 2005 by Robbie Cape and Jan Miksovsky, two former Microsoft employees who sought to simplify family logistics with technology. The company's first product, Cozi Central, was released on September 25, 2006, and included a family calendar, shopping lists, family messaging and a photo collage screensaver. The company is based in Seattle, Washington. Cozi has both a freemium version, and a paid version called Cozi Gold. Cozi Gold's additional features include Cozi Contacts, a birthday tracker, more reminders, mobile month view, and change notifications. The software can be used on desktop or mobile applications for iOS and Android. On June 5, 2011, Cozi set a Guinness World Record for the longest line of ducks in a row. The line stretched for one mile and was made up of 17,782 rubber ducks. Cozi was acquired by Time Inc. in 2014. After the Meredith Corporation acquired Time in 2018, Cozi was moved into the Parents Network division. On May 4, 2022, Cozi was acquired by OurFamilyWizard of Minneapolis, Minnesota, reporting more than 20 million registered users.

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  Neural cryptography

  Neural cryptography is a branch of cryptography dedicated to analyzing the application of stochastic algorithms, especially artificial neural network algorithms, for use in encryption and cryptanalysis. == Definition == Artificial neural networks are well known for their ability to selectively explore the solution space of a given problem. This feature finds a natural niche of application in the field of cryptanalysis. At the same time, neural networks offer a new approach to attack ciphering algorithms based on the principle that any function could be reproduced by a neural network, which is a powerful proven computational tool that can be used to find the inverse-function of any cryptographic algorithm. The ideas of mutual learning, self learning, and stochastic behavior of neural networks and similar algorithms can be used for different aspects of cryptography, like public-key cryptography, solving the key distribution problem using neural network mutual synchronization, hashing or generation of pseudo-random numbers. Another idea is the ability of a neural network to separate space in non-linear pieces using "bias". It gives different probabilities of activating the neural network or not. This is very useful in the case of Cryptanalysis. Two names are used to design the same domain of research: Neuro-Cryptography and Neural Cryptography. The first work that it is known on this topic can be traced back to 1995 in an IT Master Thesis. == Applications == In 1995, Sebastien Dourlens applied neural networks to cryptanalyze DES by allowing the networks to learn how to invert the S-tables of the DES. The bias in DES studied through Differential Cryptanalysis by Adi Shamir is highlighted. The experiment shows about 50% of the key bits can be found, allowing the complete key to be found in a short time. Hardware application with multi micro-controllers have been proposed due to the easy implementation of multilayer neural networks in hardware. One example of a public-key protocol is given by Khalil Shihab . He describes the decryption scheme and the public key creation that are based on a backpropagation neural network. The encryption scheme and the private key creation process are based on Boolean algebra. This technique has the advantage of small time and memory complexities. A disadvantage is the property of backpropagation algorithms: because of huge training sets, the learning phase of a neural network is very long. Therefore, the use of this protocol is only theoretical so far. == Neural key exchange protocol == The most used protocol for key exchange between two parties A and B in the practice is Diffie–Hellman key exchange protocol. Neural key exchange, which is based on the synchronization of two tree parity machines, should be a secure replacement for this method. Synchronizing these two machines is similar to synchronizing two chaotic oscillators in chaos communications. === Tree parity machine === The tree parity machine is a special type of multi-layer feedforward neural network. It consists of one output neuron, K hidden neurons and K×N input neurons. Inputs to the network take three values: x i j ∈ { − 1 , 0 , + 1 } {\displaystyle x_{ij}\in \left\{-1,0,+1\right\}} The weights between input and hidden neurons take the values: w i j ∈ { − L , . . . , 0 , . . . , + L } {\displaystyle w_{ij}\in \left\{-L,...,0,...,+L\right\}} Output value of each hidden neuron is calculated as a sum of all multiplications of input neurons and these weights: σ i = sgn ⁡ ( ∑ j = 1 N w i j x i j ) {\displaystyle \sigma _{i}=\operatorname {sgn}(\sum _{j=1}^{N}w_{ij}x_{ij})} Signum is a simple function, which returns −1,0 or 1: sgn ⁡ ( x ) = { − 1 if x < 0 , 0 if x = 0 , 1 if x > 0. {\displaystyle \operatorname {sgn}(x)={\begin{cases}-1&{\text{if }}x<0,\\0&{\text{if }}x=0,\\1&{\text{if }}x>0.\end{cases}}} If the scalar product is 0, the output of the hidden neuron is mapped to −1 in order to ensure a binary output value. The output of neural network is then computed as the multiplication of all values produced by hidden elements: τ = ∏ i = 1 K σ i {\displaystyle \tau =\prod _{i=1}^{K}\sigma _{i}} Output of the tree parity machine is binary. === Protocol === Each party (A and B) uses its own tree parity machine. Synchronization of the tree parity machines is achieved in these steps Initialize random weight values Execute these steps until the full synchronization is achieved Generate random input vector X Compute the values of the hidden neurons Compute the value of the output neuron Compare the values of both tree parity machines Outputs are the same: one of the suitable learning rules is applied to the weights Outputs are different: go to 2.1 After the full synchronization is achieved (the weights wij of both tree parity machines are same), A and B can use their weights as keys. This method is known as a bidirectional learning. One of the following learning rules can be used for the synchronization: Hebbian learning rule: w i + = g ( w i + σ i x i Θ ( σ i τ ) Θ ( τ A τ B ) ) {\displaystyle w_{i}^{+}=g(w_{i}+\sigma _{i}x_{i}\Theta (\sigma _{i}\tau )\Theta (\tau ^{A}\tau ^{B}))} Anti-Hebbian learning rule: w i + = g ( w i − σ i x i Θ ( σ i τ ) Θ ( τ A τ B ) ) {\displaystyle w_{i}^{+}=g(w_{i}-\sigma _{i}x_{i}\Theta (\sigma _{i}\tau )\Theta (\tau ^{A}\tau ^{B}))} Random walk: w i + = g ( w i + x i Θ ( σ i τ ) Θ ( τ A τ B ) ) {\displaystyle w_{i}^{+}=g(w_{i}+x_{i}\Theta (\sigma _{i}\tau )\Theta (\tau ^{A}\tau ^{B}))} Where: Θ ( a , b ) = 0 {\displaystyle \Theta (a,b)=0} if a ≠ b {\displaystyle a\neq b} otherwise Θ ( a , b ) = 1 {\displaystyle \Theta (a,b)=1} And: g ( x ) {\displaystyle g(x)} is a function that keeps the w i {\displaystyle w_{i}} in the range { − L , − L + 1 , . . . , 0 , . . . , L − 1 , L } {\displaystyle \{-L,-L+1,...,0,...,L-1,L\}} === Attacks and security of this protocol === In every attack it is considered, that the attacker E can eavesdrop messages between the parties A and B, but does not have an opportunity to change them. ==== Brute force ==== To provide a brute force attack, an attacker has to test all possible keys (all possible values of weights wij). By K hidden neurons, K×N input neurons and boundary of weights L, this gives (2L+1)KN possibilities. For example, the configuration K = 3, L = 3 and N = 100 gives us 310253 key possibilities, making the attack impossible with today's computer power. ==== Learning with own tree parity machine ==== One of the basic attacks can be provided by an attacker, who owns the same tree parity machine as the parties A and B. He wants to synchronize his tree parity machine with these two parties. In each step there are three situations possible: Output(A) ≠ Output(B): None of the parties updates its weights. Output(A) = Output(B) = Output(E): All the three parties update weights in their tree parity machines. Output(A) = Output(B) ≠ Output(E): Parties A and B update their tree parity machines, but the attacker can not do that. Because of this situation his learning is slower than the synchronization of parties A and B. It has been proven, that the synchronization of two parties is faster than learning of an attacker. It can be improved by increasing of the synaptic depth L of the neural network. That gives this protocol enough security and an attacker can find out the key only with small probability. ==== Other attacks ==== For conventional cryptographic systems, we can improve the security of the protocol by increasing of the key length. In the case of neural cryptography, we improve it by increasing of the synaptic depth L of the neural networks. Changing this parameter increases the cost of a successful attack exponentially, while the effort for the users grows polynomially. Therefore, breaking the security of neural key exchange belongs to the complexity class NP. Alexander Klimov, Anton Mityaguine, and Adi Shamir say that the original neural synchronization scheme can be broken by at least three different attacks—geometric, probabilistic analysis, and using genetic algorithms. Even though this particular implementation is insecure, the ideas behind chaotic synchronization could potentially lead to a secure implementation. === Permutation parity machine === The permutation parity machine is a binary variant of the tree parity machine. It consists of one input layer, one hidden layer and one output layer. The number of neurons in the output layer depends on the number of hidden units K. Each hidden neuron has N binary input neurons: x i j ∈ { 0 , 1 } {\displaystyle x_{ij}\in \left\{0,1\right\}} The weights between input and hidden neurons are also binary: w i j ∈ { 0 , 1 } {\displaystyle w_{ij}\in \left\{0,1\right\}} Output value of each hidden neuron is calculated as a sum of all exclusive disjunctions (exclusive or) of input neurons and these weights: σ i = θ N ( ∑ j = 1 N w i j ⊕ x i j ) {\displaystyle \sigma _{i}=\theta _{N}(\sum _{j=1}^{N}w_{ij}\oplus x_{ij})} (⊕ means XOR). Th

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  Ho–Kashyap algorithm

  The Ho–Kashyap algorithm is an iterative method in machine learning for finding a linear decision boundary that separates two linearly separable classes. It was developed by Yu-Chi Ho and Rangasami L. Kashyap in 1965, and usually presented as a problem in linear programming. == Setup == Given a training set consisting of samples from two classes, the Ho–Kashyap algorithm seeks to find a weight vector w {\displaystyle \mathbf {w} } and a margin vector b {\displaystyle \mathbf {b} } such that: Y w = b {\displaystyle \mathbf {Yw} =\mathbf {b} } where Y {\displaystyle \mathbf {Y} } is the augmented data matrix with samples from both classes (with appropriate sign conventions, e.g., samples from class 2 are negated), w {\displaystyle \mathbf {w} } is the weight vector to be determined, and b {\displaystyle \mathbf {b} } is a positive margin vector. The algorithm minimizes the criterion function: J ( w , b ) = | | Y w − b | | 2 {\displaystyle J(\mathbf {w} ,\mathbf {b} )=||\mathbf {Yw} -\mathbf {b} ||^{2}} subject to the constraint that b > 0 {\displaystyle \mathbf {b} >\mathbf {0} } (element-wise). Given a problem of linearly separating two classes, we consider a dataset of elements { ( x i , y i ) } i ∈ 1 : N {\displaystyle \{(\mathbf {x_{i}} ,y_{i})\}_{i\in 1:N}} where y i ∈ { − 1 , + 1 } {\displaystyle y_{i}\in \{-1,+1\}} . Linearly separating them by a perceptron is equivalent to finding weight and bias w , b {\displaystyle \mathbf {w} ,b} for a perceptron, such that: [ y 1 x 1 1 ⋮ ⋮ y N x N 1 ] [ w b ] > 0 {\displaystyle {\begin{bmatrix}y_{1}\mathbf {x} _{1}&1\\\vdots &\vdots \\y_{N}\mathbf {x} _{N}&1\\\end{bmatrix}}{\begin{bmatrix}\mathbf {w} \\b\end{bmatrix}}>0} == Algorithm == The idea of the Ho–Kashyap algorithm is as follows: Given any b {\displaystyle \mathbf {b} } , the corresponding w {\displaystyle \mathbf {w} } is known: It is simply w = Y + b {\displaystyle \mathbf {w} =\mathbf {Y} ^{+}\mathbf {b} } , where Y + {\displaystyle \mathbf {Y} ^{+}} denotes the Moore–Penrose pseudoinverse of Y {\displaystyle \mathbf {Y} } . Therefore, it only remains to find b {\displaystyle \mathbf {b} } by gradient descent. However, the gradient descent may sometimes decrease some of the coordinates of b {\displaystyle \mathbf {b} } , which may cause some coordinates of b {\displaystyle \mathbf {b} } to become negative, which is undesirable. Therefore, whenever some coordinates of b {\displaystyle \mathbf {b} } would have decreased, those coordinates are unchanged instead. As for the coordinates of b {\displaystyle \mathbf {b} } that would increase, those would increase without issue. Formally, the algorithm is as follows: Initialization: Set b ( 0 ) {\displaystyle \mathbf {b} (0)} to an arbitrary positive vector, typically b ( 0 ) = 1 {\displaystyle \mathbf {b} (0)=\mathbf {1} } (a vector of ones). Set the iteration counter k = 0 {\displaystyle k=0} . Set w ( 0 ) = Y + b ( 0 ) {\displaystyle \mathbf {w} (0)=\mathbf {Y} ^{+}\mathbf {b} (0)} Loop until convergence, or until iteration counter exceeds some k m a x {\displaystyle k_{max}} . Error calculation: Compute the error vector: e ( k ) = Y w ( k ) − b ( k ) {\displaystyle \mathbf {e} (k)=\mathbf {Yw} (k)-\mathbf {b} (k)} . Margin update: Update the margin vector: b ( k + 1 ) = b ( k ) + 2 η k ( e ( k ) + | e ( k ) | ) {\displaystyle \mathbf {b} (k+1)=\mathbf {b} (k)+2\eta _{k}(\mathbf {e} (k)+|\mathbf {e} (k)|)} where η k {\displaystyle \eta _{k}} is a positive learning rate parameter, and | e ( k ) | {\displaystyle |\mathbf {e} (k)|} denotes the element-wise absolute value. Weight calculation: Compute the weight vector using the pseudoinverse: w ( k + 1 ) = Y + b ( k + 1 ) {\displaystyle \mathbf {w} (k+1)=\mathbf {Y} ^{+}\mathbf {b} (k+1)} . Convergence check: If | | e ( k ) | | ≤ θ {\displaystyle ||\mathbf {e} (k)||\leq \theta } for some predetermined threshold θ {\displaystyle \theta } (close to zero), then return b ( k + 1 ) , w ( k + 1 ) {\displaystyle \mathbf {b} (k+1),\mathbf {w} (k+1)} . if e ( k ) ≤ 0 {\displaystyle \mathbf {e} (k)\leq \mathbf {0} } (all components non-positive), return "Samples not separable.". Return "Algorithm failed to converge in time.". == Properties == If the training data is linearly separable, the algorithm converges to a solution (where e ( k ) = 0 {\displaystyle \mathbf {e} (k)=\mathbf {0} } ) in a finite number of iterations. If the data is not linearly separable, the algorithm may or may not ever reach the point where e ( k ) = 0 {\displaystyle \mathbf {e} (k)=\mathbf {0} } . However, if it does happen that e ( k ) ≤ 0 {\displaystyle \mathbf {e} (k)\leq \mathbf {0} } at some iteration, this proves non-separability. The convergence rate depends on the choice of the learning rate parameter ρ {\displaystyle \rho } and the degree of linear separability of the data. == Relationship to other algorithms == Perceptron algorithm: Both seek linear separators. The perceptron updates weights incrementally based on individual misclassified samples, while Ho–Kashyap is a batch method that processes all samples to compute the pseudoinverse and updates based on an overall error vector. Linear discriminant analysis (LDA): LDA assumes underlying Gaussian distributions with equal covariances for the classes and derives the decision boundary from these statistical assumptions. Ho–Kashyap makes no explicit distributional assumptions and instead tries to solve a system of linear inequalities directly. Support vector machines (SVM): For linearly separable data, SVMs aim to find the maximum-margin hyperplane. The Ho–Kashyap algorithm finds a separating hyperplane but not necessarily the one with the maximum margin. If the data is not separable, soft-margin SVMs allow for some misclassifications by optimizing a trade-off between margin size and misclassification penalty, while Ho–Kashyap provides a least-squares solution. == Variants == Modified Ho–Kashyap algorithm changes weight calculation step w ( k + 1 ) = Y + b ( k + 1 ) {\displaystyle \mathbf {w} (k+1)=\mathbf {Y} ^{+}\mathbf {b} (k+1)} to w ( k + 1 ) = w ( k ) + η k Y + | e ( k ) | {\displaystyle \mathbf {w} (k+1)=\mathbf {w} (k)+\eta _{k}\mathbf {Y} ^{+}|\mathbf {e} (k)|} . Kernel Ho–Kashyap algorithm: Applies kernel methods (the "kernel trick") to the Ho–Kashyap framework to enable non-linear classification by implicitly mapping data to a higher-dimensional feature space.

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  Operational taxonomic unit

  An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "operational taxonomic unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. == Molecular OTU by clustering of marker gene sequences == In the approach represented by DNA barcoding, a particular locus is chosen to be used as the marker gene for classification. This locus should be universally present in the scope selected, variable enough to be different among close-related species, and be flanked by conservative sequences that allow for easy amplification and detection. There are databases containing sequences for such marker genes from many different species, allowing for comparison. (Sometimes only using one locus does not provide sufficient resolution, so multiple marker genes are used. This is the case for plants, where rbcL+matK is common.) Sequences obtained this way can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold set by the researcher. The exact threshold depends on the taxa in question and the mutational rates of the selected locus in the taxon. 97–99% are commonly used, but "it is now recognized to be somewhat arbitrary as sequence variation within and among species varies across taxa". 100% similarity (fully identical) is also common, also known as single variants. It remains debatable how well this commonly used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, research by Schmidt et al. (2014) demonstrated that 16S-derived microbial OTUs were generally ecologically consistent across habitats and several clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing. === OTU clustering approaches === There are three main approaches to clustering OTUs: De novo, for which the clustering is based on similarities between sequencing reads. Closed-reference, for which the clustering is performed against a reference database of sequences. Open-reference, where clustering is first performed against a reference database of sequences, then any remaining sequences that could not be mapped to the reference are clustered de novo. Using a reference provides taxonomic context for the OTUs found. Alternatively, taxonomic context can be found after the construction of clusters by comparing representative sequences from clusters against a reference database. There are also specialized classifiers for this purpose which are much faster than naive comparison using BLAST. === OTU clustering algorithms === Hierarchical clustering algorithms (HCA): uclust & cd-hit & ESPRIT Bayesian clustering: CROP == Molecular OTU by other methods == In addition to similarity-based grouping, marker gene sequences can be sorted into OTUs using molecular phylogeny, k-mer composition, or hybrid methods combining these methods with similarity. There are also Bayesian tree-less methods and machine learning approaches. Using phylogeny often involves manually assigning terminal clades or single nodes to an OTU, so this is usually only done for refinement. Genome skimming can be used to obtain high-copy DNA without the need to choose marker genes or to design PCR primers for the chosen genes. It can provide fairly good coverage of organelle DNA and repetitive elements such as ribosomal DNA, both of which can be used like marker genes in OTU analysis. Whole-genome sequencing is more expensive and involves the production and processing of more data. By considering the entire genome, many (sometimes over 100) marker genes can be used at the same time, producing highly resolved phylogenies that correctly identify problematic taxa. It is also possible to use entire genomes for OTU assignment. For example, genomes from different bacterial species almost always have an average nucleotide identity lower than 95%, a fact that can be used to define new OTUs (and likely new species).

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  Vulnerability assessment (computing)

  Vulnerability assessment is a process of defining, identifying and classifying the security holes in information technology systems. An attacker can exploit a vulnerability to violate the security of a system. Some known vulnerabilities are Authentication Vulnerability, Authorization Vulnerability and Input Validation Vulnerability. == Purpose == Before deploying a system, it first must go through from a series of vulnerability assessments that will ensure that the build system is secure from all the known security risks. When a new vulnerability is discovered, the system administrator can again perform an assessment, discover which modules are vulnerable, and start the patch process. After the fixes are in place, another assessment can be run to verify that the vulnerabilities were actually resolved. This cycle of assess, patch, and re-assess has become the standard method for many organizations to manage their security issues. The primary purpose of the assessment is to find the vulnerabilities in the system, but the assessment report conveys to stakeholders that the system is secured from these vulnerabilities. If an intruder gained access to a network consisting of vulnerable Web servers, it is safe to assume that he gained access to those systems as well. Because of assessment report, the security administrator will be able to determine how intrusion occurred, identify compromised assets and take appropriate security measures to prevent critical damage to the system. == Assessment types == Depending on the system a vulnerability assessment can have many types and level. === Host assessment === A host assessment looks for system-level vulnerabilities such as insecure file permissions, application level bugs, backdoor and Trojan horse installations. It requires specialized tools for the operating system and software packages being used, in addition to administrative access to each system that should be tested. Host assessment is often very costly in term of time, and thus is only used in the assessment of critical systems. Tools like COPS and Tiger are popular in host assessment. === Network assessment === In a network assessment one assess the network for known vulnerabilities. It locates all systems on a network, determines what network services are in use, and then analyzes those services for potential vulnerabilities. This process does not require any configuration changes on the systems being assessed. Unlike host assessment, network assessment requires little computational cost and effort. == Vulnerability assessment vs penetration testing == Vulnerability assessment and penetration testing are two different testing methods. They are differentiated on the basis of certain specific parameters. == Regulatory requirements == Vulnerability assessments are mandated or strongly recommended by several regulatory frameworks. In the United States healthcare sector, the Health Insurance Portability and Accountability Act (HIPAA) Security Rule requires covered entities to conduct periodic evaluations of their security posture, and a December 2024 Notice of Proposed Rulemaking would explicitly require vulnerability scanning at least every six months for systems containing electronic protected health information. The Payment Card Industry Data Security Standard (PCI DSS) requires quarterly vulnerability scans for organizations that process credit card transactions, and the NIST Cybersecurity Framework includes vulnerability assessment as a core component of its Identify function.

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  Vapnik–Chervonenkis dimension

  In Vapnik–Chervonenkis theory, the Vapnik–Chervonenkis (VC) dimension is a measure of the size (capacity, complexity, expressive power, richness, or flexibility) of a class of sets. The notion can be extended to classes of binary functions. It is defined as the cardinality of the largest set of points that the function class can shatter—that is, for which all possible binary labelings can be realized by some function in the class. It was originally defined by Vladimir Vapnik and Alexey Chervonenkis. Informally, the capacity of a classification model is related to how complicated it can be. For example, consider the thresholding of a high-degree polynomial: if the polynomial evaluates above zero, that point is classified as positive, otherwise as negative. A high-degree polynomial can be wiggly, so that it can fit a given set of training points well. Such a polynomial has a high capacity. A much simpler alternative is to threshold a linear function. This function may not fit the training set well, because it has a low capacity. This notion of capacity is made rigorous below. == Definitions == === VC dimension of a set-family === Let C = { C } C ∈ C {\displaystyle {\mathcal {C}}=\{C\}_{C\in {\mathcal {C}}}} be a family of sets (also called set family, collection of sets or set of sets) and X {\displaystyle X} a set. Their intersection is defined as the following set family: C ∩ X := { C ∩ X ∣ C ∈ C } . {\displaystyle {\mathcal {C}}\cap X:=\{C\cap X\mid C\in {\mathcal {C}}\}.} Here typically X {\displaystyle X} and each C ∈ C {\displaystyle C\in {\mathcal {C}}} are subsets of a big "universe" of possibilities U {\displaystyle U} where intersection takes place. We say that a set X {\displaystyle X} is shattered by C {\displaystyle {\mathcal {C}}} if P ( X ) = C ∩ X {\displaystyle {\mathcal {P}}(X)={\mathcal {C}}\cap X} i.e. the set of intersections contains (hence is equal to) all the subsets of X {\displaystyle X} . For finite sets X {\displaystyle X} this is equivalent to | C ∩ X | = 2 | X | . {\displaystyle |{\mathcal {C}}\cap X|=2^{|X|}.} The VC dimension D {\displaystyle D} of C {\displaystyle {\mathcal {C}}} is the cardinality of the largest set that is shattered by C {\displaystyle {\mathcal {C}}} . If arbitrarily large sets can be shattered, the VC dimension of C {\displaystyle {\mathcal {C}}} is ∞ {\displaystyle \infty } . === VC dimension of a classification model === A binary classification model f {\displaystyle f} with some parameter vector θ {\displaystyle \theta } is said to shatter a set of generally positioned data points ( x 1 , x 2 , … , x n ) {\displaystyle (x_{1},x_{2},\ldots ,x_{n})} if, for every assignment of labels to those points, there exists a θ {\displaystyle \theta } such that the model f {\displaystyle f} makes no errors when evaluating that set of data points. The VC dimension of a model f {\displaystyle f} is the maximum number of points that can be arranged so that f {\displaystyle f} shatters them. More formally, it is the maximum cardinal D {\displaystyle D} such that there exists a generally positioned data point set of cardinality D {\displaystyle D} that can be shattered by f {\displaystyle f} . == Examples == f {\displaystyle f} is a constant classifier (with no parameters); Its VC dimension is 0 since it cannot shatter even a single point. In general, the VC dimension of a finite classification model, which can return at most 2 d {\displaystyle 2^{d}} different classifiers, is at most d {\displaystyle d} (this is an upper bound on the VC dimension; the Sauer–Shelah lemma gives a lower bound on the dimension). f {\displaystyle f} is a single-parametric threshold classifier on real numbers; i.e., for a certain threshold θ {\displaystyle \theta } , the classifier f θ {\displaystyle f_{\theta }} returns 1 if the input number is larger than θ {\displaystyle \theta } and 0 otherwise. The VC dimension of f {\displaystyle f} is 1 because: (a) It can shatter a single point. For every point x {\displaystyle x} , a classifier f θ {\displaystyle f_{\theta }} labels it as 0 if θ > x {\displaystyle \theta >x} and labels it as 1 if θ < x {\displaystyle \theta x + 2 {\displaystyle \theta >x+2} , as (1,0) if θ ∈ [ x − 4 , x − 2 ) {\displaystyle \theta \in [x-4,x-2)} , as (1,1) if θ ∈ [ x − 2 , x ] {\displaystyle \theta \in [x-2,x]} , and as (0,1) if θ ∈ ( x , x + 2 ] {\displaystyle \theta \in (x,x+2]} . (b) It cannot shatter any set of three points. For every set of three numbers, if the smallest and the largest are labeled 1, then the middle one must also be labeled 1, so not all labelings are possible. f {\displaystyle f} is a straight line as a classification model on points in a two-dimensional plane (this is the model used by a perceptron). The line should separate positive data points from negative data points. There exist sets of 3 points that can indeed be shattered using this model (any 3 points that are not collinear can be shattered). However, no set of 4 points can be shattered: by Radon's theorem, any four points can be partitioned into two subsets with intersecting convex hulls, so it is not possible to separate one of these two subsets from the other. Thus, the VC dimension of this particular classifier is 3. It is important to remember that while one can choose any arrangement of points, the arrangement of those points cannot change when attempting to shatter for some label assignment. Note, only 3 of the 23 = 8 possible label assignments are shown for the three points. f {\displaystyle f} is a single-parametric sine classifier, i.e., for a certain parameter θ {\displaystyle \theta } , the classifier f θ {\displaystyle f_{\theta }} returns 1 if the input number x {\displaystyle x} has sin ⁡ ( θ x ) > 0 {\displaystyle \sin(\theta x)>0} and 0 otherwise. The VC dimension of f {\displaystyle f} is infinite, since it can shatter any finite subset of the set { 2 − m ∣ m ∈ N } {\displaystyle \{2^{-m}\mid m\in \mathbb {N} \}} . == Uses == === In statistical learning theory === The VC dimension can predict a probabilistic upper bound on the test error of a classification model. Vapnik proved that the probability of the test error (i.e., risk with 0–1 loss function) distancing from an upper bound (on data that is drawn i.i.d. from the same distribution as the training set) is given by: Pr ( test error ⩽ training error + 1 N [ D ( log ⁡ ( 2 N D ) + 1 ) − log ⁡ ( η 4 ) ] ) = 1 − η , {\displaystyle \Pr \left({\text{test error}}\leqslant {\text{training error}}+{\sqrt {{\frac {1}{N}}\left[D\left(\log \left({\tfrac {2N}{D}}\right)+1\right)-\log \left({\tfrac {\eta }{4}}\right)\right]}}\,\right)=1-\eta ,} where D {\displaystyle D} is the VC dimension of the classification model, 0 < η ⩽ 1 {\displaystyle 0<\eta \leqslant 1} , and N {\displaystyle N} is the size of the training set (restriction: this formula is valid when D ≪ N {\displaystyle D\ll N} . When D {\displaystyle D} is larger, the test-error may be much higher than the training-error. This is due to overfitting). The VC dimension also appears in sample-complexity bounds. A space of binary functions with VC dimension D {\displaystyle D} can be learned with: N = Θ ( D + ln ⁡ 1 δ ε 2 ) {\displaystyle N=\Theta \left({\frac {D+\ln {1 \over \delta }}{\varepsilon ^{2}}}\right)} samples, where ε {\displaystyle \varepsilon } is the learning error and δ {\displaystyle \delta } is the failure probability. Thus, the sample-complexity is a linear function of the VC dimension of the hypothesis space. === In computational geometry === The VC dimension is one of the critical parameters in the size of ε-nets, which determines the complexity of approximation algorithms based on them; range sets without finite VC dimension may not have finite ε-nets at all. == Bounds == The VC dimension of the dual set-family of C {\displaystyle {\mathcal {C}}} is strictly less than 2 vc ⁡ ( C ) + 1 {\displaystyle 2^{\operatorname {vc} ({\mathcal {C}})+1}} , and this is best possible. The VC dimension of a finite set-family C {\displaystyle {\mathcal {C}}} is at most log 2 ⁡ | C | {\displaystyle \log _{2}|{\mathcal {C}}|} . This is because | C ∩ X | ≤ | X | {\displaystyle |{\mathcal {C}}\cap X|\leq |X|} by definition. Given a set-fa

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  Operational taxonomic unit

  An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "operational taxonomic unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. == Molecular OTU by clustering of marker gene sequences == In the approach represented by DNA barcoding, a particular locus is chosen to be used as the marker gene for classification. This locus should be universally present in the scope selected, variable enough to be different among close-related species, and be flanked by conservative sequences that allow for easy amplification and detection. There are databases containing sequences for such marker genes from many different species, allowing for comparison. (Sometimes only using one locus does not provide sufficient resolution, so multiple marker genes are used. This is the case for plants, where rbcL+matK is common.) Sequences obtained this way can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold set by the researcher. The exact threshold depends on the taxa in question and the mutational rates of the selected locus in the taxon. 97–99% are commonly used, but "it is now recognized to be somewhat arbitrary as sequence variation within and among species varies across taxa". 100% similarity (fully identical) is also common, also known as single variants. It remains debatable how well this commonly used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, research by Schmidt et al. (2014) demonstrated that 16S-derived microbial OTUs were generally ecologically consistent across habitats and several clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing. === OTU clustering approaches === There are three main approaches to clustering OTUs: De novo, for which the clustering is based on similarities between sequencing reads. Closed-reference, for which the clustering is performed against a reference database of sequences. Open-reference, where clustering is first performed against a reference database of sequences, then any remaining sequences that could not be mapped to the reference are clustered de novo. Using a reference provides taxonomic context for the OTUs found. Alternatively, taxonomic context can be found after the construction of clusters by comparing representative sequences from clusters against a reference database. There are also specialized classifiers for this purpose which are much faster than naive comparison using BLAST. === OTU clustering algorithms === Hierarchical clustering algorithms (HCA): uclust & cd-hit & ESPRIT Bayesian clustering: CROP == Molecular OTU by other methods == In addition to similarity-based grouping, marker gene sequences can be sorted into OTUs using molecular phylogeny, k-mer composition, or hybrid methods combining these methods with similarity. There are also Bayesian tree-less methods and machine learning approaches. Using phylogeny often involves manually assigning terminal clades or single nodes to an OTU, so this is usually only done for refinement. Genome skimming can be used to obtain high-copy DNA without the need to choose marker genes or to design PCR primers for the chosen genes. It can provide fairly good coverage of organelle DNA and repetitive elements such as ribosomal DNA, both of which can be used like marker genes in OTU analysis. Whole-genome sequencing is more expensive and involves the production and processing of more data. By considering the entire genome, many (sometimes over 100) marker genes can be used at the same time, producing highly resolved phylogenies that correctly identify problematic taxa. It is also possible to use entire genomes for OTU assignment. For example, genomes from different bacterial species almost always have an average nucleotide identity lower than 95%, a fact that can be used to define new OTUs (and likely new species).

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  TabPFN

  TabPFN (Tabular Prior-data Fitted Network) is a machine learning model for tabular datasets proposed in 2022. It uses a transformer architecture. It is intended for supervised classification and regression analysis on tabular datasets, particularly focusing on small- to medium-sized datasets. The latest version, TabPFN-3, was released in May 2026 and supports datasets with up to one million rows and 200 features. == History == TabPFN was first introduced in a 2022 pre-print and presented at ICLR 2023. TabPFN v2 was published in 2025 in Nature by Hollmann and co-authors. The source code is published on GitHub under a modified Apache License and on PyPi. Writing for ICLR blogs, McCarter states that the model has attracted attention due to its performance on small dataset benchmarks. TabPFN v2.5 was released on November 6, 2025. TabPFN-3 was released on May 12, 2026. Prior Labs, founded in 2024, aims to commercialize TabPFN. As of April 2026, the open-source TabPFN repository had more than 6,000 stars on GitHub. == Overview and pre-training == TabPFN supports classification, regression and generative tasks. It leverages "Prior-Data Fitted Networks" models to model tabular data. By using a transformer pre-trained on synthetic tabular datasets, TabPFN avoids benchmark contamination and costs of curating real-world data. TabPFN v2 was pre-trained on approximately 130 million such datasets. Synthetic datasets are generated using causal models or Bayesian neural networks; this can include simulating missing values, imbalanced data, and noise. Random inputs are passed through these models to generate outputs, with a bias towards simpler causal structures. During pre-training, TabPFN predicts the masked target values of new data points given training data points and their known targets, effectively learning a generic learning algorithm that is executed by running a neural network forward pass. The new dataset is then processed in a single forward pass without retraining. The model's transformer encoder processes features and labels by alternating attention across rows and columns. TabPFN v2 handles numerical and categorical features, missing values, and supports tasks like regression and synthetic data generation, while TabPFN-2.5 scales this approach to datasets with up to 50,000 rows and 2,000 features. TabPFN-3 introduced a redesigned architecture with row-compression, an attention-based many-class decoder, native missing-value handling, and inference optimizations such as row chunking and a reduced key-value cache, with benchmark-validated regimes of up to 1 million rows with 200 features, 100,000 rows with 2,000 features, or 1,000 rows with 20,000 features. Since TabPFN is pre-trained, in contrast to other deep learning methods, it does not require costly hyperparameter optimization. == Research == TabPFN is the subject of on-going research. Applications for TabPFN have been investigated for domains such as chemoproteomics, insurance risk classification, and metagenomics. In clinical research, TabPFN was used in a study on the early detection of pancreatic cancer from blood samples, where it was combined with metabolomic data and reported high diagnostic performance. == Applications == TabPFN has been used in industrial and biomedical contexts. Hitachi Ltd. has been reported to use the model for predictive maintenance in rail networks, with its use described as helping to identify track issues earlier and reduce manual inspections. In the biomedical domain, Oxford Cancer Analytics has used TabPFN in the analysis of proteomic data in lung disease research. A 2025 ML Contests report noted that the winners of DrivenData's PREPARE challenge used TabPFN to generate features for gradient-boosted decision tree models. == Limitations == TabPFN has been criticized for its "one large neural network is all you need" approach to modeling problems. Further, its performance is limited in high-dimensional and large-scale datasets. == Scaling Mode == In late November 2025, Prior Labs introduced ‘‘Scaling Mode’’, an operating mode for TabPFN designed to remove the fixed upper bound on training set size. Earlier versions of TabPFN had been optimized and validated primarily for datasets of up to 100,000 rows, whereas Scaling Mode was reported to extend support to substantially larger datasets, with benchmarked experiments on datasets containing up to 10 million rows. According to Prior Labs, Scaling Mode preserves the existing TabPFN architecture, including its alternating row-attention and column-attention design, as well as the same feature-count limits as prior releases. Inference remains based on a single forward pass rather than dataset-specific gradient-descent training, while scalability is described as being constrained primarily by available compute and memory resources. Prior Labs reported benchmark results on an internal collection of datasets ranging from 1 million to 10 million rows across industry and scientific applications. In these benchmarks, Scaling Mode was compared with CatBoost, XGBoost, LightGBM, and TabPFN 2.5 using 50,000-row subsampling. The company stated that predictive performance improved monotonically with increasing training set size and that no diminishing returns from scaling were observed within the tested range. Prior Labs also announced the release through company and executive social media channels. TabPFN-3 later incorporated related scaling improvements, including row chunking and a reduced key-value cache, into the model architecture and inference pipeline.

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  Final Cut Express

  Final Cut Express was a video editing software suite created by Apple Inc. It was the consumer version of Final Cut Pro and was designed for advanced editing of digital video as well as high-definition video, which was used by many amateur and professional videographers. Final Cut Express was considered a step above iMovie in terms of capabilities, but a step underneath Final Cut Pro and its suite of applications. As of June 21, 2011, Final Cut Express was discontinued in favor of Final Cut Pro X. == History == Final Cut Express 1.0, based on Final Cut Pro 3, was released at Macworld Conference and Expo in San Francisco in 2003. The second version, based on Final Cut Pro 4, was released at Macworld San Francisco in 2004. The third version, capable of editing high definition video, was also announced at Macworld San Francisco a year later, and was released as Final Cut Express HD in February 2005. It was based on Final Cut Pro HD (version 4.5) and included LiveType 1.2 and Soundtrack 1.2. Final Cut Express version 3.5 was released with little fanfare in May 2006 as a Universal Binary. In addition to improving real-time rendering with Dynamic RT, version 3.5 upgraded LiveType to version 2.0 and Soundtrack to version 1.5. In November 2007, Apple released Final Cut Express 4, which although it did not support real-time editing in the AVCHD format (it only allowed for transcoding AVCHD to Apple Intermediate Codec (AIC) provided that the camera was actually attached to the computer - it did not convert AVCHD files stored elsewhere and is currently for Intel processors only), imported iMovie '08 projects and included 50 new filters. It did not include Soundtrack 1.5, but it still included LiveType which enables users to create advanced text for the movies they created in Final Cut. The price was dropped from $299 for version 3.5 to $199 for version 4.0. In June 2011, Final Cut Express was officially discontinued, in favor of Final Cut Pro X. == Features == Final Cut Express' interface was identical to that of Final Cut Pro, but lacks some film-specific features, including Cinema Tools, multi-cam editing, batch capture, and a time code view. The program performed 32 undo operations, while Final Cut Pro did 99 [2]. Features the program did include were: The ability to keyframe filters Dynamic RT, which changes real-time settings on-the-fly Motion path keyframing Opacity keyframing Ripple, roll, slip, slide and blade edits Picture-in-picture and split-screen effects Up to 99 video tracks and 12 compositing modes Up to 99 audio tracks Motion project import Two-way color correction. Chroma key One feature of Final Cut Express that was not available in Final Cut Pro is the ability to import iMovie '08 projects (though transitions are not preserved). === RT Extreme === Inherited from Final Cut Pro, Final Cut Express features RT Extreme, which allows previews of some video filters and transitions without rendering. Audio that is not in the native AIFF file format needs rendering before it can be played back. RT Extreme has three modes: 'Safe', for seeing multiple video layers at a quality that more or less guarantees a smooth playback; 'Unlimited', which allows the maximum number of composited video layers to be viewed at the same time; and 'Dynamic', which alternates between these settings depending on how many simultaneous video tracks are present. Frame dropping may result from using 'Unlimited' on low-resource machines. === Boris Calligraphy === Like Final Cut Pro, Express also comes with Boris Calligraphy, a plugin for advanced titling and scrolling/crawling titles more sophisticated than the ones that can be created with the built-in title overlays. Calligraphy has a WYSIWYG interface and features wrapping, alignment, leading, kerning and tracking features, as well as allowing up to five custom outlines and five custom drop shadows to be defined for a selected portion of the title. == Soundtrack == Prior to version 4, Final Cut Express included Soundtrack 1.5, a music program similar to the consumer-level GarageBand, but designed for videographers who wish to add music to their films. Soundtrack comes with around 4,000 professionally recorded instrument loops and sound effects that can be arranged in multiple tracks beneath the video track. To use Soundtrack, users export their Final Cut Express sequence, or a marked portion thereof, as a reference file, which can include scoring markers defined in the timeline. This reference file can be imported as the video track in Soundtrack. Soundtrack is functionally and visually identical to Soundtrack Pro's multitrack editing mode, but includes fewer Logic plugins and lacks the highly regarded noise removal tool. Soundtrack was removed from Final Cut Express 4, which lowered its price and may have encouraged people to buy Logic Express.

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  Latent Dirichlet allocation

  In natural language processing, latent Dirichlet allocation (LDA) is a generative statistical model that explains how a collection of text documents can be described by a set of unobserved "topics." For example, given a set of news articles, LDA might discover that one topic is characterized by words like "president", "government", and "election", while another is characterized by "team", "game", and "score". It is one of the most common topic models. The LDA model was first presented as a graphical model for population genetics by J. K. Pritchard, M. Stephens and P. Donnelly in 2000. The model was subsequently applied to machine learning by David Blei, Andrew Ng, and Michael I. Jordan in 2003. Although its most frequent application is in modeling text corpora, it has also been used for other problems, such as in clinical psychology, social science, and computational musicology. The core assumption of LDA is that documents are represented as a random mixture of latent topics, and each topic is characterized by a probability distribution over words. The model is a generalization of probabilistic latent semantic analysis (pLSA), differing primarily in that LDA treats the topic mixture as a Dirichlet prior, leading to more reasonable mixtures and less susceptibility to overfitting. Learning the latent topics and their associated probabilities from a corpus is typically done using Bayesian inference, often with methods like Gibbs sampling or variational Bayes. == History == In the context of population genetics, LDA was proposed by J. K. Pritchard, M. Stephens and P. Donnelly in 2000. LDA was applied in machine learning by David Blei, Andrew Ng and Michael I. Jordan in 2003. == Overview == === Population genetics === In population genetics, the model is used to detect the presence of structured genetic variation in a group of individuals. The model assumes that alleles carried by individuals under study have origin in various extant or past populations. The model and various inference algorithms allow scientists to estimate the allele frequencies in those source populations and the origin of alleles carried by individuals under study. The source populations can be interpreted ex-post in terms of various evolutionary scenarios. In association studies, detecting the presence of genetic structure is considered a necessary preliminary step to avoid confounding. === Clinical psychology, mental health, and social science === In clinical psychology research, LDA has been used to identify common themes of self-images experienced by young people in social situations. Other social scientists have used LDA to examine large sets of topical data from discussions on social media (e.g., tweets about prescription drugs). Additionally, supervised Latent Dirichlet Allocation with covariates (SLDAX) has been specifically developed to combine latent topics identified in texts with other manifest variables. This approach allows for the integration of text data as predictors in statistical regression analyses, improving the accuracy of mental health predictions. One of the main advantages of SLDAX over traditional two-stage approaches is its ability to avoid biased estimates and incorrect standard errors, allowing for a more accurate analysis of psychological texts. In the field of social sciences, LDA has proven to be useful for analyzing large datasets, such as social media discussions. For instance, researchers have used LDA to investigate tweets discussing socially relevant topics, like the use of prescription drugs and cultural differences in China. By analyzing these large text corpora, it is possible to uncover patterns and themes that might otherwise go unnoticed, offering valuable insights into public discourse and perception in real time. === Musicology === In the context of computational musicology, LDA has been used to discover tonal structures in different corpora. === Machine learning === One application of LDA in machine learning – specifically, topic discovery, a subproblem in natural language processing – is to discover topics in a collection of documents, and then automatically classify any individual document within the collection in terms of how "relevant" it is to each of the discovered topics. A topic is considered to be a set of terms (i.e., individual words or phrases) that, taken together, suggest a shared theme. For example, in a document collection related to pet animals, the terms dog, spaniel, beagle, golden retriever, puppy, bark, and woof would suggest a DOG_related theme, while the terms cat, siamese, Maine coon, tabby, manx, meow, purr, and kitten would suggest a CAT_related theme. There may be many more topics in the collection – e.g., related to diet, grooming, healthcare, behavior, etc. that we do not discuss for simplicity's sake. (Very common, so called stop words in a language – e.g., "the", "an", "that", "are", "is", etc., – would not discriminate between topics and are usually filtered out by pre-processing before LDA is performed. Pre-processing also converts terms to their "root" lexical forms – e.g., "barks", "barking", and "barked" would be converted to "bark".) If the document collection is sufficiently large, LDA will discover such sets of terms (i.e., topics) based upon the co-occurrence of individual terms, though the task of assigning a meaningful label to an individual topic (i.e., that all the terms are DOG_related) is up to the user, and often requires specialized knowledge (e.g., for collection of technical documents). The LDA approach assumes that: The semantic content of a document is composed by combining one or more terms from one or more topics. Certain terms are ambiguous, belonging to more than one topic, with different probability. (For example, the term training can apply to both dogs and cats, but are more likely to refer to dogs, which are used as work animals or participate in obedience or skill competitions.) However, in a document, the accompanying presence of specific neighboring terms (which belong to only one topic) will disambiguate their usage. Most documents will contain only a relatively small number of topics. In the collection, e.g., individual topics will occur with differing frequencies. That is, they have a probability distribution, so that a given document is more likely to contain some topics than others. Within a topic, certain terms will be used much more frequently than others. In other words, the terms within a topic will also have their own probability distribution. When LDA machine learning is employed, both sets of probabilities are computed during the training phase, using Bayesian methods and an expectation–maximization algorithm. LDA is a generalization of older approach of probabilistic latent semantic analysis (pLSA), The pLSA model is equivalent to LDA under a uniform Dirichlet prior distribution. pLSA relies on only the first two assumptions above and does not care about the remainder. While both methods are similar in principle and require the user to specify the number of topics to be discovered before the start of training (as with k-means clustering) LDA has the following advantages over pLSA: LDA yields better disambiguation of words and a more precise assignment of documents to topics. Computing probabilities allows a "generative" process by which a collection of new "synthetic documents" can be generated that would closely reflect the statistical characteristics of the original collection. Unlike LDA, pLSA is vulnerable to overfitting especially when the size of corpus increases. The LDA algorithm is more readily amenable to scaling up for large data sets using the MapReduce approach on a computing cluster. == Model == With plate notation, which is often used to represent probabilistic graphical models (PGMs), the dependencies among the many variables can be captured concisely. The boxes are "plates" representing replicates, which are repeated entities. The outer plate represents documents, while the inner plate represents the repeated word positions in a given document; each position is associated with a choice of topic and word. The variable names are defined as follows: M denotes the number of documents N is number of words in a given document (document i has N i {\displaystyle N_{i}} words) α is the parameter of the Dirichlet prior on the per-document topic distributions β is the parameter of the Dirichlet prior on the per-topic word distribution θ i {\displaystyle \theta _{i}} is the topic distribution for document i φ k {\displaystyle \varphi _{k}} is the word distribution for topic k z i j {\displaystyle z_{ij}} is the topic for the j-th word in document i w i j {\displaystyle w_{ij}} is the specific word. The fact that W is grayed out means that words w i j {\displaystyle w_{ij}} are the only observable variables, and the other variables are latent variables. As proposed in the original paper, a sparse Dirichlet prior can be used to model the to

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  FastICA

  FastICA is an efficient and popular algorithm for independent component analysis invented by Aapo Hyvärinen at Helsinki University of Technology. Like most ICA algorithms, FastICA seeks an orthogonal rotation of prewhitened data, through a fixed-point iteration scheme, that maximizes a measure of non-Gaussianity of the rotated components. Non-gaussianity serves as a proxy for statistical independence, which is a very strong condition and requires infinite data to verify. FastICA can also be alternatively derived as an approximative Newton iteration. == Algorithm == === Prewhitening the data === Let the X := ( x i j ) ∈ R N × M {\displaystyle \mathbf {X} :=(x_{ij})\in \mathbb {R} ^{N\times M}} denote the input data matrix, M {\displaystyle M} the number of columns corresponding with the number of samples of mixed signals and N {\displaystyle N} the number of rows corresponding with the number of independent source signals. The input data matrix X {\displaystyle \mathbf {X} } must be prewhitened, or centered and whitened, before applying the FastICA algorithm to it. Centering the data entails demeaning each component of the input data X {\displaystyle \mathbf {X} } , that is, for each i = 1 , … , N {\displaystyle i=1,\ldots ,N} and j = 1 , … , M {\displaystyle j=1,\ldots ,M} . After centering, each row of X {\displaystyle \mathbf {X} } has an expected value of 0 {\displaystyle 0} . Whitening the data requires a linear transformation L : R N × M → R N × M {\displaystyle \mathbf {L} :\mathbb {R} ^{N\times M}\to \mathbb {R} ^{N\times M}} of the centered data so that the components of L ( X ) {\displaystyle \mathbf {L} (\mathbf {X} )} are uncorrelated and have variance one. More precisely, if X {\displaystyle \mathbf {X} } is a centered data matrix, the covariance of L x := L ( X ) {\displaystyle \mathbf {L} _{\mathbf {x} }:=\mathbf {L} (\mathbf {X} )} is the ( N × N ) {\displaystyle (N\times N)} -dimensional identity matrix, that is, A common method for whitening is by performing an eigenvalue decomposition on the covariance matrix of the centered data X {\displaystyle \mathbf {X} } , E { X X T } = E D E T {\displaystyle E\left\{\mathbf {X} \mathbf {X} ^{T}\right\}=\mathbf {E} \mathbf {D} \mathbf {E} ^{T}} , where E {\displaystyle \mathbf {E} } is the matrix of eigenvectors and D {\displaystyle \mathbf {D} } is the diagonal matrix of eigenvalues. The whitened data matrix is defined thus by === Single component extraction === The iterative algorithm finds the direction for the weight vector w ∈ R N {\displaystyle \mathbf {w} \in \mathbb {R} ^{N}} that maximizes a measure of non-Gaussianity of the projection w T X {\displaystyle \mathbf {w} ^{T}\mathbf {X} } , with X ∈ R N × M {\displaystyle \mathbf {X} \in \mathbb {R} ^{N\times M}} denoting a prewhitened data matrix as described above. Note that w {\displaystyle \mathbf {w} } is a column vector. To measure non-Gaussianity, FastICA relies on a nonquadratic nonlinear function f ( u ) {\displaystyle f(u)} , its first derivative g ( u ) {\displaystyle g(u)} , and its second derivative g ′ ( u ) {\displaystyle g^{\prime }(u)} . Hyvärinen states that the functions are useful for general purposes, while may be highly robust. The steps for extracting the weight vector w {\displaystyle \mathbf {w} } for single component in FastICA are the following: Randomize the initial weight vector w {\displaystyle \mathbf {w} } Let w + ← E { X g ( w T X ) T } − E { g ′ ( w T X ) } w {\displaystyle \mathbf {w} ^{+}\leftarrow E\left\{\mathbf {X} g(\mathbf {w} ^{T}\mathbf {X} )^{T}\right\}-E\left\{g'(\mathbf {w} ^{T}\mathbf {X} )\right\}\mathbf {w} } , where E { . . . } {\displaystyle E\left\{...\right\}} means averaging over all column-vectors of matrix X {\displaystyle \mathbf {X} } Let w ← w + / ‖ w + ‖ {\displaystyle \mathbf {w} \leftarrow \mathbf {w} ^{+}/\|\mathbf {w} ^{+}\|} If not converged, go back to 2 === Multiple component extraction === The single unit iterative algorithm estimates only one weight vector which extracts a single component. Estimating additional components that are mutually "independent" requires repeating the algorithm to obtain linearly independent projection vectors - note that the notion of independence here refers to maximizing non-Gaussianity in the estimated components. Hyvärinen provides several ways of extracting multiple components with the simplest being the following. Here, 1 M {\displaystyle \mathbf {1_{M}} } is a column vector of 1's of dimension M {\displaystyle M} . Algorithm FastICA Input: C {\displaystyle C} Number of desired components Input: X ∈ R N × M {\displaystyle \mathbf {X} \in \mathbb {R} ^{N\times M}} Prewhitened matrix, where each column represents an N {\displaystyle N} -dimensional sample, where C <= N {\displaystyle C<=N} Output: W ∈ R N × C {\displaystyle \mathbf {W} \in \mathbb {R} ^{N\times C}} Un-mixing matrix where each column projects X {\displaystyle \mathbf {X} } onto independent component. Output: S ∈ R C × M {\displaystyle \mathbf {S} \in \mathbb {R} ^{C\times M}} Independent components matrix, with M {\displaystyle M} columns representing a sample with C {\displaystyle C} dimensions. for p in 1 to C: w p ← {\displaystyle \mathbf {w_{p}} \leftarrow } Random vector of length N while w p {\displaystyle \mathbf {w_{p}} } changes w p ← 1 M X g ( w p T X ) T − 1 M g ′ ( w p T X ) 1 M w p {\displaystyle \mathbf {w_{p}} \leftarrow {\frac {1}{M}}\mathbf {X} g(\mathbf {w_{p}} ^{T}\mathbf {X} )^{T}-{\frac {1}{M}}g'(\mathbf {w_{p}} ^{T}\mathbf {X} )\mathbf {1_{M}} \mathbf {w_{p}} } w p ← w p − ∑ j = 1 p − 1 ( w p T w j ) w j {\displaystyle \mathbf {w_{p}} \leftarrow \mathbf {w_{p}} -\sum _{j=1}^{p-1}(\mathbf {w_{p}} ^{T}\mathbf {w_{j}} )\mathbf {w_{j}} } w p ← w p ‖ w p ‖ {\displaystyle \mathbf {w_{p}} \leftarrow {\frac {\mathbf {w_{p}} }{\|\mathbf {w_{p}} \|}}} output W ← [ w 1 , … , w C ] {\displaystyle \mathbf {W} \leftarrow {\begin{bmatrix}\mathbf {w_{1}} ,\dots ,\mathbf {w_{C}} \end{bmatrix}}} output S ← W T X {\displaystyle \mathbf {S} \leftarrow \mathbf {W^{T}} \mathbf {X} }

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  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

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  Elasticity (data store)

  The elasticity of a data store relates to the flexibility of its data model and clustering capabilities. The greater the number of data model changes that can be tolerated, and the more easily the clustering can be managed, the more elastic the data store is considered to be. == Types == === Clustering elasticity === Clustering elasticity is the ease of adding or removing nodes from the distributed data store. Usually, this is a difficult and delicate task to be done by an expert in a relational database system. Some NoSQL data stores, like Apache Cassandra have an easy solution, and a node can be added/removed with a few changes in the properties and by adding specifying at least one seed. === Data-modelling elasticity === Relational databases are most often very inelastic, as they have a predefined data model that can only be adapted through redesign. Most NoSQL data stores, however, do not have a fixed schema. Each row can have a different number and even different type of columns. Concerning the data store, modifications in the schema are no problem. This makes this kind of data stores more elastic concerning the data model. The drawback is that the programmer has to take into account that the data model may change over time.

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  Genetic representation

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

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  GeWorkbench

  geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing funded through the NIH Roadmap (NIH Common Fund). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins. == Features == Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc. Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence and protein structure data (e.g., MarkUs). Integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. Component integration through platform management of inputs and outputs. Among data that can be shared between components are expression datasets, interaction networks, sample and marker (gene) sets and sequences. Dataset history tracking - complete record of data sets used and input settings. Integration with 3rd party tools such as GenePattern, Cytoscape, and Genomespace. Demonstrations of each feature described can be found at GeWorkbench-web Tutorials. == Versions == geWorkbench is open-source software that can be downloaded and installed locally. A zip file of the released version Java source is also available. Prepackaged installer versions also exist for Windows, Macintosh, and Linux.

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