AI Writing Helper

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  • Aggregation (linguistics)

    Aggregation (linguistics)

    In linguistics, aggregation is a subtask of natural language generation, which involves merging syntactic constituents (such as sentences and phrases) together. Sometimes aggregation can be done at a conceptual level. == Examples == A simple example of syntactic aggregation is merging the two sentences John went to the shop and John bought an apple into the single sentence John went to the shop and bought an apple. Syntactic aggregation can be much more complex than this. For example, aggregation can embed one of the constituents in the other; e.g., we can aggregate John went to the shop and The shop was closed into the sentence John went to the shop, which was closed. From a pragmatic perspective, aggregating sentences together often suggests to the reader that these sentences are related to each other. If this is not the case, the reader may be confused. For example, someone who reads John went to the shop and bought an apple may infer that the apple was bought in the shop; if this is not the case, then these sentences should not be aggregated. == Algorithms and issues == Aggregation algorithms must do two things: Decide when two constituents should be aggregated Decide how two constituents should be aggregated, and create the aggregated structure The first issue, deciding when to aggregate, is poorly understood. Aggegration decisions certainly depend on the semantic relations between the constituents, as mentioned above; they also depend on the genre (e.g., bureaucratic texts tend to be more aggregated than instruction manuals). They probably should depend on rhetorical and discourse structure. The literacy level of the reader is also probably important (poor readers need shorter sentences). But we have no integrated model which brings all these factors together into a single algorithm. With regard to the second issue, there have been some studies of different types of aggregation, and how they should be carried out. Harbusch and Kempen describe several syntactic aggregation strategies. In their terminology, John went to the shop and bought an apple is an example of forward conjunction Reduction Much less is known about conceptual aggregation. Di Eugenio et al. show how conceptual aggregation can be done in an intelligent tutoring system, and demonstrate that performing such aggregation makes the system more effective (and that conceptual aggregation make a bigger impact than syntactic aggregation). == Software == Unfortunately there is not much software available for performing aggregation. However the SimpleNLG system does include limited support for basic aggregation. For example, the following code causes SimpleNLG to print out The man is hungry and buys an apple.

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  • Prototype methods

    Prototype methods

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

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  • Operational taxonomic unit

    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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  • Types of artificial neural networks

    Types of artificial neural networks

    Types of neural networks (NN) include a family of techniques. The simplest types have static components, including number of units, number of layers, unit weights and topology. Dynamic NNs evolve via learning. Some types allow/require learning to be "supervised" by the operator, while others operate independently. Some types operate purely in hardware, while others are purely software and run on general purpose computers. The main types are: Transformers: these use attention to analyze every token in the input stream against every other token in the stream. That technique has enabled neural networks to reach the general public via chatbots, code generators and many other forms. Convolutional neural networks (CNN): a FNN that uses kernels and regularization to evade problems in prior generations of NNs. They are typically used to analyze visual and other two-dimensional data. Generative adversarial networks set networks (of varying structure) against each other, each trying to push the other(s) to produce better results such as winning a game or to deceive the opponent about the authenticity of an input. == Feedforward == In feedforward neural networks the information moves from the input to output directly in every layer. There can be hidden layers with or without cycles/loops to sequence inputs. Feedforward networks can be constructed with various types of units, such as binary McCulloch–Pitts neurons, the simplest of which is the perceptron. Continuous neurons, frequently with sigmoidal activation, are used in the context of backpropagation. == Group method of data handling == The Group Method of Data Handling (GMDH) features fully automatic structural and parametric model optimization. The node activation functions are Kolmogorov–Gabor polynomials that permit additions and multiplications. It uses a deep multilayer perceptron with eight layers. It is a supervised learning network that grows layer by layer, where each layer is trained by regression analysis. Useless items are detected using a validation set, and pruned through regularization. The size and depth of the resulting network depends on the task. == Autoencoder == An autoencoder, autoassociator or Diabolo network is similar to the multilayer perceptron (MLP) – with an input layer, an output layer and one or more hidden layers connecting them. However, the output layer has the same number of units as the input layer. Its purpose is to reconstruct its own inputs (instead of emitting a target value). Therefore, autoencoders are unsupervised learning models. An autoencoder is used for unsupervised learning of efficient codings, typically for the purpose of dimensionality reduction and for learning generative models of data. == Probabilistic == A probabilistic neural network (PNN) is a four-layer feedforward neural network. The layers are Input, hidden pattern, hidden summation, and output. In the PNN algorithm, the parent probability distribution function (PDF) of each class is approximated by a Parzen window and a non-parametric function. Then, using PDF of each class, the class probability of a new input is estimated and Bayes’ rule is employed to allocate it to the class with the highest posterior probability. It was derived from the Bayesian network and a statistical algorithm called Kernel Fisher discriminant analysis. It is used for classification and pattern recognition. == Time delay == A time delay neural network (TDNN) is a feedforward architecture for sequential data that recognizes features independent of sequence position. In order to achieve time-shift invariance, delays are added to the input so that multiple data points (points in time) are analyzed together. It usually forms part of a larger pattern recognition system. It has been implemented using a perceptron network whose connection weights were trained with back propagation (supervised learning). == Convolutional == A convolutional neural network (CNN, or ConvNet or shift invariant or space invariant) is a class of deep network, composed of one or more convolutional layers with fully connected layers (matching those in typical ANNs) on top. It uses tied weights and pooling layers. In particular, max-pooling. It is often structured via Fukushima's convolutional architecture. They are variations of multilayer perceptrons that use minimal preprocessing. This architecture allows CNNs to take advantage of the 2D structure of input data. Its unit connectivity pattern is inspired by the organization of the visual cortex. Units respond to stimuli in a restricted region of space known as the receptive field. Receptive fields partially overlap, over-covering the entire visual field. Unit response can be approximated mathematically by a convolution operation. CNNs are suitable for processing visual and other two-dimensional data. They have shown superior results in both image and speech applications. They can be trained with standard backpropagation. CNNs are easier to train than other regular, deep, feed-forward neural networks and have many fewer parameters to estimate. Capsule Neural Networks (CapsNet) add structures called capsules to a CNN and reuse output from several capsules to form more stable (with respect to various perturbations) representations. Examples of applications in computer vision include DeepDream and robot navigation. They have wide applications in image and video recognition, recommender systems and natural language processing. == Deep stacking network == A deep stacking network (DSN) (deep convex network) is based on a hierarchy of blocks of simplified neural network modules. It was introduced in 2011 by Deng and Yu. It formulates the learning as a convex optimization problem with a closed-form solution, emphasizing the mechanism's similarity to stacked generalization. Each DSN block is a simple module that is easy to train by itself in a supervised fashion without backpropagation for the entire blocks. Each block consists of a simplified multi-layer perceptron (MLP) with a single hidden layer. The hidden layer h has logistic sigmoidal units, and the output layer has linear units. Connections between these layers are represented by weight matrix U; input-to-hidden-layer connections have weight matrix W. Target vectors t form the columns of matrix T, and the input data vectors x form the columns of matrix X. The matrix of hidden units is H = σ ( W T X ) {\displaystyle {\boldsymbol {H}}=\sigma ({\boldsymbol {W}}^{T}{\boldsymbol {X}})} . Modules are trained in order, so lower-layer weights W are known at each stage. The function performs the element-wise logistic sigmoid operation. Each block estimates the same final label class y, and its estimate is concatenated with original input X to form the expanded input for the next block. Thus, the input to the first block contains the original data only, while downstream blocks' input adds the output of preceding blocks. Then learning the upper-layer weight matrix U given other weights in the network can be formulated as a convex optimization problem: min U T f = ‖ U T H − T ‖ F 2 , {\displaystyle \min _{U^{T}}f=\|{\boldsymbol {U}}^{T}{\boldsymbol {H}}-{\boldsymbol {T}}\|_{F}^{2},} which has a closed-form solution. Unlike other deep architectures, such as DBNs, the goal is not to discover the transformed feature representation. The structure of the hierarchy of this kind of architecture makes parallel learning straightforward, as a batch-mode optimization problem. In purely discriminative tasks, DSNs outperform conventional DBNs. === Tensor deep stacking networks === This architecture is a DSN extension. It offers two important improvements: it uses higher-order information from covariance statistics, and it transforms the non-convex problem of a lower-layer to a convex sub-problem of an upper-layer. TDSNs use covariance statistics in a bilinear mapping from each of two distinct sets of hidden units in the same layer to predictions, via a third-order tensor. While parallelization and scalability are not considered seriously in conventional DNNs, all learning for DSNs and TDSNs is done in batch mode, to allow parallelization. Parallelization allows scaling the design to larger (deeper) architectures and data sets. The basic architecture is suitable for diverse tasks such as classification and regression. == Physics-informed == Such a neural network is designed for the numerical solution of mathematical equations, such as differential, integral, delay, fractional and others. As input parameters, PINN accepts variables (spatial, temporal, and others), transmits them through the network block. At the output, it produces an approximate solution and substitutes it into the mathematical model, considering the initial and boundary conditions. If the solution does not satisfy the required accuracy, one uses the backpropagation and rectify the solution. Besides PINN, other architectures have been developed to produce surrogate models for scientific comput

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  • Wetware (brain)

    Wetware (brain)

    Wetware is a term drawn from the computer-related idea of hardware or software, but applied to biological life forms. == Usage == The prefix "wet" is a reference to the water found in living creatures. Wetware is used to describe the elements equivalent to hardware and software found in a person, especially the central nervous system (CNS) and the human mind. The term wetware finds use in works of fiction, in scholarly publications and in popularizations. The "hardware" component of wetware concerns the bioelectric and biochemical properties of the CNS, specifically the brain. If the sequence of impulses traveling across the various neurons are thought of symbolically as software, then the physical neurons would be the hardware. The amalgamated interaction of this software and hardware is manifested through continuously changing physical connections, and chemical and electrical influences that spread across the body. The process by which the mind and brain interact to produce the collection of experiences that we define as self-awareness is in question. == History == Although the exact definition has shifted over time, the term Wetware and its fundamental reference to "the physical mind" has been around at least since the mid-1950s. Mostly used in relatively obscure articles and papers, it was not until the heyday of cyberpunk, however, that the term found broad adoption. Among the first uses of the term in popular culture was the Bruce Sterling novel Schismatrix (1985) and the Michael Swanwick novel Vacuum Flowers (1987). Rudy Rucker references the term in a number of books, including one entitled Wetware (1988): ... all sparks and tastes and tangles, all its stimulus/response patterns – the whole bio-cybernetic software of mind. Rucker did not use the word to simply mean a brain, nor in the human-resources sense of employees. He used wetware to stand for the data found in any biological system, analogous perhaps to the firmware that is found in a ROM chip. In Rucker's sense, a seed, a plant graft, an embryo, or a biological virus are all wetware. DNA, the immune system, and the evolved neural architecture of the brain are further examples of wetware in this sense. Rucker describes his conception in a 1992 compendium The Mondo 2000 User's Guide to the New Edge, which he quotes in a 2007 blog entry. Early cyber-guru Arthur Kroker used the term in his blog. With the term getting traction in trendsetting publications, it became a buzzword in the early 1990s. In 1991, Dutch media theorist Geert Lovink organized the Wetware Convention in Amsterdam, which was supposed to be an antidote to the "out-of-body" experiments conducted in high-tech laboratories, such as experiments in virtual reality. Timothy Leary, in an appendix to Info-Psychology originally written in 1975–76 and published in 1989, used the term wetware, writing that "psychedelic neuro-transmitters were the hot new technology for booting-up the 'wetware' of the brain". Another common reference is: "Wetware has 7 plus or minus 2 temporary registers." The numerical allusion is to a classic 1957 article by George A. Miller, The magical number 7 plus or minus two: some limits in our capacity for processing information, which later gave way to Miller's law.

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  • NSynth

    NSynth

    NSynth (a portmanteau of "Neural Synthesis") is a WaveNet-based autoencoder for synthesizing audio, outlined in a paper in April 2017. == Overview == The model generates sounds through a neural network based synthesis, employing a WaveNet-style autoencoder to learn its own temporal embeddings from four different sounds. Google then released an open source hardware interface for the algorithm called NSynth Super, used by notable musicians such as Grimes and YACHT to generate experimental music using artificial intelligence. The research and development of the algorithm was part of a collaboration between Google Brain, Magenta and DeepMind. == Technology == === Dataset === The NSynth dataset is composed of 305,979 one-shot instrumental notes featuring a unique pitch, timbre, and envelope, sampled from 1,006 instruments from commercial sample libraries. For each instrument the dataset contains four-second 16 kHz audio snippets by ranging over every pitch of a standard MIDI piano, as well as five different velocities. The dataset is made available under a Creative Commons Attribution 4.0 International (CC BY 4.0) license. === Machine learning model === A spectral autoencoder model and a WaveNet autoencoder model are publicly available on GitHub. The baseline model uses a spectrogram with fft_size 1024 and hop_size 256, MSE loss on the magnitudes, and the Griffin-Lim algorithm for reconstruction. The WaveNet model trains on mu-law encoded waveform chunks of size 6144. It learns embeddings with 16 dimensions that are downsampled by 512 in time. == NSynth Super == In 2018 Google released a hardware interface for the NSynth algorithm, called NSynth Super, designed to provide an accessible physical interface to the algorithm for musicians to use in their artistic production. Design files, source code and internal components are released under an open source Apache License 2.0, enabling hobbyists and musicians to freely build and use the instrument. At the core of the NSynth Super there is a Raspberry Pi, extended with a custom printed circuit board to accommodate the interface elements. == Influence == Despite not being publicly available as a commercial product, NSynth Super has been used by notable artists, including Grimes and YACHT. Grimes reported using the instrument in her 2020 studio album Miss Anthropocene. YACHT announced an extensive use of NSynth Super in their album Chain Tripping. Claire L. Evans compared the potential influence of the instrument to the Roland TR-808. The NSynth Super design was honored with a D&AD Yellow Pencil award in 2018.

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  • Aleph (ILP)

    Aleph (ILP)

    Aleph (A Learning Engine for Proposing Hypotheses) is an inductive logic programming system introduced by Ashwin Srinivasan in 2001. As of 2022 it is still one of the most widely used inductive logic programming systems. It is based on the earlier system Progol. == Learning task == The input to Aleph is background knowledge, specified as a logic program, a language bias in the form of mode declarations, as well as positive and negative examples specified as ground facts. As output it returns a logic program which, together with the background knowledge, entails all of the positive examples and none of the negative examples. == Basic algorithm == Starting with an empty hypothesis, Aleph proceeds as follows: It chooses a positive example to generalise; if none are left, it aborts and outputs the current hypothesis. Then it constructs the bottom clause, that is, the most specific clause that is allowed by the mode declarations and covers the example. It then searches for a generalisation of the bottom clause that scores better on the chosen metric. It then adds the new clause to the hypothesis program and removes all examples that are covered by the new clause. == Search algorithm == Aleph searches for clauses in a top-down manner, using the bottom clause constructed in the preceding step to bound the search from below. It searches the refinement graph in a breadth-first manner, with tunable parameters to bound the maximal clause size and proof depth. It scores each clause using one of 13 different evaluation metrics, as chosen in advance by the user.

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  • Genetic representation

    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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  • Coupled pattern learner

    Coupled pattern learner

    Coupled Pattern Learner (CPL) is a machine learning algorithm which couples the semi-supervised learning of categories and relations to forestall the problem of semantic drift associated with boot-strap learning methods. == Coupled Pattern Learner == Semi-supervised learning approaches using a small number of labeled examples with many unlabeled examples are usually unreliable as they produce an internally consistent, but incorrect set of extractions. CPL solves this problem by simultaneously learning classifiers for many different categories and relations in the presence of an ontology defining constraints that couple the training of these classifiers. It was introduced by Andrew Carlson, Justin Betteridge, Estevam R. Hruschka Jr. and Tom M. Mitchell in 2009. == CPL overview == CPL is an approach to semi-supervised learning that yields more accurate results by coupling the training of many information extractors. Basic idea behind CPL is that semi-supervised training of a single type of extractor such as ‘coach’ is much more difficult than simultaneously training many extractors that cover a variety of inter-related entity and relation types. Using prior knowledge about the relationships between these different entities and relations CPL makes unlabeled data as a useful constraint during training. For e.g., ‘coach(x)’ implies ‘person(x)’ and ‘not sport(x)’. == CPL description == === Coupling of predicates === CPL primarily relies on the notion of coupling the learning of multiple functions so as to constrain the semi-supervised learning problem. CPL constrains the learned function in two ways. Sharing among same-arity predicates according to logical relations Relation argument type-checking === Sharing among same-arity predicates === Each predicate P in the ontology has a list of other same-arity predicates with which P is mutually exclusive. If A is mutually exclusive with predicate B, A’s positive instances and patterns become negative instances and negative patterns for B. For example, if ‘city’, having an instance ‘Boston’ and a pattern ‘mayor of arg1’, is mutually exclusive with ‘scientist’, then ‘Boston’ and ‘mayor of arg1’ will become a negative instance and a negative pattern respectively for ‘scientist.’ Further, Some categories are declared to be a subset of another category. For e.g., ‘athlete’ is a subset of ‘person’. === Relation argument type-checking === This is a type checking information used to couple the learning of relations and categories. For example, the arguments of the ‘ceoOf’ relation are declared to be of the categories ‘person’ and ‘company’. CPL does not promote a pair of noun phrases as an instance of a relation unless the two noun phrases are classified as belonging to the correct argument types. === Algorithm description === Following is a quick summary of the CPL algorithm. Input: An ontology O, and a text corpus C Output: Trusted instances/patterns for each predicate for i=1,2,...,∞ do foreach predicate p in O do EXTRACT candidate instances/contextual patterns using recently promoted patterns/instances; FILTER candidates that violate coupling; RANK candidate instances/patterns; PROMOTE top candidates; end end ==== Inputs ==== A large corpus of Part-Of-Speech tagged sentences and an initial ontology with predefined categories, relations, mutually exclusive relationships between same-arity predicates, subset relationships between some categories, seed instances for all predicates, and seed patterns for the categories. ==== Candidate extraction ==== CPL finds new candidate instances by using newly promoted patterns to extract the noun phrases that co-occur with those patterns in the text corpus. CPL extracts, Category Instances Category Patterns Relation Instances Relation Patterns ==== Candidate filtering ==== Candidate instances and patterns are filtered to maintain high precision, and to avoid extremely specific patterns. An instance is only considered for assessment if it co-occurs with at least two promoted patterns in the text corpus, and if its co-occurrence count with all promoted patterns is at least three times greater than its co-occurrence count with negative patterns. ==== Candidate ranking ==== CPL ranks candidate instances using the number of promoted patterns that they co-occur with so that candidates that occur with more patterns are ranked higher. Patterns are ranked using an estimate of the precision of each pattern. ==== Candidate promotion ==== CPL ranks the candidates according to their assessment scores and promotes at most 100 instances and 5 patterns for each predicate. Instances and patterns are only promoted if they co-occur with at least two promoted patterns or instances, respectively. == Meta-Bootstrap Learner == Meta-Bootstrap Learner (MBL) was also proposed by the authors of CPL. Meta-Bootstrap learner couples the training of multiple extraction techniques with a multi-view constraint, which requires the extractors to agree. It makes addition of coupling constraints on top of existing extraction algorithms, while treating them as black boxes, feasible. MBL assumes that the errors made by different extraction techniques are independent. Following is a quick summary of MBL. Input: An ontology O, a set of extractors ε Output: Trusted instances for each predicate for i=1,2,...,∞ do foreach predicate p in O do foreach extractor e in ε do Extract new candidates for p using e with recently promoted instances; end FILTER candidates that violate mutual-exclusion or type-checking constraints; PROMOTE candidates that were extracted by all extractors; end end Subordinate algorithms used with MBL do not promote any instance on their own, they report the evidence about each candidate to MBL and MBL is responsible for promoting instances. == Applications == In their paper authors have presented results showing the potential of CPL to contribute new facts to existing repository of semantic knowledge, Freebase

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  • Count sketch

    Count sketch

    Count sketch is a type of dimensionality reduction that is particularly efficient in statistics, machine learning and algorithms. It was invented by Moses Charikar, Kevin Chen and Martin Farach-Colton in an effort to speed up the AMS Sketch by Alon, Matias and Szegedy for approximating the frequency moments of streams (these calculations require counting of the number of occurrences for the distinct elements of the stream). The sketch is nearly identical to the Feature hashing algorithm by John Moody, but differs in its use of hash functions with low dependence, which makes it more practical. In order to still have a high probability of success, the median trick is used to aggregate multiple count sketches, rather than the mean. These properties allow use for explicit kernel methods, bilinear pooling in neural networks and is a cornerstone in many numerical linear algebra algorithms. == Intuitive explanation == The inventors of this data structure offer the following iterative explanation of its operation: at the simplest level, the output of a single hash function s mapping stream elements q into {+1, -1} is feeding a single up/down counter C. After a single pass over the data, the frequency n ( q ) {\displaystyle n(q)} of a stream element q can be approximated, although extremely poorly, by the expected value E [ C ⋅ s ( q ) ] {\displaystyle {\mathbf {E}}[C\cdot s(q)]} ; a straightforward way to improve the variance of the previous estimate is to use an array of different hash functions s i {\displaystyle s_{i}} , each connected to its own counter C i {\displaystyle C_{i}} . For each i, the E [ C i ⋅ s i ( q ) ] = n ( q ) {\displaystyle {\mathbf {E}}[C_{i}\cdot s_{i}(q)]=n(q)} still holds, so averaging across the i range will tighten the approximation; the previous construct still has a major deficiency: if a lower-frequency-but-still-important output element a exhibits a hash collision with a high-frequency element even for one of the s i {\displaystyle s_{i}} hashes, n ( a ) {\displaystyle n(a)} estimate can be significantly affected. Avoiding this requires reducing the frequency of collision counter updates between any two distinct elements. This is achieved by replacing each C i {\displaystyle C_{i}} in the previous construct with an array of m counters (making the counter set into a two-dimensional matrix C i , j {\displaystyle C_{i,j}} ), with index j of a particular counter to be incremented/decremented selected via another set of hash functions h i {\displaystyle h_{i}} that map element q into the range {1..m}. Since E [ C i , h i ( q ) ⋅ s i ( q ) ] = n ( q ) {\displaystyle {\mathbf {E}}[C_{i,h_{i}(q)}\cdot s_{i}(q)]=n(q)} , averaging across all values of i will work. == Mathematical definition == 1. For constants w {\displaystyle w} and t {\displaystyle t} (to be defined later) independently choose d = 2 t + 1 {\displaystyle d=2t+1} random hash functions h 1 , … , h d {\displaystyle h_{1},\dots ,h_{d}} and s 1 , … , s d {\displaystyle s_{1},\dots ,s_{d}} such that h i : [ n ] → [ w ] {\displaystyle h_{i}:[n]\to [w]} and s i : [ n ] → { ± 1 } {\displaystyle s_{i}:[n]\to \{\pm 1\}} . It is necessary that the hash families from which h i {\displaystyle h_{i}} and s i {\displaystyle s_{i}} are chosen be pairwise independent. 2. For each item q i {\displaystyle q_{i}} in the stream, add s j ( q i ) {\displaystyle s_{j}(q_{i})} to the h j ( q i ) {\displaystyle h_{j}(q_{i})} th bucket of the j {\displaystyle j} th hash. At the end of this process, one has w d {\displaystyle wd} sums ( C i j ) {\displaystyle (C_{ij})} where C i , j = ∑ h i ( k ) = j s i ( k ) . {\displaystyle C_{i,j}=\sum _{h_{i}(k)=j}s_{i}(k).} To estimate the count of q {\displaystyle q} s one computes the following value: r q = median i = 1 d s i ( q ) ⋅ C i , h i ( q ) . {\displaystyle r_{q}={\text{median}}_{i=1}^{d}\,s_{i}(q)\cdot C_{i,h_{i}(q)}.} The values s i ( q ) ⋅ C i , h i ( q ) {\displaystyle s_{i}(q)\cdot C_{i,h_{i}(q)}} are unbiased estimates of how many times q {\displaystyle q} has appeared in the stream. The estimate r q {\displaystyle r_{q}} has variance O ( m i n { m 1 2 / w 2 , m 2 2 / w } ) {\displaystyle O(\mathrm {min} \{m_{1}^{2}/w^{2},m_{2}^{2}/w\})} , where m 1 {\displaystyle m_{1}} is the length of the stream and m 2 2 {\displaystyle m_{2}^{2}} is ∑ q ( ∑ i [ q i = q ] ) 2 {\displaystyle \sum _{q}(\sum _{i}[q_{i}=q])^{2}} . Furthermore, r q {\displaystyle r_{q}} is guaranteed to never be more than 2 m 2 / w {\displaystyle 2m_{2}/{\sqrt {w}}} off from the true value, with probability 1 − e − O ( t ) {\displaystyle 1-e^{-O(t)}} . === Vector formulation === Alternatively Count-Sketch can be seen as a linear mapping with a non-linear reconstruction function. Let M ( i ∈ [ d ] ) ∈ { − 1 , 0 , 1 } w × n {\displaystyle M^{(i\in [d])}\in \{-1,0,1\}^{w\times n}} , be a collection of d = 2 t + 1 {\displaystyle d=2t+1} matrices, defined by M h i ( j ) , j ( i ) = s i ( j ) {\displaystyle M_{h_{i}(j),j}^{(i)}=s_{i}(j)} for j ∈ [ w ] {\displaystyle j\in [w]} and 0 everywhere else. Then a vector v ∈ R n {\displaystyle v\in \mathbb {R} ^{n}} is sketched by C ( i ) = M ( i ) v ∈ R w {\displaystyle C^{(i)}=M^{(i)}v\in \mathbb {R} ^{w}} . To reconstruct v {\displaystyle v} we take v j ∗ = median i C j ( i ) s i ( j ) {\displaystyle v_{j}^{}={\text{median}}_{i}C_{j}^{(i)}s_{i}(j)} . This gives the same guarantees as stated above, if we take m 1 = ‖ v ‖ 1 {\displaystyle m_{1}=\|v\|_{1}} and m 2 = ‖ v ‖ 2 {\displaystyle m_{2}=\|v\|_{2}} . == Relation to Tensor sketch == The count sketch projection of the outer product of two vectors is equivalent to the convolution of two component count sketches. The count sketch computes a vector convolution C ( 1 ) x ∗ C ( 2 ) x T {\displaystyle C^{(1)}x\ast C^{(2)}x^{T}} , where C ( 1 ) {\displaystyle C^{(1)}} and C ( 2 ) {\displaystyle C^{(2)}} are independent count sketch matrices. Pham and Pagh show that this equals C ( x ⊗ x T ) {\displaystyle C(x\otimes x^{T})} – a count sketch C {\displaystyle C} of the outer product of vectors, where ⊗ {\displaystyle \otimes } denotes Kronecker product. The fast Fourier transform can be used to do fast convolution of count sketches. By using the face-splitting product such structures can be computed much faster than normal matrices.

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  • Multilinear subspace learning

    Multilinear subspace learning

    Multilinear subspace learning is an approach for disentangling the causal factor of data formation and performing dimensionality reduction. The Dimensionality reduction can be performed on a data tensor that contains a collection of observations that have been vectorized, or observations that are treated as matrices and concatenated into a data tensor. Here are some examples of data tensors whose observations are vectorized or whose observations are matrices concatenated into data tensor images (2D/3D), video sequences (3D/4D), and hyperspectral cubes (3D/4D). The mapping from a high-dimensional vector space to a set of lower dimensional vector spaces is a multilinear projection. When observations are retained in the same organizational structure as matrices or higher order tensors, their representations are computed by performing linear projections into the column space, row space and fiber space. Multilinear subspace learning algorithms are higher-order generalizations of linear subspace learning methods such as principal component analysis (PCA), independent component analysis (ICA), linear discriminant analysis (LDA) and canonical correlation analysis (CCA). == Background == Multilinear methods may be causal in nature and perform causal inference, or they may be simple regression methods from which no causal conclusion are drawn. Linear subspace learning algorithms are traditional dimensionality reduction techniques that are well suited for datasets that are the result of varying a single causal factor. Unfortunately, they often become inadequate when dealing with datasets that are the result of multiple causal factors. . Multilinear subspace learning can be applied to observations whose measurements were vectorized and organized into a data tensor for causally aware dimensionality reduction. These methods may also be employed in reducing horizontal and vertical redundancies irrespective of the causal factors when the observations are treated as a "matrix" (ie. a collection of independent column/row observations) and concatenated into a tensor. == Algorithms == === Multilinear principal component analysis === Historically, multilinear principal component analysis has been referred to as "M-mode PCA", a terminology which was coined by Peter Kroonenberg. In 2005, Vasilescu and Terzopoulos introduced the Multilinear PCA terminology as a way to better differentiate between multilinear tensor decompositions that computed 2nd order statistics associated with each data tensor mode, and subsequent work on Multilinear Independent Component Analysis that computed higher order statistics for each tensor mode. MPCA is an extension of PCA. === Multilinear independent component analysis === Multilinear independent component analysis is an extension of ICA. === Multilinear linear discriminant analysis === Multilinear extension of LDA TTP-based: Discriminant Analysis with Tensor Representation (DATER) TTP-based: General tensor discriminant analysis (GTDA) TVP-based: Uncorrelated Multilinear Discriminant Analysis (UMLDA) === Multilinear canonical correlation analysis === Multilinear extension of CCA TTP-based: Tensor Canonical Correlation Analysis (TCCA) TVP-based: Multilinear Canonical Correlation Analysis (MCCA) TVP-based: Bayesian Multilinear Canonical Correlation Analysis (BMTF) A TTP is a direct projection of a high-dimensional tensor to a low-dimensional tensor of the same order, using N projection matrices for an Nth-order tensor. It can be performed in N steps with each step performing a tensor-matrix multiplication (product). The N steps are exchangeable. This projection is an extension of the higher-order singular value decomposition (HOSVD) to subspace learning. Hence, its origin is traced back to the Tucker decomposition in 1960s. A TVP is a direct projection of a high-dimensional tensor to a low-dimensional vector, which is also referred to as the rank-one projections. As TVP projects a tensor to a vector, it can be viewed as multiple projections from a tensor to a scalar. Thus, the TVP of a tensor to a P-dimensional vector consists of P projections from the tensor to a scalar. The projection from a tensor to a scalar is an elementary multilinear projection (EMP). In EMP, a tensor is projected to a point through N unit projection vectors. It is the projection of a tensor on a single line (resulting a scalar), with one projection vector in each mode. Thus, the TVP of a tensor object to a vector in a P-dimensional vector space consists of P EMPs. This projection is an extension of the canonical decomposition, also known as the parallel factors (PARAFAC) decomposition. === Typical approach in MSL === There are N sets of parameters to be solved, one in each mode. The solution to one set often depends on the other sets (except when N=1, the linear case). Therefore, the suboptimal iterative procedure in is followed. Initialization of the projections in each mode For each mode, fixing the projection in all the other mode, and solve for the projection in the current mode. Do the mode-wise optimization for a few iterations or until convergence. This is originated from the alternating least square method for multi-way data analysis. == Code == MATLAB Tensor Toolbox by Sandia National Laboratories. The MPCA algorithm written in Matlab (MPCA+LDA included). The UMPCA algorithm written in Matlab (data included). The UMLDA algorithm written in Matlab (data included). == Tensor data sets == 3D gait data (third-order tensors): 128x88x20(21.2M); 64x44x20(9.9M); 32x22x10(3.2M);

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  • Genetic representation

    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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  • Identity column

    Identity column

    An identity column is a column (also known as a field) in a database table that is made up of values generated by the database. This is much like an AutoNumber field in Microsoft Access or a sequence in Oracle. Because the concept is so important in database science, many RDBMS systems implement some type of generated key, although each has its own terminology. Today a popular technique for generating identity is to generate a random UUID. An identity column differs from a primary key in that its values are managed by the server and usually cannot be modified. In many cases an identity column is used as a primary key; however, this is not always the case. It is a common misconception that an identity column will enforce uniqueness; however, this is not the case. If you want to enforce uniqueness on the column you must include the appropriate constraint too. In Microsoft SQL Server you have options for both the seed (starting value) and the increment. By default the seed and increment are both 1. == Code samples == or In PostgreSQL == Related functions == It is often useful or necessary to know what identity value was generated by an INSERT command. Microsoft SQL Server provides several functions to do this: @@IDENTITY provides the last value generated on the current connection in the current scope, while IDENT_CURRENT(tablename) provides the last value generated, regardless of the connection or scope it was created on. Example:

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  • Gremlin (query language)

    Gremlin (query language)

    Gremlin is a graph traversal language and virtual machine developed by Apache TinkerPop of the Apache Software Foundation. Gremlin works for both OLTP-based graph databases as well as OLAP-based graph processors. Gremlin's automata and functional language foundation enable Gremlin to naturally support imperative and declarative querying, host language agnosticism, user-defined domain specific languages, an extensible compiler/optimizer, single- and multi-machine execution models, and hybrid depth- and breadth-first evaluation with Turing completeness. As an explanatory analogy, Apache TinkerPop and Gremlin are to graph databases what the JDBC and SQL are to relational databases. Likewise, the Gremlin traversal machine is to graph computing as what the Java virtual machine is to general purpose computing. == History == 2009-10-30 the project is born, and immediately named "TinkerPop" 2009-12-25 v0.1 is the first release 2011-05-21 v1.0 is released 2012-05-24 v2.0 is released 2015-01-16 TinkerPop becomes an Apache Incubator project 2015-07-09 v3.0.0-incubating is released 2016-05-23 Apache TinkerPop becomes a top-level project 2016-07-18 v3.1.3 and v3.2.1 are first releases as Apache TinkerPop 2017-12-17 v3.3.1 is released 2018-05-08 v3.3.3 is released 2019-08-05 v3.4.3 is released 2020-02-20 v3.4.6 is released 2021-05-01 v3.5.0 is released 2022-04-04 v3.6.0 is released 2023-07-31 v3.7.0 is released 2025-11-12 v3.8.0 is released == Vendor integration == Gremlin is an Apache2-licensed graph traversal language that can be used by graph system vendors. There are typically two types of graph system vendors: OLTP graph databases and OLAP graph processors. The table below outlines those graph vendors that support Gremlin. == Traversal examples == The following examples of Gremlin queries and responses in a Gremlin-Groovy environment are relative to a graph representation of the MovieLens dataset. The dataset includes users who rate movies. Users each have one occupation, and each movie has one or more categories associated with it. The MovieLens graph schema is detailed below. === Simple traversals === For each vertex in the graph, emit its label, then group and count each distinct label. What year was the oldest movie made? What is Die Hard's average rating? === Projection traversals === For each category, emit a map of its name and the number of movies it represents. For each movie with at least 11 ratings, emit a map of its name and average rating. Sort the maps in decreasing order by their average rating. Emit the first 10 maps (i.e. top 10). === Declarative pattern matching traversals === Gremlin supports declarative graph pattern matching similar to SPARQL. For instance, the following query below uses Gremlin's match()-step. What 80's action movies do 30-something programmers like? Group count the movies by their name and sort the group count map in decreasing order by value. Clip the map to the top 10 and emit the map entries. === OLAP traversal === Which movies are most central in the implicit 5-stars graph? == Gremlin graph traversal machine == Gremlin is a virtual machine composed of an instruction set as well as an execution engine. An analogy is drawn between Gremlin and Java. === Gremlin steps (instruction set) === The following traversal is a Gremlin traversal in the Gremlin-Java8 dialect. The Gremlin language (i.e. the fluent-style of expressing a graph traversal) can be represented in any host language that supports function composition and function nesting. Due to this simple requirement, there exists various Gremlin dialects including Gremlin-Groovy, Gremlin-Scala, Gremlin-Clojure, etc. The above Gremlin-Java8 traversal is ultimately compiled down to a step sequence called a traversal. A string representation of the traversal above provided below. The steps are the primitives of the Gremlin graph traversal machine. They are the parameterized instructions that the machine ultimately executes. The Gremlin instruction set is approximately 30 steps. These steps are sufficient to provide general purpose computing and what is typically required to express the common motifs of any graph traversal query. Given that Gremlin is a language, an instruction set, and a virtual machine, it is possible to design another traversal language that compiles to the Gremlin traversal machine (analogous to how Scala compiles to the JVM). For instance, the popular SPARQL graph pattern match language can be compiled to execute on the Gremlin machine. The following SPARQL query would compile to In Gremlin-Java8, the SPARQL query above would be represented as below and compile to the identical Gremlin step sequence (i.e. traversal). === Gremlin Machine (virtual machine) === The Gremlin graph traversal machine can execute on a single machine or across a multi-machine compute cluster. Execution agnosticism allows Gremlin to run over both graph databases (OLTP) and graph processors (OLAP).

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  • Variable-order Bayesian network

    Variable-order Bayesian network

    Variable-order Bayesian network (VOBN) models provide an important extension of both the Bayesian network models and the variable-order Markov models. VOBN models are used in machine learning in general and have shown great potential in bioinformatics applications. These models extend the widely used position weight matrix (PWM) models, Markov models, and Bayesian network (BN) models. In contrast to the BN models, where each random variable depends on a fixed subset of random variables, in VOBN models these subsets may vary based on the specific realization of observed variables. The observed realizations are often called the context and, hence, VOBN models are also known as context-specific Bayesian networks. The flexibility in the definition of conditioning subsets of variables turns out to be a real advantage in classification and analysis applications, as the statistical dependencies between random variables in a sequence of variables (not necessarily adjacent) may be taken into account efficiently, and in a position-specific and context-specific manner.

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