Dan Hendrycks (born 1994 or 1995) is an American machine learning researcher. He serves as the director of the Center for AI Safety, a nonprofit research organization based in San Francisco, California. == Early life and education == Hendrycks was raised in a Christian evangelical household in Marshfield, Missouri. He received a B.S. from the University of Chicago in 2018 and a Ph.D. from the University of California, Berkeley in Computer Science in 2022. == Career and research == Hendrycks' research focuses on topics that include machine learning safety, machine ethics, and robustness. He credits his participation in the effective altruism (EA) movement-linked 80,000 Hours program for his career focus towards AI safety, though denies being an advocate for EA. Hendrycks is the main author of the research paper that introduced the activation function GELU in 2016, and of the paper that introduced the language model benchmark MMLU (Massive Multitask Language Understanding) in 2020. In February 2022, Hendrycks co-authored recommendations for the US National Institute of Standards and Technology (NIST) to inform the management of risks from artificial intelligence. In September 2022, Hendrycks wrote a paper providing a framework for analyzing the impact of AI research on societal risks. He later published a paper in March 2023 examining how natural selection and competitive pressures could shape the goals of artificial agents. This was followed by "An Overview of Catastrophic AI Risks", which discusses four categories of risks: malicious use, AI race dynamics, organizational risks, and rogue AI agents. Hendrycks is the safety adviser of xAI, an AI startup company founded by Elon Musk in 2023. To avoid any potential conflicts of interest, he receives a symbolic one-dollar salary and holds no company equity. In November 2024, he also joined Scale AI as an advisor collecting a one-dollar salary. Hendrycks is the creator of Humanity's Last Exam, a benchmark for evaluating the capabilities of large language models, which he developed in collaboration with Scale AI. In 2024, Hendrycks published the textbook Introduction to AI Safety, Ethics, and Society, based on courseware he had previously developed. == Selected publications == Hendrycks, Dan; Gimpel, Kevin (2020-07-08). "Gaussian Error Linear Units (GELUs)". arXiv:1606.08415 [cs.LG]. Hendrycks, Dan; Gimpel, Kevin (2018-10-03). "A Baseline for Detecting Misclassified and Out-of-Distribution Examples in Neural Networks". International Conference on Learning Representations 2017. arXiv:1610.02136. Hendrycks, Dan; Mazeika, Mantas; Dietterich, Thomas (2019-01-28). "Deep Anomaly Detection with Outlier Exposure". International Conference on Learning Representations 2019. arXiv:1812.04606. Hendrycks, Dan; Mazeika, Mantas; Zou, Andy (2021-10-25). "What Would Jiminy Cricket Do? Towards Agents That Behave Morally". Conference on Neural Information Processing Systems 2021. arXiv:2110.13136.
Luminoso
Luminoso is a Cambridge, MA-based text analytics and artificial intelligence company. It spun out of the MIT Media Lab and its crowd-sourced Open Mind Common Sense (OMCS) project. The company has raised $20.6 million in financing, and its clients include Sony, Autodesk, Scotts Miracle-Gro, and GlaxoSmithKline. == History == Luminoso was co-founded in 2010 by Dennis Clark, Jason Alonso, Robyn Speer, and Catherine Havasi, a research scientist at MIT in artificial intelligence and computational linguistics. The company builds on the knowledge base of MIT’s Open Mind Common Sense (OMCS) project, co-founded in 1999 by Havasi, who continues to serve as its director. The OCMS knowledge base has since been combined with knowledge from other crowdsourced resources to become ConceptNet. ConceptNet consists of approximately 28 million statements in 304 languages, with full support for 10 languages and moderate support for 77 languages. ConceptNet is a resource for making an AI that understands the meanings of the words people use. During the World Cup in June 2014, the company provided a widely reported real-time sentiment analysis of the U.S. vs. Germany match, analyzing 900,000 posts on Twitter, Facebook and Google+. == Applications == The company uses artificial intelligence, natural language processing, and machine learning to derive insights from unstructured data such as contact center interactions, chatbot and live chat transcripts, product reviews, open-ended survey responses, and email. Luminoso's software identifies and quantifies patterns and relationships in text-based data, including domain-specific or creative language. Rather than human-powered keyword searches of data, the software automates taxonomy creation around concepts, allowing related words and phrases to be dynamically generated and tracked. Commercial applications include analyzing, prioritizing, and routing contact center interactions; identifying consumer complaints before they begin to trend; and tracking sentiment during product launches. The software natively analyzes text in fourteen languages, as well as emoji. == Products == Luminoso's technology can be accessed via two products: Luminoso Daylight and Luminoso Compass. Luminoso Daylight enables a deep-dive analysis into batch or real-time data, whereas Luminoso Compass automates the categorization of real-time data. Both products offer a user interface as well as an API. Luminoso's products can be implemented through either a cloud-based or an on-premise solution. == Research == Luminoso continues to actively conduct research in natural language processing and word embeddings and regularly participates in evaluations such as SemEval. At SemEval 2017, Luminoso participated in Task 2, measuring the semantic similarity of word pairs within and across five languages. Its solution outperformed all competing systems in every language pair tested, with the exception of Persian. == Recognition == Luminoso has been listed as a "Cool Vendor in AI for Marketing" by Gartner, and has also been named a "Boston Artificial Intelligence Startup to Watch" by BostInno. In May 2017, Luminoso was recognized as having the Best Application for AI in the Enterprise by AI Business, and was also shortlisted as the Best AI Breakthrough and Best Innovation in NLP. == Competitors == Major competitors include Clarabridge and Lexalytics. == Investors == The company raised $1.5 million from angel investors led by Basis Technology in 2012. Its first institutional funding round of $6.5 was completed in July 2014, led by Acadia Woods with participation from Japan’s Digital Garage. The company followed that with a $10M series B funding round in December 2018, led by DVI Equity Partners, with participation from Liberty Global Ventures, DF Enterprises, Raptor Holdco, Acadia Woods Partners, and Accord Ventures, among others.
Random forest
Random forests or random decision forests is an ensemble learning method for classification, regression and other tasks that works by creating a multitude of decision trees during training. For classification tasks, the output of the random forest is the class selected by most trees. For regression tasks, the output is the average of the predictions of the trees. Random forests correct for decision trees' habit of overfitting to their training set. The first algorithm for random decision forests was created in 1995 by Tin Kam Ho using the random subspace method, which, in Ho's formulation, is a way to implement the "stochastic discrimination" approach to classification proposed by Eugene Kleinberg. An extension of the algorithm was developed by Leo Breiman and Adele Cutler, who registered "Random Forests" as a trademark in 2006 (as of 2019, owned by Minitab, Inc.). The extension combines Breiman's "bagging" idea and random selection of features, introduced first by Ho and later independently by Amit and Geman in order to construct a collection of decision trees with controlled variance. == History == The general method of random decision forests was first proposed by Salzberg and Heath in 1993, with a method that used a randomized decision tree algorithm to create multiple trees and then combine them using majority voting. This idea was developed further by Ho in 1995. Ho established that forests of trees splitting with oblique hyperplanes can gain accuracy as they grow without suffering from overtraining, as long as the forests are randomly restricted to be sensitive to only selected feature dimensions. A subsequent work along the same lines concluded that other splitting methods behave similarly, as long as they are randomly forced to be insensitive to some feature dimensions. This observation that a more complex classifier (a larger forest) gets more accurate nearly monotonically is in sharp contrast to the common belief that the complexity of a classifier can only grow to a certain level of accuracy before being hurt by overfitting. The explanation of the forest method's resistance to overtraining can be found in Kleinberg's theory of stochastic discrimination. The early development of Breiman's notion of random forests was influenced by the work of Amit and Geman who introduced the idea of searching over a random subset of the available decisions when splitting a node, in the context of growing a single tree. The idea of random subspace selection from Ho was also influential in the design of random forests. This method grows a forest of trees, and introduces variation among the trees by projecting the training data into a randomly chosen subspace before fitting each tree or each node. Finally, the idea of randomized node optimization, where the decision at each node is selected by a randomized procedure, rather than a deterministic optimization was first introduced by Thomas G. Dietterich. The proper introduction of random forests was made in a paper by Leo Breiman, that has become one of the world's most cited papers. This paper describes a method of building a forest of uncorrelated trees using a CART like procedure, combined with randomized node optimization and bagging. In addition, this paper combines several ingredients, some previously known and some novel, which form the basis of the modern practice of random forests, in particular: Using out-of-bag error as an estimate of the generalization error. Measuring variable importance through permutation. The report also offers the first theoretical result for random forests in the form of a bound on the generalization error which depends on the strength of the trees in the forest and their correlation. == Algorithm == === Preliminaries: decision tree learning === Decision trees are a popular method for various machine learning tasks. Tree learning is almost "an off-the-shelf procedure for data mining", say Hastie et al., "because it is invariant under scaling and various other transformations of feature values, is robust to inclusion of irrelevant features, and produces inspectable models. However, they are seldom accurate". In particular, trees that are grown very deep tend to learn highly irregular patterns: they overfit their training sets, i.e. have low bias, but very high variance. Random forests are a way of averaging multiple deep decision trees, trained on different parts of the same training set, with the goal of reducing the variance. This comes at the expense of a small increase in the bias and some loss of interpretability, but generally greatly boosts the performance in the final model. === Bagging === The training algorithm for random forests applies the general technique of bootstrap aggregating, or bagging, to tree learners. Given a training set X = x1, ..., xn with responses Y = y1, ..., yn, bagging repeatedly (B times) selects a random sample with replacement of the training set and fits trees to these samples: After training, predictions for unseen samples x' can be made by averaging the predictions from all the individual regression trees on x': f ^ = 1 B ∑ b = 1 B f b ( x ′ ) {\displaystyle {\hat {f}}={\frac {1}{B}}\sum _{b=1}^{B}f_{b}(x')} or by taking the plurality vote in the case of classification trees. This bootstrapping procedure leads to better model performance because it decreases the variance of the model, without increasing the bias. This means that while the predictions of a single tree are highly sensitive to noise in its training set, the average of many trees is not, as long as the trees are not correlated. Simply training many trees on a single training set would give strongly correlated trees (or even the same tree many times, if the training algorithm is deterministic); bootstrap sampling is a way of de-correlating the trees by showing them different training sets. Additionally, an estimate of the uncertainty of the prediction can be made as the standard deviation of the predictions from all the individual regression trees on x′: σ = ∑ b = 1 B ( f b ( x ′ ) − f ^ ) 2 B − 1 . {\displaystyle \sigma ={\sqrt {\frac {\sum _{b=1}^{B}(f_{b}(x')-{\hat {f}})^{2}}{B-1}}}.} The number B of samples (equivalently, of trees) is a free parameter. Typically, a few hundred to several thousand trees are used, depending on the size and nature of the training set. B can be optimized using cross-validation, or by observing the out-of-bag error: the mean prediction error on each training sample xi, using only the trees that did not have xi in their bootstrap sample. The training and test error tend to level off after some number of trees have been fit. === From bagging to random forests === The above procedure describes the original bagging algorithm for trees. Random forests also include another type of bagging scheme: they use a modified tree learning algorithm that selects, at each candidate split in the learning process, a random subset of the features. This process is sometimes called "feature bagging". The reason for doing this is the correlation of the trees in an ordinary bootstrap sample: if one or a few features are very strong predictors for the response variable (target output), these features will be selected in many of the B trees, causing them to become correlated. An analysis of how bagging and random subspace projection contribute to accuracy gains under different conditions is given by Ho. Typically, for a classification problem with p {\displaystyle p} features, p {\displaystyle {\sqrt {p}}} (rounded down) features are used in each split. For regression problems the inventors recommend p / 3 {\displaystyle p/3} (rounded down) with a minimum node size of 5 as the default. In practice, the best values for these parameters should be tuned on a case-to-case basis for every problem. === ExtraTrees === Adding one further step of randomization yields extremely randomized trees, or ExtraTrees. As with ordinary random forests, they are an ensemble of individual trees, but there are two main differences: (1) each tree is trained using the whole learning sample (rather than a bootstrap sample), and (2) the top-down splitting is randomized: for each feature under consideration, a number of random cut-points are selected, instead of computing the locally optimal cut-point (based on, e.g., information gain or the Gini impurity). The values are chosen from a uniform distribution within the feature's empirical range (in the tree's training set). Then, of all the randomly chosen splits, the split that yields the highest score is chosen to split the node. Similar to ordinary random forests, the number of randomly selected features to be considered at each node can be specified. Default values for this parameter are p {\displaystyle {\sqrt {p}}} for classification and p {\displaystyle p} for regression, where p {\displaystyle p} is the number of features in the model. === Random forests for high-dimensional data === The basic random forest procedure may
Distribution learning theory
The distributional learning theory or learning of probability distribution is a framework in computational learning theory. It has been proposed from Michael Kearns, Yishay Mansour, Dana Ron, Ronitt Rubinfeld, Robert Schapire and Linda Sellie in 1994 and it was inspired from the PAC-framework introduced by Leslie Valiant. In this framework the input is a number of samples drawn from a distribution that belongs to a specific class of distributions. The goal is to find an efficient algorithm that, based on these samples, determines with high probability the distribution from which the samples have been drawn. Because of its generality, this framework has been used in a large variety of different fields like machine learning, approximation algorithms, applied probability and statistics. This article explains the basic definitions, tools and results in this framework from the theory of computation point of view. == Definitions == Let X {\displaystyle \textstyle X} be the support of the distributions of interest. As in the original work of Kearns et al. if X {\displaystyle \textstyle X} is finite it can be assumed without loss of generality that X = { 0 , 1 } n {\displaystyle \textstyle X=\{0,1\}^{n}} where n {\displaystyle \textstyle n} is the number of bits that have to be used in order to represent any y ∈ X {\displaystyle \textstyle y\in X} . We focus in probability distributions over X {\displaystyle \textstyle X} . There are two possible representations of a probability distribution D {\displaystyle \textstyle D} over X {\displaystyle \textstyle X} . probability distribution function (or evaluator) an evaluator E D {\displaystyle \textstyle E_{D}} for D {\displaystyle \textstyle D} takes as input any y ∈ X {\displaystyle \textstyle y\in X} and outputs a real number E D [ y ] {\displaystyle \textstyle E_{D}[y]} which denotes the probability that of y {\displaystyle \textstyle y} according to D {\displaystyle \textstyle D} , i.e. E D [ y ] = Pr [ Y = y ] {\displaystyle \textstyle E_{D}[y]=\Pr[Y=y]} if Y ∼ D {\displaystyle \textstyle Y\sim D} . generator a generator G D {\displaystyle \textstyle G_{D}} for D {\displaystyle \textstyle D} takes as input a string of truly random bits y {\displaystyle \textstyle y} and outputs G D [ y ] ∈ X {\displaystyle \textstyle G_{D}[y]\in X} according to the distribution D {\displaystyle \textstyle D} . Generator can be interpreted as a routine that simulates sampling from the distribution D {\displaystyle \textstyle D} given a sequence of fair coin tosses. A distribution D {\displaystyle \textstyle D} is called to have a polynomial generator (respectively evaluator) if its generator (respectively evaluator) exists and can be computed in polynomial time. Let C X {\displaystyle \textstyle C_{X}} a class of distribution over X, that is C X {\displaystyle \textstyle C_{X}} is a set such that every D ∈ C X {\displaystyle \textstyle D\in C_{X}} is a probability distribution with support X {\displaystyle \textstyle X} . The C X {\displaystyle \textstyle C_{X}} can also be written as C {\displaystyle \textstyle C} for simplicity. In order to evaluate learnability, it is necessary to have a way to measure how well an approximated distribution D ′ {\displaystyle \textstyle D'} fits the sampled distribution D {\displaystyle \textstyle D} . There are several ways to measure the divergence between two distributions. Three common possibilities are Kullback–Leibler divergence Total variation distance of probability measures Kolmogorov distance Total variation and Kolmogorov distance are true metrics, while KL divergence is not (it lacks symmetry). These measures are ordered by convergence strength: closeness in KL divergence implies closeness in total variation (via Pinsker's inequality), which in turn implies closeness in Kolmogorov distance. Therefore, a learnability result proven under KL divergence automatically holds under the weaker measures, but not vice versa. Since certain measures may be more appropriate in specific applications, we will use d ( D , D ′ ) {\displaystyle \textstyle d(D,D')} to denote a selected divergence between the distribution D {\displaystyle \textstyle D} and the distribution D ′ {\displaystyle \textstyle D'} . The basic input that we use in order to learn a distribution is a number of samples drawn by this distribution. For the computational point of view the assumption is that such a sample is given in a constant amount of time. So it's like having access to an oracle G E N ( D ) {\displaystyle \textstyle GEN(D)} that returns a sample from the distribution D {\displaystyle \textstyle D} . Sometimes the interest is, apart from measuring the time complexity, to measure the number of samples that have to be used in order to learn a specific distribution D {\displaystyle \textstyle D} in class of distributions C {\displaystyle \textstyle C} . This quantity is called sample complexity of the learning algorithm. In order for the problem of distribution learning to be more clear consider the problem of supervised learning as defined in. In this framework of statistical learning theory a training set S = { ( x 1 , y 1 ) , … , ( x n , y n ) } {\displaystyle \textstyle S=\{(x_{1},y_{1}),\dots ,(x_{n},y_{n})\}} and the goal is to find a target function f : X → Y {\displaystyle \textstyle f:X\rightarrow Y} that minimizes some loss function, e.g. the square loss function. More formally f = arg min g ∫ V ( y , g ( x ) ) d ρ ( x , y ) {\displaystyle f=\arg \min _{g}\int V(y,g(x))d\rho (x,y)} , where V ( ⋅ , ⋅ ) {\displaystyle V(\cdot ,\cdot )} is the loss function, e.g. V ( y , z ) = ( y − z ) 2 {\displaystyle V(y,z)=(y-z)^{2}} and ρ ( x , y ) {\displaystyle \rho (x,y)} the probability distribution according to which the elements of the training set are sampled. If the conditional probability distribution ρ x ( y ) {\displaystyle \rho _{x}(y)} is known then the target function has the closed form f ( x ) = ∫ y y d ρ x ( y ) {\displaystyle f(x)=\int _{y}yd\rho _{x}(y)} . So the set S {\displaystyle S} is a set of samples from the probability distribution ρ ( x , y ) {\displaystyle \rho (x,y)} . Now the goal of distributional learning theory if to find ρ {\displaystyle \rho } given S {\displaystyle S} which can be used to find the target function f {\displaystyle f} . Definition of learnability A class of distributions C {\displaystyle \textstyle C} is called efficiently learnable if for every ϵ > 0 {\displaystyle \textstyle \epsilon >0} and 0 < δ ≤ 1 {\displaystyle \textstyle 0<\delta \leq 1} given access to G E N ( D ) {\displaystyle \textstyle GEN(D)} for an unknown distribution D ∈ C {\displaystyle \textstyle D\in C} , there exists a polynomial time algorithm A {\displaystyle \textstyle A} , called learning algorithm of C {\displaystyle \textstyle C} , that outputs a generator or an evaluator of a distribution D ′ {\displaystyle \textstyle D'} such that Pr [ d ( D , D ′ ) ≤ ϵ ] ≥ 1 − δ {\displaystyle \Pr[d(D,D')\leq \epsilon ]\geq 1-\delta } If we know that D ′ ∈ C {\displaystyle \textstyle D'\in C} then A {\displaystyle \textstyle A} is called proper learning algorithm, otherwise is called improper learning algorithm. In some settings the class of distributions C {\displaystyle \textstyle C} is a class with well known distributions which can be described by a set of parameters. For instance C {\displaystyle \textstyle C} could be the class of all the Gaussian distributions N ( μ , σ 2 ) {\displaystyle \textstyle N(\mu ,\sigma ^{2})} . In this case the algorithm A {\displaystyle \textstyle A} should be able to estimate the parameters μ , σ {\displaystyle \textstyle \mu ,\sigma } . In this case A {\displaystyle \textstyle A} is called parameter learning algorithm. Obviously the parameter learning for simple distributions is a very well studied field that is called statistical estimation and there is a very long bibliography on different estimators for different kinds of simple known distributions. But distributions learning theory deals with learning class of distributions that have more complicated description. == First results == In their seminal work, Kearns et al. deal with the case where A {\displaystyle \textstyle A} is described in term of a finite polynomial sized circuit and they proved the following for some specific classes of distribution. O R {\displaystyle \textstyle OR} gate distributions for this kind of distributions there is no polynomial-sized evaluator, unless # P ⊆ P / poly {\displaystyle \textstyle \#P\subseteq P/{\text{poly}}} . On the other hand, this class is efficiently learnable with generator. Parity gate distributions this class is efficiently learnable with both generator and evaluator. Mixtures of Hamming Balls this class is efficiently learnable with both generator and evaluator. Probabilistic Finite Automata this class is not efficiently learnable with evaluator under the Noisy Parity Assumption which is an impossibility assumption in the PAC learning fram
Waffles (machine learning)
Waffles is a collection of command-line tools for performing machine learning operations developed at Brigham Young University. These tools are written in C++, and are available under the GNU Lesser General Public License. == Description == The Waffles machine learning toolkit contains command-line tools for performing various operations related to machine learning, data mining, and predictive modeling. The primary focus of Waffles is to provide tools that are simple to use in scripted experiments or processes. For example, the supervised learning algorithms included in Waffles are all designed to support multi-dimensional labels, classification and regression, automatically impute missing values, and automatically apply necessary filters to transform the data to a type that the algorithm can support, such that arbitrary learning algorithms can be used with arbitrary data sets. Many other machine learning toolkits provide similar functionality, but require the user to explicitly configure data filters and transformations to make it compatible with a particular learning algorithm. The algorithms provided in Waffles also have the ability to automatically tune their own parameters (with the cost of additional computational overhead). Because Waffles is designed for script-ability, it deliberately avoids presenting its tools in a graphical environment. It does, however, include a graphical "wizard" tool that guides the user to generate a command that will perform a desired task. This wizard does not actually perform the operation, but requires the user to paste the command that it generates into a command terminal or a script. The idea motivating this design is to prevent the user from becoming "locked in" to a graphical interface. All of the Waffles tools are implemented as thin wrappers around functionality in a C++ class library. This makes it possible to convert scripted processes into native applications with minimal effort. Waffles was first released as an open source project in 2005. Since that time, it has been developed at Brigham Young University, with a new version having been released approximately every 6–9 months. Waffles is not an acronym—the toolkit was named after the food for historical reasons. == Advantages == Some of the advantages of Waffles in contrast with other popular open source machine learning toolkits include: Waffles automatically takes care of many issues related to data format in order to simplify its tools. Because it is implemented in C++, many of its algorithms are particularly fast. Also, the lack of dependency on any virtual machine makes it easier to deploy in conjunction with other applications. The functionality included in Waffles is very broad, including algorithms for dimensionality reduction, collaborative filtering, visualization, clustering, supervised learning, optimization, linear algebra, data transformation, image and signal processing, policy learning, and sparse matrix operations. == Disadvantages == Although Waffles provides significant breadth, it lacks the depth of many toolkits that focus on a particular area of machine learning. The Weka (machine learning) toolkit, for example, provides many more classification algorithms than Waffles provides. Waffles only has a limited graphical interface.
Scale space
Scale-space theory is a framework for multi-scale signal representation developed by the computer vision, image processing and signal processing communities with complementary motivations from physics and biological vision. It is a formal theory for handling image structures at different scales, by representing an image as a one-parameter family of smoothed images, the scale-space representation, parametrized by the size of the smoothing kernel used for suppressing fine-scale structures. The parameter t {\displaystyle t} in this family is referred to as the scale parameter, with the interpretation that image structures of spatial size smaller than about t {\displaystyle {\sqrt {t}}} have largely been smoothed away in the scale-space level at scale t {\displaystyle t} . The main type of scale space is the linear (Gaussian) scale space, which has wide applicability as well as the attractive property of being possible to derive from a small set of scale-space axioms. The corresponding scale-space framework encompasses a theory for Gaussian derivative operators, which can be used as a basis for expressing a large class of visual operations for computerized systems that process visual information. This framework also allows visual operations to be made scale invariant, which is necessary for dealing with the size variations that may occur in image data, because real-world objects may be of different sizes and in addition the distance between the object and the camera may be unknown and may vary depending on the circumstances. == Definition == The notion of scale space applies to signals of arbitrary numbers of variables. The most common case in the literature applies to two-dimensional images, which is what is presented here. Consider a given image f {\displaystyle f} where f ( x , y ) {\displaystyle f(x,y)} is the greyscale value of the pixel at position ( x , y ) {\displaystyle (x,y)} . The linear (Gaussian) scale-space representation of f {\displaystyle f} is a family of derived signals L ( x , y ; t ) {\displaystyle L(x,y;t)} defined by the convolution of f ( x , y ) {\displaystyle f(x,y)} with the two-dimensional Gaussian kernel g ( x , y ; t ) = 1 2 π t e − ( x 2 + y 2 ) / 2 t {\displaystyle g(x,y;t)={\frac {1}{2\pi t}}e^{-(x^{2}+y^{2})/2t}\,} such that L ( ⋅ , ⋅ ; t ) = g ( ⋅ , ⋅ ; t ) ∗ f ( ⋅ , ⋅ ) , {\displaystyle L(\cdot ,\cdot ;t)\ =g(\cdot ,\cdot ;t)f(\cdot ,\cdot ),} where the semicolon in the argument of L {\displaystyle L} implies that the convolution is performed only over the variables x , y {\displaystyle x,y} , while the scale parameter t {\displaystyle t} after the semicolon just indicates which scale level is being defined. This definition of L {\displaystyle L} works for a continuum of scales t ≥ 0 {\displaystyle t\geq 0} , but typically only a finite discrete set of levels in the scale-space representation would be actually considered. The scale parameter t = σ 2 {\displaystyle t=\sigma ^{2}} is the variance of the Gaussian filter and as a limit for t = 0 {\displaystyle t=0} the filter g {\displaystyle g} becomes an impulse function such that L ( x , y ; 0 ) = f ( x , y ) , {\displaystyle L(x,y;0)=f(x,y),} that is, the scale-space representation at scale level t = 0 {\displaystyle t=0} is the image f {\displaystyle f} itself. As t {\displaystyle t} increases, L {\displaystyle L} is the result of smoothing f {\displaystyle f} with a larger and larger filter, thereby removing more and more of the details that the image contains. Since the standard deviation of the filter is σ = t {\displaystyle \sigma ={\sqrt {t}}} , details that are significantly smaller than this value are to a large extent removed from the image at scale parameter t {\displaystyle t} , see the following figures and for graphical illustrations. === Why a Gaussian filter? === When faced with the task of generating a multi-scale representation one may ask: could any filter g of low-pass type and with a parameter t which determines its width be used to generate a scale space? The answer is no, as it is of crucial importance that the smoothing filter does not introduce new spurious structures at coarse scales that do not correspond to simplifications of corresponding structures at finer scales. In the scale-space literature, a number of different ways have been expressed to formulate this criterion in precise mathematical terms. The conclusion from several different axiomatic derivations that have been presented is that the Gaussian scale space constitutes the canonical way to generate a linear scale space, based on the essential requirement that new structures must not be created when going from a fine scale to any coarser scale. Conditions, referred to as scale-space axioms, that have been used for deriving the uniqueness of the Gaussian kernel include linearity, shift invariance, semi-group structure, non-enhancement of local extrema, scale invariance and rotational invariance. In the works, the uniqueness claimed in the arguments based on scale invariance has been criticized, and alternative self-similar scale-space kernels have been proposed. The Gaussian kernel is, however, a unique choice according to the scale-space axiomatics based on causality or non-enhancement of local extrema. === Alternative definition === Equivalently, the scale-space family can be defined as the solution of the diffusion equation (for example in terms of the heat equation), ∂ t L = 1 2 ∇ 2 L , {\displaystyle \partial _{t}L={\frac {1}{2}}\nabla ^{2}L,} with initial condition L ( x , y ; 0 ) = f ( x , y ) {\displaystyle L(x,y;0)=f(x,y)} . This formulation of the scale-space representation L means that it is possible to interpret the intensity values of the image f as a "temperature distribution" in the image plane and that the process that generates the scale-space representation as a function of t corresponds to heat diffusion in the image plane over time t (assuming the thermal conductivity of the material equal to the arbitrarily chosen constant 1/2). Although this connection may appear superficial for a reader not familiar with differential equations, it is indeed the case that the main scale-space formulation in terms of non-enhancement of local extrema is expressed in terms of a sign condition on partial derivatives in the 2+1-D volume generated by the scale space, thus within the framework of partial differential equations. Furthermore, a detailed analysis of the discrete case shows that the diffusion equation provides a unifying link between continuous and discrete scale spaces, which also generalizes to nonlinear scale spaces, for example, using anisotropic diffusion. Hence, one may say that the primary way to generate a scale space is by the diffusion equation, and that the Gaussian kernel arises as the Green's function of this specific partial differential equation. == Motivations == The motivation for generating a scale-space representation of a given data set originates from the basic observation that real-world objects are composed of different structures at different scales. This implies that real-world objects, in contrast to idealized mathematical entities such as points or lines, may appear in different ways depending on the scale of observation. For example, the concept of a "tree" is appropriate at the scale of meters, while concepts such as leaves and molecules are more appropriate at finer scales. For a computer vision system analysing an unknown scene, there is no way to know a priori what scales are appropriate for describing the interesting structures in the image data. Hence, the only reasonable approach is to consider descriptions at multiple scales in order to be able to capture the unknown scale variations that may occur. Taken to the limit, a scale-space representation considers representations at all scales. Another motivation to the scale-space concept originates from the process of performing a physical measurement on real-world data. In order to extract any information from a measurement process, one has to apply operators of non-infinitesimal size to the data. In many branches of computer science and applied mathematics, the size of the measurement operator is disregarded in the theoretical modelling of a problem. The scale-space theory on the other hand explicitly incorporates the need for a non-infinitesimal size of the image operators as an integral part of any measurement as well as any other operation that depends on a real-world measurement. There is a close link between scale-space theory and biological vision. Many scale-space operations show a high degree of similarity with receptive field profiles recorded from the mammalian retina and the first stages in the visual cortex. In these respects, the scale-space framework can be seen as a theoretically well-founded paradigm for early vision, which in addition has been thoroughly tested by algorithms and experiments. == Gaussian derivatives == At any scale in scale space, we c
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).