Species distribution modelling

Species distribution modelling (SDM), also known as environmental (or ecological) niche modelling (ENM), habitat suitability modelling, predictive habitat distribution modelling, and range mapping uses ecological models to predict the distribution of a species across geographic space and time using environmental data. The environmental data are most often climate data (e.g. temperature, precipitation), but can include other variables such as soil type, water depth, and land cover. SDMs are used in several research areas in conservation biology, ecology and evolution. These models can be used to understand how environmental conditions influence the occurrence or abundance of a species, and for predictive purposes (ecological forecasting). Predictions from an SDM may be of a species' future distribution under climate change, a species' past distribution in order to assess evolutionary relationships, or the potential future distribution of an invasive species. Predictions of current and/or future habitat suitability can be useful for management applications (e.g. reintroduction or translocation of vulnerable species, reserve placement in anticipation of climate change). There are two main types of SDMs. Correlative SDMs, also known as climate envelope models, bioclimatic models, or resource selection function models, model the observed distribution of a species as a function of environmental conditions. Mechanistic SDMs, also known as process-based models or biophysical models, use independently derived information about a species' physiology to develop a model of the environmental conditions under which the species can exist. The extent to which such modelled data reflect real-world species distributions will depend on a number of factors, including the nature, complexity, and accuracy of the models used and the quality of the available environmental data layers; the availability of sufficient and reliable species distribution data as model input; and the influence of various factors such as barriers to dispersal, geologic history, or biotic interactions, that increase the difference between the realized niche and the fundamental niche. Environmental niche modelling may be considered a part of the discipline of biodiversity informatics. == History == A. F. W. Schimper used geographical and environmental factors to explain plant distributions in his 1898 Pflanzengeographie auf physiologischer Grundlage (Plant Geography Upon a Physiological Basis) and his 1908 work of the same name. Andrew Murray used the environment to explain the distribution of mammals in his 1866 The Geographical Distribution of Mammals. Robert Whittaker's work with plants and Robert MacArthur's work with birds strongly established the role the environment plays in species distributions. Elgene O. Box constructed environmental envelope models to predict the range of tree species. His computer simulations were among the earliest uses of species distribution modelling. The adoption of more sophisticated generalised linear models (GLMs) made it possible to create more sophisticated and realistic species distribution models. The expansion of remote sensing and the development of GIS-based environmental modelling increase the amount of environmental information available for model-building and made it easier to use. == Correlative vs mechanistic models == === Correlative SDMs === SDMs originated as correlative models. Correlative SDMs model the observed distribution of a species as a function of geographically referenced climatic predictor variables using multiple regression approaches. Given a set of geographically referred observed presences of a species and a set of climate maps, a model defines the most likely environmental ranges within which a species lives. Correlative SDMs assume that species are at equilibrium with their environment and that the relevant environmental variables have been adequately sampled. The models allow for interpolation between a limited number of species occurrences. For these models to be effective, it is required to gather observations not only of species presences, but also of absences, that is, where the species does not live. Records of species absences are typically not as common as records of presences, thus often "random background" or "pseudo-absence" data are used to fit these models. If there are incomplete records of species occurrences, pseudo-absences can introduce bias. Since correlative SDMs are models of a species' observed distribution, they are models of the realized niche (the environments where a species is found), as opposed to the fundamental niche (the environments where a species can be found, or where the abiotic environment is appropriate for the survival). For a given species, the realized and fundamental niches might be the same, but if a species is geographically confined due to dispersal limitation or species interactions, the realized niche will be smaller than the fundamental niche. Correlative SDMs are easier and faster to implement than mechanistic SDMs, and can make ready use of available data. Since they are correlative however, they do not provide much information about causal mechanisms and are not good for extrapolation. They will also be inaccurate if the observed species range is not at equilibrium (e.g. if a species has been recently introduced and is actively expanding its range). In standard SDMs, the distribution of a single species is often modeled, with unique parameters describing how environmental (abiotic) factors influence its occurrence probability. This allows for differentiated responses to environmental drivers among species, but can be problematic for data-deficient species. In contrast, similarities in environmental responses can be accounted for in multi-species SDMs, which model several species jointly using shared or hierarchically related parameters. However, neither approach explicitly accounts for community-level biotic interactions, which can be important in explaining species diversity patterns. Joint species distribution models (joint SDMs or J-SDMs) address this by modeling species co-occurrence patterns directly. The occurrence probability of a given species is thus influenced not only by abiotic drivers but also by inferred biotic associations with other species. This can improve accuracy for rarer taxa and provide insights into community ecology. Both standard SDMs and J-SDMs can be used to generate community-level metrics, such as species richness, by aggregating outputs across multiple species. These can be important for decision-making such as conservation planning. === Mechanistic SDMs === Mechanistic SDMs are more recently developed. In contrast to correlative models, mechanistic SDMs use physiological information about a species (taken from controlled field or laboratory studies) to determine the range of environmental conditions within which the species can persist. These models aim to directly characterize the fundamental niche, and to project it onto the landscape. A simple model may simply identify threshold values outside of which a species can't survive. A more complex model may consist of several sub-models, e.g. micro-climate conditions given macro-climate conditions, body temperature given micro-climate conditions, fitness or other biological rates (e.g. survival, fecundity) given body temperature (thermal performance curves), resource or energy requirements, and population dynamics. Geographically referenced environmental data are used as model inputs. Because the species distribution predictions are independent of the species' known range, these models are especially useful for species whose range is actively shifting and not at equilibrium, such as invasive species. Mechanistic SDMs incorporate causal mechanisms and are better for extrapolation and non-equilibrium situations. However, they are more labor-intensive to create than correlational models and require the collection and validation of a lot of physiological data, which may not be readily available. The models require many assumptions and parameter estimates, and they can become very complicated. Dispersal, biotic interactions, and evolutionary processes present challenges, as they aren't usually incorporated into either correlative or mechanistic models. Correlational and mechanistic models can be used in combination to gain additional insights. For example, a mechanistic model could be used to identify areas that are clearly outside the species' fundamental niche, and these areas can be marked as absences or excluded from analysis. See for a comparison between mechanistic and correlative models. == Niche models (correlative) == There are a variety of mathematical methods that can be used for fitting, selecting, and evaluating correlative SDMs. Models include "profile" methods, which are simple statistical techniques that use e.g. environmental distance to known sites of occurrence such as

Nobody (username)

In many Unix variants, "nobody" is the conventional name of a user identifier which owns no files, is in no privileged groups, and has no abilities except those which every other user has. It is normally not enabled as a user account, i.e. has no home directory or login credentials assigned. Some systems also define an equivalent group "nogroup". == Uses == The pseudo-user "nobody" and group "nogroup" are used, for example, in the NFSv4 implementation of Linux by idmapd, if a user or group name in an incoming packet does not match any known username on the system. It was once common to run daemons as nobody, especially on servers, in order to limit the damage that could be done by a malicious user who gained control of them. However, the usefulness of this technique is reduced if more than one daemon is run like this, because then gaining control of one daemon would provide control of them all. The reason is that processes owned by the same user have the ability to send signals to each other and use debugging facilities to read or even modify each other's memory. Modern practice, as recommended by the Linux Standard Base, is to create a separate user account for each daemon.

Softplus

In mathematics and machine learning, the softplus function is f ( x ) = ln ⁡ ( 1 + e x ) . {\displaystyle f(x)=\ln(1+e^{x}).} It is a smooth approximation (in fact, an analytic function) to the ramp function, which is known as the rectifier or ReLU (rectified linear unit) in machine learning. For large negative x {\displaystyle x} it is ln ⁡ ( 1 + e x ) = ln ⁡ ( 1 + ϵ ) ⪆ ln ⁡ 1 = 0 {\displaystyle \ln(1+e^{x})=\ln(1+\epsilon )\gtrapprox \ln 1=0} , so just above 0, while for large positive x {\displaystyle x} it is ln ⁡ ( 1 + e x ) ⪆ ln ⁡ ( e x ) = x {\displaystyle \ln(1+e^{x})\gtrapprox \ln(e^{x})=x} , so just above x {\displaystyle x} . The names softplus and SmoothReLU are used in machine learning. The name "softplus" (2000), by analogy with the earlier softmax (1989) is presumably because it is a smooth (soft) approximation of the positive part of x, which is sometimes denoted with a superscript plus, x + := max ( 0 , x ) {\displaystyle x^{+}:=\max(0,x)} . == Alternative forms == This function can be approximated as: ln ⁡ ( 1 + e x ) ≈ { ln ⁡ 2 , x = 0 , x 1 − e − x / ln ⁡ 2 , x ≠ 0 {\displaystyle \ln \left(1+e^{x}\right)\approx {\begin{cases}\ln 2,&x=0,\\[6pt]{\frac {x}{1-e^{-x/\ln 2}}},&x\neq 0\end{cases}}} By making the change of variables x = y ln ⁡ ( 2 ) {\displaystyle x=y\ln(2)} , this is equivalent to log 2 ⁡ ( 1 + 2 y ) ≈ { 1 , y = 0 , y 1 − e − y , y ≠ 0. {\displaystyle \log _{2}(1+2^{y})\approx {\begin{cases}1,&y=0,\\[6pt]{\frac {y}{1-e^{-y}}},&y\neq 0.\end{cases}}} A sharpness parameter k {\displaystyle k} may be included: f ( x ) = ln ⁡ ( 1 + e k x ) k , f ′ ( x ) = e k x 1 + e k x = 1 1 + e − k x . {\displaystyle f(x)={\frac {\ln(1+e^{kx})}{k}},\qquad \qquad f'(x)={\frac {e^{kx}}{1+e^{kx}}}={\frac {1}{1+e^{-kx}}}.} Additionally, the softplus function is equivalent to the log of the sigmoid function in the following way: − ln ⁡ ( sigmoid ( − x ) ) = − ln ⁡ ( 1 1 + e x ) = ln ⁡ ( 1 + e x ) = softplus ( x ) {\displaystyle -\ln({\text{sigmoid}}(-x))=-\ln \left({\frac {1}{1+e^{x}}}\right)=\ln \left(1+e^{x}\right)={\text{softplus}}(x)} == Related functions == The derivative of softplus is the standard logistic function: f ′ ( x ) = e x 1 + e x = 1 1 + e − x {\displaystyle f'(x)={\frac {e^{x}}{1+e^{x}}}={\frac {1}{1+e^{-x}}}} The logistic function or the sigmoid function is a smooth approximation of the rectifier, the Heaviside step function. === LogSumExp === The multivariable generalization of single-variable softplus is the LogSumExp with the first argument set to zero: L S E 0 + ⁡ ( x 1 , … , x n ) := LSE ⁡ ( 0 , x 1 , … , x n ) = ln ⁡ ( 1 + e x 1 + ⋯ + e x n ) . {\displaystyle \operatorname {LSE_{0}} ^{+}(x_{1},\dots ,x_{n}):=\operatorname {LSE} (0,x_{1},\dots ,x_{n})=\ln(1+e^{x_{1}}+\cdots +e^{x_{n}}).} The LogSumExp function is LSE ⁡ ( x 1 , … , x n ) = ln ⁡ ( e x 1 + ⋯ + e x n ) , {\displaystyle \operatorname {LSE} (x_{1},\dots ,x_{n})=\ln(e^{x_{1}}+\cdots +e^{x_{n}}),} and its gradient is the softmax; the softmax with the first argument set to zero is the multivariable generalization of the logistic function. Both LogSumExp and softmax are used in machine learning. === Convex conjugate === The convex conjugate (specifically, the Legendre transformation) of the softplus function is the negative binary entropy function (with base e). This is because (following the definition of the Legendre transformation: the derivatives are inverse functions) the derivative of softplus is the logistic function, whose inverse function is the logit, which is the derivative of negative binary entropy. Softplus can be interpreted as logistic loss (as a positive number), so, by duality, minimizing logistic loss corresponds to maximizing entropy. This justifies the principle of maximum entropy as loss minimization.

Ensemble learning

In statistics and machine learning, ensemble methods use multiple learning algorithms to obtain better predictive performance than could be obtained from any of the constituent learning algorithms alone. Unlike a statistical ensemble in statistical mechanics, which is usually infinite, a machine learning ensemble consists of only a concrete finite set of alternative models, but typically allows for much more flexible structure to exist among those alternatives. == Overview == Supervised learning algorithms search through a hypothesis space to find a suitable hypothesis that will make good predictions with a particular problem. Even if this space contains hypotheses that are very well-suited for a particular problem, it may be very difficult to find a good one. Ensembles combine multiple hypotheses to form one which should be theoretically better. Ensemble learning trains two or more machine learning algorithms on a specific classification or regression task. The algorithms within the ensemble model are generally referred as "base models", "base learners", or "weak learners" in literature. These base models can be constructed using a single modelling algorithm, or several different algorithms. The idea is to train a diverse set of weak models on the same modelling task, such that the outputs of each weak learner have poor predictive ability (i.e., high bias), and among all weak learners, the outcome and error values exhibit high variance. Fundamentally, an ensemble learning model trains at least two high-bias (weak) and high-variance (diverse) models to be combined into a better-performing model. The set of weak models — which would not produce satisfactory predictive results individually — are combined or averaged to produce a single, high performing, accurate, and low-variance model to fit the task as required. Ensemble learning typically refers to bagging (bootstrap aggregating), boosting or stacking/blending techniques to induce high variance among the base models. Bagging creates diversity by generating random samples from the training observations and fitting the same model to each different sample — also known as homogeneous parallel ensembles. Boosting follows an iterative process by sequentially training each base model on the up-weighted errors of the previous base model, producing an additive model to reduce the final model errors — also known as sequential ensemble learning. Stacking or blending consists of different base models, each trained independently (i.e. diverse/high variance) to be combined into the ensemble model — producing a heterogeneous parallel ensemble. Common applications of ensemble learning include random forests (an extension of bagging), Boosted Tree models, and Gradient Boosted Tree Models. Models in applications of stacking are generally more task-specific — such as combining clustering techniques with other parametric and/or non-parametric techniques. Evaluating the prediction of an ensemble typically requires more computation than evaluating the prediction of a single model. In one sense, ensemble learning may be thought of as a way to compensate for poor learning algorithms by performing a lot of extra computation. On the other hand, the alternative is to do a lot more learning with one non-ensemble model. An ensemble may be more efficient at improving overall accuracy for the same increase in compute, storage, or communication resources by using that increase on two or more methods, than would have been improved by increasing resource use for a single method. Fast algorithms such as decision trees are commonly used in ensemble methods (e.g., random forests), although slower algorithms can benefit from ensemble techniques as well. By analogy, ensemble techniques have been used also in unsupervised learning scenarios, for example in consensus clustering or in anomaly detection. == Ensemble theory == Empirically, ensembles tend to yield better results when there is a significant diversity among the models. Many ensemble methods, therefore, seek to promote diversity among the models they combine. Although perhaps non-intuitive, more random algorithms (like random decision trees) can be used to produce a stronger ensemble than very deliberate algorithms (like entropy-reducing decision trees). Using a variety of strong learning algorithms, however, has been shown to be more effective than using techniques that attempt to dumb-down the models in order to promote diversity. It is possible to increase diversity in the training stage of the model using correlation for regression tasks or using information measures such as cross entropy for classification tasks. Theoretically, one can justify the diversity concept because the lower bound of the error rate of an ensemble system can be decomposed into accuracy, diversity, and the other term. === The geometric framework === Ensemble learning, including both regression and classification tasks, can be explained using a geometric framework. Within this framework, the output of each individual classifier or regressor for the entire dataset can be viewed as a point in a multi-dimensional space. Additionally, the target result is also represented as a point in this space, referred to as the "ideal point." The Euclidean distance is used as the metric to measure both the performance of a single classifier or regressor (the distance between its point and the ideal point) and the dissimilarity between two classifiers or regressors (the distance between their respective points). This perspective transforms ensemble learning into a deterministic problem. For example, within this geometric framework, it can be proved that the averaging of the outputs (scores) of all base classifiers or regressors can lead to equal or better results than the average of all the individual models. It can also be proved that if the optimal weighting scheme is used, then a weighted averaging approach can outperform any of the individual classifiers or regressors that make up the ensemble or as good as the best performer at least. == Ensemble size == While the number of component classifiers of an ensemble has a great impact on the accuracy of prediction, there is a limited number of studies addressing this problem. A priori determining of ensemble size and the volume and velocity of big data streams make this even more crucial for online ensemble classifiers. Mostly statistical tests were used for determining the proper number of components. More recently, a theoretical framework suggested that there is an ideal number of component classifiers for an ensemble such that having more or less than this number of classifiers would deteriorate the accuracy. It is called "the law of diminishing returns in ensemble construction." Their theoretical framework shows that using the same number of independent component classifiers as class labels gives the highest accuracy. == Common types of ensembles == === Bayes optimal classifier === The Bayes optimal classifier is a classification technique. It is an ensemble of all the hypotheses in the hypothesis space. On average, no other ensemble can outperform it. The Naive Bayes classifier is a version of this that assumes that the data is conditionally independent on the class and makes the computation more feasible. Each hypothesis is given a vote proportional to the likelihood that the training dataset would be sampled from a system if that hypothesis were true. To facilitate training data of finite size, the vote of each hypothesis is also multiplied by the prior probability of that hypothesis. The Bayes optimal classifier can be expressed with the following equation: y = a r g m a x c j ∈ C ∑ h i ∈ H P ( c j | h i ) P ( T | h i ) P ( h i ) {\displaystyle y={\underset {c_{j}\in C}{\mathrm {argmax} }}\sum _{h_{i}\in H}{P(c_{j}|h_{i})P(T|h_{i})P(h_{i})}} where y {\displaystyle y} is the predicted class, C {\displaystyle C} is the set of all possible classes, H {\displaystyle H} is the hypothesis space, P {\displaystyle P} refers to a probability, and T {\displaystyle T} is the training data. As an ensemble, the Bayes optimal classifier represents a hypothesis that is not necessarily in H {\displaystyle H} . The hypothesis represented by the Bayes optimal classifier, however, is the optimal hypothesis in ensemble space (the space of all possible ensembles consisting only of hypotheses in H {\displaystyle H} ). This formula can be restated using Bayes' theorem, which says that the posterior is proportional to the likelihood times the prior: P ( h i | T ) ∝ P ( T | h i ) P ( h i ) {\displaystyle P(h_{i}|T)\propto P(T|h_{i})P(h_{i})} hence, y = a r g m a x c j ∈ C ∑ h i ∈ H P ( c j | h i ) P ( h i | T ) {\displaystyle y={\underset {c_{j}\in C}{\mathrm {argmax} }}\sum _{h_{i}\in H}{P(c_{j}|h_{i})P(h_{i}|T)}} === Bootstrap aggregating (bagging) === Bootstrap aggregation (bagging) involves training an ensemble on bootstrapped data sets. A bootstrapped set is cr

Feature selection

In machine learning, feature selection is the process of selecting a subset of relevant features (variables, predictors) for use in model construction. Feature selection techniques are used for several reasons: simplification of models to make them easier to interpret, shorter training times, to avoid the curse of dimensionality, improve the compatibility of the data with a certain learning model class, to encode inherent symmetries present in the input space. The central premise when using feature selection is that data sometimes contains features that are redundant or irrelevant, and can thus be removed without incurring much loss of information. Redundancy and irrelevance are two distinct notions, since one relevant feature may be redundant in the presence of another relevant feature with which it is strongly correlated. Feature extraction creates new features from functions of the original features, whereas feature selection finds a subset of the features. Feature selection techniques are often used in domains where there are many features and comparatively few samples (data points). == Introduction == A feature selection algorithm can be seen as the combination of a search technique for proposing new feature subsets, along with an evaluation measure which scores the different feature subsets. The simplest algorithm is to test each possible subset of features finding the one which minimizes the error rate. This is an exhaustive search of the space, and is computationally intractable for all but the smallest of feature sets. The choice of evaluation metric heavily influences the algorithm, and it is these evaluation metrics which distinguish between the three main categories of feature selection algorithms: wrappers, filters and embedded methods. Wrapper methods use a predictive model to score feature subsets. Each new subset is used to train a model, which is tested on a hold-out set. Counting the number of mistakes made on that hold-out set (the error rate of the model) gives the score for that subset. As wrapper methods train a new model for each subset, they are very computationally intensive, but usually provide the best performing feature set for that particular type of model or typical problem. Filter methods use a proxy measure instead of the error rate to score a feature subset. This measure is chosen to be fast to compute, while still capturing the usefulness of the feature set. Common measures include the mutual information, the pointwise mutual information, Pearson product-moment correlation coefficient, Relief-based algorithms, and inter/intra class distance or the scores of significance tests for each class/feature combinations. Filters are usually less computationally intensive than wrappers, but they produce a feature set which is not tuned to a specific type of predictive model. This lack of tuning means a feature set from a filter is more general than the set from a wrapper, usually giving lower prediction performance than a wrapper. However the feature set doesn't contain the assumptions of a prediction model, and so is more useful for exposing the relationships between the features. Many filters provide a feature ranking rather than an explicit best feature subset, and the cut off point in the ranking is chosen via cross-validation. Filter methods have also been used as a preprocessing step for wrapper methods, allowing a wrapper to be used on larger problems. One other popular approach is the Recursive Feature Elimination algorithm, commonly used with Support Vector Machines to repeatedly construct a model and remove features with low weights. Embedded methods are a catch-all group of techniques which perform feature selection as part of the model construction process. The exemplar of this approach is the LASSO method for constructing a linear model, which penalizes the regression coefficients with an L1 penalty, shrinking many of them to zero. Any features which have non-zero regression coefficients are 'selected' by the LASSO algorithm. Improvements to the LASSO include Bolasso which bootstraps samples; Elastic net regularization, which combines the L1 penalty of LASSO with the L2 penalty of ridge regression; and FeaLect which scores all the features based on combinatorial analysis of regression coefficients. AEFS further extends LASSO to nonlinear scenario with autoencoders. These approaches tend to be between filters and wrappers in terms of computational complexity. In traditional regression analysis, the most popular form of feature selection is stepwise regression, which is a wrapper technique. It is a greedy algorithm that adds the best feature (or deletes the worst feature) at each round. The main control issue is deciding when to stop the algorithm. In machine learning, this is typically done by cross-validation. In statistics, some criteria are optimized. This leads to the inherent problem of nesting. More robust methods have been explored, such as branch and bound and piecewise linear network. == Subset selection == Subset selection evaluates a subset of features as a group for suitability. Subset selection algorithms can be broken up into wrappers, filters, and embedded methods. Wrappers use a search algorithm to search through the space of possible features and evaluate each subset by running a model on the subset. Wrappers can be computationally expensive and have a risk of over fitting to the model. Filters are similar to wrappers in the search approach, but instead of evaluating against a model, a simpler filter is evaluated. Embedded techniques are embedded in, and specific to, a model. Many popular search approaches use greedy hill climbing, which iteratively evaluates a candidate subset of features, then modifies the subset and evaluates if the new subset is an improvement over the old. Evaluation of the subsets requires a scoring metric that grades a subset of features. Exhaustive search is generally impractical, so at some implementor (or operator) defined stopping point, the subset of features with the highest score discovered up to that point is selected as the satisfactory feature subset. The stopping criterion varies by algorithm; possible criteria include: a subset score exceeds a threshold, a program's maximum allowed run time has been surpassed, etc. Alternative search-based techniques are based on targeted projection pursuit which finds low-dimensional projections of the data that score highly: the features that have the largest projections in the lower-dimensional space are then selected. Search approaches include: Exhaustive Best first Simulated annealing Genetic algorithm Greedy forward selection Greedy backward elimination Particle swarm optimization Targeted projection pursuit Scatter search Variable neighborhood search Two popular filter metrics for classification problems are correlation and mutual information, although neither are true metrics or 'distance measures' in the mathematical sense, since they fail to obey the triangle inequality and thus do not compute any actual 'distance' – they should rather be regarded as 'scores'. These scores are computed between a candidate feature (or set of features) and the desired output category. There are, however, true metrics that are a simple function of the mutual information; see here. Other available filter metrics include: Class separability Error probability Inter-class distance Probabilistic distance Entropy Consistency-based feature selection Correlation-based feature selection == Optimality criteria == The choice of optimality criteria is difficult as there are multiple objectives in a feature selection task. Many common criteria incorporate a measure of accuracy, penalised by the number of features selected. Examples include Akaike information criterion (AIC) and Mallows's Cp, which have a penalty of 2 for each added feature. AIC is based on information theory, and is effectively derived via the maximum entropy principle. Other criteria are Bayesian information criterion (BIC), which uses a penalty of log ⁡ n {\displaystyle {\sqrt {\log {n}}}} for each added feature, minimum description length (MDL) which asymptotically uses log ⁡ n {\displaystyle {\sqrt {\log {n}}}} , Bonferroni / RIC which use 2 log ⁡ p {\displaystyle {\sqrt {2\log {p}}}} , maximum dependency feature selection, and a variety of new criteria that are motivated by false discovery rate (FDR), which use something close to 2 log ⁡ p q {\displaystyle {\sqrt {2\log {\frac {p}{q}}}}} . A maximum entropy rate criterion may also be used to select the most relevant subset of features. == Structure learning == Filter feature selection is a specific case of a more general paradigm called structure learning. Feature selection finds the relevant feature set for a specific target variable whereas structure learning finds the relationships between all the variables, usually by expressing these relationships as a graph. The most common structure learning algorithms

Bayesian programming

Bayesian programming is a formalism and a methodology for having a technique to specify probabilistic models and solve problems when less than the necessary information is available. Edwin T. Jaynes proposed that probability could be considered as an alternative and an extension of logic for rational reasoning with incomplete and uncertain information. In his founding book Probability Theory: The Logic of Science he developed this theory and proposed what he called "the robot," which was not a physical device, but an inference engine to automate probabilistic reasoning—a kind of Prolog for probability instead of logic. Bayesian programming is a formal and concrete implementation of this "robot". Bayesian programming may also be seen as an algebraic formalism to specify graphical models such as, for instance, Bayesian networks, dynamic Bayesian networks, Kalman filters or hidden Markov models. Indeed, Bayesian programming is more general than Bayesian networks and has a power of expression equivalent to probabilistic factor graphs. == Formalism == A Bayesian program is a means of specifying a family of probability distributions. The constituent elements of a Bayesian program are presented below: Program { Description { Specification ( π ) { Variables Decomposition Forms Identification (based on δ ) Question {\displaystyle {\text{Program}}{\begin{cases}{\text{Description}}{\begin{cases}{\text{Specification}}(\pi ){\begin{cases}{\text{Variables}}\\{\text{Decomposition}}\\{\text{Forms}}\\\end{cases}}\\{\text{Identification (based on }}\delta )\end{cases}}\\{\text{Question}}\end{cases}}} A program is constructed from a description and a question. A description is constructed using some specification ( π {\displaystyle \pi } ) as given by the programmer and an identification or learning process for the parameters not completely specified by the specification, using a data set ( δ {\displaystyle \delta } ). A specification is constructed from a set of pertinent variables, a decomposition and a set of forms. Forms are either parametric forms or questions to other Bayesian programs. A question specifies which probability distribution has to be computed. === Description === The purpose of a description is to specify an effective method of computing a joint probability distribution on a set of variables { X 1 , X 2 , ⋯ , X N } {\displaystyle \left\{X_{1},X_{2},\cdots ,X_{N}\right\}} given a set of experimental data δ {\displaystyle \delta } and some specification π {\displaystyle \pi } . This joint distribution is denoted as: P ( X 1 ∧ X 2 ∧ ⋯ ∧ X N ∣ δ ∧ π ) {\displaystyle P\left(X_{1}\wedge X_{2}\wedge \cdots \wedge X_{N}\mid \delta \wedge \pi \right)} . To specify preliminary knowledge π {\displaystyle \pi } , the programmer must undertake the following: Define the set of relevant variables { X 1 , X 2 , ⋯ , X N } {\displaystyle \left\{X_{1},X_{2},\cdots ,X_{N}\right\}} on which the joint distribution is defined. Decompose the joint distribution (break it into relevant independent or conditional probabilities). Define the forms of each of the distributions (e.g., for each variable, one of the list of probability distributions). ==== Decomposition ==== Given a partition of { X 1 , X 2 , … , X N } {\displaystyle \left\{X_{1},X_{2},\ldots ,X_{N}\right\}} containing K {\displaystyle K} subsets, K {\displaystyle K} variables are defined L 1 , ⋯ , L K {\displaystyle L_{1},\cdots ,L_{K}} , each corresponding to one of these subsets. Each variable L k {\displaystyle L_{k}} is obtained as the conjunction of the variables { X k 1 , X k 2 , ⋯ } {\displaystyle \left\{X_{k_{1}},X_{k_{2}},\cdots \right\}} belonging to the k t h {\displaystyle k^{th}} subset. Recursive application of Bayes' theorem leads to: P ( X 1 ∧ X 2 ∧ ⋯ ∧ X N ∣ δ ∧ π ) = P ( L 1 ∧ ⋯ ∧ L K ∣ δ ∧ π ) = P ( L 1 ∣ δ ∧ π ) × P ( L 2 ∣ L 1 ∧ δ ∧ π ) × ⋯ × P ( L K ∣ L K − 1 ∧ ⋯ ∧ L 1 ∧ δ ∧ π ) {\displaystyle {\begin{aligned}&P\left(X_{1}\wedge X_{2}\wedge \cdots \wedge X_{N}\mid \delta \wedge \pi \right)\\={}&P\left(L_{1}\wedge \cdots \wedge L_{K}\mid \delta \wedge \pi \right)\\={}&P\left(L_{1}\mid \delta \wedge \pi \right)\times P\left(L_{2}\mid L_{1}\wedge \delta \wedge \pi \right)\times \cdots \times P\left(L_{K}\mid L_{K-1}\wedge \cdots \wedge L_{1}\wedge \delta \wedge \pi \right)\end{aligned}}} Conditional independence hypotheses then allow further simplifications. A conditional independence hypothesis for variable L k {\displaystyle L_{k}} is defined by choosing some variable X n {\displaystyle X_{n}} among the variables appearing in the conjunction L k − 1 ∧ ⋯ ∧ L 2 ∧ L 1 {\displaystyle L_{k-1}\wedge \cdots \wedge L_{2}\wedge L_{1}} , labelling R k {\displaystyle R_{k}} as the conjunction of these chosen variables and setting: P ( L k ∣ L k − 1 ∧ ⋯ ∧ L 1 ∧ δ ∧ π ) = P ( L k ∣ R k ∧ δ ∧ π ) {\displaystyle P\left(L_{k}\mid L_{k-1}\wedge \cdots \wedge L_{1}\wedge \delta \wedge \pi \right)=P\left(L_{k}\mid R_{k}\wedge \delta \wedge \pi \right)} We then obtain: P ( X 1 ∧ X 2 ∧ ⋯ ∧ X N ∣ δ ∧ π ) = P ( L 1 ∣ δ ∧ π ) × P ( L 2 ∣ R 2 ∧ δ ∧ π ) × ⋯ × P ( L K ∣ R K ∧ δ ∧ π ) {\displaystyle {\begin{aligned}&P\left(X_{1}\wedge X_{2}\wedge \cdots \wedge X_{N}\mid \delta \wedge \pi \right)\\={}&P\left(L_{1}\mid \delta \wedge \pi \right)\times P\left(L_{2}\mid R_{2}\wedge \delta \wedge \pi \right)\times \cdots \times P\left(L_{K}\mid R_{K}\wedge \delta \wedge \pi \right)\end{aligned}}} Such a simplification of the joint distribution as a product of simpler distributions is called a decomposition, derived using the chain rule. This ensures that each variable appears at the most once on the left of a conditioning bar, which is the necessary and sufficient condition to write mathematically valid decompositions. ==== Forms ==== Each distribution P ( L k ∣ R k ∧ δ ∧ π ) {\displaystyle P\left(L_{k}\mid R_{k}\wedge \delta \wedge \pi \right)} appearing in the product is then associated with either a parametric form (i.e., a function f μ ( L k ) {\displaystyle f_{\mu }\left(L_{k}\right)} ) or a question to another Bayesian program P ( L k ∣ R k ∧ δ ∧ π ) = P ( L ∣ R ∧ δ ^ ∧ π ^ ) {\displaystyle P\left(L_{k}\mid R_{k}\wedge \delta \wedge \pi \right)=P\left(L\mid R\wedge {\widehat {\delta }}\wedge {\widehat {\pi }}\right)} . When it is a form f μ ( L k ) {\displaystyle f_{\mu }\left(L_{k}\right)} , in general, μ {\displaystyle \mu } is a vector of parameters that may depend on R k {\displaystyle R_{k}} or δ {\displaystyle \delta } or both. Learning takes place when some of these parameters are computed using the data set δ {\displaystyle \delta } . An important feature of Bayesian programming is this capacity to use questions to other Bayesian programs as components of the definition of a new Bayesian program. P ( L k ∣ R k ∧ δ ∧ π ) {\displaystyle P\left(L_{k}\mid R_{k}\wedge \delta \wedge \pi \right)} is obtained by some inferences done by another Bayesian program defined by the specifications π ^ {\displaystyle {\widehat {\pi }}} and the data δ ^ {\displaystyle {\widehat {\delta }}} . This is similar to calling a subroutine in classical programming and provides an easy way to build hierarchical models. === Question === Given a description (i.e., P ( X 1 ∧ X 2 ∧ ⋯ ∧ X N ∣ δ ∧ π ) {\displaystyle P\left(X_{1}\wedge X_{2}\wedge \cdots \wedge X_{N}\mid \delta \wedge \pi \right)} ), a question is obtained by partitioning { X 1 , X 2 , ⋯ , X N } {\displaystyle \left\{X_{1},X_{2},\cdots ,X_{N}\right\}} into three sets: the searched variables, the known variables and the free variables. The 3 variables S e a r c h e d {\displaystyle Searched} , K n o w n {\displaystyle Known} and F r e e {\displaystyle Free} are defined as the conjunction of the variables belonging to these sets. A question is defined as the set of distributions: P ( S e a r c h e d ∣ Known ∧ δ ∧ π ) {\displaystyle P\left(Searched\mid {\text{Known}}\wedge \delta \wedge \pi \right)} made of many "instantiated questions" as the cardinal of K n o w n {\displaystyle Known} , each instantiated question being the distribution: P ( Searched ∣ Known ∧ δ ∧ π ) {\displaystyle P\left({\text{Searched}}\mid {\text{Known}}\wedge \delta \wedge \pi \right)} === Inference === Given the joint distribution P ( X 1 ∧ X 2 ∧ ⋯ ∧ X N ∣ δ ∧ π ) {\displaystyle P\left(X_{1}\wedge X_{2}\wedge \cdots \wedge X_{N}\mid \delta \wedge \pi \right)} , it is always possible to compute any possible question using the following general inference: P ( Searched ∣ Known ∧ δ ∧ π ) = ∑ Free [ P ( Searched ∧ Free ∣ Known ∧ δ ∧ π ) ] = ∑ Free [ P ( Searched ∧ Free ∧ Known ∣ δ ∧ π ) ] P ( Known ∣ δ ∧ π ) = ∑ Free [ P ( Searched ∧ Free ∧ Known ∣ δ ∧ π ) ] ∑ Free ∧ Searched [ P ( Searched ∧ Free ∧ Known ∣ δ ∧ π ) ] = 1 Z × ∑ Free [ P ( Searched ∧ Free ∧ Known ∣ δ ∧ π ) ] {\displaystyle {\begin{aligned}&P\left({\text{Searched}}\mid {\text{Known}}\wedge \delta \wedge \pi \right)\\={}&\sum _{\text{Free}}\left[P\left({\text{Searched}}\wedge {\text{Free}}\mid {\text{Known}}\wedge \delta \wedge \

Quadratic unconstrained binary optimization

Quadratic unconstrained binary optimization (QUBO), also known as unconstrained binary quadratic programming (UBQP), is a combinatorial optimization problem with a wide range of applications from finance and economics to machine learning. QUBO is an NP hard problem, and for many classical problems from theoretical computer science, like maximum cut, graph coloring and the partition problem, embeddings into QUBO have been formulated. Embeddings for machine learning models include support-vector machines, clustering and probabilistic graphical models. Moreover, due to its close connection to Ising models, QUBO constitutes a central problem class for adiabatic quantum computation, where it is solved through a physical process called quantum annealing. == Definition == Let B = { 0 , 1 } {\displaystyle \mathbb {B} =\lbrace 0,1\rbrace } the set of binary digits (or bits), then B n {\displaystyle \mathbb {B} ^{n}} is the set of binary vectors of fixed length n ∈ N {\displaystyle n\in \mathbb {N} } . Given a symmetric or upper triangular matrix Q ∈ R n × n {\displaystyle {\boldsymbol {Q}}\in \mathbb {R} ^{n\times n}} , whose entries Q i j {\displaystyle Q_{ij}} define a weight for each pair of indices i , j ∈ { 1 , … , n } {\displaystyle i,j\in \lbrace 1,\dots ,n\rbrace } , we can define the function f Q : B n → R {\displaystyle f_{\boldsymbol {Q}}:\mathbb {B} ^{n}\rightarrow \mathbb {R} } that assigns a value to each binary vector x {\displaystyle {\boldsymbol {x}}} through f Q ( x ) = x ⊺ Q x = ∑ i = 1 n ∑ j = 1 n Q i j x i x j . {\displaystyle f_{\boldsymbol {Q}}({\boldsymbol {x}})={\boldsymbol {x}}^{\intercal }{\boldsymbol {Qx}}=\sum _{i=1}^{n}\sum _{j=1}^{n}Q_{ij}x_{i}x_{j}.} Alternatively, the linear and quadratic parts can be separated as f Q ′ , q ( x ) = x ⊺ Q ′ x + q ⊺ x , {\displaystyle f_{{\boldsymbol {Q}}',{\boldsymbol {q}}}({\boldsymbol {x}})={\boldsymbol {x}}^{\intercal }{\boldsymbol {Q}}'{\boldsymbol {x}}+{\boldsymbol {q}}^{\intercal }{\boldsymbol {x}},} where Q ′ ∈ R n × n {\displaystyle {\boldsymbol {Q}}'\in \mathbb {R} ^{n\times n}} and q ∈ R n {\displaystyle {\boldsymbol {q}}\in \mathbb {R} ^{n}} . This is equivalent to the previous definition through Q = Q ′ + diag ⁡ [ q ] {\displaystyle {\boldsymbol {Q}}={\boldsymbol {Q}}'+\operatorname {diag} [{\boldsymbol {q}}]} using the diag operator, exploiting that x = x ⋅ x {\displaystyle x=x\cdot x} for all binary values x {\displaystyle x} . Intuitively, the weight Q i j {\displaystyle Q_{ij}} is added if both x i = 1 {\displaystyle x_{i}=1} and x j = 1 {\displaystyle x_{j}=1} . The QUBO problem consists of finding a binary vector x ∗ {\displaystyle {\boldsymbol {x}}^{}} that minimizes f Q {\displaystyle f_{\boldsymbol {Q}}} , i.e., ∀ x ∈ B n : f Q ( x ∗ ) ≤ f Q ( x ) {\displaystyle \forall {\boldsymbol {x}}\in \mathbb {B} ^{n}:~f_{\boldsymbol {Q}}({\boldsymbol {x}}^{})\leq f_{\boldsymbol {Q}}({\boldsymbol {x}})} . In general, x ∗ {\displaystyle {\boldsymbol {x}}^{}} is not unique, meaning there may be a set of minimizing vectors with equal value w.r.t. f Q {\displaystyle f_{\boldsymbol {Q}}} . The complexity of QUBO arises from the number of candidate binary vectors to be evaluated, as | B n | = 2 n {\displaystyle \left|\mathbb {B} ^{n}\right|=2^{n}} grows exponentially in n {\displaystyle n} . Sometimes, QUBO is defined as the problem of maximizing f Q {\displaystyle f_{\boldsymbol {Q}}} , which is equivalent to minimizing f − Q = − f Q {\displaystyle f_{-{\boldsymbol {Q}}}=-f_{\boldsymbol {Q}}} . == Properties == QUBO is scale invariant for positive factors α > 0 {\displaystyle \alpha >0} , which leave the optimum x ∗ {\displaystyle {\boldsymbol {x}}^{}} unchanged: f α Q ( x ) = x ⊺ ( α Q ) x = α ( x ⊺ Q x ) = α f Q ( x ) {\displaystyle f_{\alpha {\boldsymbol {Q}}}({\boldsymbol {x}})={\boldsymbol {x}}^{\intercal }(\alpha {\boldsymbol {Q}}){\boldsymbol {x}}=\alpha ({\boldsymbol {x}}^{\intercal }{\boldsymbol {Qx}})=\alpha f_{\boldsymbol {Q}}({\boldsymbol {x}})} . In its general form, QUBO is NP-hard and cannot be solved efficiently by any known polynomial-time algorithm. However, there are polynomially-solvable special cases, where Q {\displaystyle {\boldsymbol {Q}}} has certain properties, for example: If all coefficients are positive, the optimum is trivially x ∗ = ( 0 , … , 0 ) ⊺ {\displaystyle {\boldsymbol {x}}^{}=(0,\dots ,0)^{\intercal }} . Similarly, if all coefficients are negative, the optimum is x ∗ = ( 1 , … , 1 ) ⊺ {\displaystyle {\boldsymbol {x}}^{}=(1,\dots ,1)^{\intercal }} . If Q {\displaystyle {\boldsymbol {Q}}} is diagonal, the bits can be optimized independently, and the problem is solvable in O ( n ) {\displaystyle {\mathcal {O}}(n)} . The optimal variable assignments are simply x i ∗ = 1 {\displaystyle x_{i}^{}=1} if Q i i < 0 {\displaystyle Q_{ii}<0} , and x i ∗ = 0 {\displaystyle x_{i}^{}=0} otherwise. If all off-diagonal elements of Q {\displaystyle {\boldsymbol {Q}}} are non-positive, the corresponding QUBO problem is solvable in polynomial time. QUBO can be solved using integer linear programming solvers like CPLEX or Gurobi Optimizer. This is possible since QUBO can be reformulated as a linear constrained binary optimization problem. To achieve this, substitute the product x i x j {\displaystyle x_{i}x_{j}} by an additional binary variable z i j ∈ B {\displaystyle z_{ij}\in \mathbb {B} } and add the constraints x i ≥ z i j {\displaystyle x_{i}\geq z_{ij}} , x j ≥ z i j {\displaystyle x_{j}\geq z_{ij}} and x i + x j − 1 ≤ z i j {\displaystyle x_{i}+x_{j}-1\leq z_{ij}} . Note that z i j {\displaystyle z_{ij}} can also be relaxed to continuous variables within the bounds zero and one. == Applications == QUBO is a structurally simple, yet computationally hard optimization problem. It can be used to encode a wide range of optimization problems from various scientific areas. === Maximum Cut === Given a graph G = ( V , E ) {\displaystyle G=(V,E)} with vertex set V = { 1 , … , n } {\displaystyle V=\lbrace 1,\dots ,n\rbrace } and edges E ⊆ V × V {\displaystyle E\subseteq V\times V} , the maximum cut (max-cut) problem consists of finding two subsets S , T ⊆ V {\displaystyle S,T\subseteq V} with T = V ∖ S {\displaystyle T=V\setminus S} , such that the number of edges between S {\displaystyle S} and T {\displaystyle T} is maximized. The more general weighted max-cut problem assumes edge weights w i j ≥ 0 ∀ i , j ∈ V {\displaystyle w_{ij}\geq 0~\forall i,j\in V} , with ( i , j ) ∉ E ⇒ w i j = 0 {\displaystyle (i,j)\notin E\Rightarrow w_{ij}=0} , and asks for a partition S , T ⊆ V {\displaystyle S,T\subseteq V} that maximizes the sum of edge weights between S {\displaystyle S} and T {\displaystyle T} , i.e., max S ⊆ V ∑ i ∈ S , j ∉ S w i j . {\displaystyle \max _{S\subseteq V}\sum _{i\in S,j\notin S}w_{ij}.} By setting w i j = 1 {\displaystyle w_{ij}=1} for all ( i , j ) ∈ E {\displaystyle (i,j)\in E} this becomes equivalent to the original max-cut problem above, which is why we focus on this more general form in the following. For every vertex in i ∈ V {\displaystyle i\in V} we introduce a binary variable x i {\displaystyle x_{i}} with the interpretation x i = 0 {\displaystyle x_{i}=0} if i ∈ S {\displaystyle i\in S} and x i = 1 {\displaystyle x_{i}=1} if i ∈ T {\displaystyle i\in T} . As T = V ∖ S {\displaystyle T=V\setminus S} , every i {\displaystyle i} is in exactly one set, meaning there is a 1:1 correspondence between binary vectors x ∈ B n {\displaystyle {\boldsymbol {x}}\in \mathbb {B} ^{n}} and partitions of V {\displaystyle V} into two subsets. We observe that, for any i , j ∈ V {\displaystyle i,j\in V} , the expression x i ( 1 − x j ) + ( 1 − x i ) x j {\displaystyle x_{i}(1-x_{j})+(1-x_{i})x_{j}} evaluates to 1 if and only if i {\displaystyle i} and j {\displaystyle j} are in different subsets, equivalent to logical XOR. Let W ∈ R + n × n {\displaystyle {\boldsymbol {W}}\in \mathbb {R} _{+}^{n\times n}} with W i j = w i j ∀ i , j ∈ V {\displaystyle W_{ij}=w_{ij}~\forall i,j\in V} . By extending above expression to matrix-vector form we find that x ⊺ W ( 1 − x ) + ( 1 − x ) ⊺ W x = − 2 x ⊺ W x + ( W 1 + W ⊺ 1 ) ⊺ x {\displaystyle {\boldsymbol {x}}^{\intercal }{\boldsymbol {W}}({\boldsymbol {1}}-{\boldsymbol {x}})+({\boldsymbol {1}}-{\boldsymbol {x}})^{\intercal }{\boldsymbol {Wx}}=-2{\boldsymbol {x}}^{\intercal }{\boldsymbol {Wx}}+({\boldsymbol {W1}}+{\boldsymbol {W}}^{\intercal }{\boldsymbol {1}})^{\intercal }{\boldsymbol {x}}} is the sum of weights of all edges between S {\displaystyle S} and T {\displaystyle T} , where 1 = ( 1 , 1 , … , 1 ) ⊺ ∈ R n {\displaystyle {\boldsymbol {1}}=(1,1,\dots ,1)^{\intercal }\in \mathbb {R} ^{n}} . As this is a quadratic function over x {\displaystyle {\boldsymbol {x}}} , it is a QUBO problem whose parameter matrix we can read from above expression as Q = 2 W − diag ⁡ [ W 1 + W ⊺ 1 ] , {\displaystyle {\boldsymbol {Q}}=2{\boldsymbol {W}}-\operatorname {diag} [{\boldsymbol {W1}}+{\boldsymbol {W}}^{\intercal }{\bol