AI Analytics Data

AI Analytics Data — independent reviews, comparisons, pricing and step-by-step guides on Aizhi.

  • Curve (tonality)

    Curve (tonality)

    In image editing, a curve is a remapping of image tonality, specified as a function from input level to output level, used as a way to emphasize colours or other elements in a picture. Curves can usually be applied to all channels together in an image, or to each channel individually. Applying a curve to all channels typically changes the brightness in part of the spectrum. Light parts of a picture can be easily made lighter and dark parts darker to increase contrast. Applying a curve to individual channels can be used to stress a colour. This is particularly efficient in the Lab colour space due to the separation of luminance and chromaticity, but it can also be used in RGB, CMYK or whatever other colour models the software supports.

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  • Multiclass classification

    Multiclass classification

    In machine learning and statistical classification, multiclass classification or multinomial classification is the problem of classifying instances into one of three or more classes (classifying instances into one of two classes is called binary classification). For example, deciding on whether an image is showing a banana, peach, orange, or an apple is a multiclass classification problem, with four possible classes (banana, peach, orange, apple), while deciding on whether an image contains an apple or not is a binary classification problem (with the two possible classes being: apple, no apple). While many classification algorithms (e.g., decision trees, k-NN, neural networks and multinomial logistic regression) naturally permit the use of more than two classes, some are by nature binary algorithms (e.g., classical binary support vector machine) and require decomposition strategies such as one-vs-all, one-vs-one, or ECOC to solve multiclass problems. Multiclass classification should not be confused with multi-label classification, where multiple labels are to be predicted for each instance (e.g., predicting that an image contains both an apple and an orange, in the previous example). == Better-than-random multiclass models == From the confusion matrix of a multiclass model, we can determine whether a model does better than chance. Let K ≥ 3 {\displaystyle K\geq 3} be the number of classes, O {\displaystyle {\mathcal {O}}} a set of observations, y ^ : O → { 1 , . . . , K } {\displaystyle {\hat {y}}:{\mathcal {O}}\to \{1,...,K\}} a model of the target variable y : O → { 1 , . . . , K } {\displaystyle y:{\mathcal {O}}\to \{1,...,K\}} and n i , j {\displaystyle n_{i,j}} be the number of observations in the set { y = i } ∩ { y ^ = j } {\displaystyle \{y=i\}\cap \{{\hat {y}}=j\}} . We note n i . = ∑ j n i , j {\displaystyle n_{i.}=\sum _{j}n_{i,j}} , n . j = ∑ i n i , j {\displaystyle n_{.j}=\sum _{i}n_{i,j}} , n = ∑ j n . j = ∑ i n i . {\displaystyle n=\sum _{j}n_{.j}=\sum _{i}n_{i.}} , λ i = n i . n {\displaystyle \lambda _{i}={\frac {n_{i.}}{n}}} and μ j = n . j n {\displaystyle \mu _{j}={\frac {n_{.j}}{n}}} . It is assumed that the confusion matrix ( n i , j ) i , j {\displaystyle (n_{i,j})_{i,j}} contains at least one non-zero entry in each row, that is λ i > 0 {\displaystyle \lambda _{i}>0} for any i {\displaystyle i} . Finally we call "normalized confusion matrix" the matrix of conditional probabilities ( P ( y ^ = j ∣ y = i ) ) i , j = ( n i , j n i . ) i , j {\displaystyle (\mathbb {P} ({\hat {y}}=j\mid y=i))_{i,j}=\left({\frac {n_{i,j}}{n_{i.}}}\right)_{i,j}} . === Intuitive explanation === The lift is a way of measuring the deviation from independence of two events A {\displaystyle A} and B {\displaystyle B} : L i f t ( A , B ) = P ( A ∩ B ) P ( A ) P ( B ) = P ( A ∣ B ) P ( A ) = P ( B ∣ A ) P ( B ) {\displaystyle \mathrm {Lift} (A,B)={\frac {\mathbb {P} (A\cap B)}{\mathbb {P} (A)\mathbb {P} (B)}}={\frac {\mathbb {P} (A\mid B)}{\mathbb {P} (A)}}={\frac {\mathbb {P} (B\mid A)}{\mathbb {P} (B)}}} We have L i f t ( A , B ) > 1 {\displaystyle \mathrm {Lift} (A,B)>1} if and only if events A {\displaystyle A} and B {\displaystyle B} occur simultaneously with a greater probability than if they were independent. In other words, if one of the two events occurs, the probability of observing the other event increases. A first condition to satisfy is to have L i f t ( y = i , y ^ = i ) ≥ 1 {\displaystyle \mathrm {Lift} (y=i,{\hat {y}}=i)\geq 1} for any i {\displaystyle i} . And the quality of a model (better or worse than chance) does not change if we over- or undersample the dataset, that is if we multiply each row R i {\displaystyle R_{i}} of the confusion matrix by a constant c i {\displaystyle c_{i}} . Thus the second condition is that the necessary and sufficient conditions for doing better than chance need only depend on the normalized confusion matrix. The condition on lifts can be reformulated with One versus Rest binary models : for any i {\displaystyle i} , we define the binary target variable y i {\displaystyle y_{i}} which is the indicator of event { y = i } {\displaystyle \{y=i\}} , and the binary model y ^ i {\displaystyle {\hat {y}}_{i}} of y i {\displaystyle y_{i}} which is the indicator of event { y ^ = i } {\displaystyle \{{\hat {y}}=i\}} . Each of the y ^ i {\displaystyle {\hat {y}}_{i}} models is a "One versus Rest" model. L i f t ( y = i , y ^ = i ) {\displaystyle \mathrm {Lift} (y=i,{\hat {y}}=i)} only depends on the events { y = i } {\displaystyle \{y=i\}} and { y ^ = i } {\displaystyle \{{\hat {y}}=i\}} , so merging or not merging the other classes doesn't change its value. We therefore have L i f t ( y = i , y ^ = i ) = L i f t ( y i = 1 , y ^ i = 1 ) {\displaystyle \mathrm {Lift} (y=i,{\hat {y}}=i)=\mathrm {Lift} (y_{i}=1,{\hat {y}}_{i}=1)} and the first condition is that all binary One versus Rest models are better than chance. ==== Example ==== If K = 2 {\displaystyle K=2} and 2 is the class of interest , the normalized confusion matrix is ( s p e c i f i c i t y 1 − s p e c i f i c i t y 1 − s e n s i t i v i t y s e n s i t i v i t y ) {\displaystyle {\begin{pmatrix}\mathrm {specificity} &1-\mathrm {specificity} \\1-\mathrm {sensitivity} &\mathrm {sensitivity} \end{pmatrix}}} and we have L i f t ( y = 1 , y ^ = 1 ) − 1 = P ( y = y ^ = 1 ) λ 1 μ 1 − 1 = n 1 , 1 n n 1. n .1 − 1 {\displaystyle \mathrm {Lift} (y=1,{\hat {y}}=1)-1={\frac {\mathbb {P} (y={\hat {y}}=1)}{\lambda _{1}\mu _{1}}}-1={\frac {n_{1,1}n}{n_{1.}n_{.1}}}-1} = n 1 , 1 ( n 1 , 1 + n 1 , 2 + n 2 , 1 + n 2 , 2 ) − ( n 1 , 1 + n 1 , 2 ) ( n 1 , 1 + n 2 , 1 ) n 1. n .1 = n 1 , 1 n 2 , 2 − n 1 , 2 n 2 , 1 n 1. n .1 {\displaystyle ={\frac {n_{1,1}(n_{1,1}+n_{1,2}+n_{2,1}+n_{2,2})-(n_{1,1}+n_{1,2})(n_{1,1}+n_{2,1})}{n_{1.}n_{.1}}}={\frac {n_{1,1}n_{2,2}-n_{1,2}n_{2,1}}{n_{1.}n_{.1}}}} . Thus L i f t ( y = 1 , y ^ = 1 ) ≥ 1 ⟺ n 1 , 1 n 2 , 2 − n 1 , 2 n 2 , 1 ≥ 0 {\displaystyle \mathrm {Lift} (y=1,{\hat {y}}=1)\geq 1\iff n_{1,1}n_{2,2}-n_{1,2}n_{2,1}\geq 0} . Similarly, by swapping the roles of 1 and 2, we find that L i f t ( y = 2 , y ^ = 2 ) ≥ 1 ⟺ n 1 , 1 n 2 , 2 − n 1 , 2 n 2 , 1 ≥ 0 {\displaystyle \mathrm {Lift} (y=2,{\hat {y}}=2)\geq 1\iff n_{1,1}n_{2,2}-n_{1,2}n_{2,1}\geq 0} . Dividing by n 1. n 2. {\displaystyle n_{1.}n_{2.}} we find that the necessary and sufficient condition on the normalized confusion matrix is s e n s i t i v i t y s p e c i f i c i t y − ( 1 − s e n s i t i v i t y ) ( 1 − s p e c i f i c i t y ) ≥ 0 ⟺ s e n s i t i v i t y + s p e c i f i c i t y − 1 ≥ 0 ⟺ J ≥ 0 {\displaystyle \mathrm {sensitivity} \ \mathrm {specificity} -(1-\mathrm {sensitivity} )(1-\mathrm {specificity} )\geq 0\iff \mathrm {sensitivity} +\mathrm {specificity} -1\geq 0\iff J\geq 0} . This brings us back to the classical binary condition: Youden's J must be positive (or zero for random models). === Random models === A random model is a model that is independent of the target variable. This property is easily reformulated with the confusion matrix. This proposition shows that the model y ^ {\displaystyle {\hat {y}}} of y {\displaystyle y} is uninformative if and only if there are two families of numbers ( α i ) i {\displaystyle (\alpha _{i})_{i}} and ( β j ) j {\displaystyle (\beta _{j})_{j}} such that P ( { y = i } ∩ { y ^ = j } ) = α i β j {\displaystyle \mathbb {P} (\{y=i\}\cap \{{\hat {y}}=j\})=\alpha _{i}\beta _{j}} for any i {\displaystyle i} and j {\displaystyle j} . === Multiclass likelihood ratios and diagnostic odds ratios === We define generalized likelihood ratios calculated from the normalized confusion matrix: for any i {\displaystyle i} and j ≠ i {\displaystyle j\not =i} , let L R i , j = P ( y ^ = j ∣ y = j ) P ( y ^ = j ∣ y = i ) {\displaystyle \mathrm {LR} _{i,j}={\frac {\mathbb {P} ({\hat {y}}=j\mid y=j)}{\mathbb {P} ({\hat {y}}=j\mid y=i)}}} . When K = 2 {\displaystyle K=2} , if 2 is the class of interest,, we find the classical likelihood ratios L R 1 , 2 = L R + {\displaystyle \mathrm {LR} _{1,2}=\mathrm {LR} _{+}} and L R 2 , 1 = 1 L R − {\displaystyle \mathrm {LR} _{2,1}={\frac {1}{\mathrm {LR} _{-}}}} . Multiclass diagnostic odds ratios can also be defined using the formula D O R i , j = D O R j , i = L R i , j L R j , i = n i , i n j , j n i , j n j , i = P ( y ^ = j ∣ y = j ) / P ( y ^ = i ∣ y = j ) P ( y ^ = j ∣ y = i ) / P ( y ^ = i ∣ y = i ) {\displaystyle \mathrm {DOR} _{i,j}=\mathrm {DOR} _{j,i}=\mathrm {LR} _{i,j}\mathrm {LR} _{j,i}={\frac {n_{i,i}n_{j,j}}{n_{i,j}n_{j,i}}}={\frac {\mathbb {P} ({\hat {y}}=j\mid y=j)/\mathbb {P} ({\hat {y}}=i\mid y=j)}{\mathbb {P} ({\hat {y}}=j\mid y=i)/\mathbb {P} ({\hat {y}}=i\mid y=i)}}} We saw above that a better-than-chance model (or a random model) must verify L i f t ( y = i , y ^ = i ) ≥ 1 {\displaystyle \mathrm {Lift} (y=i,{\hat {y}}=i)\geq 1} for any i {\displaystyle i} and λ i {\displaystyle \lambda _{i}} . According to the previous corollary, likelihood ratios are thus greater

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  • Multidimensional analysis

    Multidimensional analysis

    In statistics, econometrics and related fields, multidimensional analysis (MDA) is a data analysis process that groups data into two categories: data dimensions and measurements. For example, a data set consisting of the number of wins for a single football team at each of several years is a single-dimensional (in this case, longitudinal) data set. A data set consisting of the number of wins for several football teams in a single year is also a single-dimensional (in this case, cross-sectional) data set. A data set consisting of the number of wins for several football teams over several years is a two-dimensional data set. == Higher dimensions == In many disciplines, two-dimensional data sets are also called panel data. While, strictly speaking, two- and higher-dimensional data sets are "multi-dimensional", the term "multidimensional" tends to be applied only to data sets with three or more dimensions. For example, some forecast data sets provide forecasts for multiple target periods, conducted by multiple forecasters, and made at multiple horizons. The three dimensions provide more information than can be gleaned from two-dimensional panel data sets. == Software == Computer software for MDA include Online analytical processing (OLAP) for data in relational databases, pivot tables for data in spreadsheets, and Array DBMSs for general multi-dimensional data (such as raster data) in science, engineering, and business.

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  • Natarajan dimension

    Natarajan dimension

    In the theory of Probably Approximately Correct Machine Learning, the Natarajan dimension characterizes the complexity of learning a set of functions, generalizing from the Vapnik–Chervonenkis dimension for boolean functions to multi-class functions. Originally introduced as the Generalized Dimension by Natarajan, it was subsequently renamed the Natarajan Dimension by Haussler and Long. == Definition == Let H {\displaystyle H} be a set of functions from a set X {\displaystyle X} to a set Y {\displaystyle Y} . H {\displaystyle H} shatters a set C ⊂ X {\displaystyle C\subset X} if there exist two functions f 0 , f 1 ∈ H {\displaystyle f_{0},f_{1}\in H} such that For every x ∈ C , f 0 ( x ) ≠ f 1 ( x ) {\displaystyle x\in C,f_{0}(x)\neq f_{1}(x)} . For every B ⊂ C {\displaystyle B\subset C} , there exists a function h ∈ H {\displaystyle h\in H} such that for all x ∈ B , h ( x ) = f 0 ( x ) {\displaystyle x\in B,h(x)=f_{0}(x)} and for all x ∈ C − B , h ( x ) = f 1 ( x ) {\displaystyle x\in C-B,h(x)=f_{1}(x)} . The Natarajan dimension of H is the maximal cardinality of a set shattered by H {\displaystyle H} . It is easy to see that if | Y | = 2 {\displaystyle |Y|=2} , the Natarajan dimension collapses to the Vapnik–Chervonenkis dimension. Shalev-Shwartz and Ben-David present comprehensive material on multi-class learning and the Natarajan dimension, including uniform convergence and learnability. Recently, Cohen et al showed that the Natarajan dimension is the dominant term governing agnostic multi-class PAC learnability.

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  • Dominant resource fairness

    Dominant resource fairness

    Dominant resource fairness (DRF) is a rule for fair division. It is particularly useful for dividing computing resources in among users in cloud computing environments, where each user may require a different combination of resources. DRF was presented by Ali Ghodsi, Matei Zaharia, Benjamin Hindman, Andy Konwinski, Scott Shenker and Ion Stoica in 2011. == Motivation == In an environment with a single resource, a widely used criterion is max-min fairness, which aims to maximize the minimum amount of resource given to a user. But in cloud computing, it is required to share different types of resource, such as: memory, CPU, bandwidth and disk-space. Previous fair schedulers, such as in Apache Hadoop, reduced the multi-resource setting to a single-resource setting by defining nodes with a fixed amount of each resource (e.g. 4 CPU, 32 MB memory, etc.), and dividing slots which are fractions of nodes. But this method is inefficient, since not all users need the same ratio of resources. For example, some users need more CPU whereas other users need more memory. As a result, most tasks either under-utilize or over-utilize their resources. DRF solves the problem by maximizing the minimum amount of the dominant resource given to a user (then the second-minimum etc., in a leximin order). The dominant resource may be different for different users. For example, if user A runs CPU-heavy tasks and user B runs memory-heavy tasks, DRF will try to equalize the CPU share given to user A and the memory share given to user B. == Definition == There are m resources. The total capacities of the resources are r1,...,rm. There are n users. Each users runs individual tasks. Each task has a demand-vector (d1,..,dm), representing the amount it needs of each resource. It is implicitly assumed that the utility of a user equals the number of tasks he can perform. For example, if user A runs tasks with demand-vector [1 CPU, 4 GB RAM], and receives 3 CPU and 8 GB RAM, then his utility is 2, since he can perform only 2 tasks. More generally, the utility of a user receiving x1,...,xm resources is minj(xj/dj), that is, the users have Leontief utilities. The demand-vectors are normalized to fractions of the capacities. For example, if the system has 9 CPUs and 18 GB RAM, then the above demand-vector is normalized to [1/9 CPU, 2/9 GB]. For each user, the resource with the highest demand-fraction is called the dominant resource. In the above example, the dominant resource is memory, as 2/9 is the largest fraction. If user B runs a task with demand-vector [3 CPU, 1 GB], which is normalized to [1/3 CPU, 1/18 GB], then his dominant resource is CPU. DRF aims to find the maximum x such that all agents can receive at least x of their dominant resource. In the above example, this maximum x is 2/3: User A gets 3 tasks, which require 3/9 CPU and 2/3 GB. User B gets 2 tasks, which require 2/3 CPU and 1/9 GB. The maximum x can be found by solving a linear program; see Lexicographic max-min optimization. Alternatively, the DRF can be computed sequentially. The algorithm tracks the amount of dominant resource used by each user. At each round, it finds a user with the smallest allocated dominant resource so far, and allocates the next task of this user. Note that this procedure allows the same user to run tasks with different demand vectors. == Properties == DRF has several advantages over other policies for resource allocation. Proportionality: each user receives at least as much resources as they could get in a system in which all resources are partitioned equally among users (the authors call this condition "sharing incentive"). Strategyproofness: a user cannot get a larger allocation by lying about his needs. Strategyproofness is important, as evidence from cloud operators show that users try to manipulate the servers in order to get better allocations. Envy-freeness: no user would prefer the allocation of another user. Pareto efficiency: no other allocation is better for some users and not worse for anyone. Population monotonicity: when a user leaves the system, the allocations of remaining users do not decrease. When there is a single resource that is a bottleneck resource (highly demanded by all users), DRF reduces to max-min fairness. However, DRF violates resource monotonicity: when resources are added to the system, some allocations might decrease. == Extensions == Weighted DRF is an extension of DRF to settings in which different users have different weights (representing their different entitlements). Parkes, Procaccia and Shah formally extend weighted DRF to a setting in which some users do not need all resources (that is, they may have demand 0 to some resource). They prove that the extended version still satisfies proportionality, Pareto-efficiency, envy-freeness, strategyproofness, and even Group strategyproofness. On the other hand, they show that DRF may yield poor utilitarian social welfare, that is, the sum of utilities may be only 1/m of the optimum. However, they prove that any mechanism satisfying one of proportionality, envy-freeness or strategyproofness may suffers from the same low utilitarian welfare. They also extend DRF to the setting in which the users' demands are indivisible (as in fair item allocation). For the indivisible setting, they relax envy-freeness to EF1. They show that strategyproofness is incompatible with PO+EF1 or with PO+proportionality. However, a mechanism called SequentialMinMax satisfies efficiency, proportionality and EF1. Wang, Li and Liang present DRFH - an extension of DRF to a system with several heterogeneous servers. == Implementation == DRF was first implemented in Apache Mesos - a cluster resource manager, and it led to better throughput and fairness than previously used fair-sharing schemes.

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  • Dendrogram

    Dendrogram

    A dendrogram is a diagram representing a tree graph. This diagrammatic representation is frequently used in different contexts: in hierarchical clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses. in computational biology, it shows the clustering of genes or samples, sometimes in the margins of heatmaps. in phylogenetics, it displays the evolutionary relationships among various biological taxa. In this case, the dendrogram is also called a phylogenetic tree. The name dendrogram derives from the two ancient greek words δένδρον (déndron), meaning "tree", and γράμμα (grámma), meaning "drawing, mathematical figure". == Clustering example == For a clustering example, suppose that five taxa ( a {\displaystyle a} to e {\displaystyle e} ) have been clustered by UPGMA based on a matrix of genetic distances. The hierarchical clustering dendrogram would show a column of five nodes representing the initial data (here individual taxa), and the remaining nodes represent the clusters to which the data belong, with the arrows representing the distance (dissimilarity). The distance between merged clusters is monotone, increasing with the level of the merger: the height of each node in the plot is proportional to the value of the intergroup dissimilarity between its two daughters (the nodes on the right representing individual observations all plotted at zero height).

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  • Evolutionary algorithm

    Evolutionary algorithm

    Evolutionary algorithms (EA) reproduce essential elements of biological evolution in a computer algorithm in order to solve "difficult" problems, at least approximately, for which no exact or satisfactory solution methods are known. They are metaheuristics and population-based bio-inspired algorithms and evolutionary computation, which itself are part of the field of computational intelligence. The mechanisms of biological evolution that an EA mainly imitates are reproduction, mutation, recombination and selection. Candidate solutions to the optimization problem play the role of individuals in a population, and the fitness function determines the quality of the solutions (see also loss function). Evolution of the population then takes place after the repeated application of the above operators. Evolutionary algorithms often perform well approximating solutions to all types of problems because they ideally do not make any assumption about the underlying fitness landscape. Techniques from evolutionary algorithms applied to the modeling of biological evolution are generally limited to explorations of microevolution (microevolutionary processes) and planning models based upon cellular processes. In most real applications of EAs, computational complexity is a prohibiting factor. In fact, this computational complexity is due to fitness function evaluation. Fitness approximation is one of the solutions to overcome this difficulty. However, seemingly simple EA can solve often complex problems; therefore, there may be no direct link between algorithm complexity and problem complexity. == Generic definition == The following is an example of a generic evolutionary algorithm: Randomly generate the initial population of individuals, the first generation. Evaluate the fitness of each individual in the population. Check, if the goal is reached and the algorithm can be terminated. Select individuals as parents, preferably of higher fitness. Produce offspring with optional crossover (mimicking reproduction). Apply mutation operations on the offspring. Select individuals preferably of lower fitness for replacement with new individuals (mimicking natural selection). Return to 2 == Types == Similar techniques differ in genetic representation and other implementation details, and the nature of the particular applied problem. Genetic algorithm – This is the most popular type of EA. One seeks the solution of a problem in the form of strings of numbers (traditionally binary, although the best representations are usually those that reflect something about the problem being solved), by applying operators such as recombination and mutation (sometimes one, sometimes both). This type of EA is often used in optimization problems. Genetic programming – Here the solutions are in the form of computer programs, and their fitness is determined by their ability to solve a computational problem. There are many variants of Genetic Programming: Cartesian genetic programming Gene expression programming Grammatical evolution Linear genetic programming Multi expression programming Evolutionary programming – Similar to evolution strategy, but with a deterministic selection of all parents. Evolution strategy (ES) – Works with vectors of real numbers as representations of solutions, and typically uses self-adaptive mutation rates. The method is mainly used for numerical optimization, although there are also variants for combinatorial tasks. CMA-ES Natural evolution strategy Differential evolution – Based on vector differences and is therefore primarily suited for numerical optimization problems. Coevolutionary algorithm – Similar to genetic algorithms and evolution strategies, but the created solutions are compared on the basis of their outcomes from interactions with other solutions. Solutions can either compete or cooperate during the search process. Coevolutionary algorithms are often used in scenarios where the fitness landscape is dynamic, complex, or involves competitive interactions. Neuroevolution – Similar to genetic programming but the genomes represent artificial neural networks by describing structure and connection weights. The genome encoding can be direct or indirect. Learning classifier system – Here the solution is a set of classifiers (rules or conditions). A Michigan-LCS evolves at the level of individual classifiers whereas a Pittsburgh-LCS uses populations of classifier-sets. Initially, classifiers were only binary, but now include real, neural net, or S-expression types. Fitness is typically determined with either a strength or accuracy based reinforcement learning or supervised learning approach. Quality–Diversity algorithms – QD algorithms simultaneously aim for high-quality and diverse solutions. Unlike traditional optimization algorithms that solely focus on finding the best solution to a problem, QD algorithms explore a wide variety of solutions across a problem space and keep those that are not just high performing, but also diverse and unique. == Theoretical background == The following theoretical principles apply to all or almost all EAs. === No free lunch theorem === The no free lunch theorem of optimization states that all optimization strategies are equally effective when the set of all optimization problems is considered. Under the same condition, no evolutionary algorithm is fundamentally better than another. This can only be the case if the set of all problems is restricted. This is exactly what is inevitably done in practice. Therefore, to improve an EA, it must exploit problem knowledge in some form (e.g. by choosing a certain mutation strength or a problem-adapted coding). Thus, if two EAs are compared, this constraint is implied. In addition, an EA can use problem specific knowledge by, for example, not randomly generating the entire start population, but creating some individuals through heuristics or other procedures. Another possibility to tailor an EA to a given problem domain is to involve suitable heuristics, local search procedures or other problem-related procedures in the process of generating the offspring. This form of extension of an EA is also known as a memetic algorithm. Both extensions play a major role in practical applications, as they can speed up the search process and make it more robust. === Convergence === For EAs in which, in addition to the offspring, at least the best individual of the parent generation is used to form the subsequent generation (so-called elitist EAs), there is a general proof of convergence under the condition that an optimum exists. Without loss of generality, a maximum search is assumed for the proof: From the property of elitist offspring acceptance and the existence of the optimum it follows that per generation k {\displaystyle k} an improvement of the fitness F {\displaystyle F} of the respective best individual x ′ {\displaystyle x'} will occur with a probability P > 0 {\displaystyle P>0} . Thus: F ( x 1 ′ ) ≤ F ( x 2 ′ ) ≤ F ( x 3 ′ ) ≤ ⋯ ≤ F ( x k ′ ) ≤ ⋯ {\displaystyle F(x'_{1})\leq F(x'_{2})\leq F(x'_{3})\leq \cdots \leq F(x'_{k})\leq \cdots } I.e., the fitness values represent a monotonically non-decreasing sequence, which is bounded due to the existence of the optimum. From this follows the convergence of the sequence against the optimum. Since the proof makes no statement about the speed of convergence, it is of little help in practical applications of EAs. But it does justify the recommendation to use elitist EAs. However, when using the usual panmictic population model, elitist EAs tend to converge prematurely more than non-elitist ones. In a panmictic population model, mate selection (see step 4 of the generic definition) is such that every individual in the entire population is eligible as a mate. In non-panmictic populations, selection is suitably restricted, so that the dispersal speed of better individuals is reduced compared to panmictic ones. Thus, the general risk of premature convergence of elitist EAs can be significantly reduced by suitable population models that restrict mate selection. === Virtual alphabets === With the theory of virtual alphabets, David E. Goldberg showed in 1990 that by using a representation with real numbers, an EA that uses classical recombination operators (e.g. uniform or n-point crossover) cannot reach certain areas of the search space, in contrast to a coding with binary numbers. This results in the recommendation for EAs with real representation to use arithmetic operators for recombination (e.g. arithmetic mean or intermediate recombination). With suitable operators, real-valued representations are more effective than binary ones, contrary to earlier opinion. == Comparison to other concepts == === Biological processes === A possible limitation of many evolutionary algorithms is their lack of a clear genotype–phenotype distinction. In nature, the fertilized egg cell undergoes a complex process known as embryogenesis to become a mature p

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  • Ilastik

    Ilastik

    ilastik is free open source software for image classification and segmentation. No previous experience in image processing is required to run the software. Since 2018 ilastik is further developed and maintained by Anna Kreshuk's group at European Molecular Biology Laboratory. == Features == ilastik allows user to annotate an arbitrary number of classes in images with a mouse interface. Using these user annotations and the generic (nonlinear) image features, the user can train a random forest classifier. Trained ilastik classifiers can be applied new data not included in the training set in ilastik via its batch processing functionality, or without using the graphical user interface, in headless mode. ilastik can be integrated into various related tools: Pre-trained workflows can be executed directly from ImageJ/Fiji using the ilastik-ImageJ plugin. Pre-trained ilastik Pixel Classification workflows can be run directly in Python with the ilastik Python package, which is available via conda. ilastik has a CellProfiler module to use ilastik classifiers to process images within a CellProfiler framework. == History == ilastik was first released in 2011 by scientists at the Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg. == Application == The Interactive Learning and Segmentation Toolkit Carving Cell classification and neuron classification Synapse detection Cell tracking Neural Network Classification == Resources == ilastik project is hosted on GitHub. It is a collaborative project, any contributions such as comments, bug reports, bug fixes or code contributions are welcome. The ilastik team can be contacted for user support on the image.sc forum.

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  • Hello World: How to be Human in the Age of the Machine

    Hello World: How to be Human in the Age of the Machine

    Hello World: How to Be Human in the Age of the Machine (also titled Hello World: Being Human in the Age of Algorithms) is a book on the growing influence of algorithms and artificial intelligence (AI) on human life, authored by mathematician and science communicator Hannah Fry. The book examines how algorithms are increasingly shaping decisions in critical areas such as healthcare, transportation, justice, finance, and the arts. == Overview == Fry uses real-world examples, such as driverless cars and predictive policing, to illustrate her points. She emphasizes that algorithms are not inherently objective; they reflect biases embedded in their design and data inputs. While acknowledging their potential to improve efficiency and accuracy, Fry cautions against over-reliance on machines without human judgment. Fry explores moral questions surrounding algorithmic decision-making, such as whether machines can replace human empathy in critical situations. She advocates for greater scrutiny of algorithms to ensure fairness and avoid harmful biases. The book proposes a "cyborg future", where humans work alongside algorithms to enhance decision-making while retaining ultimate control. == Reception == Hello World has been praised for its clarity, engaging storytelling, and balanced perspective. Critics have highlighted Fry's ability to make complex topics accessible to general audiences while raising important questions about technology's impact on society. The book was shortlisted for awards such as the 2018 Baillie Gifford Prize and the Royal Society Science Book Prize.

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  • C4.5 algorithm

    C4.5 algorithm

    C4.5 is an algorithm used to generate a decision tree developed by Ross Quinlan. C4.5 is an extension of Quinlan's earlier ID3 algorithm. The decision trees generated by C4.5 can be used for classification, and for this reason, C4.5 is often referred to as a statistical classifier. In 2011, authors of the Weka machine learning software described the C4.5 algorithm as "a landmark decision tree program that is probably the machine learning workhorse most widely used in practice to date". It became quite popular after ranking #1 in the Top 10 Algorithms in Data Mining pre-eminent paper published by Springer LNCS in 2008. == Algorithm == C4.5 builds decision trees from a set of training data in the same way as ID3, using the concept of information entropy. The training data is a set S = s 1 , s 2 , . . . {\displaystyle S={s_{1},s_{2},...}} of already classified samples. Each sample s i {\displaystyle s_{i}} consists of a p-dimensional vector ( x 1 , i , x 2 , i , . . . , x p , i ) {\displaystyle (x_{1,i},x_{2,i},...,x_{p,i})} , where the x j {\displaystyle x_{j}} represent attribute values or features of the sample, as well as the class in which s i {\displaystyle s_{i}} falls. At each node of the tree, C4.5 chooses the attribute of the data that most effectively splits its set of samples into subsets enriched in one class or the other. The splitting criterion is the normalized information gain (difference in entropy). The attribute with the highest normalized information gain is chosen to make the decision. The C4.5 algorithm then recurses on the partitioned sublists. This algorithm has a few base cases. All the samples in the list belong to the same class. When this happens, it simply creates a leaf node for the decision tree saying to choose that class. None of the features provide any information gain. In this case, C4.5 creates a decision node higher up the tree using the expected value of the class. Instance of previously unseen class encountered. Again, C4.5 creates a decision node higher up the tree using the expected value. === Pseudocode === In pseudocode, the general algorithm for building decision trees is: Check for the above base cases. For each attribute a, find the normalized information gain ratio from splitting on a. Let a_best be the attribute with the highest normalized information gain. Create a decision node that splits on a_best. Recurse on the sublists obtained by splitting on a_best, and add those nodes as children of node. == Improvements from ID3 algorithm == C4.5 made a number of improvements to ID3. Some of these are: Handling both continuous and discrete attributes: In order to handle continuous attributes, C4.5 creates a threshold and then splits the list into those whose attribute value is above the threshold and those that are less than or equal to it. Handling training data with missing attribute values: C4.5 allows attribute values to be marked as missing. Missing attribute values are simply not used in gain and entropy calculations. Handling attributes with differing costs. Pruning trees after creation: C4.5 goes back through the tree once it's been created and attempts to remove branches that do not help by replacing them with leaf nodes. == Improvements in C5.0/See5 algorithm == Quinlan went on to create C5.0 and See5 (C5.0 for Unix/Linux, See5 for Windows) which he markets commercially. C5.0 offers a number of improvements on C4.5. Some of these are: Speed - C5.0 is significantly faster than C4.5 (several orders of magnitude) Memory usage - C5.0 is more memory efficient than C4.5 Smaller decision trees - C5.0 gets similar results to C4.5 with considerably smaller decision trees. Support for boosting - Boosting improves the trees and gives them more accuracy. Weighting - C5.0 allows you to weight different cases and misclassification types. Winnowing - a C5.0 option automatically winnows the attributes to remove those that may be unhelpful. Source for a single-threaded Linux version of C5.0 is available under the GNU General Public License (GPL).

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  • Stochastic gradient descent

    Stochastic gradient descent

    Stochastic gradient descent (often abbreviated SGD) is an iterative method for optimizing an objective function with suitable smoothness properties (e.g. differentiable or subdifferentiable). It can be regarded as a stochastic approximation of gradient descent optimization, since it replaces the actual gradient (calculated from the entire data set) by an estimate thereof (calculated from a randomly selected subset of the data). Especially in high-dimensional optimization problems this reduces the very high computational burden, achieving faster iterations in exchange for a lower convergence rate. The basic idea behind stochastic approximation can be traced back to the Robbins–Monro algorithm of the 1950s. Today, stochastic gradient descent has become an important optimization method in machine learning. == Background == Both statistical estimation and machine learning consider the problem of minimizing an objective function that has the form of a sum: Q ( w ) = 1 n ∑ i = 1 n Q i ( w ) , {\displaystyle Q(w)={\frac {1}{n}}\sum _{i=1}^{n}Q_{i}(w),} where the parameter w {\displaystyle w} that minimizes Q ( w ) {\displaystyle Q(w)} is to be estimated. Each summand function Q i {\displaystyle Q_{i}} is typically associated with the i {\displaystyle i} -th observation in the data set (used for training). In classical statistics, sum-minimization problems arise in least squares and in maximum-likelihood estimation (for independent observations). The general class of estimators that arise as minimizers of sums are called M-estimators. However, in statistics, it has been long recognized that requiring even local minimization is too restrictive for some problems of maximum-likelihood estimation. Therefore, contemporary statistical theorists often consider stationary points of the likelihood function (or zeros of its derivative, the score function, and other estimating equations). The sum-minimization problem also arises for empirical risk minimization. There, Q i ( w ) {\displaystyle Q_{i}(w)} is the value of the loss function at i {\displaystyle i} -th example, and Q ( w ) {\displaystyle Q(w)} is the empirical risk. When used to minimize the above function, a standard (or "batch") gradient descent method would perform the following iterations: w := w − η ∇ Q ( w ) = w − η n ∑ i = 1 n ∇ Q i ( w ) . {\displaystyle w:=w-\eta \,\nabla Q(w)=w-{\frac {\eta }{n}}\sum _{i=1}^{n}\nabla Q_{i}(w).} The step size is denoted by η {\displaystyle \eta } (sometimes called the learning rate in machine learning) and here " := {\displaystyle :=} " denotes the update of a variable in the algorithm. In many cases, the summand functions have a simple form that enables inexpensive evaluations of the sum-function and the sum gradient. For example, in statistics, one-parameter exponential families allow economical function-evaluations and gradient-evaluations. However, in other cases, evaluating the sum-gradient may require expensive evaluations of the gradients from all summand functions. When the training set is enormous and no simple formulas exist, evaluating the sums of gradients becomes very expensive, because evaluating the gradient requires evaluating all the summand functions' gradients. To economize on the computational cost at every iteration, stochastic gradient descent samples a subset of summand functions at every step. This is very effective in the case of large-scale machine learning problems. == Iterative method == In stochastic (or "on-line") gradient descent, the true gradient of Q ( w ) {\displaystyle Q(w)} is approximated by a gradient at a single sample: w := w − η ∇ Q i ( w ) . {\displaystyle w:=w-\eta \,\nabla Q_{i}(w).} As the algorithm sweeps through the training set, it performs the above update for each training sample. Several passes can be made over the training set until the algorithm converges. If this is done, the data can be shuffled for each pass to prevent cycles. Typical implementations may use an adaptive learning rate so that the algorithm converges. In pseudocode, stochastic gradient descent can be presented as : A compromise between computing the true gradient and the gradient at a single sample is to compute the gradient against more than one training sample (called a "mini-batch") at each step. This can perform significantly better than "true" stochastic gradient descent described, because the code can make use of vectorization libraries rather than computing each step separately as was first shown in where it was called "the bunch-mode back-propagation algorithm". It may also result in smoother convergence, as the gradient computed at each step is averaged over more training samples. The convergence of stochastic gradient descent has been analyzed using the theories of convex minimization and of stochastic approximation. Briefly, when the learning rates η {\displaystyle \eta } decrease with an appropriate rate, and subject to relatively mild assumptions, stochastic gradient descent converges almost surely to a global minimum when the objective function is convex or pseudoconvex, and otherwise converges almost surely to a local minimum. This is in fact a consequence of the Robbins–Siegmund theorem. == Linear regression == Suppose we want to fit a straight line y ^ = w 1 + w 2 x {\displaystyle {\hat {y}}=w_{1}+w_{2}x} to a training set with observations ( ( x 1 , y 1 ) , ( x 2 , y 2 ) … , ( x n , y n ) ) {\displaystyle ((x_{1},y_{1}),(x_{2},y_{2})\ldots ,(x_{n},y_{n}))} and corresponding estimated responses ( y ^ 1 , y ^ 2 , … , y ^ n ) {\displaystyle ({\hat {y}}_{1},{\hat {y}}_{2},\ldots ,{\hat {y}}_{n})} using least squares. The objective function to be minimized is Q ( w ) = ∑ i = 1 n Q i ( w ) = ∑ i = 1 n ( y ^ i − y i ) 2 = ∑ i = 1 n ( w 1 + w 2 x i − y i ) 2 . {\displaystyle Q(w)=\sum _{i=1}^{n}Q_{i}(w)=\sum _{i=1}^{n}\left({\hat {y}}_{i}-y_{i}\right)^{2}=\sum _{i=1}^{n}\left(w_{1}+w_{2}x_{i}-y_{i}\right)^{2}.} The last line in the above pseudocode for this specific problem will become: [ w 1 w 2 ] ← [ w 1 w 2 ] − η [ ∂ ∂ w 1 ( w 1 + w 2 x i − y i ) 2 ∂ ∂ w 2 ( w 1 + w 2 x i − y i ) 2 ] = [ w 1 w 2 ] − η [ 2 ( w 1 + w 2 x i − y i ) 2 x i ( w 1 + w 2 x i − y i ) ] . {\displaystyle {\begin{bmatrix}w_{1}\\w_{2}\end{bmatrix}}\leftarrow {\begin{bmatrix}w_{1}\\w_{2}\end{bmatrix}}-\eta {\begin{bmatrix}{\frac {\partial }{\partial w_{1}}}(w_{1}+w_{2}x_{i}-y_{i})^{2}\\{\frac {\partial }{\partial w_{2}}}(w_{1}+w_{2}x_{i}-y_{i})^{2}\end{bmatrix}}={\begin{bmatrix}w_{1}\\w_{2}\end{bmatrix}}-\eta {\begin{bmatrix}2(w_{1}+w_{2}x_{i}-y_{i})\\2x_{i}(w_{1}+w_{2}x_{i}-y_{i})\end{bmatrix}}.} Note that in each iteration or update step, the gradient is only evaluated at a single x i {\displaystyle x_{i}} . This is the key difference between stochastic gradient descent and batched gradient descent. In general, given a linear regression y ^ = ∑ k ∈ 1 : m w k x k {\displaystyle {\hat {y}}=\sum _{k\in 1:m}w_{k}x_{k}} problem, stochastic gradient descent behaves differently when m < n {\displaystyle m

  • Relationship square

    Relationship square

    In statistics, the relationship square is a graphical representation for use in the factorial analysis of a table individuals x variables. This representation completes classical representations provided by principal component analysis (PCA) or multiple correspondence analysis (MCA), namely those of individuals, of quantitative variables (correlation circle) and of the categories of qualitative variables (at the centroid of the individuals who possess them). It is especially important in factor analysis of mixed data (FAMD) and in multiple factor analysis (MFA). == Definition of relationship square in the MCA frame == The first interest of the relationship square is to represent the variables themselves, not their categories, which is all the more valuable as there are many variables. For this, we calculate for each qualitative variable j {\displaystyle j} and each factor F s {\displaystyle F_{s}} ( F s {\displaystyle F_{s}} , rank s {\displaystyle s} factor, is the vector of coordinates of the individuals along the axis of rank s {\displaystyle s} ; in PCA, F s {\displaystyle F_{s}} is called principal component of rank s {\displaystyle s} ), the square of the correlation ratio between the F s {\displaystyle F_{s}} and the variable j {\displaystyle j} , usually denoted : η 2 ( j , F s ) {\displaystyle \eta ^{2}(j,F_{s})} Thus, to each factorial plane, we can associate a representation of qualitative variables themselves. Their coordinates being between 0 and 1, the variables appear in the square having as vertices the points (0,0), ( 0,1), (1,0) and (1,1). == Example in MCA == Six individuals ( i 1 , … , i 6 ) {\displaystyle i_{1},\ldots ,i_{6})} are described by three variables ( q 1 , q 2 , q 3 ) {\displaystyle (q_{1},q_{2},q_{3})} having respectively 3, 2 and 3 categories. Example : the individual i 1 {\displaystyle i_{1}} possesses the category a {\displaystyle a} of q 1 {\displaystyle q_{1}} , d {\displaystyle d} of q 2 {\displaystyle q_{2}} and f {\displaystyle f} of q 3 {\displaystyle q_{3}} . Applied to these data, the MCA function included in the R Package FactoMineR provides to the classical graph in Figure 1. The relationship square (Figure 2) makes easier the reading of the classic factorial plane. It indicates that: The first factor is related to the three variables but especially q 3 {\displaystyle q_{3}} (which have a very high coordinate along the first axis) and then q 2 {\displaystyle q_{2}} . The second factor is related only to q 1 {\displaystyle q_{1}} and q 3 {\displaystyle q_{3}} (and not to q 2 {\displaystyle q_{2}} which has a coordinate along axis 2 equal to 0) and that in a strong and equal manner. All this is visible on the classic graphic but not so clearly. The role of the relationship square is first to assist in reading a conventional graphic. This is precious when the variables are numerous and possess numerous coordinates. == Extensions == This representation may be supplemented with those of quantitative variables, the coordinates of the latter being the square of correlation coefficients (and not of correlation ratios). Thus, the second advantage of the relationship square lies in the ability to represent simultaneously quantitative and qualitative variables. The relationship square can be constructed from any factorial analysis of a table individuals x variables. In particular, it is (or should be) used systematically: in multiple correspondences analysis (MCA); in principal components analysis (PCA) when there are many supplementary variables; in factor analysis of mixed data (FAMD). An extension of this graphic to groups of variables (how to represent a group of variables by a single point ?) is used in Multiple Factor Analysis (MFA) == History == The idea of representing the qualitative variables themselves by a point (and not the categories) is due to Brigitte Escofier. The graphic as it is used now has been introduced by Brigitte Escofier and Jérôme Pagès in the framework of multiple factor analysis == Conclusion == In MCA, the relationship square provides a synthetic view of the connections between mixed variables, all the more valuable as there are many variables having many categories. This representation iscan be useful in any factorial analysis when there are numerous mixed variables, active and/or supplementary.

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  • Visible (mobile app)

    Visible (mobile app)

    Visible is a health tracking mobile app for people with long COVID and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). The company was founded by a Harry Leeming, an engineer from London living with long Covid since 2020, and Luke Martin-Fuller. In November 2022, Visible released an open beta of an app that aims to help people pace their activities to avoid post-exertional malaise. The app gathers data on exertion levels, symptom severity, and heart-rate variability. HRV is approximated using a smartphone's camera via a technique called photoplethysmography, and according to the app's developers, can indicate how much someone needs rest. The app is currently free, but is expected to be freemium in the future. Users can also opt to allow their data be used for research purposes. In July 2023, Visible and Imperial College London announced the start of the first two studies. One is on the effects of the menstrual cycle on long COVID symptoms, and the other is on the condition's epidemiology and economic impact. Visible has announced plans to couple the app with activity trackers for continuous monitoring of heart-rate and actimetry data, which the developers claim will be more effective. As of 2022, no clinical trials on Visible's effectiveness have been conducted.

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  • Semidefinite embedding

    Semidefinite embedding

    Maximum Variance Unfolding (MVU), also known as Semidefinite Embedding (SDE), is an algorithm in computer science that uses semidefinite programming to perform non-linear dimensionality reduction of high-dimensional vectorial input data. It is motivated by the observation that kernel Principal Component Analysis (kPCA) does not reduce the data dimensionality, as it leverages the Kernel trick to non-linearly map the original data into an inner-product space. == Algorithm == MVU creates a mapping from the high dimensional input vectors to some low dimensional Euclidean vector space in the following steps: A neighbourhood graph is created. Each input is connected with its k-nearest input vectors (according to Euclidean distance metric) and all k-nearest neighbors are connected with each other. If the data is sampled well enough, the resulting graph is a discrete approximation of the underlying manifold. The neighbourhood graph is "unfolded" with the help of semidefinite programming. Instead of learning the output vectors directly, the semidefinite programming aims to find an inner product matrix that maximizes the pairwise distances between any two inputs that are not connected in the neighbourhood graph while preserving the nearest neighbors distances. The low-dimensional embedding is finally obtained by application of multidimensional scaling on the learned inner product matrix. The steps of applying semidefinite programming followed by a linear dimensionality reduction step to recover a low-dimensional embedding into a Euclidean space were first proposed by Linial, London, and Rabinovich. == Optimization formulation == Let X {\displaystyle X\,\!} be the original input and Y {\displaystyle Y\,\!} be the embedding. If i , j {\displaystyle i,j\,\!} are two neighbors, then the local isometry constraint that needs to be satisfied is: | X i − X j | 2 = | Y i − Y j | 2 {\displaystyle |X_{i}-X_{j}|^{2}=|Y_{i}-Y_{j}|^{2}\,\!} Let G , K {\displaystyle G,K\,\!} be the Gram matrices of X {\displaystyle X\,\!} and Y {\displaystyle Y\,\!} (i.e.: G i j = X i ⋅ X j , K i j = Y i ⋅ Y j {\displaystyle G_{ij}=X_{i}\cdot X_{j},K_{ij}=Y_{i}\cdot Y_{j}\,\!} ). We can express the above constraint for every neighbor points i , j {\displaystyle i,j\,\!} in term of G , K {\displaystyle G,K\,\!} : G i i + G j j − G i j − G j i = K i i + K j j − K i j − K j i {\displaystyle G_{ii}+G_{jj}-G_{ij}-G_{ji}=K_{ii}+K_{jj}-K_{ij}-K_{ji}\,\!} In addition, we also want to constrain the embedding Y {\displaystyle Y\,\!} to center at the origin: 0 = | ∑ i Y i | 2 ⇔ ( ∑ i Y i ) ⋅ ( ∑ i Y i ) ⇔ ∑ i , j Y i ⋅ Y j ⇔ ∑ i , j K i j {\displaystyle 0=|\sum _{i}Y_{i}|^{2}\Leftrightarrow (\sum _{i}Y_{i})\cdot (\sum _{i}Y_{i})\Leftrightarrow \sum _{i,j}Y_{i}\cdot Y_{j}\Leftrightarrow \sum _{i,j}K_{ij}} As described above, except the distances of neighbor points are preserved, the algorithm aims to maximize the pairwise distance of every pair of points. The objective function to be maximized is: T ( Y ) = 1 2 N ∑ i , j | Y i − Y j | 2 {\displaystyle T(Y)={\dfrac {1}{2N}}\sum _{i,j}|Y_{i}-Y_{j}|^{2}} Intuitively, maximizing the function above is equivalent to pulling the points as far away from each other as possible and therefore "unfold" the manifold. The local isometry constraint Let τ = m a x { η i j | Y i − Y j | 2 } {\displaystyle \tau =max\{\eta _{ij}|Y_{i}-Y_{j}|^{2}\}\,\!} where η i j := { 1 if i is a neighbour of j 0 otherwise . {\displaystyle \eta _{ij}:={\begin{cases}1&{\mbox{if}}\ i{\mbox{ is a neighbour of }}j\\0&{\mbox{otherwise}}.\end{cases}}} prevents the objective function from diverging (going to infinity). Since the graph has N points, the distance between any two points | Y i − Y j | 2 ≤ N τ {\displaystyle |Y_{i}-Y_{j}|^{2}\leq N\tau \,\!} . We can then bound the objective function as follows: T ( Y ) = 1 2 N ∑ i , j | Y i − Y j | 2 ≤ 1 2 N ∑ i , j ( N τ ) 2 = N 3 τ 2 2 {\displaystyle T(Y)={\dfrac {1}{2N}}\sum _{i,j}|Y_{i}-Y_{j}|^{2}\leq {\dfrac {1}{2N}}\sum _{i,j}(N\tau )^{2}={\dfrac {N^{3}\tau ^{2}}{2}}\,\!} The objective function can be rewritten purely in the form of the Gram matrix: T ( Y ) = 1 2 N ∑ i , j | Y i − Y j | 2 = 1 2 N ∑ i , j ( Y i 2 + Y j 2 − Y i ⋅ Y j − Y j ⋅ Y i ) = 1 2 N ( ∑ i , j Y i 2 + ∑ i , j Y j 2 − ∑ i , j Y i ⋅ Y j − ∑ i , j Y j ⋅ Y i ) = 1 2 N ( ∑ i , j Y i 2 + ∑ i , j Y j 2 − 0 − 0 ) = 1 N ( ∑ i Y i 2 ) = 1 N ( T r ( K ) ) {\displaystyle {\begin{aligned}T(Y)&{}={\dfrac {1}{2N}}\sum _{i,j}|Y_{i}-Y_{j}|^{2}\\&{}={\dfrac {1}{2N}}\sum _{i,j}(Y_{i}^{2}+Y_{j}^{2}-Y_{i}\cdot Y_{j}-Y_{j}\cdot Y_{i})\\&{}={\dfrac {1}{2N}}(\sum _{i,j}Y_{i}^{2}+\sum _{i,j}Y_{j}^{2}-\sum _{i,j}Y_{i}\cdot Y_{j}-\sum _{i,j}Y_{j}\cdot Y_{i})\\&{}={\dfrac {1}{2N}}(\sum _{i,j}Y_{i}^{2}+\sum _{i,j}Y_{j}^{2}-0-0)\\&{}={\dfrac {1}{N}}(\sum _{i}Y_{i}^{2})={\dfrac {1}{N}}(Tr(K))\\\end{aligned}}\,\!} Finally, the optimization can be formulated as: Maximize T r ( K ) subject to K ⪰ 0 , ∑ i j K i j = 0 and G i i + G j j − G i j − G j i = K i i + K j j − K i j − K j i , ∀ i , j where η i j = 1 , {\displaystyle {\begin{aligned}&{\text{Maximize}}&&Tr(\mathbf {K} )\\&{\text{subject to}}&&\mathbf {K} \succeq 0,\sum _{ij}\mathbf {K} _{ij}=0\\&{\text{and}}&&G_{ii}+G_{jj}-G_{ij}-G_{ji}=K_{ii}+K_{jj}-K_{ij}-K_{ji},\forall i,j{\mbox{ where }}\eta _{ij}=1,\end{aligned}}} After the Gram matrix K {\displaystyle K\,\!} is learned by semidefinite programming, the output Y {\displaystyle Y\,\!} can be obtained via Cholesky decomposition. In particular, the Gram matrix can be written as K i j = ∑ α = 1 N ( λ α V α i V α j ) {\displaystyle K_{ij}=\sum _{\alpha =1}^{N}(\lambda _{\alpha }V_{\alpha i}V_{\alpha j})\,\!} where V α i {\displaystyle V_{\alpha i}\,\!} is the i-th element of eigenvector V α {\displaystyle V_{\alpha }\,\!} of the eigenvalue λ α {\displaystyle \lambda _{\alpha }\,\!} . It follows that the α {\displaystyle \alpha \,\!} -th element of the output Y i {\displaystyle Y_{i}\,\!} is λ α V α i {\displaystyle {\sqrt {\lambda _{\alpha }}}V_{\alpha i}\,\!} .

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  • Consensus clustering

    Consensus clustering

    Consensus clustering is a method of aggregating (potentially conflicting) results from multiple clustering algorithms. Also called cluster ensembles or aggregation of clustering (or partitions), it refers to the situation in which a number of different (input) clusterings have been obtained for a particular dataset and it is desired to find a single (consensus) clustering which is a better fit in some sense than the existing clusterings. Consensus clustering is thus the problem of reconciling clustering information about the same data set coming from different sources or from different runs of the same algorithm. When cast as an optimization problem, consensus clustering is known as median partition, and has been shown to be NP-complete, even when the number of input clusterings is three. Consensus clustering for unsupervised learning is analogous to ensemble learning in supervised learning. == Issues with existing clustering techniques == Current clustering techniques do not address all the requirements adequately. Dealing with large number of dimensions and large number of data items can be problematic because of time complexity; Effectiveness of the method depends on the definition of "distance" (for distance-based clustering) If an obvious distance measure doesn't exist, we must "define" it, which is not always easy, especially in multidimensional spaces. The result of the clustering algorithm (that, in many cases, can be arbitrary itself) can be interpreted in different ways. == Justification for using consensus clustering == There are potential shortcomings for all existing clustering techniques. This may cause interpretation of results to become difficult, especially when there is no knowledge about the number of clusters. Clustering methods are also very sensitive to the initial clustering settings, which can cause non-significant data to be amplified in non-reiterative methods. An extremely important issue in cluster analysis is the validation of the clustering results, that is, how to gain confidence about the significance of the clusters provided by the clustering technique (cluster numbers and cluster assignments). Lacking an external objective criterion (the equivalent of a known class label in supervised analysis), this validation becomes somewhat elusive. Iterative descent clustering methods, such as the SOM and k-means clustering circumvent some of the shortcomings of hierarchical clustering by providing for univocally defined clusters and cluster boundaries. Consensus clustering provides a method that represents the consensus across multiple runs of a clustering algorithm, to determine the number of clusters in the data, and to assess the stability of the discovered clusters. The method can also be used to represent the consensus over multiple runs of a clustering algorithm with random restart (such as K-means, model-based Bayesian clustering, SOM, etc.), so as to account for its sensitivity to the initial conditions. It can provide data for a visualization tool to inspect cluster number, membership, and boundaries. However, they lack the intuitive and visual appeal of hierarchical clustering dendrograms, and the number of clusters must be chosen a priori. == The Monti consensus clustering algorithm == The Monti consensus clustering algorithm is one of the most popular consensus clustering algorithms and is used to determine the number of clusters, K {\displaystyle K} . Given a dataset of N {\displaystyle N} total number of points to cluster, this algorithm works by resampling and clustering the data, for each K {\displaystyle K} and a N × N {\displaystyle N\times N} consensus matrix is calculated, where each element represents the fraction of times two samples clustered together. A perfectly stable matrix would consist entirely of zeros and ones, representing all sample pairs always clustering together or not together over all resampling iterations. The relative stability of the consensus matrices can be used to infer the optimal K {\displaystyle K} . More specifically, given a set of points to cluster, D = { e 1 , e 2 , . . . e N } {\displaystyle D=\{e_{1},e_{2},...e_{N}\}} , let D 1 , D 2 , . . . , D H {\displaystyle D^{1},D^{2},...,D^{H}} be the list of H {\displaystyle H} perturbed (resampled) datasets of the original dataset D {\displaystyle D} , and let M h {\displaystyle M^{h}} denote the N × N {\displaystyle N\times N} connectivity matrix resulting from applying a clustering algorithm to the dataset D h {\displaystyle D^{h}} . The entries of M h {\displaystyle M^{h}} are defined as follows: M h ( i , j ) = { 1 , if points i and j belong to the same cluster 0 , otherwise {\displaystyle M^{h}(i,j)={\begin{cases}1,&{\text{if}}{\text{ points i and j belong to the same cluster}}\\0,&{\text{otherwise}}\end{cases}}} Let I h {\displaystyle I^{h}} be the N × N {\displaystyle N\times N} identicator matrix where the ( i , j ) {\displaystyle (i,j)} -th entry is equal to 1 if points i {\displaystyle i} and j {\displaystyle j} are in the same perturbed dataset D h {\displaystyle D^{h}} , and 0 otherwise. The indicator matrix is used to keep track of which samples were selected during each resampling iteration for the normalisation step. The consensus matrix C {\displaystyle C} is defined as the normalised sum of all connectivity matrices of all the perturbed datasets and a different one is calculated for every K {\displaystyle K} . C ( i , j ) = ( ∑ h = 1 H M h ( i , j ) ∑ h = 1 H I h ( i , j ) ) {\displaystyle C(i,j)=\left({\frac {\textstyle \sum _{h=1}^{H}M^{h}(i,j)\displaystyle }{\sum _{h=1}^{H}I^{h}(i,j)}}\right)} That is the entry ( i , j ) {\displaystyle (i,j)} in the consensus matrix is the number of times points i {\displaystyle i} and j {\displaystyle j} were clustered together divided by the total number of times they were selected together. The matrix is symmetric and each element is defined within the range [ 0 , 1 ] {\displaystyle [0,1]} . A consensus matrix is calculated for each K {\displaystyle K} to be tested, and the stability of each matrix, that is how far the matrix is towards a matrix of perfect stability (just zeros and ones) is used to determine the optimal K {\displaystyle K} . One way of quantifying the stability of the K {\displaystyle K} th consensus matrix is examining its CDF curve (see below). == Over-interpretation potential of the Monti consensus clustering algorithm == Monti consensus clustering can be a powerful tool for identifying clusters, but it needs to be applied with caution as shown by Şenbabaoğlu et al. It has been shown that the Monti consensus clustering algorithm is able to claim apparent stability of chance partitioning of null datasets drawn from a unimodal distribution, and thus has the potential to lead to over-interpretation of cluster stability in a real study. If clusters are not well separated, consensus clustering could lead one to conclude apparent structure when there is none, or declare cluster stability when it is subtle. Identifying false positive clusters is a common problem throughout cluster research, and has been addressed by methods such as SigClust and the GAP-statistic. However, these methods rely on certain assumptions for the null model that may not always be appropriate. Şenbabaoğlu et al demonstrated the original delta K metric to decide K {\displaystyle K} in the Monti algorithm performed poorly, and proposed a new superior metric for measuring the stability of consensus matrices using their CDF curves. In the CDF curve of a consensus matrix, the lower left portion represents sample pairs rarely clustered together, the upper right portion represents those almost always clustered together, whereas the middle segment represent those with ambiguous assignments in different clustering runs. The proportion of ambiguous clustering (PAC) score measure quantifies this middle segment; and is defined as the fraction of sample pairs with consensus indices falling in the interval (u1, u2) ∈ [0, 1] where u1 is a value close to 0 and u2 is a value close to 1 (for instance u1=0.1 and u2=0.9). A low value of PAC indicates a flat middle segment, and a low rate of discordant assignments across permuted clustering runs. One can therefore infer the optimal number of clusters by the K {\displaystyle K} value having the lowest PAC. == Related work == Clustering ensemble (Strehl and Ghosh): They considered various formulations for the problem, most of which reduce the problem to a hyper-graph partitioning problem. In one of their formulations they considered the same graph as in the correlation clustering problem. The solution they proposed is to compute the best k-partition of the graph, which does not take into account the penalty for merging two nodes that are far apart. Clustering aggregation (Fern and Brodley): They applied the clustering aggregation idea to a collection of soft clusterings they obtained by random projections. They used an agglomerative algorithm

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