Fitness approximation aims to approximate the objective or fitness functions in evolutionary optimization by building up machine learning models based on data collected from numerical simulations or physical experiments. The machine learning models for fitness approximation are also known as meta-models or surrogates, and evolutionary optimization based on approximated fitness evaluations are also known as surrogate-assisted evolutionary approximation. Fitness approximation in evolutionary optimization can be seen as a sub-area of data-driven evolutionary optimization. == Approximate models in function optimization == === Motivation === In many real-world optimization problems including engineering problems, the number of fitness function evaluations needed to obtain a good solution dominates the optimization cost. In order to obtain efficient optimization algorithms, it is crucial to use prior information gained during the optimization process. Conceptually, a natural approach to utilizing the known prior information is building a model of the fitness function to assist in the selection of candidate solutions for evaluation. A variety of techniques for constructing such a model, often also referred to as surrogates, metamodels or approximation models – for computationally expensive optimization problems have been considered. === Approaches === Common approaches to constructing approximate models based on learning and interpolation from known fitness values of a small population include: Low-degree polynomials and regression models Fourier surrogate modeling Artificial neural networks including Multilayer perceptrons Radial basis function network Support vector machines Due to the limited number of training samples and high dimensionality encountered in engineering design optimization, constructing a globally valid approximate model remains difficult. As a result, evolutionary algorithms using such approximate fitness functions may converge to local optima. Therefore, it can be beneficial to selectively use the original fitness function together with the approximate model.
Halloween Problem
In computing, the Halloween Problem refers to a phenomenon in databases in which an update operation causes a change in the physical location of a row, potentially allowing the row to be visited again later in the same update operation. This could even cause an infinite loop in some cases where updates continually place the updated record ahead of the scan performing the update operation. The potential for this database error was first discovered by Don Chamberlin, Pat Selinger, and Morton Astrahan in the mid-1970s, on Halloween day, while working on query optimization. They wrote a SQL query supposed to give a ten percent raise to every employee who earned less than $25,000. This query would run successfully, with no errors, but when finished all the employees in the database earned at least $25,000, because it kept giving them a raise until they reached that level. The expectation was that the query would iterate over each of the employee records with a salary less than $25,000 precisely once. In fact, because even updated records were visible to the query execution engine and so continued to match the query's criteria, salary records were matching multiple times and each time being given a 10% raise until they were all greater than $25,000. Contrary to what some believe, the name is not descriptive of the nature of the problem but rather was given due to the day it was discovered on. As recounted by Don Chamberlin: Pat and Morton discovered this problem on Halloween... I remember they came into my office and said, "Chamberlin, look at this. We have to make sure that when the optimizer is making a plan for processing an update, it doesn't use an index that is based on the field that is being updated. How are we going to do that?" It happened to be on a Friday, and we said, "Listen, we are not going to be able to solve this problem this afternoon. Let's just give it a name. We'll call it the Halloween Problem and we'll work on it next week." And it turns out it has been called that ever since.
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).
ID3 algorithm
In decision tree learning, ID3 (Iterative Dichotomiser 3) is a greedy algorithm invented by Ross Quinlan used to generate a decision tree from a dataset. ID3 is the precursor to the C4.5 algorithm. The 3 in the name is meant to signify that this was Quinlan's third attempt at a model based on entropy-based splitting, and the term dichotimser is a misnomer as it implies a binary split, but the ID3 algorithm can split on multi-valued attributes. == Algorithm == The ID3 algorithm begins with the original set S {\displaystyle S} as the root node. On each iteration of the algorithm, it iterates through every unused attribute of the set S {\displaystyle S} and calculates the entropy H ( S ) {\displaystyle \mathrm {H} {(S)}} or the information gain I G ( S ) {\displaystyle IG(S)} of that attribute. It then selects the attribute which has the smallest entropy (or largest information gain) value. The set S {\displaystyle S} is then split or partitioned by the selected attribute to produce subsets of the data. (For example, a node can be split into child nodes based upon the subsets of the population whose ages are less than 50, between 50 and 100, and greater than 100.) The algorithm continues to recurse on each subset, considering only attributes never selected before. Recursion on a subset may stop in one of these cases: every element in the subset belongs to the same class; in which case the node is turned into a leaf node and labelled with the class of the examples. there are no more attributes to be selected, but the examples still do not belong to the same class. In this case, the node is made a leaf node and labelled with the most common class of the examples in the subset. there are no examples in the subset, which happens when no example in the parent set was found to match a specific value of the selected attribute. An example could be the absence of a person among the population with age over 100 years. Then a leaf node is created and labelled with the most common class of the examples in the parent node's set. Throughout the algorithm, the decision tree is constructed with each non-terminal node (internal node) representing the selected attribute on which the data was split, and terminal nodes (leaf nodes) representing the class label of the final subset of this branch. === Summary === Calculate the entropy of every attribute a {\displaystyle a} of the data set S {\displaystyle S} . Partition ("split") the set S {\displaystyle S} into subsets using the attribute for which the resulting entropy after splitting is minimized; or, equivalently, information gain is maximum. Make a decision tree node containing that attribute. Recurse on subsets using the remaining attributes. === Properties === ID3 does not guarantee an optimal solution. It can converge upon local optima. It uses a greedy strategy by selecting the locally best attribute to split the dataset on each iteration. The algorithm's optimality can be improved by using backtracking during the search for the optimal decision tree at the cost of possibly taking longer. ID3 can overfit the training data. To avoid overfitting, smaller decision trees should be preferred over larger ones. This algorithm usually produces small trees, but it does not always produce the smallest possible decision tree. ID3 is harder to use on continuous data than on factored data (factored data has a discrete number of possible values, thus reducing the possible branch points). If the values of any given attribute are continuous, then there are many more places to split the data on this attribute, and searching for the best value to split by can be time-consuming. === Usage === The ID3 algorithm is used by training on a data set S {\displaystyle S} to produce a decision tree which is stored in memory. At runtime, this decision tree is used to classify new test cases (feature vectors) by traversing the decision tree using the features of the datum to arrive at a leaf node. == The ID3 metrics == === Entropy === Entropy H ( S ) {\displaystyle \mathrm {H} {(S)}} is a measure of the amount of uncertainty in the (data) set S {\displaystyle S} (i.e. entropy characterizes the (data) set S {\displaystyle S} ). H ( S ) = ∑ x ∈ X − p ( x ) log 2 p ( x ) {\displaystyle \mathrm {H} {(S)}=\sum _{x\in X}{-p(x)\log _{2}p(x)}} Where, S {\displaystyle S} – The current dataset for which entropy is being calculated This changes at each step of the ID3 algorithm, either to a subset of the previous set in the case of splitting on an attribute or to a "sibling" partition of the parent in case the recursion terminated previously. X {\displaystyle X} – The set of classes in S {\displaystyle S} p ( x ) {\displaystyle p(x)} – The proportion of the number of elements in class x {\displaystyle x} to the number of elements in set S {\displaystyle S} When H ( S ) = 0 {\displaystyle \mathrm {H} {(S)}=0} , the set S {\displaystyle S} is perfectly classified (i.e. all elements in S {\displaystyle S} are of the same class). In ID3, entropy is calculated for each remaining attribute. The attribute with the smallest entropy is used to split the set S {\displaystyle S} on this iteration. Entropy in information theory measures how much information is expected to be gained upon measuring a random variable; as such, it can also be used to quantify the amount to which the distribution of the quantity's values is unknown. A constant quantity has zero entropy, as its distribution is perfectly known. In contrast, a uniformly distributed random variable (discretely or continuously uniform) maximizes entropy. Therefore, the greater the entropy at a node, the less information is known about the classification of data at this stage of the tree; and therefore, the greater the potential to improve the classification here. As such, ID3 is a greedy heuristic performing a best-first search for locally optimal entropy values. Its accuracy can be improved by preprocessing the data. === Information gain === Information gain I G ( A ) {\displaystyle IG(A)} is the measure of the difference in entropy from before to after the set S {\displaystyle S} is split on an attribute A {\displaystyle A} . In other words, how much uncertainty in S {\displaystyle S} was reduced after splitting set S {\displaystyle S} on attribute A {\displaystyle A} . I G ( S , A ) = H ( S ) − ∑ t ∈ T p ( t ) H ( t ) = H ( S ) − H ( S | A ) . {\displaystyle IG(S,A)=\mathrm {H} {(S)}-\sum _{t\in T}p(t)\mathrm {H} {(t)}=\mathrm {H} {(S)}-\mathrm {H} {(S|A)}.} Where, H ( S ) {\displaystyle \mathrm {H} (S)} – Entropy of set S {\displaystyle S} T {\displaystyle T} – The subsets created from splitting set S {\displaystyle S} by attribute A {\displaystyle A} such that S = ⋃ t ∈ T t {\displaystyle S=\bigcup _{t\in T}t} p ( t ) {\displaystyle p(t)} – The proportion of the number of elements in t {\displaystyle t} to the number of elements in set S {\displaystyle S} H ( t ) {\displaystyle \mathrm {H} (t)} – Entropy of subset t {\displaystyle t} In ID3, information gain can be calculated (instead of entropy) for each remaining attribute. The attribute with the largest information gain is used to split the set S {\displaystyle S} on this iteration.
Prefrontal cortex basal ganglia working memory
Prefrontal cortex basal ganglia working memory (PBWM) is an algorithm that models working memory in the prefrontal cortex and the basal ganglia. It can be compared to long short-term memory (LSTM) in functionality, but is more biologically explainable. It uses the primary value learned value model to train prefrontal cortex working-memory updating system, based on the biology of the prefrontal cortex and basal ganglia. It is used as part of the Leabra framework and was implemented in Emergent in 2019. == Abstract == The prefrontal cortex has long been thought to subserve both working memory (the holding of information online for processing) and "executive" functions (deciding how to manipulate working memory and perform processing). Although many computational models of working memory have been developed, the mechanistic basis of executive function remains elusive. PBWM is a computational model of the prefrontal cortex to control both itself and other brain areas in a strategic, task-appropriate manner. These learning mechanisms are based on subcortical structures in the midbrain, basal ganglia and amygdala, which together form an actor/critic architecture. The critic system learns which prefrontal representations are task-relevant and trains the actor, which in turn provides a dynamic gating mechanism for controlling working memory updating. Computationally, the learning mechanism is designed to simultaneously solve the temporal and structural credit assignment problems. The model's performance compares favorably with standard backpropagation-based temporal learning mechanisms on the challenging 1-2-AX working memory task, and other benchmark working memory tasks. == Model == First, there are multiple separate stripes (groups of units) in the prefrontal cortex and striatum layers. Each stripe can be independently updated, such that this system can remember several different things at the same time, each with a different "updating policy" of when memories are updated and maintained. The active maintenance of the memory is in prefrontal cortex (PFC), and the updating signals (and updating policy more generally) come from the striatum units (a subset of basal ganglia units). PVLV provides reinforcement learning signals to train up the dynamic gating system in the basal ganglia. === Sensory input and motor output === The sensory input is connected to the posterior cortex which is connected to the motor output. The sensory input is also linked to the PVLV system. === Posterior cortex === The posterior cortex form the hidden layers of the input/output mapping. The PFC is connected with the posterior cortex to contextualize this input/output mapping. === PFC === The PFC (for output gating) has a localist one-to-one representation of the input units for every stripe. Thus, you can look at these PFC representations and see directly what the network is maintaining. The PFC maintains the working memory needed to perform the task. === Striatum === This is the dynamic gating system representing the striatum units of the basal ganglia. Every even-index unit within a stripe represents "Go", while the odd-index units represent "NoGo." The Go units cause updating of the PFC, while the NoGo units cause the PFC to maintain its existing memory representation. There are groups of units for every stripe. In the PBWM model in Emergent, the matrices represent the striatum. === PVLV === All of these layers are part of PVLV system. The PVLV system controls the dopaminergic modulation of the basal ganglia (BG). Thus, BG/PVLV form an actor-critic architecture where the PVLV system learns when to update. ==== SNrThal ==== SNrThal represents the substantia nigra pars reticulata (SNr) and the associated area of the thalamus, which produce a competition among the Go/NoGo units within a given stripe and mediates competition using k-winners-take-all dynamics. If there is more overall Go activity in a given stripe, then the associated SNrThal unit gets activated, and it drives updating in PFC. For every stripe, there is one unit in SNrThal. ==== VTA and SNc ==== Ventral tegmental area (VTA) and substantia nigra pars compacta (SNc) are part of the dopamine layer. This layer models midbrain dopamine neurons. They control the dopaminergic modulation of the basal ganglia.
Rake (software)
Rake is a software task management and a build automation tool created by Jim Weirich. It allows the user to specify tasks and to describe dependencies as well as to group tasks into namespaces. It is similar to SCons and Make. Rake was written in Ruby and has been part of the standard library of Ruby since version 1.9. == Examples == The tasks that should be executed need to be defined in a configuration file called Rakefile. A Rakefile has no special syntax and contains executable Ruby code. === Tasks === The basic unit in Rake is the task. A task has a name and an action block, that defines its functionality. The following code defines a task called greet that will output the text "Hello, Rake!" to the console. When defining a task, you can optionally add dependencies, that is one task can depend on the successful completion of another task. Calling the "seed" task from the following example will first execute the "migrate" task and only then proceed with the execution of the "seed" task.Tasks can also be made more versatile by accepting arguments. For example, the "generate_report" task will take a date as argument. If no argument is supplied the current date is used.A special type of task is the file task, which can be used to specify file creation tasks. The following task, for example, is given two object files, i.e. "a.o" and "b.o", to create an executable program.Another useful tool is the directory convenience method, that can be used to create directories upon demand. === Rules === When a file is named as a prerequisite but it does not have a file task defined for it, Rake will attempt to synthesize a task by looking at a list of rules supplied in the Rakefile. For example, suppose we were trying to invoke task "mycode.o" with no tasks defined for it. If the Rakefile has a rule that looks like this: This rule will synthesize any task that ends in ".o". It has as a prerequisite that a source file with an extension of ".c" must exist. If Rake is able to find a file named "mycode.c", it will automatically create a task that builds "mycode.o" from "mycode.c". If the file "mycode.c" does not exist, Rake will attempt to recursively synthesize a rule for it. When a task is synthesized from a rule, the source attribute of the task is set to the matching source file. This allows users to write rules with actions that reference the source file. === Advanced rules === Any regular expression may be used as the rule pattern. Additionally, a proc may be used to calculate the name of the source file. This allows for complex patterns and sources. The following rule is equivalent to the example above: NOTE: Because of a quirk in Ruby syntax, parentheses are required around a rule when the first argument is a regular expression. The following rule might be used for Java files: === Namespaces === To better organize big Rakefiles, tasks can be grouped into namespaces. Below is an example of a simple Rake recipe:
Markov model
In probability theory, a Markov model is a stochastic model used to model pseudo-randomly changing systems. It is assumed that future states depend only on the current state, not on the events that occurred before it (that is, it assumes the Markov property). Generally, this assumption enables reasoning and computation with the model that would otherwise be intractable. For this reason, in the fields of predictive modelling and probabilistic forecasting, it is desirable for a given model to exhibit the Markov property. == Introduction == Andrey Andreyevich Markov (14 June 1856 – 20 July 1922) was a Russian mathematician best known for his work on stochastic processes. A primary subject of his research later became known as the Markov chain. There are four common Markov models used in different situations, depending on whether every sequential state is observable or not, and whether the system is to be adjusted on the basis of observations made: == Markov chain == The simplest Markov model is the Markov chain. It models the state of a system with a random variable that changes through time. In this context, the Markov property indicates that the distribution for this variable depends only on the distribution of a previous state. An example use of a Markov chain is Markov chain Monte Carlo, which uses the Markov property to prove that a particular method for performing a random walk will sample from the joint distribution. == Hidden Markov model == A hidden Markov model is a Markov chain for which the state is only partially observable or noisily observable. In other words, observations are related to the state of the system, but they are typically insufficient to precisely determine the state. Several well-known algorithms for hidden Markov models exist. For example, given a sequence of observations, the Viterbi algorithm will compute the most-likely corresponding sequence of states, the forward algorithm will compute the probability of the sequence of observations, and the Baum–Welch algorithm will estimate the starting probabilities, the transition function, and the observation function of a hidden Markov model. One common use is for speech recognition, where the observed data is the speech audio waveform and the hidden state is the spoken text. In this example, the Viterbi algorithm finds the most likely sequence of spoken words given the speech audio. == Markov decision process == A Markov decision process is a Markov chain in which state transitions depend on the current state and an action vector that is applied to the system. Typically, a Markov decision process is used to compute a policy of actions that will maximize some utility with respect to expected rewards. == Partially observable Markov decision process == A partially observable Markov decision process (POMDP) is a Markov decision process in which the state of the system is only partially observed. POMDPs are known to be NP complete, but recent approximation techniques have made them useful for a variety of applications, such as controlling simple agents or robots. == Markov random field == A Markov random field, or Markov network, may be considered to be a generalization of a Markov chain in multiple dimensions. In a Markov chain, state depends only on the previous state in time, whereas in a Markov random field, each state depends on its neighbors in any of multiple directions. A Markov random field may be visualized as a field or graph of random variables, where the distribution of each random variable depends on the neighboring variables with which it is connected. More specifically, the joint distribution for any random variable in the graph can be computed as the product of the "clique potentials" of all the cliques in the graph that contain that random variable. Modeling a problem as a Markov random field is useful because it implies that the joint distributions at each vertex in the graph may be computed in this manner. == Hierarchical Markov models == Hierarchical Markov models can be applied to categorize human behavior at various levels of abstraction. For example, a series of simple observations, such as a person's location in a room, can be interpreted to determine more complex information, such as in what task or activity the person is performing. Two kinds of Hierarchical Markov Models are the Hierarchical hidden Markov model and the Abstract Hidden Markov Model. Both have been used for behavior recognition and certain conditional independence properties between different levels of abstraction in the model allow for faster learning and inference. == Tolerant Markov model == A Tolerant Markov model (TMM) is a probabilistic-algorithmic Markov chain model. It assigns the probabilities according to a conditioning context that considers the last symbol, from the sequence to occur, as the most probable instead of the true occurring symbol. A TMM can model three different natures: substitutions, additions or deletions. Successful applications have been efficiently implemented in DNA sequences compression. == Markov-chain forecasting models == Markov-chains have been used as a forecasting methods for several topics, for example price trends, wind power and solar irradiance. The Markov-chain forecasting models utilize a variety of different settings, from discretizing the time-series to hidden Markov-models combined with wavelets and the Markov-chain mixture distribution model (MCM).