Gene expression programming

Gene expression programming

Gene expression programming (GEP) in computer programming is an evolutionary algorithm that creates computer programs or models. These computer programs are complex tree structures that learn and adapt by changing their sizes, shapes, and composition, much like a living organism. And like living organisms, the computer programs of GEP are also encoded in simple linear chromosomes of fixed length. Thus, GEP is a genotype–phenotype system, benefiting from a simple genome to keep and transmit the genetic information and a complex phenotype to explore the environment and adapt to it. == Background == Evolutionary algorithms use populations of individuals, select individuals according to fitness, and introduce genetic variation using one or more genetic operators. Their use in artificial computational systems dates back to the 1950s where they were used to solve optimization problems (e.g. Box 1957 and Friedman 1959). But it was with the introduction of evolution strategies by Rechenberg in 1965 that evolutionary algorithms gained popularity. A good overview text on evolutionary algorithms is the book "An Introduction to Genetic Algorithms" by Mitchell (1996). Gene expression programming belongs to the family of evolutionary algorithms and is closely related to genetic algorithms and genetic programming. From genetic algorithms it inherited the linear chromosomes of fixed length; and from genetic programming it inherited the expressive parse trees of varied sizes and shapes. In gene expression programming the linear chromosomes work as the genotype and the parse trees as the phenotype, creating a genotype/phenotype system. This genotype/phenotype system is multigenic, thus encoding multiple parse trees in each chromosome. This means that the computer programs created by GEP are composed of multiple parse trees. Because these parse trees are the result of gene expression, in GEP they are called expression trees. Masood Nekoei, et al. utilized this expression programming style in ABC optimization to conduct ABCEP as a method that outperformed other evolutionary algorithms.ABCEP == Encoding: the genotype == The genome of gene expression programming consists of a linear, symbolic string or chromosome of fixed length composed of one or more genes of equal size. These genes, despite their fixed length, code for expression trees of different sizes and shapes. An example of a chromosome with two genes, each of size 9, is the string (position zero indicates the start of each gene): 012345678012345678 L+a-baccdcLabacd where “L” represents the natural logarithm function and “a”, “b”, “c”, and “d” represent the variables and constants used in a problem. == Expression trees: the phenotype == As shown above, the genes of gene expression programming have all the same size. However, these fixed length strings code for expression trees of different sizes. This means that the size of the coding regions varies from gene to gene, allowing for adaptation and evolution to occur smoothly. For example, the mathematical expression: ( a − b ) ( c + d ) {\displaystyle {\sqrt {(a-b)(c+d)}}\,} can also be represented as an expression tree: where "Q” represents the square root function. This kind of expression tree consists of the phenotypic expression of GEP genes, whereas the genes are linear strings encoding these complex structures. For this particular example, the linear string corresponds to: 01234567 Q-+abcd which is the straightforward reading of the expression tree from top to bottom and from left to right. These linear strings are called k-expressions (from Karva notation). Going from k-expressions to expression trees is also very simple. For example, the following k-expression: 01234567890 Qb+baQba is composed of two different terminals (the variables “a” and “b”), two different functions of two arguments (“” and “+”), and a function of one argument (“Q”). Its expression gives: == K-expressions and genes == The k-expressions of gene expression programming correspond to the region of genes that gets expressed. This means that there might be sequences in the genes that are not expressed, which is indeed true for most genes. The reason for these noncoding regions is to provide a buffer of terminals so that all k-expressions encoded in GEP genes correspond always to valid programs or expressions. The genes of gene expression programming are therefore composed of two different domains – a head and a tail – each with different properties and functions. The head is used mainly to encode the functions and variables chosen to solve the problem at hand, whereas the tail, while also used to encode the variables, provides essentially a reservoir of terminals to ensure that all programs are error-free. For GEP genes the length of the tail is given by the formula: t = h ( n max − 1 ) + 1 {\displaystyle t=h(n_{\max }-1)+1} where h is the head's length and nmax is maximum arity. For example, for a gene created using the set of functions F = {Q, +, −, ∗, /} and the set of terminals T = {a, b}, nmax = 2. And if we choose a head length of 15, then t = 15 (2–1) + 1 = 16, which gives a gene length g of 15 + 16 = 31. The randomly generated string below is an example of one such gene: 0123456789012345678901234567890 b+a-aQab+//+b+babbabbbababbaaa It encodes the expression tree: which, in this case, only uses 8 of the 31 elements that constitute the gene. It's not hard to see that, despite their fixed length, each gene has the potential to code for expression trees of different sizes and shapes, with the simplest composed of only one node (when the first element of a gene is a terminal) and the largest composed of as many nodes as there are elements in the gene (when all the elements in the head are functions with maximum arity). It's also not hard to see that it is trivial to implement all kinds of genetic modification (mutation, inversion, insertion, recombination, and so on) with the guarantee that all resulting offspring encode correct, error-free programs. == Multigenic chromosomes == The chromosomes of gene expression programming are usually composed of more than one gene of equal length. Each gene codes for a sub-expression tree (sub-ET) or sub-program. Then the sub-ETs can interact with one another in different ways, forming a more complex program. The figure shows an example of a program composed of three sub-ETs. In the final program the sub-ETs could be linked by addition or some other function, as there are no restrictions to the kind of linking function one might choose. Some examples of more complex linkers include taking the average, the median, the midrange, thresholding their sum to make a binomial classification, applying the sigmoid function to compute a probability, and so on. These linking functions are usually chosen a priori for each problem, but they can also be evolved elegantly and efficiently by the cellular system of gene expression programming. == Cells and code reuse == In gene expression programming, homeotic genes control the interactions of the different sub-ETs or modules of the main program. The expression of such genes results in different main programs or cells, that is, they determine which genes are expressed in each cell and how the sub-ETs of each cell interact with one another. In other words, homeotic genes determine which sub-ETs are called upon and how often in which main program or cell and what kind of connections they establish with one another. === Homeotic genes and the cellular system === Homeotic genes have exactly the same kind of structural organization as normal genes and they are built using an identical process. They also contain a head domain and a tail domain, with the difference that the heads contain now linking functions and a special kind of terminals – genic terminals – that represent the normal genes. The expression of the normal genes results as usual in different sub-ETs, which in the cellular system are called ADFs (automatically defined functions). As for the tails, they contain only genic terminals, that is, derived features generated on the fly by the algorithm. For example, the chromosome in the figure has three normal genes and one homeotic gene and encodes a main program that invokes three different functions a total of four times, linking them in a particular way. From this example it is clear that the cellular system not only allows the unconstrained evolution of linking functions but also code reuse. And it shouldn't be hard to implement recursion in this system. === Multiple main programs and multicellular systems === Multicellular systems are composed of more than one homeotic gene. Each homeotic gene in this system puts together a different combination of sub-expression trees or ADFs, creating multiple cells or main programs. For example, the program shown in the figure was created using a cellular system with two cells and three normal genes. The applications of these multicellular systems are mu

Shape factor (image analysis and microscopy)

Shape factors are dimensionless quantities used in image analysis and microscopy that numerically describe the shape of a particle, independent of its size. Shape factors are calculated from measured dimensions, such as diameter, chord lengths, area, perimeter, centroid, moments, etc. The dimensions of the particles are usually measured from two-dimensional cross-sections or projections, as in a microscope field, but shape factors also apply to three-dimensional objects. The particles could be the grains in a metallurgical or ceramic microstructure, or the microorganisms in a culture, for example. The dimensionless quantities often represent the degree of deviation from an ideal shape, such as a circle, sphere or equilateral polyhedron. Shape factors are often normalized, that is, the value ranges from zero to one. A shape factor equal to one usually represents an ideal case or maximum symmetry, such as a circle, sphere, square or cube. == Aspect ratio == The most common shape factor is the aspect ratio, a function of the largest diameter and the smallest diameter orthogonal to it: A R = d min d max {\displaystyle A_{R}={\frac {d_{\min }}{d_{\max }}}} The normalized aspect ratio varies from approaching zero for a very elongated particle, such as a grain in a cold-worked metal, to near unity for an equiaxed grain. The reciprocal of the right side of the above equation is also used, such that the AR varies from one to approaching infinity. == Circularity == Another very common shape factor is the circularity (or isoperimetric quotient), a function of the perimeter P and the area A: f circ = 4 π A P 2 {\displaystyle f_{\text{circ}}={\frac {4\pi A}{P^{2}}}} The circularity of a circle is 1, and much less than one for a starfish footprint. The reciprocal of the circularity equation is also used, such that fcirc varies from one for a circle to infinity. == Elongation shape factor == The less-common elongation shape factor is defined as the square root of the ratio of the two second moments in of the particle around its principal axes. f elong = i 2 i 1 {\displaystyle f_{\text{elong}}={\sqrt {\frac {i_{2}}{i_{1}}}}} == Compactness shape factor == The compactness shape factor is a function of the polar second moment in of a particle and a circle of equal area A. f comp = A 2 2 π i 1 2 + i 2 2 {\displaystyle f_{\text{comp}}={\frac {A^{2}}{2\pi {\sqrt {{i_{1}}^{2}+{i_{2}}^{2}}}}}} The fcomp of a circle is one, and much less than one for the cross-section of an I-beam. == Waviness shape factor == The waviness shape factor of the perimeter is a function of the convex portion Pcvx of the perimeter to the total. f wav = P cvx P {\displaystyle f_{\text{wav}}={\frac {P_{\text{cvx}}}{P}}} Some properties of metals and ceramics, such as fracture toughness, have been linked to grain shapes. == An application of shape factors == Greenland, the largest island in the world, has an area of 2,166,086 km2; a coastline (perimeter) of 39,330 km; a north–south length of 2670 km; and an east–west length of 1290 km. The aspect ratio of Greenland is A R = 1290 2670 = 0.483 {\displaystyle A_{R}={\frac {1290}{2670}}=0.483} The circularity of Greenland is f circ = 4 π ( 2166086 ) 39330 2 = 0.0176. {\displaystyle f_{\text{circ}}={\frac {4\pi (2166086)}{39330^{2}}}=0.0176.} The aspect ratio is agreeable with an eyeball-estimate on a globe. Such an estimate on a typical flat map, using the Mercator projection, would be less accurate due to the distorted scale at high latitudes. The circularity is deceptively low, due to the fjords that give Greenland a very jagged coastline (see the coastline paradox). A low value of circularity does not necessarily indicate a lack of symmetry, and shape factors are not limited to microscopic objects.

Color reproduction

Color reproduction is an aspect of color science concerned with producing light spectra that evoke a desired color, either through additive (light emitting) or subtractive (surface color) models. It converts physical correlates of color perception (CIE 1931 XYZ color space tristimulus values and related quantities) into light spectra that can be experienced by observers. In this way, it is the opposite of colorimetry. It is concerned with the faithful reproduction of a color in one medium, with a color in another, so it is a central concept in color management and relies heavily on color calibration. For example, food packaging must be able to faithfully reproduce the colors of the foods therein in order to appeal to a customer. This involves proper color calibration of at least four devices: Lighting, which must have a high color rendering index and not give a color cast to the object. Camera, which measures the reflected spectrum of the object and converts to a trichromatic color space (e.g. RGB). Screen, which reproduces color so a designer can proof the captured image and make color corrections as necessary. Printer, which reproduces the final color on paper.

Showcase Workshop

Showcase Workshop, also referred to as Showcase, is a SaaS company that develops a presentation-building application for business use. Users upload files and images to a web platform which generates presentations viewable on a suite of mobile apps. Showcase was founded in 2011. The company’s headquarters are in Wellington, New Zealand. == History == Showcase Workshop was originally developed in response to dynamically changing content being presented on iPads at the 2012 Olympics. After market-testing a beta version of the core application, Showcase Workshop launched commercially in 2012. In 2014 Showcase partnered with Vodafone Global Enterprise. == Product == Users upload pre-existing PDFs, videos, images and Microsoft Office documents to a secure server, building presentations or ‘showcases’ which can then be downloaded via the mobile apps. The presentations are used for mobile sales enablement, training, or operational/health and safety purposes. == Reception == Reviewers have praised the ease of use of Showcase, calling it a “better alternative to developing a native app” and “intuitive”. Criticisms include the lack of differing templates and a lack of complex customisation controls. Showcase was nominated for a Tabby Award in 2014 and won a Tabby Award in 2015 for its Windows app.

Apache Kudu

Apache Kudu is a free and open source column-oriented data store of the Apache Hadoop ecosystem. It is compatible with most of the data processing frameworks in the Hadoop environment. It provides completeness to Hadoop's storage layer to enable fast analytics on fast data. The open source project to build Apache Kudu began as internal project at Cloudera. The first version Apache Kudu 1.0 was released 19 September 2016. == Comparison with other storage engines == Kudu was designed and optimized for OLAP workloads. Like HBase, it is a real-time store that supports key-indexed record lookup and mutation. Kudu differs from HBase since Kudu's datamodel is a more traditional relational model, while HBase is schemaless. Kudu's "on-disk representation is truly columnar and follows an entirely different storage design than HBase/Bigtable".

Trello

Trello is a web-based, kanban-style list-making application developed by Atlassian. Created in 2011 by Fog Creek Software, it was spun out to form the basis of a separate company in New York City in 2014 and sold to Atlassian in January 2017. == History == The name Trello is derived from the word trellis, which had been a code name for the project at its early stages. Trello was released at a TechCrunch event by Fog Creek founder Joel Spolsky. In September 2011 Wired magazine named the application one of "The 7 Coolest Startups You Haven't Heard of Yet". Lifehacker said "it makes project collaboration simple and kind of enjoyable". In 2014, it raised US$10.3 million in funding from Index Ventures and Spark Capital. Prior to its acquisition, Trello had sold 22% of its shares to investors, with the remaining shares held by founders Michael Pryor and Joel Spolsky. In May 2016, Trello claimed it had more than 1.1 million daily active users and 14 million total signups. In May 2015, Trello expanded internationally with localized interfaces for Brazil, Germany, and Spain. In 2016 Trello launched the Power-Up platform, allowing 3rd party developers to build and distribute extensions known as Power-Ups to Trello. Initial integrations included Zendesk, SurveyMonkey and Giphy. By January 2022 there were a total of 247 power-ups listed in the Power-Up directory. On 9 January 2017, Atlassian announced its intent to acquire Trello for $425 million. The transaction was made with $360 million in cash and $65 million in shares and options. In December 2018, Trello announced its acquisition of Butler, a company that developed a leading power-up for automating tasks within a Trello board. Trello announced 35 million users in March 2019 and 50 million users in October 2019. In 2020 Craig Jones, then cybersecurity operations director at Sophos, found that the company exposed the personally identifiable information (PII) data of its users, exposed through public Trello boards; the researcher first tweeted about this issue in the year 2018. On 16 January 2024 Trello suffered a data breach containing over 15 million unique email addresses, names and usernames, when the data was posted on a popular hacking forum. The data was obtained by enumerating a publicly accessible resource using email addresses from previous breach corpuses; it was then added on 22 January 2024 to the famous website collecting data breaches "Have I Been Pwned?". == Uses == Users can create task boards with different columns and move the tasks between them. Typically columns include task statuses such as To Do, In Progress, Done. The tool can be used for personal and business purposes including real estate management, software project management, school bulletin boards, lesson planning, accounting, web design, gaming, and law office case management. == Architecture == According to a Fog Creek blog post in January 2012, the client was a thin web layer which downloads the main app, written in CoffeeScript and compiled to minified JavaScript, using Backbone.js, HTML5 .pushState(), and the Mustache templating language. The server was built on top of MongoDB, Node.js and a modified version of Socket.io. == Reception == On 26 January 2017, PC Magazine gave Trello a 3.5 / 5 rating, calling it "flexible" and saying that "you can get rather creative", while noting that "it may require some experimentation to figure out how to best use it for your team and the workload you manage."

CPanel

cPanel is a web hosting control panel software developed by cPanel, L.L.C. It provides a graphical interface (GUI) and automation tools designed to simplify the process of hosting a web site for the website owner or "end user". It enables administration through a standard web browser using a three-tier structure. While cPanel is limited to managing a single hosting account, cPanel & WHM allow the administration of the entire server. In addition to the GUI, cPanel also has command line and API-based access that allows third-party software vendors, web hosting organizations, and developers to automate standard system administration processes. cPanel & WHM is designed to function either as a dedicated server or virtual private server. The latest cPanel & WHM version supports installation on AlmaLinux, Rocky Linux, CloudLinux OS, and Ubuntu. == History == cPanel is currently developed by cPanel, L.L.C., a privately owned company headquartered in Houston, Texas, United States. WebPros is the parent company of cPanel, L.L.C. It was originally designed in 1996 as the control panel for Speed Hosting, a now-defunct web hosting company. The original author of cPanel, J. Nick Koston, had a stake in Speed Hosting. Webking quickly began using cPanel after its merger with Speed Hosting. The new company moved its servers to Virtual Development Inc. (VDI), a now-defunct hosting facility. Following an agreement between Koston and VDI, cPanel was only available to customers hosted directly at VDI. At the time, there was little competition in the control panel market, with the main choices being VDI and Alabanza. Eventually, due to Koston leaving for college, he and William Jensen signed an agreement in which cPanel was split into a separate program called WebPanel; this version was run by VDI. Without the lead programmer, VDI was not able to continue any work on cPanel and eventually stopped supporting it completely. Koston kept working on cPanel while also working at BurstNET. Eventually, he left BurstNET to focus fully on cPanel. cPanel 3 was released in 1999: main additions over cPanel 2 were an automatic upgrade and the Web Host Manager (WHM). The interface was also improved when Carlos Rego of WizardsHosting made what became the default theme of cPanel. With the release of cPanel 11, cPanel adopted a four-tier versioning system, "Parent.Major.Minor.Patch" (e.g., 11.32.0.3). As of version 11.52, the "Parent" representation is deprecated, with 11.54 stylized as "Version 54." cPanel 11.30 is the last major version to support FreeBSD. On August 20, 2018 cPanel L.L.C. announced that it had signed an agreement to be acquired by a group led by Oakley Capital (who also own Plesk and SolusVM). While Koston sold his interest in cPanel, he will continue to be an owner of the company that owns cPanel. In April 2026, a severe vulnerability was discovered that affected all cPanel and WHM versions after 11.40, affectively allowing unauthenticated remote attackers to access the control panel. According to some web hosters the vulnerability was already being actively exploited, with some attempts even dating back to late February 2026. == Add-ons == cPanel provides front-ends for a number of common operations, including the management of PGP keys, crontab tasks, mail and FTP accounts, and mailing lists. Several add-ons exist, some for an additional fee, including auto installers such as Installatron, Fantastico, Softaculous, and WHMSonic (SHOUTcast/radio Control Panel Add-on). The add-ons need to be enabled by the server administrator in WHM to be accessible to the cPanel user. WHM manages some software packages separately from the underlying operating system, applying upgrades to Apache, PHP, MySQL and MariaDB, Exim, FTP, and related software packages automatically. This ensures that these packages are kept up-to-date and compatible with WHM, but makes it more difficult to install newer versions of these packages. It also makes it difficult to verify that the packages have not been tampered with, since the operating system's package management verification system cannot be used to do so. == WHM == WHM, short for WebHost Manager, is a web-based tool which is used for server administration. There are at least two tiers of WHM, often referred to as "root WHM", and non-root WHM (or Reseller WHM). Root WHM is used by server administrators and non-root WHM (with fewer privileges) is used by others, like entity departments, and resellers to manage hosting accounts often referred to as cPanel accounts on a web server. WHM is also used to manage SSL certificates (both server self generated and CA provided SSL certificates), cPanel users, hosting packages, DNS zones, themes, and authentication methods. The default automatic SSL (AutoSSL) provided by cPanel is powered by Let's Encrypt. Additionally, WHM can also be used to manage FTP, Mail (POP, IMAP, and SMTP) and SSH services on the server. As well as being accessible by the root administrator, WHM is also accessible to users with reseller privileges. Reseller users of cPanel have a smaller set of features than the root user, generally limited by the server administrator, to features which they determine will affect their customers' accounts rather than the server as a whole. From root WHM, the server administrator can perform maintenance operations such as upgrading and recompiling Apache and PHP, installing Perl modules, and upgrading RPMs installed on the system. == Enkompass == A version of cPanel & WHM for Microsoft Windows, called Enkompass, was declared end-of-life as of February 2014. Version 3 remained available for download, but without further development or support. In the preceding years, Enkompass had been available for free as product development slowed. == Pricing == On June 27, 2019 cPanel announced a new account-based pricing structure. After backlash from their customers, cPanel issued a second announcement but did not change the new structure.