Timnit W. Gebru (Amharic and Tigrinya: ትምኒት ገብሩ; 1982/1983) is an Eritrean Ethiopian-born computer scientist who works in the fields of artificial intelligence (AI), algorithmic bias and data mining. She is a co-founder of Black in AI, an advocacy group that has pushed for more Black roles in AI development and research. She is the founder of the Distributed Artificial Intelligence Research Institute (DAIR). In December 2020, public controversy erupted over the circumstances surrounding Gebru's departure from Google, where she was technical co-lead of the Ethical Artificial Intelligence Team. Gebru had coauthored a paper on the risks of large language models (LLMs) acting as stochastic parrots, and submitted it for publication. According to Jeff Dean, head of Google AI, the paper was submitted without waiting for Google's internal review, which then asserted that it ignored too much relevant research. Google management requested that Gebru either withdraw the paper or remove the names of all the authors employed by Google. Gebru requested the identity and feedback of every reviewer, and stated that if Google refused, she would talk to her manager about "a last date". Google terminated her employment immediately, stating that they were accepting her resignation. Gebru maintained that she had not formally offered to resign, and only threatened to. Gebru has been widely recognized for her expertise in the ethics of artificial intelligence. She was named one of the World's 50 Greatest Leaders by Fortune and one of Nature's ten people who shaped science in 2021, and in 2022, one of Time's most influential people. == Early life and education == Gebru was raised in Addis Ababa, Ethiopia. Her father, an electrical engineer with a Doctor of Philosophy (PhD), died when she was five years old, and she was raised by her mother, an economist. Both her parents are from Eritrea. When Gebru was 15, during the Eritrean–Ethiopian War, she fled Ethiopia after some of her family were deported to Eritrea and compelled to fight in the war. She was initially denied a U.S. visa and briefly lived in Ireland, but she eventually received political asylum in the U.S., an experience she said was "miserable". Gebru settled in Somerville, Massachusetts to attend high school, where she says she immediately started to experience racial discrimination, with some teachers refusing to allow her to take certain Advanced Placement courses, despite being a high-achiever. After she completed high school, an encounter with the police set Gebru on a course toward a focus on ethics in technology. A friend of hers, a Black woman, was assaulted in a bar, and Gebru called the police to report it. She says that instead of filing the assault report, her friend was arrested and remanded to a cell. Gebru called it a pivotal moment and a "blatant example of systemic racism." In 2001, Gebru was accepted at Stanford University. There, she earned her Bachelor of Science and Master of Science degrees in electrical engineering and her PhD in computer vision in 2017. Gebru was advised during her PhD program by Fei-Fei Li. During the 2008 United States presidential election, Gebru canvassed in support of Barack Obama. Gebru presented her doctoral research at the 2017 LDV Capital Vision Summit competition, where computer vision scientists present their work to members of industry and venture capitalists. Gebru won the competition, starting a series of collaborations with other entrepreneurs and investors. Both during her PhD program in 2016 and in 2018, Gebru returned to Ethiopia with Jelani Nelson's programming campaign, AddisCoder. While working on her PhD, Gebru authored a paper that was never published about her concern over the future of AI. She wrote of the dangers of the lack of diversity in the field, centered on her experiences with the police and on a ProPublica investigation into predictive policing, which revealed a projection of human biases in machine learning. In the paper, she scathed the "boy's club culture", reflecting on her experiences at conference gatherings of drunken male attendees sexually harassing her, and criticized the hero worship of the field's celebrities. == Career == === 2004–2013: Software development at Apple === Gebru joined Apple as an intern while at Stanford, working in their hardware division making circuitry for audio components, and was offered a full-time position the following year. Of her work as an audio engineer, her manager told Wired she was "fearless", and well-liked by her colleagues. During her tenure at Apple, Gebru became more interested in building software, namely computer vision that could detect human figures. She went on to develop signal processing algorithms for the first iPad. At the time, she said she did not consider the potential use for surveillance, saying "I just found it technically interesting." Long after leaving the company, during the #AppleToo movement in the summer of 2021, which was led by Apple engineer Cher Scarlett, who consulted with Gebru, Gebru revealed she experienced "so many egregious things" and "always wondered how they manage[d] to get out of the spotlight." She said that accountability at Apple was long overdue, and warned they could not continue to fly under the radar for much longer. Gebru also criticized the way the media covers Apple and other tech giants, saying that the press helps shield such companies from public scrutiny. === 2013–2017: Research at Stanford and Microsoft === In 2013, Gebru joined Fei-Fei Li's lab at Stanford, where she combined deep learning with Google Street View to estimate the demographics of United States neighbourhoods, showing that socioeconomic attributes such as voting patterns, income, race, and education can be inferred from observations of cars. In 2015, Gebru attended the field's top conference, Neural Information Processing Systems (NIPS), in Montreal, Canada. Out of 3,700 attendees, she noted she was one of only a few Black researchers. When she attended again the following year, she kept a tally and noted that there were only five Black men and that she was the only Black woman out of 8,500 delegates. Together with her colleague Rediet Abebe, Gebru founded Black in AI, a community of Black researchers working in artificial intelligence that aims to increase the presence, visibility, and well-being of Black professionals and leaders within the field. In the summer of 2017, Gebru joined Microsoft as a postdoctoral researcher in the Fairness, Accountability, Transparency, and Ethics in AI (FATE) lab. In 2017, Gebru spoke at the Fairness and Transparency conference, where MIT Technology Review interviewed her about biases that exist in AI systems and how adding diversity in AI teams can fix that issue. In her interview with Jackie Snow, Snow asked Gebru, "How does the lack of diversity distort artificial intelligence and specifically computer vision?" and Gebru pointed out that there are biases that exist in the software developers. While at Microsoft, Gebru co-authored a research paper called Gender Shades, which became the namesake of a project of a broader Massachusetts Institute of Technology project led by co-author Joy Buolamwini. The pair investigated facial recognition software, finding that in one particular implementation Black women were 35% less likely to be recognized than White men. === 2018–2020: Artificial intelligence ethics at Google === Gebru joined Google in 2018, where she co-led a team on the ethics of artificial intelligence with Margaret Mitchell. She studied the implications of artificial intelligence, looking to improve the ability of technology to do social good. In 2019, Gebru and other artificial intelligence researchers "signed a letter calling on Amazon to stop selling its facial-recognition technology to law enforcement agencies because it is biased against women and people of color", citing a study that was conducted by MIT researchers showing that Amazon's facial recognition system had more trouble identifying darker-skinned females than any other technology company's facial recognition software. In a New York Times interview, Gebru has further expressed that she believes facial recognition is too dangerous to be used for law enforcement and security purposes at present. === Exit from Google === In 2020 Gebru and five co-authors wrote a paper titled "On the Dangers of Stochastic Parrots: Can Language Models Be Too Big? 🦜". The paper examined risks of very large language models, including their environmental footprint, financial costs, the inscrutability of large models, the potential for LLMs to display prejudice against certain groups, the inability of LLMs to understand the language they process, and the use of LLMs to spread disinformation. In December 2020, her employment with Google ended after Google management asked her to either withdraw the paper before publication, or remove the names of all the Google employees from
Non-photorealistic rendering
Non-photorealistic rendering (NPR) is an area of computer graphics that focuses on enabling a wide variety of expressive styles for digital art, in contrast to traditional computer graphics, which focuses on photorealism. NPR is inspired by other artistic modes such as painting, drawing, technical illustration, and animated cartoons. NPR has appeared in movies and video games in the form of cel-shaded animation (also known as "toon" shading) as well as in scientific visualization, architectural illustration and experimental animation. == History and criticism of the term == The term non-photorealistic rendering is believed to have been coined by the SIGGRAPH 1990 papers committee, who held a session entitled "Non Photo Realistic Rendering". The term has received some criticism: The term "photorealism" has different meanings for graphics researchers (see "photorealistic rendering") and artists. For artists—who are the target consumers of NPR techniques—it refers to a school of painting that focuses on reproducing the effect of a camera lens, with all the distortion and hyper-reflections that it creates. For graphics researchers, however, it refers to an image that is visually indistinguishable from reality. In fact, graphics researchers lump the kinds of visual distortions that are used by photorealist painters into "non-photorealism". Describing something by what it is not is problematic. Equivalent (made-up) comparisons might be "non-elephant biology" or "non-geometric mathematics". NPR researchers have stated that they expect the term will disappear eventually and be replaced by the now more general term "computer graphics", with "photorealistic graphics" being the term used to describe "traditional" computer graphics. Many techniques that are used to create 'non-photorealistic' images are not rendering techniques. They are modelling techniques, or post-processing techniques. While the latter are coming to be known as 'image-based rendering', sketch-based modelling techniques, cannot technically be included under this heading, which is very inconvenient for conference organisers. The first conference on non-photorealistic animation and rendering included a discussion of possible alternative names. Among those suggested were "expressive graphics", "artistic rendering", "non-realistic graphics", "art-based rendering", and "psychographics". All of these terms have been used in various research papers on the topic, but the "non-photorealistic" term seems to have nonetheless taken hold. The first technical meeting dedicated to NPR was the ACM-sponsored Symposium on Non-Photorealistic Rendering and Animation(NPAR) in 2000. NPAR is traditionally co-located with the Annecy Animated Film Festival, running on even numbered years. From 2007 onward, NPAR began to also run on odd-numbered years, co-located with ACM SIGGRAPH. == 3D == Three-dimensional NPR is the style that is most commonly seen in video games and movies. The output from this technique is almost always a 3D model that has been modified from the original input model to portray a new artistic style. In many cases, the geometry of the model is identical to the original geometry, and only the material applied to the surface is modified. With increased availability of programmable GPU's, shaders have allowed NPR effects to be applied to the rasterised image that is to be displayed to the screen. The majority of NPR techniques applied to 3D geometry are intended to make the scene appear two-dimensional. NPR techniques for 3D images include cel shading and Gooch shading. Many methods can be used to draw stylized outlines and strokes from 3D models, including occluding contours and Suggestive contours. For enhanced legibility, the most useful technical illustrations for technical communication are not necessarily photorealistic. Non-photorealistic renderings, such as exploded view diagrams, greatly assist in showing placement of parts in a complex system. Cartoon rendering, also called cel shading or toon shading, is a non-photorealistic rendering technique used to give 3D computer graphics a flat, cartoon-like appearance. Its defining feature is the use of distinct shading colors rather than smooth gradients, producing a look reminiscent of comic books or animated films. This technique is often used to blend 3D objects and environments with 2D hand-animated elements while maintaining a consistent look. Treasure Planet movie by Disney is an example of blending these techniques. == 2D == The input to a two dimensional NPR system is typically an image or video. The output is a typically an artistic rendering of that input imagery (for example in a watercolor, painterly or sketched style) although some 2D NPR serves non-artistic purposes e.g. data visualization. The artistic rendering of images and video (often referred to as image stylization) traditionally focused upon heuristic algorithms that seek to simulate the placement of brush strokes on a digital canvas. Arguably, the earliest example of 2D NPR is Paul Haeberli's 'Paint by Numbers' at SIGGRAPH 1990. This (and similar interactive techniques) provide the user with a canvas that they can "paint" on using the cursor — as the user paints, a stylized version of the image is revealed on the canvas. This is especially useful for people who want to simulate different sizes of brush strokes according to different areas of the image. Subsequently, basic image processing operations using gradient operators or statistical moments were used to automate this process and minimize user interaction in the late nineties (although artistic control remains with the user via setting parameters of the algorithms). This automation enabled practical application of 2D NPR to video, for the first time in the living paintings of the movie What Dreams May Come (1998). More sophisticated image abstractions techniques were developed in the early 2000s harnessing computer vision operators e.g. image salience, or segmentation operators to drive stroke placement. Around this time, machine learning began to influence image stylization algorithms notably image analogy that could learn to mimic the style of an existing artwork. The advent of deep learning has re-kindled activity in image stylization, notably with neural style transfer (NST) algorithms that can mimic a wide gamut of artistic styles from single visual examples. These algorithms underpin mobile apps capable of the same e.g. Prisma In addition to the above stylization methods, a related class of techniques in 2D NPR address the simulation of artistic media. These methods include simulating the diffusion of ink through different kinds of paper, and also of pigments through water for simulation of watercolor. == Artistic rendering == Artistic rendering is the application of visual art styles to rendering. For photorealistic rendering styles, the emphasis is on accurate reproduction of light-and-shadow and the surface properties of the depicted objects, composition, or other more generic qualities. When the emphasis is on unique interpretive rendering styles, visual information is interpreted by the artist and displayed accordingly using the chosen art medium and level of abstraction in abstract art. In computer graphics, interpretive rendering styles are known as non-photorealistic rendering styles, but may be used to simplify technical illustrations. Rendering styles that combine photorealism with non-photorealism are known as hyperrealistic rendering styles. == Notable films and games == This section lists some seminal uses of NPR techniques in films, games and software. See cel-shaded animation for a list of uses of toon-shading in games and movies.
Semantic mapping (statistics)
Semantic mapping (SM) is a statistical method for dimensionality reduction (the transformation of data from a high-dimensional space into a low-dimensional space). SM can be used in a set of multidimensional vectors of features to extract a few new features that preserves the main data characteristics. SM performs dimensionality reduction by clustering the original features in semantic clusters and combining features mapped in the same cluster to generate an extracted feature. Given a data set, this method constructs a projection matrix that can be used to map a data element from a high-dimensional space into a reduced dimensional space. SM can be applied in construction of text mining and information retrieval systems, as well as systems managing vectors of high dimensionality. SM is an alternative to random mapping, principal components analysis and latent semantic indexing methods.
Detrended correspondence analysis
Detrended correspondence analysis (DCA) is a multivariate statistical technique widely used by ecologists to find the main factors or gradients in large, species-rich but usually sparse data matrices that typify ecological community data. DCA is frequently used to suppress artifacts inherent in most other multivariate analyses when applied to gradient data. == History == DCA was created in 1979 by Mark Hill of the United Kingdom's Institute for Terrestrial Ecology (now merged into Centre for Ecology and Hydrology) and implemented in FORTRAN code package called DECORANA (Detrended Correspondence Analysis), a correspondence analysis method. DCA is sometimes erroneously referred to as DECORANA; however, DCA is the underlying algorithm, while DECORANA is a tool implementing it. == Issues addressed == According to Hill and Gauch, DCA suppresses two artifacts inherent in most other multivariate analyses when applied to gradient data. An example is a time-series of plant species colonising a new habitat; early successional species are replaced by mid-successional species, then by late successional ones (see example below). When such data are analysed by a standard ordination such as a correspondence analysis: the ordination scores of the samples will exhibit the 'edge effect', i.e. the variance of the scores at the beginning and the end of a regular succession of species will be considerably smaller than that in the middle, when presented as a graph the points will be seen to follow a horseshoe shaped curve rather than a straight line ('arch effect'), even though the process under analysis is a steady and continuous change that human intuition would prefer to see as a linear trend. Outside ecology, the same artifacts occur when gradient data are analysed (e.g. soil properties along a transect running between 2 different geologies, or behavioural data over the lifespan of an individual) because the curved projection is an accurate representation of the shape of the data in multivariate space. Ter Braak and Prentice (1987, p. 121) cite a simulation study analysing two-dimensional species packing models resulting in a better performance of DCA compared to CA. == Method == DCA is an iterative algorithm that has shown itself to be a highly reliable and useful tool for data exploration and summary in community ecology (Shaw 2003). It starts by running a standard ordination (CA or reciprocal averaging) on the data, to produce the initial horse-shoe curve in which the 1st ordination axis distorts into the 2nd axis. It then divides the first axis into segments (default = 26), and rescales each segment to have mean value of zero on the 2nd axis - this effectively squashes the curve flat. It also rescales the axis so that the ends are no longer compressed relative to the middle, so that 1 DCA unit approximates to the same rate of turnover all the way through the data: the rule of thumb is that 4 DCA units mean that there has been a total turnover in the community. Ter Braak and Prentice (1987, p. 122) warn against the non-linear rescaling of the axes due to robustness issues and recommend using detrending-by-polynomials only. == Drawbacks == No significance tests are available with DCA, although there is a constrained (canonical) version called DCCA in which the axes are forced by Multiple linear regression to correlate optimally with a linear combination of other (usually environmental) variables; this allows testing of a null model by Monte-Carlo permutation analysis. == Example == The example shows an ideal data set: The species data is in rows, samples in columns. For each sample along the gradient, a new species is introduced but another species is no longer present. The result is a sparse matrix. Ones indicate the presence of a species in a sample. Except at the edges each sample contains five species. The plot of the first two axes of the correspondence analysis result on the right hand side clearly shows the disadvantages of this procedure: the edge effect, i.e. the points are clustered at the edges of the first axis, and the arch effect. == Software == An open source implementation of DCA, based on the original FORTRAN code, is available in the vegan R-package.
GNU Octave
GNU Octave is a scientific programming language for scientific computing and numerical computation. Among other things, Octave can be used to solve linear and nonlinear problems numerically and to perform other numerical experiments using a language that is mostly compatible with MATLAB. It may also be used as a batch-oriented language. As part of the GNU Project, it is free software under the terms of the GNU General Public License. == History == The project was conceived around 1988. At first it was intended to be a companion to a chemical reactor design course. Full development was started by John W. Eaton in 1992. The first alpha release dates back to 4 January 1993 and on 17 February 1994 version 1.0 was released. Version 9.2.0 was released on 7 June 2024. The program is named after Octave Levenspiel, a former professor of the principal author. Levenspiel was known for his ability to perform quick back-of-the-envelope calculations. == Development history == == Developments == In addition to use on desktops for personal scientific computing, Octave is used in academia and industry. For example, Octave was used on a massive parallel computer at Pittsburgh Supercomputing Center to find vulnerabilities related to guessing social security numbers. Acceleration with OpenCL or CUDA is also possible with use of GPUs. == Technical details == Octave is written in C++ using the C++ standard library. Octave uses an interpreter to execute the Octave scripting language. Octave is extensible using dynamically loadable modules. Octave interpreter has an OpenGL-based graphics engine to create plots, graphs and charts and to save or print them. Alternatively, gnuplot can be used for the same purpose. Octave includes a graphical user interface (GUI) in addition to the traditional command-line interface (CLI); see #User interfaces for details. == Octave, the language == The Octave language is an interpreted programming language. It is a structured programming language (similar to C) and supports many common C standard library functions, and also certain UNIX system calls and functions. However, it does not support passing arguments by reference although function arguments are copy-on-write to avoid unnecessary duplication. Octave programs consist of a list of function calls or a script. The syntax is matrix-based and provides various functions for matrix operations. It supports various data structures and allows object-oriented programming. Its syntax is very similar to MATLAB, and careful programming of a script will allow it to run on both Octave and MATLAB. Because Octave is made available under the GNU General Public License, it may be freely changed, copied and used. The program runs on Microsoft Windows and most Unix and Unix-like operating systems, including Linux, Android, and macOS. == Notable features == === Command and variable name completion === Typing a TAB character on the command line causes Octave to attempt to complete variable, function, and file names (similar to Bash's tab completion). Octave uses the text before the cursor as the initial portion of the name to complete. === Command history === When running interactively, Octave saves the commands typed in an internal buffer so that they can be recalled and edited. === Data structures === Octave includes a limited amount of support for organizing data in structures. In this example, we see a structure x with elements a, b, and c, (an integer, an array, and a string, respectively): === Short-circuit Boolean operators === Octave's && and || logical operators are evaluated in a short-circuit fashion (like the corresponding operators in the C language), in contrast to the element-by-element operators & and |. === Increment and decrement operators === Octave includes the C-like increment and decrement operators ++ and -- in both their prefix and postfix forms. Octave also does augmented assignment, e.g. x += 5. === Unwind-protect === Octave supports a limited form of exception handling modelled after the unwind_protect of Lisp. The general form of an unwind_protect block looks like this: As a general rule, GNU Octave recognizes as termination of a given block either the keyword end (which is compatible with the MATLAB language) or a more specific keyword endblock or, in some cases, end_block. As a consequence, an unwind_protect block can be terminated either with the keyword end_unwind_protect as in the example, or with the more portable keyword end. The cleanup part of the block is always executed. In case an exception is raised by the body part, cleanup is executed immediately before propagating the exception outside the block unwind_protect. GNU Octave also supports another form of exception handling (compatible with the MATLAB language): This latter form differs from an unwind_protect block in two ways. First, exception_handling is only executed when an exception is raised by body. Second, after the execution of exception_handling the exception is not propagated outside the block (unless a rethrow( lasterror ) statement is explicitly inserted within the exception_handling code). === Variable-length argument lists === Octave has a mechanism for handling functions that take an unspecified number of arguments without explicit upper limit. To specify a list of zero or more arguments, use the special argument varargin as the last (or only) argument in the list. varargin is a cell array containing all the input arguments. === Variable-length return lists === A function can be set up to return any number of values by using the special return value varargout. For example: === C++ integration === It is also possible to execute Octave code directly in a C++ program. For example, here is a code snippet for calling rand([10,1]): C and C++ code can be integrated into GNU Octave by creating oct files, or using the MATLAB compatible MEX files. == MATLAB compatibility == Octave has been built with MATLAB compatibility in mind, and shares many features with MATLAB: % Script: myscript.m a = 5; b = a 2 % Function: myfunc.m function result = myfunc(x) result = x^2 + 3; end Matrices as fundamental data type. Built-in support for complex numbers. Powerful built-in math functions and extensive function libraries. Extensibility in the form of user-defined functions. Octave treats incompatibility with MATLAB as a bug; therefore, it could be considered a software clone, which does not infringe software copyright as per Lotus v. Borland court case. MATLAB scripts from the MathWorks' FileExchange repository in principle are compatible with Octave. However, while they are often provided and uploaded by users under an Octave compatible and proper open source BSD license, the FileExchange Terms of use prohibit any usage beside MathWorks' proprietary MATLAB. === Syntax compatibility === There are a few purposeful, albeit minor, syntax additions Archived 2012-04-26 at the Wayback Machine: Comment lines can be prefixed with the # character as well as the % character; Various C-based operators ++, --, +=, =, /= are supported; Elements can be referenced without creating a new variable by cascaded indexing, e.g. [1:10](3); Strings can be defined with the double-quote " character as well as the single-quote ' character; When the variable type is single (a single-precision floating-point number), Octave calculates the "mean" in the single-domain (MATLAB in double-domain) which is faster but gives less accurate results; Blocks can also be terminated with more specific Control structure keywords, i.e., endif, endfor, endwhile, etc.; Functions can be defined within scripts and at the Octave prompt; Presence of a do-until loop (similar to do-while in C). === Function compatibility === Many, but not all, of the numerous MATLAB functions are available in GNU Octave, some of them accessible through packages in Octave Forge. The functions available as part of either core Octave or Forge packages are listed online Archived 2024-03-14 at the Wayback Machine. A list of unavailable functions is included in the Octave function __unimplemented.m__. Unimplemented functions are also listed under many Octave Forge packages in the Octave Wiki. When an unimplemented function is called the following error message is shown: == User interfaces == Octave comes with an official graphical user interface (GUI) and an integrated development environment (IDE) based on Qt. It has been available since Octave 3.8, and has become the default interface (over the command-line interface) with the release of Octave 4.0. It was well-received by an EDN contributor, who wrote "[Octave] now has a very workable GUI" in reviewing the then-new GUI in 2014. Several 3rd-party graphical front-ends have also been developed, like ToolboX for coding education. == GUI applications == With Octave code, the user can create GUI applications. See GUI Development (GNU Octave (version 7.1.0)). Below are some examples: Button, edit control, checkboxTextboxListbox wit
Microscope image processing
Microscope image processing is a broad term that covers the use of digital image processing techniques to process, analyze and present images obtained from a microscope. Such processing is now commonplace in a number of diverse fields such as medicine, biological research, cancer research, drug testing, metallurgy, etc. A number of manufacturers of microscopes now specifically design in features that allow the microscopes to interface to an image processing system. == Image acquisition == Until the early 1990s, most image acquisition in video microscopy applications was typically done with an analog video camera, often simply closed circuit TV cameras. While this required the use of a frame grabber to digitize the images, video cameras provided images at full video frame rate (25-30 frames per second) allowing live video recording and processing. While the advent of solid state detectors yielded several advantages, the real-time video camera was actually superior in many respects. Today, acquisition is usually done using a CCD camera mounted in the optical path of the microscope. The camera may be full colour or monochrome. Very often, very high resolution cameras are employed to gain as much direct information as possible. Cryogenic cooling is also common, to minimise noise. Often digital cameras used for this application provide pixel intensity data to a resolution of 12-16 bits, much higher than is used in consumer imaging products. Ironically, in recent years, much effort has been put into acquiring data at video rates, or higher (25-30 frames per second or higher). What was once easy with off-the-shelf video cameras now requires special, high speed electronics to handle the vast digital data bandwidth. Higher speed acquisition allows dynamic processes to be observed in real time, or stored for later playback and analysis. Combined with the high image resolution, this approach can generate vast quantities of raw data, which can be a challenge to deal with, even with a modern computer system. While current CCD detectors allow very high image resolution, often this involves a trade-off because, for a given chip size, as the pixel count increases, the pixel size decreases. As the pixels get smaller, their well depth decreases, reducing the number of electrons that can be stored. In turn, this results in a poorer signal-to-noise ratio. For best results, one must select an appropriate sensor for a given application. Because microscope images have an intrinsic limiting resolution, it often makes little sense to use a noisy, high resolution detector for image acquisition. A more modest detector, with larger pixels, can often produce much higher quality images because of reduced noise. This is especially important in low-light applications such as fluorescence microscopy. Moreover, one must also consider the temporal resolution requirements of the application. A lower resolution detector will often have a significantly higher acquisition rate, permitting the observation of faster events. Conversely, if the observed object is motionless, one may wish to acquire images at the highest possible spatial resolution without regard to the time required to acquire a single image. == 2D image techniques == Image processing for microscopy application begins with fundamental techniques intended to most accurately reproduce the information contained in the microscopic sample. This might include adjusting the brightness and contrast of the image, averaging images to reduce image noise and correcting for illumination non-uniformities. Such processing involves only basic arithmetic operations between images (i.e. addition, subtraction, multiplication and division). The vast majority of processing done on microscope image is of this nature. Another class of common 2D operations called image convolution are often used to reduce or enhance image details. Such "blurring" and "sharpening" algorithms in most programs work by altering a pixel's value based on a weighted sum of that and the surrounding pixels (a more detailed description of kernel based convolution deserves an entry for itself) or by altering the frequency domain function of the image using Fourier Transform. Most image processing techniques are performed in the Frequency domain. Other basic two dimensional techniques include operations such as image rotation, warping, color balancing etc. At times, advanced techniques are employed with the goal of "undoing" the distortion of the optical path of the microscope, thus eliminating distortions and blurring caused by the instrumentation. This process is called deconvolution, and a variety of algorithms have been developed, some of great mathematical complexity. The end result is an image far sharper and clearer than could be obtained in the optical domain alone. This is typically a 3-dimensional operation, that analyzes a volumetric image (i.e. images taken at a variety of focal planes through the sample) and uses this data to reconstruct a more accurate 3-dimensional image. == 3D image techniques == Another common requirement is to take a series of images at a fixed position, but at different focal depths. Since most microscopic samples are essentially transparent, and the depth of field of the focused sample is exceptionally narrow, it is possible to capture images "through" a three-dimensional object using 2D equipment like confocal microscopes. Software is then able to reconstruct a 3D model of the original sample which may be manipulated appropriately. The processing turns a 2D instrument into a 3D instrument, which would not otherwise exist. In recent times this technique has led to a number of scientific discoveries in cell biology. == Analysis == Analysis of images will vary considerably according to application. Typical analysis includes determining where the edges of an object are, counting similar objects, calculating the area, perimeter length and other useful measurements of each object. A common approach is to create an image mask which only includes pixels that match certain criteria, then perform simpler scanning operations on the resulting mask. It is also possible to label objects and track their motion over a series of frames in a video sequence.
Relief (feature selection)
Relief is an algorithm developed by Kenji Kira and Larry Rendell in 1992 that takes a filter-method approach to feature selection that is notably sensitive to feature interactions. It was originally designed for application to binary classification problems with discrete or numerical features. Relief calculates a feature score for each feature which can then be applied to rank and select top scoring features for feature selection. Alternatively, these scores may be applied as feature weights to guide downstream modeling. Relief feature scoring is based on the identification of feature value differences between nearest neighbor instance pairs. If a feature value difference is observed in a neighboring instance pair with the same class (a 'hit'), the feature score decreases. Alternatively, if a feature value difference is observed in a neighboring instance pair with different class values (a 'miss'), the feature score increases. The original Relief algorithm has since inspired a family of Relief-based feature selection algorithms (RBAs), including the ReliefF algorithm. Beyond the original Relief algorithm, RBAs have been adapted to (1) perform more reliably in noisy problems, (2) generalize to multi-class problems (3) generalize to numerical outcome (i.e. regression) problems, and (4) to make them robust to incomplete (i.e. missing) data. To date, the development of RBA variants and extensions has focused on four areas; (1) improving performance of the 'core' Relief algorithm, i.e. examining strategies for neighbor selection and instance weighting, (2) improving scalability of the 'core' Relief algorithm to larger feature spaces through iterative approaches, (3) methods for flexibly adapting Relief to different data types, and (4) improving Relief run efficiency. Their strengths are that they are not dependent on heuristics, they run in low-order polynomial time, and they are noise-tolerant and robust to feature interactions, as well as being applicable for binary or continuous data; however, it does not discriminate between redundant features, and low numbers of training instances fool the algorithm. == Relief Algorithm == Take a data set with n instances of p features, belonging to two known classes. Within the data set, each feature should be scaled to the interval [0 1] (binary data should remain as 0 and 1). The algorithm will be repeated m times. Start with a p-long weight vector (W) of zeros. At each iteration, take the feature vector (X) belonging to one random instance, and the feature vectors of the instance closest to X (by Euclidean distance) from each class. The closest same-class instance is called 'near-hit', and the closest different-class instance is called 'near-miss'. Update the weight vector such that W i = W i − ( x i − n e a r H i t i ) 2 + ( x i − n e a r M i s s i ) 2 , {\displaystyle W_{i}=W_{i}-(x_{i}-\mathrm {nearHit} _{i})^{2}+(x_{i}-\mathrm {nearMiss} _{i})^{2},} where i {\displaystyle i} indexes the components and runs from 1 to p. Thus the weight of any given feature decreases if it differs from that feature in nearby instances of the same class more than nearby instances of the other class, and increases in the reverse case. After m iterations, divide each element of the weight vector by m. This becomes the relevance vector. Features are selected if their relevance is greater than a threshold τ. Kira and Rendell's experiments showed a clear contrast between relevant and irrelevant features, allowing τ to be determined by inspection. However, it can also be determined by Chebyshev's inequality for a given confidence level (α) that a τ of 1/sqrt(αm) is good enough to make the probability of a Type I error less than α, although it is stated that τ can be much smaller than that. Relief was also described as generalizable to multinomial classification by decomposition into a number of binary problems. == ReliefF Algorithm == Kononenko et al. propose a number of updates to Relief. Firstly, they find the near-hit and near-miss instances using the Manhattan (L1) norm rather than the Euclidean (L2) norm, although the rationale is not specified. Furthermore, they found taking the absolute differences between xi and near-hiti, and xi and near-missi to be sufficient when updating the weight vector (rather than the square of those differences). === Reliable probability estimation === Rather than repeating the algorithm m times, implement it exhaustively (i.e. n times, once for each instance) for relatively small n (up to one thousand). Furthermore, rather than finding the single nearest hit and single nearest miss, which may cause redundant and noisy attributes to affect the selection of the nearest neighbors, ReliefF searches for k nearest hits and misses and averages their contribution to the weights of each feature. k can be tuned for any individual problem. === Incomplete data === In ReliefF, the contribution of missing values to the feature weight is determined using the conditional probability that two values should be the same or different, approximated with relative frequencies from the data set. This can be calculated if one or both features are missing. === Multi-class problems === Rather than use Kira and Rendell's proposed decomposition of a multinomial classification into a number of binomial problems, ReliefF searches for k near misses from each different class and averages their contributions for updating W, weighted with the prior probability of each class. == Other Relief-based Algorithm Extensions/Derivatives == The following RBAs are arranged chronologically from oldest to most recent. They include methods for improving (1) the core Relief algorithm concept, (2) iterative approaches for scalability, (3) adaptations to different data types, (4) strategies for computational efficiency, or (5) some combination of these goals. For more on RBAs see these book chapters or this most recent review paper. === RRELIEFF === Robnik-Šikonja and Kononenko propose further updates to ReliefF, making it appropriate for regression. === Relieved-F === Introduced deterministic neighbor selection approach and a new approach for incomplete data handling. === Iterative Relief === Implemented method to address bias against non-monotonic features. Introduced the first iterative Relief approach. For the first time, neighbors were uniquely determined by a radius threshold and instances were weighted by their distance from the target instance. === I-RELIEF === Introduced sigmoidal weighting based on distance from target instance. All instance pairs (not just a defined subset of neighbors) contributed to score updates. Proposed an on-line learning variant of Relief. Extended the iterative Relief concept. Introduced local-learning updates between iterations for improved convergence. === TuRF (a.k.a. Tuned ReliefF) === Specifically sought to address noise in large feature spaces through the recursive elimination of features and the iterative application of ReliefF. === Evaporative Cooling ReliefF === Similarly seeking to address noise in large feature spaces. Utilized an iterative `evaporative' removal of lowest quality features using ReliefF scores in association with mutual information. === EReliefF (a.k.a. Extended ReliefF) === Addressing issues related to incomplete and multi-class data. === VLSReliefF (a.k.a. Very Large Scale ReliefF) === Dramatically improves the efficiency of detecting 2-way feature interactions in very large feature spaces by scoring random feature subsets rather than the entire feature space. === ReliefMSS === Introduced calculation of feature weights relative to average feature 'diff' between instance pairs. === SURF === SURF identifies nearest neighbors (both hits and misses) based on a distance threshold from the target instance defined by the average distance between all pairs of instances in the training data. Results suggest improved power to detect 2-way epistatic interactions over ReliefF. === SURF (a.k.a. SURFStar) === SURF extends the SURF algorithm to not only utilized 'near' neighbors in scoring updates, but 'far' instances as well, but employing inverted scoring updates for 'far instance pairs. Results suggest improved power to detect 2-way epistatic interactions over SURF, but an inability to detect simple main effects (i.e. univariate associations). === SWRF === SWRF extends the SURF algorithm adopting sigmoid weighting to take distance from the threshold into account. Also introduced a modular framework for further developing RBAs called MoRF. === MultiSURF (a.k.a. MultiSURFStar) === MultiSURF extends the SURF algorithm adapting the near/far neighborhood boundaries based on the average and standard deviation of distances from the target instance to all others. MultiSURF uses the standard deviation to define a dead-band zone where 'middle-distance' instances do not contribute to scoring. Evidence suggests MultiSURF performs best in detecting pure 2-way feature interactions. === Reli