In bioinformatics, GLIMMER (Gene Locator and Interpolated Markov ModelER) is used to find genes in prokaryotic DNA. "It is effective at finding genes in bacteria, archea, viruses, typically finding 98-99% of all relatively long protein coding genes". GLIMMER was the first system that used the interpolated Markov model to identify coding regions. The GLIMMER software is open source and is maintained by Steven Salzberg, Art Delcher, and their colleagues at the Center for Computational Biology at Johns Hopkins University. The original GLIMMER algorithms and software were designed by Art Delcher, Simon Kasif and Steven Salzberg and applied to bacterial genome annotation in collaboration with Owen White. == Versions == === GLIMMER 1.0 === First Version of GLIMMER "i.e., GLIMMER 1.0" was released in 1998 and it was published in the paper Microbial gene identification using interpolated Markov model. Markov models were used to identify microbial genes in GLIMMER 1.0. GLIMMER considers the local composition sequence dependencies which makes GLIMMER more flexible and more powerful when compared to fixed-order Markov model. There was a comparison made between interpolated Markov model used by GLIMMER and fifth order Markov model in the paper Microbial gene identification using interpolated Markov models. "GLIMMER algorithm found 1680 genes out of 1717 annotated genes in Haemophilus influenzae where fifth order Markov model found 1574 genes. GLIMMER found 209 additional genes which were not included in 1717 annotated genes where fifth order Markov model found 104 genes."' === GLIMMER 2.0 === Second Version of GLIMMER i.e., GLIMMER 2.0 was released in 1999 and it was published in the paper Improved microbial identification with GLIMMER. This paper provides significant technical improvements such as using interpolated context model instead of interpolated Markov model and resolving overlapping genes which improves the accuracy of GLIMMER. Interpolated context models are used instead of interpolated Markov model which gives the flexibility to select any base. In interpolated Markov model probability distribution of a base is determined from the immediate preceding bases. If the immediate preceding base is irrelevant amino acid translation, interpolated Markov model still considers the preceding base to determine the probability of given base where as interpolated context model which was used in GLIMMER 2.0 can ignore irrelevant bases. False positive predictions were increased in GLIMMER 2.0 to reduce the number of false negative predictions. Overlapped genes are also resolved in GLIMMER 2.0. Various comparisons between GLIMMER 1.0 and GLIMMER 2.0 were made in the paper Improved microbial identification with GLIMMER which shows improvement in the later version. "Sensitivity of GLIMMER 1.0 ranges from 98.4 to 99.7% with an average of 99.1% where as GLIMMER 2.0 has a sensitivity range from 98.6 to 99.8% with an average of 99.3%. GLIMMER 2.0 is very effective in finding genes of high density. The parasite Trypanosoma brucei, responsible for causing African sleeping sickness is being identified by GLIMMER 2.0" === GLIMMER 3.0 === Third version of GLIMMER, "GLIMMER 3.0" was released in 2007 and it was published in the paper Identifying bacterial genes and endosymbiont DNA with Glimmer. This paper describes several major changes made to the GLIMMER system including improved methods to identify coding regions and start codon. Scoring of ORF in GLIMMER 3.0 is done in reverse order i.e., starting from stop codon and moves back towards the start codon. Reverse scanning helps in identifying the coding portion of the gene more accurately which is contained in the context window of IMM. GLIMMER 3.0 also improves the generated training set data by comparing the long-ORF with universal amino acid distribution of widely disparate bacterial genomes."GLIMMER 3.0 has an average long-ORF output of 57% for various organisms where as GLIMMER 2.0 has an average long-ORF output of 39%." GLIMMER 3.0 reduces the rate of false positive predictions which were increased in GLIMMER 2.0 to reduce the number of false negative predictions. "GLIMMER 3.0 has a start-site prediction accuracy of 99.5% for 3'5' matches where as GLIMMER 2.0 has 99.1% for 3'5' matches. GLIMMER 3.0 uses a new algorithm for scanning coding regions, a new start site detection module, and architecture which integrates all gene predictions across an entire genome." Minimum description length === Theoretical and Biological Foundation === The GLIMMER project helped introduce and popularize the use of variable length models in Computational Biology and Bioinformatics that subsequently have been applied to numerous problems such as protein classification and others. Variable length modeling was originally pioneered by information theorists and subsequently ingeniously applied and popularized in data compression (e.g. Ziv-Lempel compression). Prediction and compression are intimately linked using Minimum Description Length Principles. The basic idea is to create a dictionary of frequent words (motifs in biological sequences). The intuition is that the frequently occurring motifs are likely to be most predictive and informative. In GLIMMER the interpolated model is a mixture model of the probabilities of these relatively common motifs. Similarly to the development of HMMs in Computational Biology, the authors of GLIMMER were conceptually influenced by the previous application of another variant of interpolated Markov models to speech recognition by researchers such as Fred Jelinek (IBM) and Eric Ristad (Princeton). The learning algorithm in GLIMMER is different from these earlier approaches. == Access == GLIMMER can be downloaded from The Glimmer home page (requires a C++ compiler). Alternatively, an online version is hosted by NCBI [1]. == How it works == GLIMMER primarily searches for long-ORFS. An open reading frame might overlap with any other open reading frame which will be resolved using the technique described in the sub section. Using these long-ORFS and following certain amino acid distribution GLIMMER generates training set data. Using these training data, GLIMMER trains all the six Markov models of coding DNA from zero to eight order and also train the model for noncoding DNA GLIMMER tries to calculate the probabilities from the data. Based on the number of observations, GLIMMER determines whether to use fixed order Markov model or interpolated Markov model. If the number of observations are greater than 400, GLIMMER uses fixed order Markov model to obtain there probabilities. If the number of observations are less than 400, GLIMMER uses interpolated Markov model which is briefly explained in the next sub section. GLIMMER obtains score for every long-ORF generated using all the six coding DNA models and also using non-coding DNA model. If the score obtained in the previous step is greater than a certain threshold then GLIMMER predicts it to be a gene. The steps explained above describes the basic functionality of GLIMMER. There are various improvements made to GLIMMER and some of them are described in the following sub-sections. === The GLIMMER system === GLIMMER system consists of two programs. First program called build-imm, which takes an input set of sequences and outputs the interpolated Markov model as follows. The probability for each base i.e., A,C,G,T for all k-mers for 0 ≤ k ≤ 8 is computed. Then, for each k-mer, GLIMMER computes weight. New sequence probability is computed as follows. where n is the length of the sequence S x {\displaystyle S_{x}} is the oligomer at position x. I M M 8 ( S x ) {\displaystyle IMM_{8}(S_{x})} , the 8 t h {\displaystyle 8^{th}} -order interpolated Markov model score is computed as "where Y k ( S x − 1 ) {\displaystyle Y_{k}(S_{x-1})} is the weight of the k-mer at position x-1 in the sequence S and P k ( S x ) {\displaystyle P_{k}(S_{x})} is the estimate obtained from the training data of the probability of the base located at position x in the k t h {\displaystyle k^{th}} -order model." The probability of base S x {\displaystyle S_{x}} given the i previous bases is computed as follows. "The value of Y i ( S x ) {\displaystyle Y_{i}(S_{x})} associated with P i ( S x ) {\displaystyle P_{i}(S_{x})} can be regarded as a measure of confidence in the accuracy of this value as an estimate of the true probability. GLIMMER uses two criteria to determine Y i ( S x ) {\displaystyle Y_{i}(S_{x})} . The first of these is simple frequency occurrence in which the number of occurrences of context string S x , i {\displaystyle S_{x,i}} in the training data exceeds a specific threshold value, then Y i ( S x ) {\displaystyle Y_{i}(S_{x})} is set to 1.0. The current default value for threshold is 400, which gives 95% confidence. When there are insufficient sample occurrences of a context string, build-imm employ additional criteria to determine Y {\displaystyle Y} value. For a
Quantum natural language processing
Quantum natural language processing (QNLP) is the application of quantum computing to natural language processing (NLP). It computes word embeddings as parameterised quantum circuits that can solve NLP tasks faster than any classical computer. It is inspired by categorical quantum mechanics and the DisCoCat framework, making use of string diagrams to translate from grammatical structure to quantum processes. == Theory == The first quantum algorithm for natural language processing used the DisCoCat framework and Grover's algorithm to show a quadratic quantum speedup for a text classification task. It was later shown that quantum language processing is BQP-Complete, i.e. quantum language models are more expressive than their classical counterpart, unless quantum mechanics can be efficiently simulated by classical computers. These two theoretical results assume fault-tolerant quantum computation and a QRAM, i.e. an efficient way to load classical data on a quantum computer. Thus, they are not applicable to the noisy intermediate-scale quantum (NISQ) computers available today. == Experiments == The algorithm of Zeng and Coecke was adapted to the constraints of NISQ computers and implemented on IBM quantum computers to solve binary classification tasks. Instead of loading classical word vectors onto a quantum memory, the word vectors are computed directly as the parameters of quantum circuits. These parameters are optimised using methods from quantum machine learning to solve data-driven tasks such as question answering, machine translation and even algorithmic music composition.
Concept class
In computational learning theory in mathematics, a concept over a domain X is a total Boolean function over X. A concept class is a class of concepts. Concept classes are a subject of computational learning theory. Concept class terminology frequently appears in model theory associated with probably approximately correct (PAC) learning. In this setting, if one takes a set Y as a set of (classifier output) labels, and X is a set of examples, the map c : X → Y {\displaystyle c:X\to Y} , i.e. from examples to classifier labels (where Y = { 0 , 1 } {\displaystyle Y=\{0,1\}} and where c is a subset of X), c is then said to be a concept. A concept class C {\displaystyle C} is then a collection of such concepts. Given a class of concepts C, a subclass D is reachable if there exists a sample s such that D contains exactly those concepts in C that are extensions to s. Not every subclass is reachable. == Background == A sample s {\displaystyle s} is a partial function from X {\displaystyle X} to { 0 , 1 } {\displaystyle \{0,1\}} . Identifying a concept with its characteristic function mapping X {\displaystyle X} to { 0 , 1 } {\displaystyle \{0,1\}} , it is a special case of a sample. Two samples are consistent if they agree on the intersection of their domains. A sample s ′ {\displaystyle s'} extends another sample s {\displaystyle s} if the two are consistent and the domain of s {\displaystyle s} is contained in the domain of s ′ {\displaystyle s'} . == Examples == Suppose that C = S + ( X ) {\displaystyle C=S^{+}(X)} . Then: the subclass { { x } } {\displaystyle \{\{x\}\}} is reachable with the sample s = { ( x , 1 ) } {\displaystyle s=\{(x,1)\}} ; the subclass S + ( Y ) {\displaystyle S^{+}(Y)} for Y ⊆ X {\displaystyle Y\subseteq X} are reachable with a sample that maps the elements of X − Y {\displaystyle X-Y} to zero; the subclass S ( X ) {\displaystyle S(X)} , which consists of the singleton sets, is not reachable. == Applications == Let C {\displaystyle C} be some concept class. For any concept c ∈ C {\displaystyle c\in C} , we call this concept 1 / d {\displaystyle 1/d} -good for a positive integer d {\displaystyle d} if, for all x ∈ X {\displaystyle x\in X} , at least 1 / d {\displaystyle 1/d} of the concepts in C {\displaystyle C} agree with c {\displaystyle c} on the classification of x {\displaystyle x} . The fingerprint dimension F D ( C ) {\displaystyle FD(C)} of the entire concept class C {\displaystyle C} is the least positive integer d {\displaystyle d} such that every reachable subclass C ′ ⊆ C {\displaystyle C'\subseteq C} contains a concept that is 1 / d {\displaystyle 1/d} -good for it. This quantity can be used to bound the minimum number of equivalence queries needed to learn a class of concepts according to the following inequality: F D ( C ) − 1 ≤ # E Q ( C ) ≤ ⌈ F D ( C ) ln ( | C | ) ⌉ {\textstyle FD(C)-1\leq \#EQ(C)\leq \lceil FD(C)\ln(|C|)\rceil } .
Tensor product network
A tensor product network, in artificial neural networks, is a network that exploits the properties of tensors to model associative concepts such as variable assignment. Orthonormal vectors are chosen to model the ideas (such as variable names and target assignments), and the tensor product of these vectors construct a network whose mathematical properties allow the user to easily extract the association from it.
Ground truth
Ground truth is information that is known to be real or true, provided by direct observation and measurement (i.e. empirical evidence) as opposed to information provided by inference. The term ground truth appeared in remote sensing literature as early as 1972, when NASA described it as essential "data about ... materials on the earth's surface" used to calibrate measurements. It was later adopted by the statistical modeling and machine learning communities. == Etymology == The Oxford English Dictionary (s.v. ground truth) records the use of the word Groundtruth in the sense of 'fundamental truth' from Henry Ellison's poem "The Siberian Exile's Tale", published in 1833. == Usage == The term "ground truth" can be used as a noun, adjective, and verb. Noun: "ground truth" (no hyphen). Example: "The ground truth is essential for training accurate models." Adjective: "ground-truth" (hyphenated compound adjective). Example: "We need to use ground-truth data to validate the model." Verb: "to ground-truth" or "to groundtruth" (compound verb,). Example: "We need to ground-truth the results to ensure their accuracy." == Statistics and machine learning == In statistics and machine learning, ground truth is the ideal expected result, used in statistical models to prove or disprove research hypotheses. "Ground truthing" is the process of gathering the good data for this test. Ground truth is typically included in labeled data. In machine learning, "ground truth" is not necessarily objectively correct or true. For example, in training AI models or relevance rankers, it may be a set of judgments made by people or inferred from user behavior, which may depend on context. For example, in Bayesian spam filtering, a supervised learning system is typically trained by examples labeled as spam and non-spam. Although these labels may be subjective or inaccurate, they are considered ground truth. True ground truth in machine learning is objective data. For example, suppose we are testing a stereo vision system to see how well it can estimate 3D positions. A calibrated laser rangefinder may provide accurate distances as ground truth. == Remote sensing == In remote sensing, "ground truth" refers to information collected at the imaged location. Ground truth allows image data to be related to real features and materials on the ground. The collection of ground truth data enables calibration of remote-sensing data, and aids in the interpretation and analysis of what is being sensed. Examples include cartography, meteorology, analysis of aerial photographs, satellite imagery and other techniques in which data are gathered at a distance. More specifically, ground truth may refer to a process in which "pixels" on a satellite image are compared to what is imaged (at the time of capture) in order to verify the contents of the "pixels" in the image (noting that the concept of "pixel" is imaging-system-dependent). In the case of a classified image, supervised classification can help to determine the accuracy of the classification by the remote sensing system which can minimize error in the classification. Ground truth is usually done on site, correlating what is known with surface observations and measurements of various properties of the features of the ground resolution cells under study in the remotely sensed digital image. The process also involves taking geographic coordinates of the ground resolution cell with GPS technology and comparing those with the coordinates of the "pixel" being studied provided by the remote sensing software to understand and analyze the location errors and how it may affect a particular study. Ground truth is important in the initial supervised classification of an image. When the identity and location of land cover types are known through a combination of field work, maps, and personal experience these areas are known as training sites. The spectral characteristics of these areas are used to train the remote sensing software using decision rules for classifying the rest of the image. These decision rules such as Maximum Likelihood Classification, Parallelopiped Classification, and Minimum Distance Classification offer different techniques to classify an image. Additional ground truth sites allow the remote sensor to establish an error matrix that validates the accuracy of the classification method used. Different classification methods may have different percentages of error for a given classification project. It is important that the remote sensor chooses a classification method that works best with the number of classifications used while providing the least amount of error. Ground truth also helps with atmospheric correction. Since images from satellites have to pass through the atmosphere, they can get distorted because of absorption in the atmosphere. So ground truth can help fully identify objects in satellite photos. === Errors of commission === An example of an error of commission is when a pixel reports the presence of a feature (such a tree) that, in reality, is absent (no tree is actually present). Ground truthing ensures that the error matrices have a higher accuracy percentage than would be the case if no pixels were ground-truthed. This value is the complement of the user's accuracy, i.e. Commission Error = 1 - user's accuracy. === Errors of omission === An example of an error of omission is when pixels of a certain type, for example, maple trees, are not classified as maple trees. The process of ground-truthing helps to ensure that the pixel is classified correctly and the error matrices are more accurate. This value is the complement of the producer's accuracy, i.e. Omission Error = 1 - producer's accuracy == Geographical information systems == In GIS the spatial data is modeled as field (like in remote sensing raster images) or as object (like in vectorial map representation). They are modeled from the real world (also named geographical reality), typically by a cartographic process (illustrated). Geographic information systems such as GIS, GPS, and GNSS, have become so widespread that the term "ground truth" has taken on special meaning in that context. If the location coordinates returned by a location method such as GPS are an estimate of a location, then the "ground truth" is the actual location on Earth. A smart phone might return a set of estimated location coordinates such as 43.87870, −103.45901. The ground truth being estimated by those coordinates is the tip of George Washington's nose on Mount Rushmore. The accuracy of the estimate is the maximum distance between the location coordinates and the ground truth. We could say in this case that the estimate accuracy is 10 meters, meaning that the point on Earth represented by the location coordinates is thought to be within 10 meters of George's nose—the ground truth. In slang, the coordinates indicate where we think George Washington's nose is located, and the ground truth is where it really is. In practice a smart phone or hand-held GPS unit is routinely able to estimate the ground truth within 6–10 meters. Specialized instruments can reduce GPS measurement error to under a centimeter. == Military usage == US military slang uses "ground truth" to refer to the facts comprising a tactical situation—as opposed to intelligence reports, mission plans, and other descriptions reflecting the conative or policy-based projections of the industrial·military complex. The term appears in the title of the Iraq War documentary film The Ground Truth (2006), and also in military publications, for example Stars and Stripes saying: "Stripes decided to figure out what the ground truth was in Iraq."
Bitstrips
Bitstrips, Inc. was a Canadian media and technology company based in Toronto, founded in 2007 by Jacob Blackstock, David Kennedy, Shahan Panth, Dorian Baldwin, and Jesse Brown. The company created and offered a web application, Bitstrips.com, which allowed users to create comic strips using personalized avatars, and preset templates and poses. Brown and Blackstock explained that the service was meant to enable self-expression without the need to have artistic skills. Bitstrips was first presented in 2008 at South by Southwest in Austin, Texas, and the service later piloted and launched a version designed for use as educational software. The service achieved increasing prominence following the launch of versions for Facebook and mobile platforms. In 2014, Bitstrips launched a spin-off app known as Bitmoji, which allows users to create personalized stickers for use in instant messaging. In July 2016, Snapchat Inc. announced that it had acquired the company; the Bitstrips comic service was shut down, but Bitmoji remains operational, and has subsequently been given greater prominence within Snapchat's overall platform. == History == Bitstrips was co-developed by Toronto-based comic artist Jacob Blackstock and his high school friend, journalist Jesse Brown. The service was originally envisioned as a means to allow anyone to create their own comic strip without needing artistic skills. Brown explained that "it's so difficult and time-consuming to tell a story in comic book form, drawing the same characters again and again in these tiny little panels, and just the amount of craftsmanship required. And even if you can do it well, which I never could, it takes years to make a story." Brown stated that the service would be "groundwork for a whole new way to communicate", and went as far as describing the service as being a "YouTube for comics". Blackstock explained that the concept of Bitstrips was influenced by his own use of comics as a form of socialization; a student, Blackstock and his friends drew comics featuring each other and shared them during classes. He felt that Bitstrips was a "medium for self-expression", stating that "It's not just about you making the comics, but since you and your friends star in these comics, it's like you're the medium. The visual nature of comics just speaks so much louder than text." The service was publicly unveiled at South by Southwest in 2008. In 2009, the service introduced a version oriented towards the educational market, Bitstrips for Schools, which was initially piloted at a number of schools in Ontario. The service was praised by educators for being engaging to students, especially within language classes. Brown noted that students were using the service to create comics outside of class as well, stating that it was "so gratifying and shocking what people do with your tool to make their own stories in ways that you never would have anticipated. Some of them are just brilliant." In December 2012, Bitstrips launched a version for Facebook; by July 2013, Bitstrips had 10 million unique users on Facebook, having created over 50 million comics. In October 2013, Bitstrips launched a mobile app; in two months, Bitstrips became a top-downloaded app in 40 countries, and over 30 million avatars had been created with it. In November 2013, Bitstrips secured a round of funding from Horizons Ventures and Li Ka-shing. In October 2014, Bitstrips launched Bitmoji, a spin-off app that allows users to create stickers featuring Bitstrips characters in various templates. In July 2016, following unconfirmed reports earlier in the year, Snapchat Inc. announced that it had acquired Bitstrips. The company's staff continue to operate out of Toronto, but the original Bitstrips comic service was shut down in favour of focusing exclusively on Bitmoji, leaving many Bitstrips users to call for a reboot of the comic service.
Effective fitness
In natural evolution and artificial evolution (e.g. artificial life and evolutionary computation) the fitness (or performance or objective measure) of a schema is rescaled to give its effective fitness which takes into account crossover and mutation. Effective fitness is used in Evolutionary Computation to understand population dynamics. While a biological fitness function only looks at reproductive success, an effective fitness function tries to encompass things that are needed to be fulfilled for survival on population level. In homogeneous populations, reproductive fitness and effective fitness are equal. When a population moves away from homogeneity a higher effective fitness is reached for the recessive genotype. This advantage will decrease while the population moves toward an equilibrium. The deviation from this equilibrium displays how close the population is to achieving a steady state. When this equilibrium is reached, the maximum effective fitness of the population is achieved. Problem solving with evolutionary computation is realized with a cost function. If cost functions are applied to swarm optimization they are called a fitness function. Strategies like reinforcement learning and NEAT neuroevolution are creating a fitness landscape which describes the reproductive success of cellular automata. The effective fitness function models the number of fit offspring and is used in calculations that include evolutionary processes, such as mutation and crossover, important on the population level. The effective fitness model is superior to its predecessor, the standard reproductive fitness model. It advances in the qualitatively and quantitatively understanding of evolutionary concepts like bloat, self-adaptation, and evolutionary robustness. While reproductive fitness only looks at pure selection, effective fitness describes the flow of a population and natural selection by taking genetic operators into account. A normal fitness function fits to a problem, while an effective fitness function is an assumption if the objective was reached. The difference is important for designing fitness functions with algorithms like novelty search in which the objective of the agents is unknown. In the case of bacteria effective fitness could include production of toxins and rate of mutation of different plasmids, which are mostly stochastically determined == Applications == When evolutionary equations of the studied population dynamics are available, one can algorithmically compute the effective fitness of a given population. Though the perfect effective fitness model is yet to be found, it is already known to be a good framework to the better understanding of the moving of the genotype-phenotype map, population dynamics, and the flow on fitness landscapes. Models using a combination of Darwinian fitness functions and effective functions are better at predicting population trends. Effective models could be used to determine therapeutic outcomes of disease treatment. Other models could determine effective protein engineering and works towards finding novel or heightened biochemistry.