AI Detector Winston

AI Detector Winston — independent reviews, comparisons, pricing and step-by-step guides on Aizhi.

  • 1.58-bit large language model

    1.58-bit large language model

    A 1.58-bit large language model (also known as a ternary LLM) is a type of large language model (LLM) designed to be computationally efficient. It achieves this by using weights that are restricted to only three values: -1, 0, and +1. This restriction significantly reduces the model's memory footprint and allows for faster processing, as computationally expensive multiplication operations can be replaced with lower-cost additions. This contrasts with traditional models that use 16-bit floating-point numbers (FP16 or BF16) for their weights. Studies have shown that for models up to several billion parameters, the performance of 1.58-bit LLMs on various tasks is comparable to their full-precision counterparts. This approach could enable powerful AI to run on less specialized and lower-power hardware. The name "1.58-bit" comes from the fact that a system with three states contains log 2 ⁡ 3 ≈ 1.58 {\displaystyle \log _{2}3\approx 1.58} bits of information. These models are sometimes also referred to as 1-bit LLMs in research papers, although this term can also refer to true binary models (with weights of -1 and +1). == BitNet == In 2024, Ma et al., researchers at Microsoft, declared that their 1.58-bit model, BitNet b1.58 is comparable in performance to the 16-bit Llama 2 and opens the era of 1-bit LLM. BitNet creators did not use the post-training quantization of weights but instead relied on the new BitLinear transform that replaced the nn.Linear layer of the traditional transformer design. In 2025, Microsoft researchers had released an open-weights and open inference code model BitNet b1.58 2B4T demonstrating performance competitive with the full precision models at 2B parameters and 4T training tokens. == Post-training quantization == BitNet derives its performance from being trained natively in 1.58 bit instead of being quantized from a full-precision model after training. Still, training is an expensive process and it would be desirable to be able to somehow convert an existing model to 1.58 bits. In 2024, HuggingFace reported a way to gradually ramp up the 1.58-bit quantization in fine-tuning an existing model down to 1.58 bits. == Critique == Some researchers point out that the scaling laws of large language models favor the low-bit weights only in case of undertrained models. As the number of training tokens increases, the deficiencies of low-bit quantization surface.

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  • Rprop

    Rprop

    Rprop, short for resilient backpropagation, is a learning heuristic for supervised learning in feedforward artificial neural networks. This is a first-order optimization algorithm. This algorithm was created by Martin Riedmiller and Heinrich Braun in 1992. Similarly to the Manhattan update rule, Rprop takes into account only the sign of the partial derivative over all patterns (not the magnitude), and acts independently on each "weight". For each weight, if there was a sign change of the partial derivative of the total error function compared to the last iteration, the update value for that weight is multiplied by a factor η−, where η− < 1. If the last iteration produced the same sign, the update value is multiplied by a factor of η+, where η+ > 1. The update values are calculated for each weight in the above manner, and finally each weight is changed by its own update value, in the opposite direction of that weight's partial derivative, so as to minimise the total error function. η+ is empirically set to 1.2 and η− to 0.5. Rprop can result in very large weight increments or decrements if the gradients are large, which is a problem when using mini-batches as opposed to full batches. RMSprop addresses this problem by keeping the moving average of the squared gradients for each weight and dividing the gradient by the square root of the mean square. RPROP is a batch update algorithm. Next to the cascade correlation algorithm and the Levenberg–Marquardt algorithm, Rprop is one of the fastest weight update mechanisms. == Variations == Martin Riedmiller developed three algorithms, all named RPROP. Igel and Hüsken assigned names to them and added a new variant: RPROP+ is defined at A Direct Adaptive Method for Faster Backpropagation Learning: The RPROP Algorithm. RPROP− is defined at Advanced Supervised Learning in Multi-layer Perceptrons – From Backpropagation to Adaptive Learning Algorithms. Backtracking is removed from RPROP+. iRPROP− is defined in Rprop – Description and Implementation Details and was reinvented by Igel and Hüsken. This variant is very popular and most simple. iRPROP+ is defined at Improving the Rprop Learning Algorithm and is very robust and typically faster than the other three variants.

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  • Perceptron

    Perceptron

    In machine learning, the perceptron is an algorithm for supervised learning of binary classifiers. A binary classifier is a function that can decide whether or not an input, represented by a vector of numbers, belongs to some specific class. It is a type of linear classifier, i.e. a classification algorithm that makes its predictions based on a linear predictor function combining a set of weights with the feature vector. == History == The artificial neuron and artificial neural network were invented in 1943 by Warren McCulloch and Walter Pitts in their seminal paper "A Logical Calculus of the Ideas Immanent in Nervous Activity". In 1957, Frank Rosenblatt was at the Cornell Aeronautical Laboratory. He simulated the perceptron on an IBM 704. Later, he obtained funding by the Information Systems Branch of the United States Office of Naval Research and the Rome Air Development Center, to build a custom-made computer, the Mark I Perceptron. It was first publicly demonstrated on 23 June 1960. The machine was "part of a previously secret four-year NPIC [the US' National Photographic Interpretation Center] effort from 1963 through 1966 to develop this algorithm into a useful tool for photo-interpreters". Rosenblatt described the details of the perceptron in a 1958 paper. His organization of a perceptron is constructed of three kinds of cells ("units"): S, A, R, which stand for "sensory", "association" and "response". He presented at the first international symposium on AI, Mechanisation of Thought Processes, which took place in 1958 November. Rosenblatt's project was funded under Contract Nonr-401(40) "Cognitive Systems Research Program", which lasted from 1959 to 1970, and Contract Nonr-2381(00) "Project PARA" ("PARA" means "Perceiving and Recognition Automata"), which lasted from 1957 to 1963. In 1959, the Institute for Defense Analysis awarded his group a $10,000 contract. By September 1961, the ONR awarded further $153,000 worth of contracts, with $108,000 committed for 1962. The ONR research manager, Marvin Denicoff, stated that ONR, instead of ARPA, funded the Perceptron project, because the project was unlikely to produce technological results in the near or medium term. Funding from ARPA go up to the order of millions dollars, while from ONR are on the order of 10,000 dollars. Meanwhile, the head of IPTO at ARPA, J.C.R. Licklider, was interested in 'self-organizing', 'adaptive' and other biologically-inspired methods in the 1950s; but by the mid-1960s he was openly critical of these, including the perceptron. Instead he strongly favored the logical AI approach of Simon and Newell. === Mark I Perceptron machine === The perceptron was intended to be a machine, rather than a program, and while its first implementation was in software for the IBM 704, it was subsequently implemented in custom-built hardware as the Mark I Perceptron with the project name "Project PARA", designed for image recognition. The machine is currently in Smithsonian National Museum of American History. The Mark I Perceptron had three layers. One version was implemented as follows: An array of 400 photocells arranged in a 20x20 grid, named "sensory units" (S-units), or "input retina". Each S-unit can connect to up to 40 A-units. A hidden layer of 512 perceptrons, named "association units" (A-units). An output layer of eight perceptrons, named "response units" (R-units). Rosenblatt called this three-layered perceptron network the alpha-perceptron, to distinguish it from other perceptron models he experimented with. The S-units are connected to the A-units randomly (according to a table of random numbers) via a plugboard (see photo), to "eliminate any particular intentional bias in the perceptron". The connection weights are fixed, not learned. Rosenblatt was adamant about the random connections, as he believed the retina was randomly connected to the visual cortex, and he wanted his perceptron machine to resemble human visual perception. The A-units are connected to the R-units, with adjustable weights encoded in potentiometers, and weight updates during learning were performed by electric motors.The hardware details are in an operators' manual. In a 1958 press conference organized by the US Navy, Rosenblatt made statements about the perceptron that caused a heated controversy among the fledgling AI community; based on Rosenblatt's statements, The New York Times reported the perceptron to be "the embryo of an electronic computer that [the Navy] expects will be able to walk, talk, see, write, reproduce itself and be conscious of its existence." The Photo Division of Central Intelligence Agency, from 1960 to 1964, studied the use of Mark I Perceptron machine for recognizing militarily interesting silhouetted targets (such as planes and ships) in aerial photos. === Principles of Neurodynamics (1962) === Rosenblatt described his experiments with many variants of the Perceptron machine in a book Principles of Neurodynamics (1962). The book is a published version of the 1961 report. Among the variants are: "cross-coupling" (connections between units within the same layer) with possibly closed loops, "back-coupling" (connections from units in a later layer to units in a previous layer), four-layer perceptrons where the last two layers have adjustable weights (and thus a proper multilayer perceptron), incorporating time-delays to perceptron units, to allow for processing sequential data, analyzing audio (instead of images). The machine was shipped from Cornell to Smithsonian in 1967, under a government transfer administered by the Office of Naval Research. === Perceptrons (1969) === Although the perceptron initially seemed promising, it was quickly proved that perceptrons could not be trained to recognise many classes of patterns. This caused the field of neural network research to stagnate for many years, before it was recognised that a feedforward neural network with two or more layers (also called a multilayer perceptron) had greater processing power than perceptrons with one layer (also called a single-layer perceptron). Single-layer perceptrons are only capable of learning linearly separable patterns. For a classification task with some step activation function, a single node will have a single line dividing the data points forming the patterns. More nodes can create more dividing lines, but those lines must somehow be combined to form more complex classifications. A second layer of perceptrons, or even linear nodes, are sufficient to solve many otherwise non-separable problems. In 1969, a famous book entitled Perceptrons by Marvin Minsky and Seymour Papert showed that it was impossible for these classes of network to learn an XOR function. It is often incorrectly believed that they also conjectured that a similar result would hold for a multi-layer perceptron network. However, this is not true, as both Minsky and Papert already knew that multi-layer perceptrons were capable of producing an XOR function. (See the page on Perceptrons (book) for more information.) Nevertheless, the often-miscited Minsky and Papert text caused a significant decline in interest and funding of neural network research. It took ten more years until neural network research experienced a resurgence in the 1980s. This text was reprinted in 1987 as "Perceptrons - Expanded Edition" where some errors in the original text are shown and corrected. === Subsequent work === Rosenblatt continued working on perceptrons despite diminishing funding. The last attempt was Tobermory, built between 1961 and 1967, built for speech recognition. It occupied an entire room. It had 4 layers with 12,000 weights implemented by toroidal magnetic cores. By the time of its completion, simulation on digital computers had become faster than purpose-built perceptron machines. He died in a boating accident in 1971. A simulation program for neural networks was written for IBM 7090/7094, and was used to study various pattern recognition applications, such as character recognition, particle tracks in bubble-chamber photographs; phoneme, isolated word, and continuous speech recognition; speaker verification; and center-of-attention mechanisms for image processing. The kernel perceptron algorithm was already introduced in 1964 by Aizerman et al. Margin bounds guarantees were given for the Perceptron algorithm in the general non-separable case first by Freund and Schapire (1998), and more recently by Mohri and Rostamizadeh (2013) who extend previous results and give new and more favorable L1 bounds. The perceptron is a simplified model of a biological neuron. While the complexity of biological neuron models is often required to fully understand neural behavior, research suggests a perceptron-like linear model can produce some behavior seen in real neurons. The solution spaces of decision boundaries for all binary functions and learning behaviors are studied in. == Definition == In the modern sense, the perceptron is an algori

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  • Out-of-bag error

    Out-of-bag error

    Out-of-bag (OOB) error, also called out-of-bag estimate, is a method of measuring the prediction error of random forests, boosted decision trees, and other machine learning models utilizing bootstrap aggregating (bagging). Bagging uses subsampling with replacement to create training samples for the model to learn from. OOB error is the mean prediction error on each training sample xi, using only the trees that did not have xi in their bootstrap sample. Bootstrap aggregating allows one to define an out-of-bag estimate of the prediction performance improvement by evaluating predictions on those observations that were not used in the building of the next base learner. == Out-of-bag dataset == When bootstrap aggregating is performed, two independent sets are created. One set, the bootstrap sample, is the data chosen to be "in-the-bag" by sampling with replacement. The out-of-bag set is all data not chosen in the sampling process. When this process is repeated, such as when building a random forest, many bootstrap samples and OOB sets are created. The OOB sets can be aggregated into one dataset, but each sample is only considered out-of-bag for the trees that do not include it in their bootstrap sample. The picture below shows that for each bag sampled, the data is separated into two groups. This example shows how bagging could be used in the context of diagnosing disease. A set of patients are the original dataset, but each model is trained only by the patients in its bag. The patients in each out-of-bag set can be used to test their respective models. The test would consider whether the model can accurately determine if the patient has the disease. == Calculating out-of-bag error == Since each out-of-bag set is not used to train the model, it is a good test for the performance of the model. The specific calculation of OOB error depends on the implementation of the model, but a general calculation is as follows. Find all models (or trees, in the case of a random forest) that are not trained by the OOB instance. Take the majority vote of these models' result for the OOB instance, compared to the true value of the OOB instance. Compile the OOB error for all instances in the OOB dataset. The bagging process can be customized to fit the needs of a model. To ensure an accurate model, the bootstrap training sample size should be close to that of the original set. Also, the number of iterations (trees) of the model (forest) should be considered to find the true OOB error. The OOB error will stabilize over many iterations so starting with a high number of iterations is a good idea. Shown in the example to the right, the OOB error can be found using the method above once the forest is set up. == Comparison to cross-validation == Out-of-bag error and cross-validation (CV) are different methods of measuring the error estimate of a machine learning model. Over many iterations, the two methods should produce a very similar error estimate. That is, once the OOB error stabilizes, it will converge to the cross-validation (specifically leave-one-out cross-validation) error. The advantage of the OOB method is that it requires less computation and allows one to test the model as it is being trained. == Accuracy and Consistency == Out-of-bag error is used frequently for error estimation within random forests but with the conclusion of a study done by Silke Janitza and Roman Hornung, out-of-bag error has shown to overestimate in settings that include an equal number of observations from all response classes (balanced samples), small sample sizes, a large number of predictor variables, small correlation between predictors, and weak effects.

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  • Yap (company)

    Yap (company)

    Yap Speech Cloud was a multimodal speech recognition system developed by American technology company Yap Inc. It offered a fully cloud-based speech-to-text transcription platform that was used by customers such as Microsoft. The Company was a contestant at the inaugural TechCrunch conference and was subsequently acquired by Amazon in September 2011 to help develop products such as Alexa Voice Service, Echo, and Fire TV.

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  • Medoid

    Medoid

    Medoids are representative objects of a data set or a cluster within a data set whose sum of dissimilarities to all the objects in the cluster is minimal. Medoids are similar in concept to means or centroids, but medoids are always restricted to be members of the data set. Medoids are most commonly used on data when a mean or centroid cannot be defined, such as graphs. They are also used in contexts where the centroid is not representative of the dataset like in images, 3-D trajectories and gene expression (where while the data is sparse the medoid need not be). These are also of interest while wanting to find a representative using some distance other than squared euclidean distance (for instance in movie-ratings). For some data sets there may be more than one medoid, as with medians. A common application of the medoid is the k-medoids clustering algorithm, which is similar to the k-means algorithm but works when a mean or centroid is not definable. This algorithm basically works as follows. First, a set of medoids is chosen at random. Second, the distances to the other points are computed. Third, data are clustered according to the medoid they are most similar to. Fourth, the medoid set is optimized via an iterative process. Note that a medoid is not equivalent to a median, a geometric median, or centroid. A median is only defined on 1-dimensional data, and it only minimizes dissimilarity to other points for metrics induced by a norm (such as the Manhattan distance or Euclidean distance). A geometric median is defined in any dimension, but unlike a medoid, it is not necessarily a point from within the original dataset. == Definition == Let X := { x 1 , x 2 , … , x n } {\textstyle {\mathcal {X}}:=\{x_{1},x_{2},\dots ,x_{n}\}} be a set of n {\textstyle n} points in a space with a distance function d. Medoid is defined as x medoid = arg ⁡ min y ∈ X ∑ i = 1 n d ( y , x i ) . {\displaystyle x_{\text{medoid}}=\arg \min _{y\in {\mathcal {X}}}\sum _{i=1}^{n}d(y,x_{i}).} == Clustering with medoids == Medoids are a popular replacement for the cluster mean when the distance function is not (squared) Euclidean distance, or not even a metric (as the medoid does not require the triangle inequality). When partitioning the data set into clusters, the medoid of each cluster can be used as a representative of each cluster. Clustering algorithms based on the idea of medoids include: Partitioning Around Medoids (PAM), the standard k-medoids algorithm Hierarchical Clustering Around Medoids (HACAM), which uses medoids in hierarchical clustering == Algorithms to compute the medoid of a set == From the definition above, it is clear that the medoid of a set X {\displaystyle {\mathcal {X}}} can be computed after computing all pairwise distances between points in the ensemble. This would take O ( n 2 ) {\textstyle O(n^{2})} distance evaluations (with n = | X | {\displaystyle n=|{\mathcal {X}}|} ). In the worst case, one can not compute the medoid with fewer distance evaluations. However, there are many approaches that allow us to compute medoids either exactly or approximately in sub-quadratic time under different statistical models. If the points lie on the real line, computing the medoid reduces to computing the median which can be done in O ( n ) {\textstyle O(n)} by Quick-select algorithm of Hoare. However, in higher dimensional real spaces, no linear-time algorithm is known. RAND is an algorithm that estimates the average distance of each point to all the other points by sampling a random subset of other points. It takes a total of O ( n log ⁡ n ϵ 2 ) {\textstyle O\left({\frac {n\log n}{\epsilon ^{2}}}\right)} distance computations to approximate the medoid within a factor of ( 1 + ϵ Δ ) {\textstyle (1+\epsilon \Delta )} with high probability, where Δ {\textstyle \Delta } is the maximum distance between two points in the ensemble. Note that RAND is an approximation algorithm, and moreover Δ {\textstyle \Delta } may not be known apriori. RAND was leveraged by TOPRANK which uses the estimates obtained by RAND to focus on a small subset of candidate points, evaluates the average distance of these points exactly, and picks the minimum of those. TOPRANK needs O ( n 5 3 log 4 3 ⁡ n ) {\textstyle O(n^{\frac {5}{3}}\log ^{\frac {4}{3}}n)} distance computations to find the exact medoid with high probability under a distributional assumption on the average distances. trimed presents an algorithm to find the medoid with O ( n 3 2 2 Θ ( d ) ) {\textstyle O(n^{\frac {3}{2}}2^{\Theta (d)})} distance evaluations under a distributional assumption on the points. The algorithm uses the triangle inequality to cut down the search space. Meddit leverages a connection of the medoid computation with multi-armed bandits and uses an upper-Confidence-bound type of algorithm to get an algorithm which takes O ( n log ⁡ n ) {\textstyle O(n\log n)} distance evaluations under statistical assumptions on the points. Correlated Sequential Halving also leverages multi-armed bandit techniques, improving upon Meddit. By exploiting the correlation structure in the problem, the algorithm is able to provably yield drastic improvement (usually around 1-2 orders of magnitude) in both number of distance computations needed and wall clock time. == Implementations == An implementation of RAND, TOPRANK, and trimed can be found here. An implementation of Meddit can be found here and here. An implementation of Correlated Sequential Halving can be found here. == Medoids in text and natural language processing (NLP) == Medoids can be applied to various text and NLP tasks to improve the efficiency and accuracy of analyses. By clustering text data based on similarity, medoids can help identify representative examples within the dataset, leading to better understanding and interpretation of the data. === Text clustering === Text clustering is the process of grouping similar text or documents together based on their content. Medoid-based clustering algorithms can be employed to partition large amounts of text into clusters, with each cluster represented by a medoid document. This technique helps in organizing, summarizing, and retrieving information from large collections of documents, such as in search engines, social media analytics and recommendation systems. === Text summarization === Text summarization aims to produce a concise and coherent summary of a larger text by extracting the most important and relevant information. Medoid-based clustering can be used to identify the most representative sentences in a document or a group of documents, which can then be combined to create a summary. This approach is especially useful for extractive summarization tasks, where the goal is to generate a summary by selecting the most relevant sentences from the original text. === Sentiment analysis === Sentiment analysis involves determining the sentiment or emotion expressed in a piece of text, such as positive, negative, or neutral. Medoid-based clustering can be applied to group text data based on similar sentiment patterns. By analyzing the medoid of each cluster, researchers can gain insights into the predominant sentiment of the cluster, helping in tasks such as opinion mining, customer feedback analysis, and social media monitoring. === Topic modeling === Topic modeling is a technique used to discover abstract topics that occur in a collection of documents. Medoid-based clustering can be applied to group documents with similar themes or topics. By analyzing the medoids of these clusters, researchers can gain an understanding of the underlying topics in the text corpus, facilitating tasks such as document categorization, trend analysis, and content recommendation. === Techniques for measuring text similarity in medoid-based clustering === When applying medoid-based clustering to text data, it is essential to choose an appropriate similarity measure to compare documents effectively. Each technique has its advantages and limitations, and the choice of the similarity measure should be based on the specific requirements and characteristics of the text data being analyzed. The following are common techniques for measuring text similarity in medoid-based clustering: ==== Cosine similarity ==== Cosine similarity is a widely used measure to compare the similarity between two pieces of text. It calculates the cosine of the angle between two document vectors in a high-dimensional space. Cosine similarity ranges between -1 and 1, where a value closer to 1 indicates higher similarity, and a value closer to -1 indicates lower similarity. By visualizing two lines originating from the origin and extending to the respective points of interest, and then measuring the angle between these lines, one can determine the similarity between the associated points. Cosine similarity is less affected by document length, so it may be better at producing medoids that are representative of the content of a cluster instead of the lengt

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  • Extremal Ensemble Learning

    Extremal Ensemble Learning

    Extremal Ensemble Learning (EEL) is a machine learning algorithmic paradigm for graph partitioning. EEL creates an ensemble of partitions and then uses information contained in the ensemble to find new and improved partitions. The ensemble evolves and learns how to form improved partitions through extremal updating procedure. The final solution is found by achieving consensus among its member partitions about what the optimal partition is. == Reduced-Network Extremal Ensemble Learning (RenEEL) == A particular implementation of the EEL paradigm is the Reduced-Network Extremal Ensemble Learning (RenEEL) scheme for partitioning a graph. RenEEL uses consensus across many partitions in an ensemble to create a reduced network that can be efficiently analyzed to find more accurate partitions. These better quality partitions are subsequently used to update the ensemble. An algorithm that utilizes the RenEEL scheme is currently the best algorithm for finding the graph partition with maximum modularity, which is an NP-hard problem.

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  • Latent and observable variables

    Latent and observable variables

    In statistics, latent variables (from Latin: present participle of lateo 'lie hidden') are variables that can only be inferred indirectly through a mathematical model from other observable variables that can be directly observed or measured. Such latent variable models are used in many disciplines, including engineering, medicine, ecology, physics, machine learning/artificial intelligence, natural language processing, bioinformatics, chemometrics, demography, economics, management, political science, psychology and the social sciences. Latent variables may correspond to aspects of physical reality. These could in principle be measured, but may not be for practical reasons. Among the earliest expressions of this idea is Francis Bacon's polemic the Novum Organum, itself a challenge to the more traditional logic expressed in Aristotle's Organon: But the latent process of which we speak, is far from being obvious to men’s minds, beset as they now are. For we mean not the measures, symptoms, or degrees of any process which can be exhibited in the bodies themselves, but simply a continued process, which, for the most part, escapes the observation of the senses. In this situation, the term hidden variables is commonly used, reflecting the fact that the variables are meaningful, but not observable. Other latent variables correspond to abstract concepts, like categories, behavioral or mental states, or data structures. The terms hypothetical variables or hypothetical constructs may be used in these situations. The use of latent variables can serve to reduce the dimensionality of data. Many observable variables can be aggregated in a model to represent an underlying concept, making it easier to understand the data. In this sense, they serve a function similar to that of scientific theories. At the same time, latent variables link observable "sub-symbolic" data in the real world to symbolic data in the modeled world. == Examples == === Psychology === Latent variables, as created by factor analytic methods, generally represent "shared" variance, or the degree to which variables "move" together. Variables that have no correlation cannot result in a latent construct based on the common factor model. The "Big Five personality traits" have been inferred using factor analysis. extraversion spatial ability wisdom: “Two of the more predominant means of assessing wisdom include wisdom-related performance and latent variable measures.” Spearman's g, or the general intelligence factor in psychometrics === Economics === Examples of latent variables from the field of economics include quality of life, business confidence, morale, happiness and conservatism: these are all variables which cannot be measured directly. However, by linking these latent variables to other, observable variables, the values of the latent variables can be inferred from measurements of the observable variables. Quality of life is a latent variable which cannot be measured directly, so observable variables are used to infer quality of life. Observable variables to measure quality of life include wealth, employment, environment, physical and mental health, education, recreation and leisure time, and social belonging. === Medicine === Latent-variable methodology is used in many branches of medicine. A class of problems that naturally lend themselves to latent variables approaches are longitudinal studies where the time scale (e.g. age of participant or time since study baseline) is not synchronized with the trait being studied. For such studies, an unobserved time scale that is synchronized with the trait being studied can be modeled as a transformation of the observed time scale using latent variables. Examples of this include disease progression modeling and modeling of growth (see box). == Inferring latent variables == There exists a range of different model classes and methodology that make use of latent variables and allow inference in the presence of latent variables. Models include: linear mixed-effects models and nonlinear mixed-effects models Hidden Markov models Factor analysis Item response theory Analysis and inference methods include: Principal component analysis Instrumented principal component analysis Partial least squares regression Latent semantic analysis and probabilistic latent semantic analysis EM algorithms Metropolis–Hastings algorithm === Bayesian algorithms and methods === Bayesian statistics is often used for inferring latent variables. Latent Dirichlet allocation The Chinese restaurant process is often used to provide a prior distribution over assignments of objects to latent categories. The Indian buffet process is often used to provide a prior distribution over assignments of latent binary features to objects.

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  • Rapid PHP Editor

    Rapid PHP Editor

    rapid PHP Editor is a PHP Editor that incorporates many functions such as AutoComplete, Syntax checker, debugger and many other tools for fast PHP development. Rapid PHP Editor also contain other development tools for helping on HTML, CSS, JavaScript and many other languages. Is part of a family of products covering most aspects of modern web development integrating as well many other capabilities used by developers. Some features: (X)HTML to HTML5 CSS to CSS3 Code intelligence Powerful search and replace Support for several frameworks Code beautifier FTP Explorer (FTP/SFTP/FTPS) File explorer Database explorer Code snippets Validators and Debuggers FAST, real fast Many other tools available (many more to describe all here) == History == Rapid PHP Editor was built using the Delphi programming language.

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  • Proper generalized decomposition

    Proper generalized decomposition

    The proper generalized decomposition (PGD) is an iterative numerical method for solving boundary value problems (BVPs), that is, partial differential equations constrained by a set of boundary conditions, such as the Poisson's equation or the Laplace's equation. The PGD algorithm computes an approximation of the solution of the BVP by successive enrichment. This means that, in each iteration, a new component (or mode) is computed and added to the approximation. In principle, the more modes obtained, the closer the approximation is to its theoretical solution. Unlike POD principal components, PGD modes are not necessarily orthogonal to each other. By selecting only the most relevant PGD modes, a reduced order model of the solution is obtained. Because of this, PGD is considered a dimensionality reduction algorithm. == Description == The proper generalized decomposition is a method characterized by a variational formulation of the problem, a discretization of the domain in the style of the finite element method, the assumption that the solution can be approximated as a separate representation and a numerical greedy algorithm to find the solution. === Variational formulation === In the Proper Generalized Decomposition method, the variational formulation involves translating the problem into a format where the solution can be approximated by minimizing (or sometimes maximizing) a functional. A functional is a scalar quantity that depends on a function, which in this case, represents our problem. The most commonly implemented variational formulation in PGD is the Bubnov-Galerkin method. This method is chosen for its ability to provide an approximate solution to complex problems, such as those described by partial differential equations (PDEs). In the Bubnov-Galerkin approach, the idea is to project the problem onto a space spanned by a finite number of basis functions. These basis functions are chosen to approximate the solution space of the problem. In the Bubnov-Galerkin method, we seek an approximate solution that satisfies the integral form of the PDEs over the domain of the problem. This is different from directly solving the differential equations. By doing so, the method transforms the problem into finding the coefficients that best fit this integral equation in the chosen function space. While the Bubnov-Galerkin method is prevalent, other variational formulations are also used in PGD, depending on the specific requirements and characteristics of the problem, such as: Petrov-Galerkin Method: This method is similar to the Bubnov-Galerkin approach but differs in the choice of test functions. In the Petrov-Galerkin method, the test functions (used to project the residual of the differential equation) are different from the trial functions (used to approximate the solution). This can lead to improved stability and accuracy for certain types of problems. Collocation Method: In collocation methods, the differential equation is satisfied at a finite number of points in the domain, known as collocation points. This approach can be simpler and more direct than the integral-based methods like Galerkin's, but it may also be less stable for some problems. Least Squares Method: This approach involves minimizing the square of the residual of the differential equation over the domain. It is particularly useful when dealing with problems where traditional methods struggle with stability or convergence. Mixed Finite Element Method: In mixed methods, additional variables (such as fluxes or gradients) are introduced and approximated along with the primary variable of interest. This can lead to more accurate and stable solutions for certain problems, especially those involving incompressibility or conservation laws. Discontinuous Galerkin Method: This is a variant of the Galerkin method where the solution is allowed to be discontinuous across element boundaries. This method is particularly useful for problems with sharp gradients or discontinuities. === Domain discretization === The discretization of the domain is a well defined set of procedures that cover (a) the creation of finite element meshes, (b) the definition of basis function on reference elements (also called shape functions) and (c) the mapping of reference elements onto the elements of the mesh. === Separate representation === PGD assumes that the solution u of a (multidimensional) problem can be approximated as a separate representation of the form u ≈ u N ( x 1 , x 2 , … , x d ) = ∑ i = 1 N X 1 i ( x 1 ) ⋅ X 2 i ( x 2 ) ⋯ X d i ( x d ) , {\displaystyle \mathbf {u} \approx \mathbf {u} ^{N}(x_{1},x_{2},\ldots ,x_{d})=\sum _{i=1}^{N}\mathbf {X_{1}} _{i}(x_{1})\cdot \mathbf {X_{2}} _{i}(x_{2})\cdots \mathbf {X_{d}} _{i}(x_{d}),} where the number of addends N and the functional products X1(x1), X2(x2), ..., Xd(xd), each depending on a variable (or variables), are unknown beforehand. === Greedy algorithm === The solution is sought by applying a greedy algorithm, usually the fixed point algorithm, to the weak formulation of the problem. For each iteration i of the algorithm, a mode of the solution is computed. Each mode consists of a set of numerical values of the functional products X1(x1), ..., Xd(xd), which enrich the approximation of the solution. Due to the greedy nature of the algorithm, the term 'enrich' is used rather than 'improve', since some modes may actually worsen the approach. The number of computed modes required to obtain an approximation of the solution below a certain error threshold depends on the stopping criterion of the iterative algorithm. == Features == PGD is suitable for solving high-dimensional problems, since it overcomes the limitations of classical approaches. In particular, PGD avoids the curse of dimensionality, as solving decoupled problems is computationally much less expensive than solving multidimensional problems. Therefore, PGD enables to re-adapt parametric problems into a multidimensional framework by setting the parameters of the problem as extra coordinates: u ≈ u N ( x 1 , … , x d ; k 1 , … , k p ) = ∑ i = 1 N X 1 i ( x 1 ) ⋯ X d i ( x d ) ⋅ K 1 i ( k 1 ) ⋯ K p i ( k p ) , {\displaystyle \mathbf {u} \approx \mathbf {u} ^{N}(x_{1},\ldots ,x_{d};k_{1},\ldots ,k_{p})=\sum _{i=1}^{N}\mathbf {X_{1}} _{i}(x_{1})\cdots \mathbf {X_{d}} _{i}(x_{d})\cdot \mathbf {K_{1}} _{i}(k_{1})\cdots \mathbf {K_{p}} _{i}(k_{p}),} where a series of functional products K1(k1), K2(k2), ..., Kp(kp), each depending on a parameter (or parameters), has been incorporated to the equation. In this case, the obtained approximation of the solution is called computational vademecum: a general meta-model containing all the particular solutions for every possible value of the involved parameters. == Sparse Subspace Learning == The Sparse Subspace Learning (SSL) method leverages the use of hierarchical collocation to approximate the numerical solution of parametric models. With respect to traditional projection-based reduced order modeling, the use of a collocation enables non-intrusive approach based on sparse adaptive sampling of the parametric space. This allows to recover the lowdimensional structure of the parametric solution subspace while also learning the functional dependency from the parameters in explicit form. A sparse low-rank approximate tensor representation of the parametric solution can be built through an incremental strategy that only needs to have access to the output of a deterministic solver. Non-intrusiveness makes this approach straightforwardly applicable to challenging problems characterized by nonlinearity or non affine weak forms.

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  • Automated Pain Recognition

    Automated Pain Recognition

    Automated Pain Recognition (APR) is a method for objectively measuring pain and at the same time represents an interdisciplinary research area that comprises elements of medicine, psychology, psychobiology, and computer science. The focus is on computer-aided objective recognition of pain, implemented on the basis of machine learning. Automated pain recognition allows for the valid, reliable detection and monitoring of pain in people who are unable to communicate verbally. The underlying machine learning processes are trained and validated in advance by means of unimodal or multimodal body signals. Signals used to detect pain may include facial expressions or gestures and may also be of a (psycho-)physiological or paralinguistic nature. To date, the focus has been on identifying pain intensity, but visionary efforts are also being made to recognize the quality, site, and temporal course of pain. However, the clinical implementation of this approach is a controversial topic in the field of pain research. Critics of automated pain recognition argue that pain diagnosis can only be performed subjectively by humans. == Background == Pain diagnosis under conditions where verbal reporting is restricted - such as in verbally and/or cognitively impaired people or in patients who are sedated or mechanically ventilated - is based on behavioral observations by trained professionals. However, all known observation procedures (e.g., Zurich Observation Pain Assessment (ZOPA)); Pain Assessment in Advanced Dementia Scale (PAINAD) require a great deal of specialist expertise. These procedures can be made more difficult by perception- and interpretation-related misjudgments on the part of the observer. With regard to the differences in design, methodology, evaluation sample, and conceptualization of the phenomenon of pain, it is difficult to compare the quality criteria of the various tools. Even if trained personnel could theoretically record pain intensity several times a day using observation instruments, it would not be possible to measure it every minute or second. In this respect, the goal of automated pain recognition is to use valid, robust pain response patterns that can be recorded multimodally for a temporally dynamic, high-resolution, automated pain intensity recognition system. == Procedure == For automated pain recognition, pain-relevant parameters are usually recorded using non-invasive sensor technology, which captures data on the (physical) responses of the person in pain. This can be achieved with camera technology that captures facial expressions, gestures, or posture, while audio sensors record paralinguistic features. (Psycho-)physiological information such as muscle tone and heart rate can be collected via biopotential sensors (electrodes). Pain recognition requires the extraction of meaningful characteristics or patterns from the data collected. This is achieved using machine learning techniques that are able to provide an assessment of the pain after training (learning), e.g., "no pain," "mild pain," or "severe pain." == Parameters == Although the phenomenon of pain comprises different components (sensory discriminative, affective (emotional), cognitive, vegetative, and (psycho-)motor), automated pain recognition currently relies on the measurable parameters of pain responses. These can be divided roughly into the two main categories of "physiological responses" and "behavioral responses". === Physiological responses === In humans, pain almost always initiates autonomic nervous processes that are reflected measurably in various physiological signals. ==== Physiological signals ==== Measurements can include electrodermal activity (EDA, also skin conductance), electromyography (EMG), electrocardiogram (ECG), blood volume pulse (BVP), electroencephalogram (EEG), respiration, and body temperature, which are regulatory mechanisms of the sympathetic and parasympathetic systems. Physiological signals are mainly recorded using special non-invasive surface electrodes (for EDA, EMG, ECG, and EEG), a blood volume pulse sensor (BVP), a respiratory belt (respiration), and a thermal sensor (body temperature). Endocrinological and immunological parameters can also be recorded, but this requires measures that are somewhat invasive (e.g., blood sampling). === Behavioral responses === Behavioral responses to pain fulfil two functions: protection of the body (e.g., through protective reflexes) and external communication of the pain (e.g., as a cry for help). The responses are particularly evident in facial expressions, gestures, and paralinguistic features. ==== Facial expressions ==== Behavioral signals captured comprise facial expression patterns (expressive behavior), which are measured with the aid of video signals. Facial expression recognition is based on the everyday clinical observation that pain often manifests itself in the patient's facial expressions but that this is not necessarily always the case, since facial expressions can be inhibited through self-control. Despite the possibility that facial expressions may be influenced consciously, facial expression behavior represents an essential source of information for pain diagnosis and is thus also a source of information for automatic pain recognition. One advantage of video-based facial expression recognition is the contact-free measurement of the face, provided that it can be captured on video, which is not possible in every position (e.g., lying face down) or may be limited by bandages covering the face. Facial expression analysis relies on rapid, spontaneous, and temporary changes in neuromuscular activity that lead to visually detectable changes in the face. ==== Gestures ==== Gestures are also captured predominantly using non-contact camera technology. Motor pain responses vary and are strongly dependent on the type and cause of the pain. They range from abrupt protective reflexes (e.g., spontaneous retraction of extremities or doubling up) to agitation (pathological restlessness) and avoidance behavior (hesitant, cautious movements). ==== Paralinguistic features of language ==== Among other things, pain leads to nonverbal linguistic behavior that manifests itself in sounds such as sighing, gasping, moaning, whining, etc. Paralinguistic features are usually recorded using highly sensitive microphones. == Algorithms == After the recording, pre-processing (e.g., filtering), and extraction of relevant features, an optional information fusion can be performed. During this process, modalities from different signal sources are merged to generate new or more precise knowledge. The pain is classified using machine learning processes. The method chosen has a significant influence on the recognition rate and depends greatly on the quality and granularity of the underlying data. Similar to the field of affective computing, the following classifiers are currently being used: Support Vector Machine (SVM): The goal of an SVM is to find a clearly defined optimal hyperplane with the greatest minimal distance to two (or more) classes to be separated. The hyperplane acts as a decision function for classifying an unknown pattern. Random Forest (RF): RF is based on the composition of random, uncorrelated decision trees. An unknown pattern is judged individually by each tree and assigned to a class. The final classification of the patterns by the RF is then based on a majority decision. k-Nearest Neighbors (k-NN): The k-NN algorithm classifies an unknown object using the class label that most commonly classifies the k neighbors closest to it. Its neighbors are determined using a selected similarity measure (e.g., Euclidean distance, Jaccard coefficient, etc.). Artificial neural networks (ANNs): ANNs are inspired by biological neural networks and model their organizational principles and processes in a very simplified manner. Class patterns are learned by adjusting the weights of the individual neuronal connections. == Databases == In order to classify pain in a valid manner, it is necessary to create representative, reliable, and valid pain databases that are available to the machine learner for training. An ideal database would be sufficiently large and would consist of natural (not experimental), high-quality pain responses. However, natural responses are difficult to record and can only be obtained to a limited extent; in most cases they are characterized by suboptimal quality. The databases currently available therefore contain experimental or quasi-experimental pain responses, and each database is based on a different pain model. The following list shows a selection of the most relevant pain databases (last updated: April 2020): UNBC-McMaster Shoulder Pain BioVid Heat Pain EmoPain SenseEmotion X-ITE Pain

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  • Soft independent modelling of class analogies

    Soft independent modelling of class analogies

    Soft independent modelling by class analogy (SIMCA) is a statistical method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes. == Method == In order to build the classification models, the samples belonging to each class need to be analysed using principal component analysis (PCA); only the significant components are retained. For a given class, the resulting model then describes either a line (for one Principal Component or PC), plane (for two PCs) or hyper-plane (for more than two PCs). For each modelled class, the mean orthogonal distance of training data samples from the line, plane, or hyper-plane (calculated as the residual standard deviation) is used to determine a critical distance for classification. This critical distance is based on the F-distribution and is usually calculated using 95% or 99% confidence intervals. New observations are projected into each PC model and the residual distances calculated. An observation is assigned to the model class when its residual distance from the model is below the statistical limit for the class. The observation may be found to belong to multiple classes and a measure of goodness of the model can be found from the number of cases where the observations are classified into multiple classes. The classification efficiency is usually indicated by Receiver operating characteristics. In the original SIMCA method, the ends of the hyper-plane of each class are closed off by setting statistical control limits along the retained principal components axes (i.e., score value between plus and minus 0.5 times score standard deviation). More recent adaptations of the SIMCA method close off the hyper-plane by construction of ellipsoids (e.g. Hotelling's T2 or Mahalanobis distance). With such modified SIMCA methods, classification of an object requires both that its orthogonal distance from the model and its projection within the model (i.e. score value within the region defined by the ellipsoid) are not significant. == Application == SIMCA as a method of classification has gained widespread use especially in applied statistical fields such as chemometrics and spectroscopic data analysis.

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  • Pixel aspect ratio

    Pixel aspect ratio

    A pixel aspect ratio (PAR) is a mathematical ratio that describes how the width of a pixel in a digital image compares to the height of that pixel. Most digital imaging systems display an image as a grid of tiny, square pixels. However, some imaging systems, especially those that must be compatible with standard-definition television motion pictures, display an image as a grid of rectangular pixels, in which the pixel width and height are different. Pixel aspect ratio describes this difference. Use of pixel aspect ratio mostly involves pictures pertaining to standard-definition television and some other exceptional cases. Most other imaging systems, including those that comply with SMPTE standards and practices, use square pixels. PAR is also known as sample aspect ratio and abbreviated SAR, though it can be confused with storage aspect ratio. == Introduction == The ratio of the width to the height of an image is known as the aspect ratio, or more precisely the display aspect ratio (DAR) – the aspect ratio of the image as displayed; for TV, DAR was traditionally 4:3 (a.k.a. fullscreen), with 16:9 (a.k.a. widescreen) now the standard for HDTV. In digital images, there is a distinction with the storage aspect ratio (SAR), which is the ratio of pixel dimensions. If an image is displayed with square pixels, then these ratios agree; if not, then non-square, "rectangular" pixels are used, and these ratios disagree. The aspect ratio of the pixels themselves is known as the pixel aspect ratio (PAR) – for square pixels this is 1:1 – and these are related by the identity: Rearranging (solving for PAR) yields: For example: A 640 × 480 VGA image has a SAR of 640/480 = 4:3, and if displayed on a 4:3 display (DAR = 4:3) has square pixels, hence a PAR of 1:1. By contrast, a 720 × 576 D-1 PAL image has a SAR of 720/576 = 5:4, but if displayed on a 4:3 display (DAR = 4:3) the PAR is 4/3 : 5/4 = 16:15 ≈ 1.066. This means that the pixels of the PAL picture must be "stretched" by this amount to fit in the 4:3 display. In analog images such as film there is no notion of pixel, nor notion of SAR or PAR, but in the digitization of analog images the resulting digital image has pixels, hence SAR (and accordingly PAR, if displayed at the same aspect ratio as the original). Non-square pixels arise often in early digital TV standards, related to digitalization of analog TV signals – whose vertical and "effective" horizontal resolutions differ and are thus best described by non-square pixels – and also in some digital video cameras and computer display modes, such as Color Graphics Adapter (CGA). Today they arise also in transcoding between resolutions with different SARs. Actual displays do not generally have non-square pixels, though digital sensors might; they are rather a mathematical abstraction used in resampling images to convert between resolutions. There are several complicating factors in understanding PAR, particularly as it pertains to digitization of analog video: First, analog video does not have pixels, but rather a raster scan, and thus has a well-defined vertical resolution (the lines of the raster), but not a well-defined horizontal resolution, since each line is an analog signal. However, by a standardized sampling rate, the effective horizontal resolution can be determined by the sampling theorem, as is done below. Second, due to overscan, some of the lines at the top and bottom of the raster are not visible, as are some of the possible image on the left and right – see Overscan: Analog to digital resolution issues. Also, the resolution may be rounded (DV NTSC uses 480 lines, rather than the 486 that are possible). Third, analog video signals are interlaced – each image (frame) is sent as two "fields", each with half the lines. Thus either the pixels are twice as tall as they would be without interlacing, or the image is deinterlaced. == Background == Video is presented as a sequential series of images called video frames. Historically, video frames were created and recorded in analog form. As digital display technology, digital broadcast technology, and digital video compression evolved separately, it resulted in video frame differences that must be addressed using pixel aspect ratio. Digital video frames are generally defined as a grid of pixels used to present each sequential image. The horizontal component is defined by pixels (or samples), and is known as a video line. The vertical component is defined by the number of lines, as in 480 lines. Standard-definition television standards and practices were developed as broadcast technologies and intended for terrestrial broadcasting, and were therefore not designed for digital video presentation. Such standards define an image as an array of well-defined horizontal "Lines", well-defined vertical "Line Duration" and a well-defined picture center. However, there is not a standard-definition television standard that properly defines image edges or explicitly demands a certain number of picture elements per line. Furthermore, analog video systems such as NTSC 480i and PAL 576i, instead of employing progressively displayed frames, employ fields or interlaced half-frames displayed in an interwoven manner to reduce flicker and double the image rate for smoother motion. === Analog-to-digital conversion === As a result of computers becoming powerful enough to serve as video editing tools, video digital-to-analog converters and analog-to-digital converters were made to overcome this incompatibility. To convert analog video lines into a series of square pixels, the industry adopted a default sampling rate at which luma values were extracted into pixels. The luma sampling rate for 480i pictures was 12+3⁄11 MHz and for 576i pictures was 14+3⁄4 MHz. The term pixel aspect ratio was first coined when ITU-R BT.601 (commonly known as Rec. 601) specified that standard-definition television pictures are made of lines of exactly 720 non-square pixels. ITU-R BT.601 did not define the exact pixel aspect ratio but did provide enough information to calculate the exact pixel aspect ratio based on industry practices: The standard luma sampling rate of precisely 13+1⁄2 MHz. Based on this information: The pixel aspect ratio for 480i would be 10:11 as: 12 3 11 ÷ 13 1 2 = 10 11 {\displaystyle 12{\tfrac {3}{11}}\div 13{\tfrac {1}{2}}={\tfrac {10}{11}}} The pixel aspect ratio for 576i would be 59:54 as: 14 3 4 ÷ 13 1 2 = 59 54 {\displaystyle 14{\tfrac {3}{4}}\div 13{\tfrac {1}{2}}={\tfrac {59}{54}}} SMPTE RP 187 further attempted to standardize the pixel aspect ratio values for 480i and 576i. It designated 177:160 for 480i or 1035:1132 for 576i. However, due to significant difference with practices in effect by industry and the computational load that they imposed upon the involved hardware, SMPTE RP 187 was simply ignored. SMPTE RP 187 information annex A.4 further suggested the use of 10:11 for 480i. As of this writing, ITU-R BT.601-6, which is the latest edition of ITU-R BT.601, still implies that the pixel aspect ratios mentioned above are correct. === Digital video processing === As stated above, ITU-R BT.601 specified that standard-definition television pictures are made of lines of 720 non-square pixels, sampled with a precisely specified sampling rate. A simple mathematical calculation reveals that a 704 pixel width would be enough to contain a 480i or 576i standard 4:3 picture: A 4:3 480-line picture, digitized with the Rec. 601-recommended sampling rate, would be 704 non-square pixels wide. x 480 × 10 11 = 4 3 ⇒ x = 480 × 11 × 4 10 × 3 = 704 {\displaystyle {\frac {x}{480}}\times {\frac {10}{11}}={\frac {4}{3}}\Rightarrow x={\frac {480\times 11\times 4}{10\times 3}}=704} A 4:3 576-line picture, digitized with the Rec. 601-recommended sampling rate, would be 702+54⁄59 non-square pixels wide. x 576 × 59 54 = 4 3 ⇒ x = 576 × 54 × 4 59 × 3 = 702 54 59 {\displaystyle {\frac {x}{576}}\times {\frac {59}{54}}={\frac {4}{3}}\Rightarrow x={\frac {576\times 54\times 4}{59\times 3}}=702{\tfrac {54}{59}}} Unfortunately, not all standard TV pictures are exactly 4:3: As mentioned earlier, in analog video, the center of a picture is well-defined but the edges of the picture are not standardized. As a result, some analog devices (mostly PAL devices but also some NTSC devices) generated motion pictures that were horizontally (slightly) wider. This also proportionately applies to anamorphic widescreen (16:9) pictures. Therefore, to maintain a safe margin of error, ITU-R BT.601 required sampling 16 more non-square pixels per line (8 more at each edge) to ensure saving all video data near the margins. This requirement, however, had implications for PAL motion pictures. PAL pixel aspect ratios for standard (4:3) and anamorphic wide screen (16:9), respectively 59:54 and 118:81, were awkward for digital image processing, especially for mixing PAL and NTSC video clips. Therefore, video editing products chose the almost equivalent value

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  • GeWorkbench

    GeWorkbench

    geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing funded through the NIH Roadmap (NIH Common Fund). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins. == Features == Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc. Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence and protein structure data (e.g., MarkUs). Integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. Component integration through platform management of inputs and outputs. Among data that can be shared between components are expression datasets, interaction networks, sample and marker (gene) sets and sequences. Dataset history tracking - complete record of data sets used and input settings. Integration with 3rd party tools such as GenePattern, Cytoscape, and Genomespace. Demonstrations of each feature described can be found at GeWorkbench-web Tutorials. == Versions == geWorkbench is open-source software that can be downloaded and installed locally. A zip file of the released version Java source is also available. Prepackaged installer versions also exist for Windows, Macintosh, and Linux.

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  • Constellation model

    Constellation model

    The constellation model is a probabilistic, generative model for category-level object recognition in computer vision. Like other part-based models, the constellation model attempts to represent an object class by a set of N parts under mutual geometric constraints. Because it considers the geometric relationship between different parts, the constellation model differs significantly from appearance-only, or "bag-of-words" representation models, which explicitly disregard the location of image features. The problem of defining a generative model for object recognition is difficult. The task becomes significantly complicated by factors such as background clutter, occlusion, and variations in viewpoint, illumination, and scale. Ideally, we would like the particular representation we choose to be robust to as many of these factors as possible. In category-level recognition, the problem is even more challenging because of the fundamental problem of intra-class variation. Even if two objects belong to the same visual category, their appearances may be significantly different. However, for structured objects such as cars, bicycles, and people, separate instances of objects from the same category are subject to similar geometric constraints. For this reason, particular parts of an object such as the headlights or tires of a car still have consistent appearances and relative positions. The Constellation Model takes advantage of this fact by explicitly modeling the relative location, relative scale, and appearance of these parts for a particular object category. Model parameters are estimated using an unsupervised learning algorithm, meaning that the visual concept of an object class can be extracted from an unlabeled set of training images, even if that set contains "junk" images or instances of objects from multiple categories. It can also account for the absence of model parts due to appearance variability, occlusion, clutter, or detector error. == History == The idea for a "parts and structure" model was originally introduced by Fischler and Elschlager in 1973. This model has since been built upon and extended in many directions. The Constellation Model, as introduced by Dr. Perona and his colleagues, was a probabilistic adaptation of this approach. In the late '90s, Burl et al. revisited the Fischler and Elschlager model for the purpose of face recognition. In their work, Burl et al. used manual selection of constellation parts in training images to construct a statistical model for a set of detectors and the relative locations at which they should be applied. In 2000, Weber et al. made the significant step of training the model using a more unsupervised learning process, which precluded the necessity for tedious hand-labeling of parts. Their algorithm was particularly remarkable because it performed well even on cluttered and occluded image data. Fergus et al. then improved upon this model by making the learning step fully unsupervised, having both shape and appearance learned simultaneously, and accounting explicitly for the relative scale of parts. == The method of Weber and Welling et al. == In the first step, a standard interest point detection method, such as Harris corner detection, is used to generate interest points. Image features generated from the vicinity of these points are then clustered using k-means or another appropriate algorithm. In this process of vector quantization, one can think of the centroids of these clusters as being representative of the appearance of distinctive object parts. Appropriate feature detectors are then trained using these clusters, which can be used to obtain a set of candidate parts from images. As a result of this process, each image can now be represented as a set of parts. Each part has a type, corresponding to one of the aforementioned appearance clusters, as well as a location in the image space. === Basic generative model === Weber & Welling here introduce the concept of foreground and background. Foreground parts correspond to an instance of a target object class, whereas background parts correspond to background clutter or false detections. Let T be the number of different types of parts. The positions of all parts extracted from an image can then be represented in the following "matrix," X o = ( x 11 , x 12 , ⋯ , x 1 N 1 x 21 , x 22 , ⋯ , x 2 N 2 ⋮ x T 1 , x T 2 , ⋯ , x T N T ) {\displaystyle X^{o}={\begin{pmatrix}x_{11},x_{12},{\cdots },x_{1N_{1}}\\x_{21},x_{22},{\cdots },x_{2N_{2}}\\\vdots \\x_{T1},x_{T2},{\cdots },x_{TN_{T}}\end{pmatrix}}} where N i {\displaystyle N_{i}\,} represents the number of parts of type i ∈ { 1 , … , T } {\displaystyle i\in \{1,\dots ,T\}} observed in the image. The superscript o indicates that these positions are observable, as opposed to missing. The positions of unobserved object parts can be represented by the vector x m {\displaystyle x^{m}\,} . Suppose that the object will be composed of F {\displaystyle F\,} distinct foreground parts. For notational simplicity, we assume here that F = T {\displaystyle F=T\,} , though the model can be generalized to F > T {\displaystyle F>T\,} . A hypothesis h {\displaystyle h\,} is then defined as a set of indices, with h i = j {\displaystyle h_{i}=j\,} , indicating that point x i j {\displaystyle x_{ij}\,} is a foreground point in X o {\displaystyle X^{o}\,} . The generative probabilistic model is defined through the joint probability density p ( X o , x m , h ) {\displaystyle p(X^{o},x^{m},h)\,} . === Model details === The rest of this section summarizes the details of Weber & Welling's model for a single component model. The formulas for multiple component models are extensions of those described here. To parametrize the joint probability density, Weber & Welling introduce the auxiliary variables b {\displaystyle b\,} and n {\displaystyle n\,} , where b {\displaystyle b\,} is a binary vector encoding the presence/absence of parts in detection ( b i = 1 {\displaystyle b_{i}=1\,} if h i > 0 {\displaystyle h_{i}>0\,} , otherwise b i = 0 {\displaystyle b_{i}=0\,} ), and n {\displaystyle n\,} is a vector where n i {\displaystyle n_{i}\,} denotes the number of background candidates included in the i t h {\displaystyle i^{th}} row of X o {\displaystyle X^{o}\,} . Since b {\displaystyle b\,} and n {\displaystyle n\,} are completely determined by h {\displaystyle h\,} and the size of X o {\displaystyle X^{o}\,} , we have p ( X o , x m , h ) = p ( X o , x m , h , n , b ) {\displaystyle p(X^{o},x^{m},h)=p(X^{o},x^{m},h,n,b)\,} . By decomposition, p ( X o , x m , h , n , b ) = p ( X o , x m | h , n , b ) p ( h | n , b ) p ( n ) p ( b ) {\displaystyle p(X^{o},x^{m},h,n,b)=p(X^{o},x^{m}|h,n,b)p(h|n,b)p(n)p(b)\,} The probability density over the number of background detections can be modeled by a Poisson distribution, p ( n ) = ∏ i = 1 T 1 n i ! ( M i ) n i e − M i {\displaystyle p(n)=\prod _{i=1}^{T}{\frac {1}{n_{i}!}}(M_{i})^{n_{i}}e^{-M_{i}}} where M i {\displaystyle M_{i}\,} is the average number of background detections of type i {\displaystyle i\,} per image. Depending on the number of parts F {\displaystyle F\,} , the probability p ( b ) {\displaystyle p(b)\,} can be modeled either as an explicit table of length 2 F {\displaystyle 2^{F}\,} , or, if F {\displaystyle F\,} is large, as F {\displaystyle F\,} independent probabilities, each governing the presence of an individual part. The density p ( h | n , b ) {\displaystyle p(h|n,b)\,} is modeled by p ( h | n , b ) = { 1 ∏ f = 1 F N f b f , if h ∈ H ( b , n ) 0 , for other h {\displaystyle p(h|n,b)={\begin{cases}{\frac {1}{\textstyle \prod _{f=1}^{F}N_{f}^{b_{f}}}},&{\mbox{if }}h\in H(b,n)\\0,&{\mbox{for other }}h\end{cases}}} where H ( b , n ) {\displaystyle H(b,n)\,} denotes the set of all hypotheses consistent with b {\displaystyle b\,} and n {\displaystyle n\,} , and N f {\displaystyle N_{f}\,} denotes the total number of detections of parts of type f {\displaystyle f\,} . This expresses the fact that all consistent hypotheses, of which there are ∏ f = 1 F N f b f {\displaystyle \textstyle \prod _{f=1}^{F}N_{f}^{b_{f}}} , are equally likely in the absence of information on part locations. And finally, p ( X o , x m | h , n ) = p f g ( z ) p b g ( x b g ) {\displaystyle p(X^{o},x^{m}|h,n)=p_{fg}(z)p_{bg}(x_{bg})\,} where z = ( x o x m ) {\displaystyle z=(x^{o}x^{m})\,} are the coordinates of all foreground detections, observed and missing, and x b g {\displaystyle x_{bg}\,} represents the coordinates of the background detections. Note that foreground detections are assumed to be independent of the background. p f g ( z ) {\displaystyle p_{fg}(z)\,} is modeled as a joint Gaussian with mean μ {\displaystyle \mu \,} and covariance Σ {\displaystyle \Sigma \,} . === Classification === The ultimate objective of this model is to classify images into classes "object present" (class C 1 {\displaystyle C_{1}\,} ) and "object absent" (class C 0 {\displaystyle C_{0}\,} ) given t

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