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  • Latent semantic analysis

    Latent semantic analysis

    Latent semantic analysis (LSA) is a technique in natural language processing, in particular distributional semantics, of analyzing relationships between a set of documents and the terms they contain by producing a set of concepts related to the documents and terms. LSA assumes that words that are close in meaning will occur in similar pieces of text (the distributional hypothesis). A matrix containing word counts per document (rows represent unique words and columns represent each document) is constructed from a large piece of text and a mathematical technique called singular value decomposition (SVD) is used to reduce the number of rows while preserving the similarity structure among columns. Documents are then compared by cosine similarity between any two columns. Values close to 1 represent very similar documents while values close to 0 represent very dissimilar documents. An information retrieval technique using latent semantic structure was patented in 1988 by Scott Deerwester, Susan Dumais, George Furnas, Richard Harshman, Thomas Landauer, Karen Lochbaum and Lynn Streeter. In the context of its application to information retrieval, it is sometimes called latent semantic indexing (LSI). == Overview == === Occurrence matrix === LSA can use a document-term matrix which describes the occurrences of terms in documents; it is a sparse matrix whose rows correspond to terms and whose columns correspond to documents. A typical example of the weighting of the elements of the matrix is tf-idf (term frequency–inverse document frequency): the weight of an element of the matrix is proportional to the number of times the terms appear in each document, where rare terms are upweighted to reflect their relative importance. This matrix is also common to standard semantic models, though it is not necessarily explicitly expressed as a matrix, since the mathematical properties of matrices are not always used. === Rank lowering === After the construction of the occurrence matrix, LSA finds a low-rank approximation to the term-document matrix. There could be various reasons for these approximations: The original term-document matrix is presumed too large for the computing resources; in this case, the approximated low rank matrix is interpreted as an approximation (a "least and necessary evil"). The original term-document matrix is presumed noisy: for example, anecdotal instances of terms are to be eliminated. From this point of view, the approximated matrix is interpreted as a de-noisified matrix (a better matrix than the original). The original term-document matrix is presumed overly sparse relative to the "true" term-document matrix. That is, the original matrix lists only the words actually in each document, whereas we might be interested in all words related to each document—generally a much larger set due to synonymy. The consequence of the rank lowering is that some dimensions are combined and depend on more than one term: {(car), (truck), (flower)} → {(1.3452 car + 0.2828 truck), (flower)} This mitigates the problem of identifying synonymy, as the rank lowering is expected to merge the dimensions associated with terms that have similar meanings. It also partially mitigates the problem with polysemy, since components of polysemous words that point in the "right" direction are added to the components of words that share a similar meaning. Conversely, components that point in other directions tend to either simply cancel out, or, at worst, to be smaller than components in the directions corresponding to the intended sense. === Derivation === Let X {\displaystyle X} be a matrix where element ( i , j ) {\displaystyle (i,j)} describes the occurrence of term i {\displaystyle i} in document j {\displaystyle j} (this can be, for example, the frequency). X {\displaystyle X} will look like this: d j ↓ t i T → [ x 1 , 1 … x 1 , j … x 1 , n ⋮ ⋱ ⋮ ⋱ ⋮ x i , 1 … x i , j … x i , n ⋮ ⋱ ⋮ ⋱ ⋮ x m , 1 … x m , j … x m , n ] {\displaystyle {\begin{matrix}&{\textbf {d}}_{j}\\&\downarrow \\{\textbf {t}}_{i}^{T}\rightarrow &{\begin{bmatrix}x_{1,1}&\dots &x_{1,j}&\dots &x_{1,n}\\\vdots &\ddots &\vdots &\ddots &\vdots \\x_{i,1}&\dots &x_{i,j}&\dots &x_{i,n}\\\vdots &\ddots &\vdots &\ddots &\vdots \\x_{m,1}&\dots &x_{m,j}&\dots &x_{m,n}\\\end{bmatrix}}\end{matrix}}} Now a row in this matrix will be a vector corresponding to a term, giving its relation to each document: t i T = [ x i , 1 … x i , j … x i , n ] {\displaystyle {\textbf {t}}_{i}^{T}={\begin{bmatrix}x_{i,1}&\dots &x_{i,j}&\dots &x_{i,n}\end{bmatrix}}} Likewise, a column in this matrix will be a vector corresponding to a document, giving its relation to each term: d j = [ x 1 , j ⋮ x i , j ⋮ x m , j ] {\displaystyle {\textbf {d}}_{j}={\begin{bmatrix}x_{1,j}\\\vdots \\x_{i,j}\\\vdots \\x_{m,j}\\\end{bmatrix}}} Now the dot product t i T t p {\displaystyle {\textbf {t}}_{i}^{T}{\textbf {t}}_{p}} between two term vectors gives the correlation between the terms over the set of documents. The matrix product X X T {\displaystyle XX^{T}} contains all these dot products. Element ( i , p ) {\displaystyle (i,p)} (which is equal to element ( p , i ) {\displaystyle (p,i)} ) contains the dot product t i T t p {\displaystyle {\textbf {t}}_{i}^{T}{\textbf {t}}_{p}} ( = t p T t i {\displaystyle ={\textbf {t}}_{p}^{T}{\textbf {t}}_{i}} ). Likewise, the matrix X T X {\displaystyle X^{T}X} contains the dot products between all the document vectors, giving their correlation over the terms: d j T d q = d q T d j {\displaystyle {\textbf {d}}_{j}^{T}{\textbf {d}}_{q}={\textbf {d}}_{q}^{T}{\textbf {d}}_{j}} . Now, from the theory of linear algebra, there exists a decomposition of X {\displaystyle X} such that U {\displaystyle U} and V {\displaystyle V} are orthogonal matrices and Σ {\displaystyle \Sigma } is a diagonal matrix. This is called a singular value decomposition (SVD): X = U Σ V T {\displaystyle {\begin{matrix}X=U\Sigma V^{T}\end{matrix}}} The matrix products giving us the term and document correlations then become X X T = ( U Σ V T ) ( U Σ V T ) T = ( U Σ V T ) ( V T T Σ T U T ) = U Σ V T V Σ T U T = U Σ Σ T U T X T X = ( U Σ V T ) T ( U Σ V T ) = ( V T T Σ T U T ) ( U Σ V T ) = V Σ T U T U Σ V T = V Σ T Σ V T {\displaystyle {\begin{matrix}XX^{T}&=&(U\Sigma V^{T})(U\Sigma V^{T})^{T}=(U\Sigma V^{T})(V^{T^{T}}\Sigma ^{T}U^{T})=U\Sigma V^{T}V\Sigma ^{T}U^{T}=U\Sigma \Sigma ^{T}U^{T}\\X^{T}X&=&(U\Sigma V^{T})^{T}(U\Sigma V^{T})=(V^{T^{T}}\Sigma ^{T}U^{T})(U\Sigma V^{T})=V\Sigma ^{T}U^{T}U\Sigma V^{T}=V\Sigma ^{T}\Sigma V^{T}\end{matrix}}} Since Σ Σ T {\displaystyle \Sigma \Sigma ^{T}} and Σ T Σ {\displaystyle \Sigma ^{T}\Sigma } are diagonal we see that U {\displaystyle U} must contain the eigenvectors of X X T {\displaystyle XX^{T}} , while V {\displaystyle V} must be the eigenvectors of X T X {\displaystyle X^{T}X} . Both products have the same non-zero eigenvalues, given by the non-zero entries of Σ Σ T {\displaystyle \Sigma \Sigma ^{T}} , or equally, by the non-zero entries of Σ T Σ {\displaystyle \Sigma ^{T}\Sigma } . Now the decomposition looks like this: X U Σ V T ( d j ) ( d ^ j ) ↓ ↓ ( t i T ) → [ x 1 , 1 … x 1 , j … x 1 , n ⋮ ⋱ ⋮ ⋱ ⋮ x i , 1 … x i , j … x i , n ⋮ ⋱ ⋮ ⋱ ⋮ x m , 1 … x m , j … x m , n ] = ( t ^ i T ) → [ [ u 1 ] … [ u l ] ] ⋅ [ σ 1 … 0 ⋮ ⋱ ⋮ 0 … σ l ] ⋅ [ [ v 1 ] ⋮ [ v l ] ] {\displaystyle {\begin{matrix}&X&&&U&&\Sigma &&V^{T}\\&({\textbf {d}}_{j})&&&&&&&({\hat {\textbf {d}}}_{j})\\&\downarrow &&&&&&&\downarrow \\({\textbf {t}}_{i}^{T})\rightarrow &{\begin{bmatrix}x_{1,1}&\dots &x_{1,j}&\dots &x_{1,n}\\\vdots &\ddots &\vdots &\ddots &\vdots \\x_{i,1}&\dots &x_{i,j}&\dots &x_{i,n}\\\vdots &\ddots &\vdots &\ddots &\vdots \\x_{m,1}&\dots &x_{m,j}&\dots &x_{m,n}\\\end{bmatrix}}&=&({\hat {\textbf {t}}}_{i}^{T})\rightarrow &{\begin{bmatrix}{\begin{bmatrix}\,\\\,\\{\textbf {u}}_{1}\\\,\\\,\end{bmatrix}}\dots {\begin{bmatrix}\,\\\,\\{\textbf {u}}_{l}\\\,\\\,\end{bmatrix}}\end{bmatrix}}&\cdot &{\begin{bmatrix}\sigma _{1}&\dots &0\\\vdots &\ddots &\vdots \\0&\dots &\sigma _{l}\\\end{bmatrix}}&\cdot &{\begin{bmatrix}{\begin{bmatrix}&&{\textbf {v}}_{1}&&\end{bmatrix}}\\\vdots \\{\begin{bmatrix}&&{\textbf {v}}_{l}&&\end{bmatrix}}\end{bmatrix}}\end{matrix}}} The values σ 1 , … , σ l {\displaystyle \sigma _{1},\dots ,\sigma _{l}} are called the singular values, and u 1 , … , u l {\displaystyle u_{1},\dots ,u_{l}} and v 1 , … , v l {\displaystyle v_{1},\dots ,v_{l}} the left and right singular vectors. Notice the only part of U {\displaystyle U} that contributes to t i {\displaystyle {\textbf {t}}_{i}} is the i 'th {\displaystyle i{\textrm {'th}}} row. Let this row vector be called t ^ i T {\displaystyle {\hat {\textrm {t}}}_{i}^{T}} . Likewise, the only part of V T {\displaystyle V^{T}} that contributes to d j {\displaystyle {\textbf {d}}_{j}} is the j 'th {\displaystyle j{\textrm {'th}}} column, d ^ j {\displaystyle {\hat {\textrm {d}}}_{j}} . These are not the eigenvectors, but depend on all the eigenvectors. I

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  • Expectation–maximization algorithm

    Expectation–maximization algorithm

    In statistics, an expectation–maximization (EM) algorithm is an iterative method to find (local) maximum likelihood or maximum a posteriori (MAP) estimates of parameters in statistical models, where the model depends on unobserved latent variables. The EM iteration alternates between performing an expectation (E) step, which creates a function for the expectation of the log-likelihood evaluated using the current estimate for the parameters, and a maximization (M) step, which computes parameters maximizing the expected log-likelihood found on the E step. These parameter-estimates are then used to determine the distribution of the latent variables in the next E step. It can be used, for example, to estimate a mixture of gaussians, or to solve the multiple linear regression problem. == History == The EM algorithm was explained and given its name in a classic 1977 paper by Arthur Dempster, Nan Laird, and Donald Rubin. They pointed out that the method had been "proposed many times in special circumstances" by earlier authors. One of the earliest is the gene-counting method for estimating allele frequencies by Cedric Smith. Another was proposed by H.O. Hartley in 1958, and Hartley and Hocking in 1977, from which many of the ideas in the Dempster–Laird–Rubin paper originated. Another one by S.K Ng, Thriyambakam Krishnan and G.J McLachlan in 1977. Hartley's ideas can be broadened to any grouped discrete distribution. A very detailed treatment of the EM method for exponential families was published by Rolf Sundberg in his thesis and several papers, following his collaboration with Per Martin-Löf and Anders Martin-Löf. The Dempster–Laird–Rubin paper in 1977 generalized the method and sketched a convergence analysis for a wider class of problems. The Dempster–Laird–Rubin paper established the EM method as an important tool of statistical analysis. See also Meng and van Dyk (1997). The convergence analysis of the Dempster–Laird–Rubin algorithm was flawed and a correct convergence analysis was published by C. F. Jeff Wu in 1983. Wu's proof established the EM method's convergence also outside of the exponential family, as claimed by Dempster–Laird–Rubin. == Introduction == The EM algorithm is used to find (local) maximum likelihood parameters of a statistical model in cases where the equations cannot be solved directly. Typically these models involve latent variables in addition to unknown parameters and known data observations. That is, either missing values exist among the data, or the model can be formulated more simply by assuming the existence of further unobserved data points. For example, a mixture model can be described more simply by assuming that each observed data point has a corresponding unobserved data point, or latent variable, specifying the mixture component to which each data point belongs. Finding a maximum likelihood solution typically requires taking the derivatives of the likelihood function with respect to all the unknown values, the parameters and the latent variables, and simultaneously solving the resulting equations. In statistical models with latent variables, this is usually impossible. Instead, the result is typically a set of interlocking equations in which the solution to the parameters requires the values of the latent variables and vice versa, but substituting one set of equations into the other produces an unsolvable equation. The EM algorithm proceeds from the observation that there is a way to solve these two sets of equations numerically. One can simply pick arbitrary values for one of the two sets of unknowns, use them to estimate the second set, then use these new values to find a better estimate of the first set, and then keep alternating between the two until the resulting values both converge to fixed points. It's not obvious that this will work, but it can be proven in this context. Additionally, it can be proven that the derivative of the likelihood is (arbitrarily close to) zero at that point, which in turn means that the point is either a local maximum or a saddle point. In general, multiple maxima may occur, with no guarantee that the global maximum will be found. Some likelihoods also have singularities in them, i.e., nonsensical maxima. For example, one of the solutions that may be found by EM in a mixture model involves setting one of the components to have zero variance and the mean parameter for the same component to be equal to one of the data points. == Description == === The symbols === Given the statistical model which generates a set X {\displaystyle \mathbf {X} } of observed data, a set of unobserved latent data or missing values Z {\displaystyle \mathbf {Z} } , and a vector of unknown parameters θ {\displaystyle {\boldsymbol {\theta }}} , along with a likelihood function L ( θ ; X , Z ) = p ( X , Z ∣ θ ) {\displaystyle L({\boldsymbol {\theta }};\mathbf {X} ,\mathbf {Z} )=p(\mathbf {X} ,\mathbf {Z} \mid {\boldsymbol {\theta }})} , the maximum likelihood estimate (MLE) of the unknown parameters is determined by maximizing the marginal likelihood of the observed data L ( θ ; X ) = p ( X ∣ θ ) = ∫ p ( X , Z ∣ θ ) d Z = ∫ p ( X ∣ Z , θ ) p ( Z ∣ θ ) d Z {\displaystyle {\begin{aligned}L({\boldsymbol {\theta }};\mathbf {X} )=p(\mathbf {X} \mid {\boldsymbol {\theta }})&=\int p(\mathbf {X} ,\mathbf {Z} \mid {\boldsymbol {\theta }})\,d\mathbf {Z} \\&=\int p(\mathbf {X} \mid \mathbf {Z} ,{\boldsymbol {\theta }})p(\mathbf {Z} \mid {\boldsymbol {\theta }})\,d\mathbf {Z} \end{aligned}}} However, this quantity is often intractable since Z {\displaystyle \mathbf {Z} } is unobserved and the distribution of Z {\displaystyle \mathbf {Z} } is unknown before attaining θ {\displaystyle {\boldsymbol {\theta }}} . === The EM algorithm === The EM algorithm seeks to find the maximum likelihood estimate of the marginal likelihood by iteratively applying these two steps: More succinctly, we can write it as one equation: θ ( t + 1 ) = arg ⁡ max θ ⁡ E Z ∼ p ( ⋅ | X , θ ( t ) ) ⁡ [ log ⁡ p ( X , Z | θ ) ] {\displaystyle {\boldsymbol {\theta }}^{(t+1)}=\mathop {\arg \max } _{\boldsymbol {\theta }}\operatorname {E} _{\mathbf {Z} \sim p(\cdot |\mathbf {X} ,{\boldsymbol {\theta }}^{(t)})}\left[\log p(\mathbf {X} ,\mathbf {Z} |{\boldsymbol {\theta }})\right]\,} === Interpretation of the variables === The typical models to which EM is applied use Z {\displaystyle \mathbf {Z} } as a latent variable indicating membership in one of a set of groups: The observed data points X {\displaystyle \mathbf {X} } may be discrete (taking values in a finite or countably infinite set) or continuous (taking values in an uncountably infinite set). Associated with each data point may be a vector of observations. The missing values (aka latent variables) Z {\displaystyle \mathbf {Z} } are discrete, drawn from a fixed number of values, and with one latent variable per observed unit. The parameters are continuous, and are of two kinds: Parameters that are associated with all data points, and those associated with a specific value of a latent variable (i.e., associated with all data points whose corresponding latent variable has that value). However, it is possible to apply EM to other sorts of models. The motivation is as follows. If the value of the parameters θ {\displaystyle {\boldsymbol {\theta }}} is known, usually the value of the latent variables Z {\displaystyle \mathbf {Z} } can be found by maximizing the log-likelihood over all possible values of Z {\displaystyle \mathbf {Z} } , either simply by iterating over Z {\displaystyle \mathbf {Z} } or through an algorithm such as the Viterbi algorithm for hidden Markov models. Conversely, if we know the value of the latent variables Z {\displaystyle \mathbf {Z} } , we can find an estimate of the parameters θ {\displaystyle {\boldsymbol {\theta }}} fairly easily, typically by simply grouping the observed data points according to the value of the associated latent variable and averaging the values, or some function of the values, of the points in each group. This suggests an iterative algorithm, in the case where both θ {\displaystyle {\boldsymbol {\theta }}} and Z {\displaystyle \mathbf {Z} } are unknown: First, initialize the parameters θ {\displaystyle {\boldsymbol {\theta }}} to some random values. Compute the probability of each possible value of ⁠ Z {\displaystyle \mathbf {Z} } ⁠, given ⁠ θ {\displaystyle {\boldsymbol {\theta }}} ⁠. Then, use the just-computed values of Z {\displaystyle \mathbf {Z} } to compute a better estimate for the parameters ⁠ θ {\displaystyle {\boldsymbol {\theta }}} ⁠. Iterate steps 2 and 3 until convergence. The algorithm as just described monotonically approaches a local minimum of the cost function. == Properties == Although an EM iteration does increase the observed data (i.e., marginal) likelihood function, no guarantee exists that the sequence converges to a maximum likelihood estimator. For multimodal distributions, this means that an EM algorithm may co

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  • CN2 algorithm

    CN2 algorithm

    The CN2 induction algorithm is a learning algorithm for rule induction. It is designed to work even when the training data is imperfect. It is based on ideas from the AQ algorithm and the ID3 algorithm. As a consequence it creates a rule set like that created by AQ but is able to handle noisy data like ID3. == Description of algorithm == The algorithm must be given a set of examples, TrainingSet, which have already been classified in order to generate a list of classification rules. A set of conditions, SimpleConditionSet, which can be applied, alone or in combination, to any set of examples is predefined to be used for the classification. routine CN2(TrainingSet) let the ClassificationRuleList be empty repeat let the BestConditionExpression be Find_BestConditionExpression(TrainingSet) if the BestConditionExpression is not nil then let the TrainingSubset be the examples covered by the BestConditionExpression remove from the TrainingSet the examples in the TrainingSubset let the MostCommonClass be the most common class of examples in the TrainingSubset append to the ClassificationRuleList the rule 'if ' the BestConditionExpression ' then the class is ' the MostCommonClass until the TrainingSet is empty or the BestConditionExpression is nil return the ClassificationRuleList routine Find_BestConditionExpression(TrainingSet) let the ConditionalExpressionSet be empty let the BestConditionExpression be nil repeat let the TrialConditionalExpressionSet be the set of conditional expressions, {x and y where x belongs to the ConditionalExpressionSet and y belongs to the SimpleConditionSet}. remove all formulae in the TrialConditionalExpressionSet that are either in the ConditionalExpressionSet (i.e., the unspecialized ones) or null (e.g., big = y and big = n) for every expression, F, in the TrialConditionalExpressionSet if F is statistically significant and F is better than the BestConditionExpression by user-defined criteria when tested on the TrainingSet then replace the current value of the BestConditionExpression by F while the number of expressions in the TrialConditionalExpressionSet > user-defined maximum remove the worst expression from the TrialConditionalExpressionSet let the ConditionalExpressionSet be the TrialConditionalExpressionSet until the ConditionalExpressionSet is empty return the BestConditionExpression

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  • Teaching dimension

    Teaching dimension

    In computational learning theory, the teaching dimension of a concept class C is defined to be max c ∈ C { w C ( c ) } {\displaystyle \max _{c\in C}\{w_{C}(c)\}} , where w C ( c ) {\displaystyle {w_{C}(c)}} is the minimum size of a witness set for c in C. Intuitively, this measures the number of instances that are needed to identify a concept in the class, using supervised learning with examples provided by a helpful teacher who is trying to convey the concept as succinctly as possible. This definition was formulated in 1995 by Sally Goldman and Michael Kearns, based on earlier work by Goldman, Ron Rivest, and Robert Schapire. The teaching dimension of a finite concept class can be used to give a lower and an upper bound on the membership query cost of the concept class. In Stasys Jukna's book "Extremal Combinatorics", a lower bound is given for the teaching dimension in general: Let C be a concept class over a finite domain X. If the size of C is greater than 2 k ( | X | k ) , {\displaystyle 2^{k}{|X| \choose k},} then the teaching dimension of C is greater than k. However, there are more specific teaching models that make assumptions about teacher or learner, and can get lower values for the teaching dimension. For instance, several models are the classical teaching (CT) model, the optimal teacher (OT) model, recursive teaching (RT), preference-based teaching (PBT), and non-clashing teaching (NCT).

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  • Plotly

    Plotly

    Plotly is a technical computing company headquartered in Montreal, Quebec, that develops online data analytics and visualization tools. Plotly provides online graphing, analytics, and statistics tools for individuals and collaboration, as well as scientific graphing libraries for Python, R, MATLAB, Perl, Julia, Arduino, JavaScript and REST. == History == Plotly was founded by Alex Johnson, Jack Parmer, Chris Parmer, and Matthew Sundquist. The founders' backgrounds are in science, energy, and data analysis and visualization. Early employees include Christophe Viau, a Canadian software engineer and Ben Postlethwaite, a Canadian geophysicist. Plotly was named one of the Top 20 Hottest Innovative Companies in Canada by the Canadian Innovation Exchange. Plotly was featured in "startup row" at PyCon 2013, and sponsored the SciPy 2018 conference. Plotly raised $5.5 million during its Series A funding, led by MHS Capital, Siemens Venture Capital, Rho Ventures, Real Ventures, and Silicon Valley Bank. The Boston Globe and Washington Post newsrooms have produced data journalism using Plotly. In 2020, Plotly was named a Best Place to Work by the Canadian SME National Business Awards, and nominated as Business of the Year. == Products == Plotly offers open-source and enterprise products. Dash is an open-source Python, R, and Julia framework for building web-based analytic applications. Many specialized open-source Dash libraries exist that are tailored for building domain-specific Dash components and applications. Some examples are Dash DAQ, for building data acquisition GUIs to use with scientific instruments, and Dash Bio, which enables users to build custom chart types, sequence analysis tools, and 3D rendering tools for bioinformatics applications. Dash Enterprise is Plotly's paid product for building, testing, deploying, managing and scaling Dash applications organization-wide. Chart Studio Cloud is a free, online tool for creating interactive graphs. It has a point-and-click graphical user interface for importing and analyzing data into a grid and using stats tools. Graphs can be embedded or downloaded. Chart Studio Enterprise is a paid product that allows teams to create, style, and share interactive graphs on a single platform. It offers expanded authentication and file export options, and does not limit sharing and viewing. Data visualization libraries Plotly.js is an open-source JavaScript library for creating graphs and powers Plotly.py for Python, as well as Plotly.R for R, MATLAB, Node.js, Julia, and Arduino and a REST API. Plotly can also be used to style interactive graphs with Jupyter notebook. Figure converters which convert matplotlib, ggplot2, and IGOR Pro graphs into interactive, online graphs. == Data visualization libraries == Plotly provides a collection of supported chart types across several programming languages: == Dash == Dash is a Python framework built on top of React, a JavaScript library. Dash also works for R, and most recently supports Julia. While still described as a Python framework, Python isn't used for the other languages: "... describing Dash as a Python framework misses a key feature of its design: the Python side (the back end/server) of Dash was built to be lightweight and stateless [allowing] multiple back-end languages to coexist on an equal footing". It is possible to integrate D3.js charts as Dash components. Dash provides the default CSS (plus HTML and JavaScript), but for custom styling Dash applications, CSS can be added, or Dash Enterprise used. === Dash Enterprise === Dash Enterprise is Plotly's paid product for building, testing, deploying, managing and scaling Dash applications organization-wide. The product integrates with enterprise IT systems to enable organizations to build, deploy and scale low-code Dash applications. With open-source Dash, analytic applications can be run from a local machine, but cannot be easily accessed by others in the organization. ==== Enterprise IT integration ==== Dash Enterprise installs on cloud environments and on-premises. Amazon Web Services, Google Cloud Platform, and Microsoft Azure are supported, as are multiple Linux on-premises servers. Authentication integrations include LDAP, AD, PKI, Okta, SAML, OAuth2, SSO, and email authentication, and Dash application access is managed through a GUI rather than code. Dash Enterprise connects to major big data backends, including Salesforce, PostgreSQL, Databricks via PySpark, Snowflake, Dask, Datashader, and Vaex. In 2020, Plotly partnered with NVIDIA to integrate Dash with RAPIDS, and NVIDIA participated in Plotly's Series C funding round. ==== Low-code capabilities ==== Dash Enterprise enables low-code development of Dash applications, which is not possible with open-source Dash. Enterprise users can write applications in multiple development environments, including Jupyter Notebook. Dash Enterprise ships with several “development engines” for drag-and-drop application editing, application design, and automated reporting, as well as dozens of artificial intelligence and machine learning application templates. ==== Deployment and scaling ==== Dash application code is deployed to Dash Enterprise using the git-push command. Dash application deployments are containerized to avoid dependency conflicts, and can be embedded in existing web platforms without iframes. Deployed applications can be managed and accessed in a single portal called App Manager, where administrators can control user authentication and view usage analytics. Dash Enterprise scales horizontally with Kubernetes. Jobs queuing, GPU acceleration, and CPU parallelization support high performance computing requirements. Plotly also offers professional services for application development and workshop training.

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  • Operational taxonomic unit

    Operational taxonomic unit

    An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "operational taxonomic unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. == Molecular OTU by clustering of marker gene sequences == In the approach represented by DNA barcoding, a particular locus is chosen to be used as the marker gene for classification. This locus should be universally present in the scope selected, variable enough to be different among close-related species, and be flanked by conservative sequences that allow for easy amplification and detection. There are databases containing sequences for such marker genes from many different species, allowing for comparison. (Sometimes only using one locus does not provide sufficient resolution, so multiple marker genes are used. This is the case for plants, where rbcL+matK is common.) Sequences obtained this way can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold set by the researcher. The exact threshold depends on the taxa in question and the mutational rates of the selected locus in the taxon. 97–99% are commonly used, but "it is now recognized to be somewhat arbitrary as sequence variation within and among species varies across taxa". 100% similarity (fully identical) is also common, also known as single variants. It remains debatable how well this commonly used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, research by Schmidt et al. (2014) demonstrated that 16S-derived microbial OTUs were generally ecologically consistent across habitats and several clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing. === OTU clustering approaches === There are three main approaches to clustering OTUs: De novo, for which the clustering is based on similarities between sequencing reads. Closed-reference, for which the clustering is performed against a reference database of sequences. Open-reference, where clustering is first performed against a reference database of sequences, then any remaining sequences that could not be mapped to the reference are clustered de novo. Using a reference provides taxonomic context for the OTUs found. Alternatively, taxonomic context can be found after the construction of clusters by comparing representative sequences from clusters against a reference database. There are also specialized classifiers for this purpose which are much faster than naive comparison using BLAST. === OTU clustering algorithms === Hierarchical clustering algorithms (HCA): uclust & cd-hit & ESPRIT Bayesian clustering: CROP == Molecular OTU by other methods == In addition to similarity-based grouping, marker gene sequences can be sorted into OTUs using molecular phylogeny, k-mer composition, or hybrid methods combining these methods with similarity. There are also Bayesian tree-less methods and machine learning approaches. Using phylogeny often involves manually assigning terminal clades or single nodes to an OTU, so this is usually only done for refinement. Genome skimming can be used to obtain high-copy DNA without the need to choose marker genes or to design PCR primers for the chosen genes. It can provide fairly good coverage of organelle DNA and repetitive elements such as ribosomal DNA, both of which can be used like marker genes in OTU analysis. Whole-genome sequencing is more expensive and involves the production and processing of more data. By considering the entire genome, many (sometimes over 100) marker genes can be used at the same time, producing highly resolved phylogenies that correctly identify problematic taxa. It is also possible to use entire genomes for OTU assignment. For example, genomes from different bacterial species almost always have an average nucleotide identity lower than 95%, a fact that can be used to define new OTUs (and likely new species).

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  • Santa Fe Trail problem

    Santa Fe Trail problem

    The Santa Fe Trail problem is a genetic programming exercise in which artificial ants search for food pellets according to a programmed set of instructions. The layout of food pellets in the Santa Fe Trail problem has become a standard for comparing different genetic programming algorithms and solutions. One method for programming and testing algorithms on the Santa Fe Trail problem is by using the NetLogo application. There is at least one case of a student creating a Lego robotic ant to solve the problem.

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  • Joseph Nechvatal

    Joseph Nechvatal

    Joseph Nechvatal (born January 15, 1951) is an American post-conceptual digital artist and art theoretician who creates computer-assisted paintings and computer animations, often using custom computer viruses. == Life and work == Joseph Nechvatal was born in Chicago. He studied fine art and philosophy at Southern Illinois University Carbondale, Cornell University, and Columbia University. He earned a Doctor of Philosophy in Philosophy of Art and Technology at the Planetary Collegium at University of Wales, Newport and has taught art theory and art history at the School of Visual Arts. He has had many solo exhibitions and is one of five artists that art historian Patrick Frank examines in his 2024 book Art of the 1980s: As If the Digital Mattered. His work in the late 1970s and early 1980s chiefly consisted of postminimal gray palimpsest-like drawings that were often photo-mechanically enlarged. Beginning in 1979 he became associated with the artist group Colab, organized the Public Arts International/Free Speech series, and helped established the non-profit group ABC No Rio. In 1983 he co-founded the avant-garde electronic art music audio project Tellus Audio Cassette Magazine. In 1984, Nechvatal began work on an opera called XS: The Opera Opus (1984-6) with the no wave musical composer Rhys Chatham. He began using computers and robotics to make post-conceptual paintings in 1986 and later, in his signature work, began to employ self-created computer viruses. From 1991 to 1993, he was artist-in-residence at the Louis Pasteur Atelier in Arbois, France and at the Saline Royale/Ledoux Foundation's computer lab. There he worked on The Computer Virus Project, his first artistic experiment with computer viruses and computer virus animation. He exhibited computer-robotic paintings at Documenta 8 in 1987. In 2002 he extended his experimentation into viral artificial life through a collaboration with the programmer Stephane Sikora of music2eye in a work called the Computer Virus Project II. Nechvatal has also created a noise music work called viral symphOny, a collaborative sound symphony created by using his computer virus software at the Institute for Electronic Arts at Alfred University. In 2021 Pentiments released Nechvatal's retrospective audio cassette called Selected Sound Works (1981-2021) and in 2022 his The Viral Tempest, a double vinyl LP of new audio work. In 2025, he joined the roster of artists/musicians at Table of the Elements with two CD/book releases: Selected Sound Works (1981-2021) and The Marriage of Orlando and Artaud, Even. From 1999 to 2013, Nechvatal taught art theories of immersive virtual reality and the viractual at the School of Visual Arts in New York City (SVA). A book of his collected essays entitled Towards an Immersive Intelligence: Essays on the Work of Art in the Age of Computer Technology and Virtual Reality (1993–2006) was published by Edgewise Press in 2009. Also in 2009, his virtual reality art theory and art history book Immersive Ideals / Critical Distances was published. In 2011, his book Immersion Into Noise was published by Open Humanities Press in conjunction with the University of Michigan Library's Scholarly Publishing Office. Nechvatal has also published three books with Punctum Books: Minóy (noise music—ed.—2014), Destroyer of Naivetés (poetry—2015), and Styling Sagaciousness (poetry—2022). In 2023 his art theory cybersex farce novella venus©~Ñ~vibrator, even was published by Orbis Tertius Press The Joseph Nechvatal archive is housed at The Fales Library Downtown Collection at the NYU Special Collections Library in New York City. === Viractualism === Viractualism is an art theory concept developed by Nechvatal in 1999 from Ph.D. research Nechvatal conducted at the Planetary Collegium at University of Wales, Newport. There he developed his concept of the viractual, which strives to create an interface between the actual and the virtual.

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  • Josh (app)

    Josh (app)

    Josh (stylized as JOSH) was a video-sharing social networking service but it has since evolved into a live call and chat application owned by VerSe Innovation – an Indian technology company based in Bangalore, India. Josh was an Indian short video app that was launched in immediately after the Indian Government banned TikTok and other Chinese apps in June 2020. The founders of the platform have promoted the app as the “Instagram for Bharat” referring to their focus on the Indian audience that speaks its own regional and state languages. Josh was among the top 10 most downloaded apps social and entertainment apps in India of 2021 and had 150 million monthly active users as per April 2022. The word 'Josh' translates to fervour or passion. The app was launched under the aegis of the Atmanirbhar Bharat campaign and to compete with the duopoly of Google and Facebook in India. Josh's parent company VerSe Innovations Pvt. Ltd. owns another startup Dailyhunt, which a content and news aggregator application. Both Dailyhunt and Josh are a part of the VerSe's focus on the "next billion" regional language users of India. Founders Virendra Gupta and Umang Bedi conceptualised Josh as a short-video platform that made content creation accessible to vernacular language users, essentially the non-English speaking audience in India. == Features == Josh is currently available in 12 Indian languages and allows users to upload, share, remix bite-sized videos of up to 120 seconds. There are various categories across the video section including viral, trending, glamour, dance, devotion, yoga and cooking among others. Similar to Instagram and TikTok, it has a video feed which is curated for individuals on the basis of their app behaviour. The app hosts many daily, weekly and monthly social media challenges. == Funding == In December 2020, within 3 months of its launch, Josh's parent app VerSe Innovation raised more than $100 million from investors including Alphabet Inc's Google and Microsoft. In February 2021, VerSe Innovation raised $100 million in Series H funding from Qatar Investment Authority, the sovereign wealth fund of the State of Qatar, and Glade Brook Capital Partners. In August 2021, VerSe raised over $450 million in its Series I financing round with a valuation of $1 billion. Investors included Canada Pension Plan Investment Board (CPPIB), Siguler Guff, Baillie Gifford, Carlyle Asia Partners Growth II affiliates, and others. The startup announced its plan to expand overseas and broaden its ecommerce play for both Dailyhunt and Josh. In April 2022, VerSe announced that it has raised $805 million in funding from investors at a valuation of nearly $5 billion. ByteDance Offloads Stake In Josh Parent VerSe, Exits At 56% Discount == Partnerships == In February 2021, Saregama and Josh signed a music licensing deal, wherein Josh expanded its musical library with 1.3 lakh songs from Saregama in 25 different languages. To improve their user experience, Josh partnered with computer vision company D-ID in August 2021. The company helped Josh introduce photo-to-video features, live portrait technology, animate their photos etc. In order to solidify their efforts in enhancing Josh, VerSe acquired Indian social networking platform GolBol in October 2021. The move came as an effort by the startup to strengthen their discovery initiatives on the platform and classify content at scale and understand the core behaviour of Indian regional audiences. Josh has also announced its plans to include live commerce as a potential revenue stream through its partnership with multiple large e-commerce players. == Notable campaigns == Say No To Dowry – In association with Josh, the Kerala Police partook in the #SayNo2Dowry online social media campaign that was started to highlight and stop the social evil in the state. Salute India – Josh entered the Guinness World Records by creating the largest online video album of people saluting (29,529). It organised an online campaign #SaluteIndia on the app during the 75th Independence Day of India during 10–15 August 2021.

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  • Multiple kernel learning

    Multiple kernel learning

    Multiple kernel learning refers to a set of machine learning methods that use a predefined set of kernels and learn an optimal linear or non-linear combination of kernels as part of the algorithm. Reasons to use multiple kernel learning include a) the ability to select for an optimal kernel and parameters from a larger set of kernels, reducing bias due to kernel selection while allowing for more automated machine learning methods, and b) combining data from different sources (e.g. sound and images from a video) that have different notions of similarity and thus require different kernels. Instead of creating a new kernel, multiple kernel algorithms can be used to combine kernels already established for each individual data source. Multiple kernel learning approaches have been used in many applications, such as event recognition in video, object recognition in images, and biomedical data fusion. == Algorithms == Multiple kernel learning algorithms have been developed for supervised, semi-supervised, as well as unsupervised learning. Most work has been done on the supervised learning case with linear combinations of kernels, however, many algorithms have been developed. The basic idea behind multiple kernel learning algorithms is to add an extra parameter to the minimization problem of the learning algorithm. As an example, consider the case of supervised learning of a linear combination of a set of n {\displaystyle n} kernels K {\displaystyle K} . We introduce a new kernel K ′ = ∑ i = 1 n β i K i {\displaystyle K'=\sum _{i=1}^{n}\beta _{i}K_{i}} , where β {\displaystyle \beta } is a vector of coefficients for each kernel. Because the kernels are additive (due to properties of reproducing kernel Hilbert spaces), this new function is still a kernel. For a set of data X {\displaystyle X} with labels Y {\displaystyle Y} , the minimization problem can then be written as min β , c E ( Y , K ′ c ) + R ( K , c ) {\displaystyle \min _{\beta ,c}\mathrm {E} (Y,K'c)+R(K,c)} where E {\displaystyle \mathrm {E} } is an error function and R {\displaystyle R} is a regularization term. E {\displaystyle \mathrm {E} } is typically the square loss function (Tikhonov regularization) or the hinge loss function (for SVM algorithms), and R {\displaystyle R} is usually an ℓ n {\displaystyle \ell _{n}} norm or some combination of the norms (i.e. elastic net regularization). This optimization problem can then be solved by standard optimization methods. Adaptations of existing techniques such as the Sequential Minimal Optimization have also been developed for multiple kernel SVM-based methods. === Supervised learning === For supervised learning, there are many other algorithms that use different methods to learn the form of the kernel. The following categorization has been proposed by Gonen and Alpaydın (2011) ==== Fixed rules approaches ==== Fixed rules approaches such as the linear combination algorithm described above use rules to set the combination of the kernels. These do not require parameterization and use rules like summation and multiplication to combine the kernels. The weighting is learned in the algorithm. Other examples of fixed rules include pairwise kernels, which are of the form k ( ( x 1 i , x 1 j ) , ( x 2 i , x 2 j ) ) = k ( x 1 i , x 2 i ) k ( x 1 j , x 2 j ) + k ( x 1 i , x 2 j ) k ( x 1 j , x 2 i ) {\displaystyle k((x_{1i},x_{1j}),(x_{2i},x_{2j}))=k(x_{1i},x_{2i})k(x_{1j},x_{2j})+k(x_{1i},x_{2j})k(x_{1j},x_{2i})} . These pairwise approaches have been used in predicting protein-protein interactions. ==== Heuristic approaches ==== These algorithms use a combination function that is parameterized. The parameters are generally defined for each individual kernel based on single-kernel performance or some computation from the kernel matrix. Examples of these include the kernel from Tenabe et al. (2008). Letting π m {\displaystyle \pi _{m}} be the accuracy obtained using only K m {\displaystyle K_{m}} , and letting δ {\displaystyle \delta } be a threshold less than the minimum of the single-kernel accuracies, we can define β m = π m − δ ∑ h = 1 n ( π h − δ ) {\displaystyle \beta _{m}={\frac {\pi _{m}-\delta }{\sum _{h=1}^{n}(\pi _{h}-\delta )}}} Other approaches use a definition of kernel similarity, such as A ( K 1 , K 2 ) = ⟨ K 1 , K 2 ⟩ ⟨ K 1 , K 1 ⟩ ⟨ K 2 , K 2 ⟩ {\displaystyle A(K_{1},K_{2})={\frac {\langle K_{1},K_{2}\rangle }{\sqrt {\langle K_{1},K_{1}\rangle \langle K_{2},K_{2}\rangle }}}} Using this measure, Qui and Lane (2009) used the following heuristic to define β m = A ( K m , Y Y T ) ∑ h = 1 n A ( K h , Y Y T ) {\displaystyle \beta _{m}={\frac {A(K_{m},YY^{T})}{\sum _{h=1}^{n}A(K_{h},YY^{T})}}} ==== Optimization approaches ==== These approaches solve an optimization problem to determine parameters for the kernel combination function. This has been done with similarity measures and structural risk minimization approaches. For similarity measures such as the one defined above, the problem can be formulated as follows: max β , tr ⁡ ( K t r a ′ ) = 1 , K ′ ≥ 0 A ( K t r a ′ , Y Y T ) . {\displaystyle \max _{\beta ,\operatorname {tr} (K'_{tra})=1,K'\geq 0}A(K'_{tra},YY^{T}).} where K t r a ′ {\displaystyle K'_{tra}} is the kernel of the training set. Structural risk minimization approaches that have been used include linear approaches, such as that used by Lanckriet et al. (2002). We can define the implausibility of a kernel ω ( K ) {\displaystyle \omega (K)} to be the value of the objective function after solving a canonical SVM problem. We can then solve the following minimization problem: min tr ⁡ ( K t r a ′ ) = c ω ( K t r a ′ ) {\displaystyle \min _{\operatorname {tr} (K'_{tra})=c}\omega (K'_{tra})} where c {\displaystyle c} is a positive constant. Many other variations exist on the same idea, with different methods of refining and solving the problem, e.g. with nonnegative weights for individual kernels and using non-linear combinations of kernels. ==== Bayesian approaches ==== Bayesian approaches put priors on the kernel parameters and learn the parameter values from the priors and the base algorithm. For example, the decision function can be written as f ( x ) = ∑ i = 0 n α i ∑ m = 1 p η m K m ( x i m , x m ) {\displaystyle f(x)=\sum _{i=0}^{n}\alpha _{i}\sum _{m=1}^{p}\eta _{m}K_{m}(x_{i}^{m},x^{m})} η {\displaystyle \eta } can be modeled with a Dirichlet prior and α {\displaystyle \alpha } can be modeled with a zero-mean Gaussian and an inverse gamma variance prior. This model is then optimized using a customized multinomial probit approach with a Gibbs sampler. These methods have been used successfully in applications such as protein fold recognition and protein homology problems ==== Boosting approaches ==== Boosting approaches add new kernels iteratively until some stopping criteria that is a function of performance is reached. An example of this is the MARK model developed by Bennett et al. (2002) f ( x ) = ∑ i = 1 N ∑ m = 1 P α i m K m ( x i m , x m ) + b {\displaystyle f(x)=\sum _{i=1}^{N}\sum _{m=1}^{P}\alpha _{i}^{m}K_{m}(x_{i}^{m},x^{m})+b} The parameters α i m {\displaystyle \alpha _{i}^{m}} and b {\displaystyle b} are learned by gradient descent on a coordinate basis. In this way, each iteration of the descent algorithm identifies the best kernel column to choose at each particular iteration and adds that to the combined kernel. The model is then rerun to generate the optimal weights α i {\displaystyle \alpha _{i}} and b {\displaystyle b} . === Semisupervised learning === Semisupervised learning approaches to multiple kernel learning are similar to other extensions of supervised learning approaches. An inductive procedure has been developed that uses a log-likelihood empirical loss and group LASSO regularization with conditional expectation consensus on unlabeled data for image categorization. We can define the problem as follows. Let L = ( x i , y i ) {\displaystyle L={(x_{i},y_{i})}} be the labeled data, and let U = x i {\displaystyle U={x_{i}}} be the set of unlabeled data. Then, we can write the decision function as follows. f ( x ) = α 0 + ∑ i = 1 | L | α i K i ( x ) {\displaystyle f(x)=\alpha _{0}+\sum _{i=1}^{|L|}\alpha _{i}K_{i}(x)} The problem can be written as min f L ( f ) + λ R ( f ) + γ Θ ( f ) {\displaystyle \min _{f}L(f)+\lambda R(f)+\gamma \Theta (f)} where L {\displaystyle L} is the loss function (weighted negative log-likelihood in this case), R {\displaystyle R} is the regularization parameter (Group LASSO in this case), and Θ {\displaystyle \Theta } is the conditional expectation consensus (CEC) penalty on unlabeled data. The CEC penalty is defined as follows. Let the marginal kernel density for all the data be g m π ( x ) = ⟨ ϕ m π , ψ m ( x ) ⟩ {\displaystyle g_{m}^{\pi }(x)=\langle \phi _{m}^{\pi },\psi _{m}(x)\rangle } where ψ m ( x ) = [ K m ( x 1 , x ) , … , K m ( x L , x ) ] T {\displaystyle \psi _{m}(x)=[K_{m}(x_{1},x),\ldots ,K_{m}(x_{L},x)]^{T}} (the kernel distance between the labe

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  • Relationship square

    Relationship square

    In statistics, the relationship square is a graphical representation for use in the factorial analysis of a table individuals x variables. This representation completes classical representations provided by principal component analysis (PCA) or multiple correspondence analysis (MCA), namely those of individuals, of quantitative variables (correlation circle) and of the categories of qualitative variables (at the centroid of the individuals who possess them). It is especially important in factor analysis of mixed data (FAMD) and in multiple factor analysis (MFA). == Definition of relationship square in the MCA frame == The first interest of the relationship square is to represent the variables themselves, not their categories, which is all the more valuable as there are many variables. For this, we calculate for each qualitative variable j {\displaystyle j} and each factor F s {\displaystyle F_{s}} ( F s {\displaystyle F_{s}} , rank s {\displaystyle s} factor, is the vector of coordinates of the individuals along the axis of rank s {\displaystyle s} ; in PCA, F s {\displaystyle F_{s}} is called principal component of rank s {\displaystyle s} ), the square of the correlation ratio between the F s {\displaystyle F_{s}} and the variable j {\displaystyle j} , usually denoted : η 2 ( j , F s ) {\displaystyle \eta ^{2}(j,F_{s})} Thus, to each factorial plane, we can associate a representation of qualitative variables themselves. Their coordinates being between 0 and 1, the variables appear in the square having as vertices the points (0,0), ( 0,1), (1,0) and (1,1). == Example in MCA == Six individuals ( i 1 , … , i 6 ) {\displaystyle i_{1},\ldots ,i_{6})} are described by three variables ( q 1 , q 2 , q 3 ) {\displaystyle (q_{1},q_{2},q_{3})} having respectively 3, 2 and 3 categories. Example : the individual i 1 {\displaystyle i_{1}} possesses the category a {\displaystyle a} of q 1 {\displaystyle q_{1}} , d {\displaystyle d} of q 2 {\displaystyle q_{2}} and f {\displaystyle f} of q 3 {\displaystyle q_{3}} . Applied to these data, the MCA function included in the R Package FactoMineR provides to the classical graph in Figure 1. The relationship square (Figure 2) makes easier the reading of the classic factorial plane. It indicates that: The first factor is related to the three variables but especially q 3 {\displaystyle q_{3}} (which have a very high coordinate along the first axis) and then q 2 {\displaystyle q_{2}} . The second factor is related only to q 1 {\displaystyle q_{1}} and q 3 {\displaystyle q_{3}} (and not to q 2 {\displaystyle q_{2}} which has a coordinate along axis 2 equal to 0) and that in a strong and equal manner. All this is visible on the classic graphic but not so clearly. The role of the relationship square is first to assist in reading a conventional graphic. This is precious when the variables are numerous and possess numerous coordinates. == Extensions == This representation may be supplemented with those of quantitative variables, the coordinates of the latter being the square of correlation coefficients (and not of correlation ratios). Thus, the second advantage of the relationship square lies in the ability to represent simultaneously quantitative and qualitative variables. The relationship square can be constructed from any factorial analysis of a table individuals x variables. In particular, it is (or should be) used systematically: in multiple correspondences analysis (MCA); in principal components analysis (PCA) when there are many supplementary variables; in factor analysis of mixed data (FAMD). An extension of this graphic to groups of variables (how to represent a group of variables by a single point ?) is used in Multiple Factor Analysis (MFA) == History == The idea of representing the qualitative variables themselves by a point (and not the categories) is due to Brigitte Escofier. The graphic as it is used now has been introduced by Brigitte Escofier and Jérôme Pagès in the framework of multiple factor analysis == Conclusion == In MCA, the relationship square provides a synthetic view of the connections between mixed variables, all the more valuable as there are many variables having many categories. This representation iscan be useful in any factorial analysis when there are numerous mixed variables, active and/or supplementary.

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  • Multiple discriminant analysis

    Multiple discriminant analysis

    Multiple Discriminant Analysis (MDA) is a multivariate dimensionality reduction technique. It has been used to predict signals as diverse as neural memory traces and corporate failure. MDA is not directly used to perform classification. It merely supports classification by yielding a compressed signal amenable to classification. The method described in Duda et al. (2001) §3.8.3 projects the multivariate signal down to an M−1 dimensional space where M is the number of categories. MDA is useful because most classifiers are strongly affected by the curse of dimensionality. In other words, when signals are represented in very-high-dimensional spaces, the classifier's performance is catastrophically impaired by the overfitting problem. This problem is reduced by compressing the signal down to a lower-dimensional space as MDA does. MDA has been used to reveal neural codes.

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  • Cognition Network Technology

    Cognition Network Technology

    Cognition Network Technology (CNT), also known as Definiens Cognition Network Technology, is an object-based image analysis method developed by Nobel laureate Gerd Binnig together with a team of researchers at Definiens AG in Munich, Germany. It serves for extracting information from images using a hierarchy of image objects (groups of pixels), as opposed to traditional pixel processing methods. To emulate the human mind's cognitive powers, Definiens used patented image segmentation and classification processes, and developed a method to render knowledge in a semantic network. CNT examines pixels not in isolation, but in context. It builds up a picture iteratively, recognizing groups of pixels as objects. It uses the color, shape, texture and size of objects as well as their context and relationships to draw conclusions and inferences, similar to human analysis. == History == In 1994 Professor Gerd Binnig founded Definiens. CNT was first available with the launch of the eCognition software in May 2000. In June 2010, Trimble Navigation Ltd (NASDAQ: TRMB) acquired Definiens business asset in earth sciences markets, including eCognition software, and also licensed Definiens' patented CNT. In 2014, Definiens was acquired by MedImmune, the global biologics research and development arm of AstraZeneca, for an initial consideration of $150 million. == Software == Definiens Tissue Studio Definiens Tissue Studio is a digital pathology image analysis software application based on CNT. The intended use of Definiens Tissue Studio is for biomarker translational research in formalin-fixed, paraffin-embedded tissue samples which have been treated with immunohistochemical staining assays, or hematoxylin and eosin (H&E). The central concept behind Definiens Tissue Studio is a user interface that facilitates machine learning from example digital histopathology images to derive an image analysis solution suitable for the measurement of biomarkers and/or histological features within pre-defined regions of interest on a cell-by-cell basis, and within sub-cellular compartments. The derived image analysis solution is then automatically applied to subsequent digital images to objectively measure defined sets of multiparametric image features. These data sets are used for further understanding the underlying biological processes that drive cancer and other diseases. Image processing and data analysis are performed either on a local desktop computer workstation, or on a server grid. eCognition The eCognition suite offers three components that can be used stand-alone or in combination to solve image analysis tasks. eCognition Developer is a development environment for object-based image analysis. It is used in earth sciences to develop rule sets (or applications) for the analysis of remote sensing data. eCognition Architect enables non-technical users to configure, calibrate and execute image analysis workflows created in eCognition Developer. eCognition Server software provides a processing environment for batch execution of image analysis jobs. eCognition software is utilized in numerous remote sensing and geospatial application scenarios and environments, using a variety of data types: Generic: Rapid Mapping, Change Detection, Object Recognition By environment: Diverse Landcover Mapping, Urban Analysis (i.e. impervious surface area analysis for taxation, property assessment for insurance, inventory of green infrastructure), Forestry (i.e. biomass measurement, species identification, firescar measurement), Agriculture (i.e. regional planning, precision farming, crisis response), Marine and Riparian (i.e. ecosystem evaluation, disaster management, harbor monitoring). Other: Defense, security, atmosphere and climate The online eCognition community was launched in July 2009 and had 2813 members as of July 9, 2010. Membership is distributed globally and user conferences are held regularly, the last having taken place in November 2009 in Munich, Germany. The bi-annual GEOBIA (Geographic Object-Based Image Analysis) conference is heavily attended by eCognition users, with the majority of presentations based on eCognition software.

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  • Rule-based machine learning

    Rule-based machine learning

    Rule-based machine learning (RBML) is a term in computer science intended to encompass any machine learning method that identifies, learns, or evolves 'rules' to store, manipulate or apply. The defining characteristic of a rule-based machine learner is the identification and utilization of a set of relational rules that collectively represent the knowledge captured by the system. Rule-based machine learning approaches include learning classifier systems, association rule learning, artificial immune systems, and any other method that relies on a set of rules, each covering contextual knowledge. While rule-based machine learning is conceptually a type of rule-based system, it is distinct from traditional rule-based systems, which are often hand-crafted, and other rule-based decision makers. This is because rule-based machine learning applies some form of learning algorithm such as Rough sets theory to identify and minimise the set of features and to automatically identify useful rules, rather than a human needing to apply prior domain knowledge to manually construct rules and curate a rule set. == Rules == Rules typically take the form of an '{IF:THEN} expression', (e.g. {IF 'condition' THEN 'result'}, or as a more specific example, {IF 'red' AND 'octagon' THEN 'stop-sign}). An individual rule is not in itself a model, since the rule is only applicable when its condition is satisfied. Therefore rule-based machine learning methods typically comprise a set of rules, or knowledge base, that collectively make up the prediction model usually known as decision algorithm. Rules can also be interpreted in various ways depending on the domain knowledge, data types(discrete or continuous) and in combinations. == RIPPER == Repeated incremental pruning to produce error reduction (RIPPER) is a propositional rule learner proposed by William W. Cohen as an optimized version of IREP.

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  • Blockmodeling

    Blockmodeling

    Blockmodeling is a set or a coherent framework, that is used for analyzing social structure and also for setting procedure(s) for partitioning (clustering) social network's units (nodes, vertices, actors), based on specific patterns, which form a distinctive structure through interconnectivity. It is primarily used in statistics, machine learning and network science. As an empirical procedure, blockmodeling assumes that all the units in a specific network can be grouped together to such extent to which they are equivalent. Regarding equivalency, it can be structural, regular or generalized. Using blockmodeling, a network can be analyzed using newly created blockmodels, which transforms large and complex network into a smaller and more comprehensible one. At the same time, the blockmodeling is used to operationalize social roles. While some contend that the blockmodeling is just clustering methods, Bonacich and McConaghy state that "it is a theoretically grounded and algebraic approach to the analysis of the structure of relations". Blockmodeling's unique ability lies in the fact that it considers the structure not just as a set of direct relations, but also takes into account all other possible compound relations that are based on the direct ones. The principles of blockmodeling were first introduced by Francois Lorrain and Harrison C. White in 1971. Blockmodeling is considered as "an important set of network analytic tools" as it deals with delineation of role structures (the well-defined places in social structures, also known as positions) and the discerning the fundamental structure of social networks. According to Batagelj, the primary "goal of blockmodeling is to reduce a large, potentially incoherent network to a smaller comprehensible structure that can be interpreted more readily". Blockmodeling was at first used for analysis in sociometry and psychometrics, but has now spread also to other sciences. == Definition == A network as a system is composed of (or defined by) two different sets: one set of units (nodes, vertices, actors) and one set of links between the units. Using both sets, it is possible to create a graph, describing the structure of the network. During blockmodeling, the researcher is faced with two problems: how to partition the units (e.g., how to determine the clusters (or classes), that then form vertices in a blockmodel) and then how to determine the links in the blockmodel (and at the same time the values of these links). In the social sciences, the networks are usually social networks, composed of several individuals (units) and selected social relationships among them (links). Real-world networks can be large and complex; blockmodeling is used to simplify them into smaller structures that can be easier to interpret. Specifically, blockmodeling partitions the units into clusters and then determines the ties among the clusters. At the same time, blockmodeling can be used to explain the social roles existing in the network, as it is assumed that the created cluster of units mimics (or is closely associated with) the units' social roles. Blockmodeling can thus be defined as a set of approaches for partitioning units into clusters (also known as positions) and links into blocks, which are further defined by the newly obtained clusters. A block (also blockmodel) is defined as a submatrix, that shows interconnectivity (links) between nodes, present in the same or different clusters. Each of these positions in the cluster is defined by a set of (in)direct ties to and from other social positions. These links (connections) can be directed or undirected; there can be multiple links between the same pair of objects or they can have weights on them. If there are not any multiple links in a network, it is called a simple network. A matrix representation of a graph is composed of ordered units, in rows and columns, based on their names. The ordered units with similar patterns of links are partitioned together in the same clusters. Clusters are then arranged together so that units from the same clusters are placed next to each other, thus preserving interconnectivity. In the next step, the units (from the same clusters) are transformed into a blockmodel. With this, several blockmodels are usually formed, one being core cluster and others being cohesive; a core cluster is always connected to cohesive ones, while cohesive ones cannot be linked together. Clustering of nodes is based on the equivalence, such as structural and regular. The primary objective of the matrix form is to visually present relations between the persons included in the cluster. These ties are coded dichotomously (as present or absent), and the rows in the matrix form indicate the source of the ties, while the columns represent the destination of the ties. Equivalence can have two basic approaches: the equivalent units have the same connection pattern to the same neighbors or these units have same or similar connection pattern to different neighbors. If the units are connected to the rest of network in identical ways, then they are structurally equivalent. Units can also be regularly equivalent, when they are equivalently connected to equivalent others. With blockmodeling, it is necessary to consider the issue of results being affected by measurement errors in the initial stage of acquiring the data. == Different approaches == Regarding what kind of network is undergoing blockmodeling, a different approach is necessary. Networks can be one–mode or two–mode. In the former all units can be connected to any other unit and where units are of the same type, while in the latter the units are connected only to the unit(s) of a different type. Regarding relationships between units, they can be single–relational or multi–relational networks. Further more, the networks can be temporal or multilevel and also binary (only 0 and 1) or signed (allowing negative ties)/values (other values are possible) networks. Different approaches to blockmodeling can be grouped into two main classes: deterministic blockmodeling and stochastic blockmodeling approaches. Deterministic blockmodeling is then further divided into direct and indirect blockmodeling approaches. Among direct blockmodeling approaches are: structural equivalence and regular equivalence. Structural equivalence is a state, when units are connected to the rest of the network in an identical way(s), while regular equivalence occurs when units are equally related to equivalent others (units are not necessarily sharing neighbors, but have neighbour that are themselves similar). Indirect blockmodeling approaches, where partitioning is dealt with as a traditional cluster analysis problem (measuring (dis)similarity results in a (dis)similarity matrix), are: conventional blockmodeling, generalized blockmodeling: generalized blockmodeling of binary networks, generalized blockmodeling of valued networks and generalized homogeneity blockmodeling, prespecified blockmodeling. According to Brusco and Steinley (2011), the blockmodeling can be categorized (using a number of dimensions): deterministic or stochastic blockmodeling, one–mode or two–mode networks, signed or unsigned networks, exploratory or confirmatory blockmodeling. == Blockmodels == Blockmodels (sometimes also block models) are structures in which: vertices (e.g., units, nodes) are assembled within a cluster, with each cluster identified as a vertex; from such vertices a graph can be constructed; combinations of all the links (ties), represented in a block as a single link between positions, while at the same time constructing one tie for each block. In a case, when there are no ties in a block, there will be no ties between the two positions that define the block. Computer programs can partition the social network according to pre-set conditions. When empirical blocks can be reasonably approximated in terms of ideal blocks, such blockmodels can be reduced to a blockimage, which is a representation of the original network, capturing its underlying 'functional anatomy'. Thus, blockmodels can "permit the data to characterize their own structure", and at the same time not seek to manifest a preconceived structure imposed by the researcher. Blockmodels can be created indirectly or directly, based on the construction of the criterion function. Indirect construction refers to a function, based on "compatible (dis)similarity measure between paris of units", while the direct construction is "a function measuring the fit of real blocks induced by a given clustering to the corresponding ideal blocks with perfect relations within each cluster and between clusters according to the considered types of connections (equivalence)". === Types === Blockmodels can be specified regarding the intuition, substance or the insight into the nature of the studied network; this can result in such models as follows: parent-child role systems, organizational hierarchies, systems of

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