Data profiling is the process of examining the data available from an existing information source (e.g. a database or a file) and collecting statistics or informative summaries about that data. The purpose of these statistics may be to: Find out whether existing data can be easily used for other purposes Improve the ability to search data by tagging it with keywords, descriptions, or assigning it to a category Assess data quality, including whether the data conforms to particular standards or patterns Assess the risk involved in integrating data in new applications, including the challenges of joins Discover metadata of the source database, including value patterns and distributions, key candidates, foreign-key candidates, and functional dependencies Assess whether known metadata accurately describes the actual values in the source database Understanding data challenges early in any data intensive project, so that late project surprises are avoided. Finding data problems late in the project can lead to delays and cost overruns. Have an enterprise view of all data, for uses such as master data management, where key data is needed, or data governance for improving data quality. == Introduction == Data profiling refers to the analysis of information for use in a data warehouse in order to clarify the structure, content, relationships, and derivation rules of the data. Profiling helps to not only understand anomalies and assess data quality, but also to discover, register, and assess enterprise metadata. The result of the analysis is used to determine the suitability of the candidate source systems, usually giving the basis for an early go/no-go decision, and also to identify problems for later solution design. == How data profiling is conducted == Data profiling utilizes methods of descriptive statistics such as minimum, maximum, mean, mode, percentile, standard deviation, frequency, variation, aggregates such as count and sum, and additional metadata information obtained during data profiling such as data type, length, discrete values, uniqueness, occurrence of null values, typical string patterns, and abstract type recognition. The metadata can then be used to discover problems such as illegal values, misspellings, missing values, varying value representation, and duplicates. Different analyses are performed for different structural levels. E.g. single columns could be profiled individually to get an understanding of frequency distribution of different values, type, and use of each column. Embedded value dependencies can be exposed in a cross-columns analysis. Finally, overlapping value sets possibly representing foreign key relationships between entities can be explored in an inter-table analysis. Normally, purpose-built tools are used for data profiling to ease the process. The computational complexity increases when going from single column, to single table, to cross-table structural profiling. Therefore, performance is an evaluation criterion for profiling tools. == When is data profiling conducted? == According to Kimball, data profiling is performed several times and with varying intensity throughout the data warehouse developing process. A light profiling assessment should be undertaken immediately after candidate source systems have been identified and DW/BI business requirements have been satisfied. The purpose of this initial analysis is to clarify at an early stage if the correct data is available at the appropriate detail level and that anomalies can be handled subsequently. If this is not the case the project may be terminated. Additionally, more in-depth profiling is done prior to the dimensional modeling process in order assess what is required to convert data into a dimensional model. Detailed profiling extends into the ETL system design process in order to determine the appropriate data to extract and which filters to apply to the data set. Additionally, data profiling may be conducted in the data warehouse development process after data has been loaded into staging, the data marts, etc. Conducting data at these stages helps ensure that data cleaning and transformations have been done correctly and in compliance of requirements. == Benefits and examples == Data profiling can improve data quality, shorten the implementation cycle of major projects, and improve users' understanding of data. Discovering business knowledge embedded in data itself is one of the significant benefits derived from data profiling. It can improve data accuracy in corporate databases.
XRX (web application architecture)
In software development XRX is a web application architecture based on XForms, REST and XQuery. XRX applications store data on both the web client and on the web server in XML format and do not require a translation between data formats. XRX is considered a simple and elegant application architecture due to the minimal number of translations needed to transport data between client and server systems. The XRX architecture is also tightly coupled to W3C standards (CSS, XHTML 2.0, XPath, XML Schema) to ensure XRX applications will be robust in the future. Because XRX applications leverage modern declarative languages on the client and functional languages on the server they are designed to empower non-developers who are not familiar with traditional imperative languages such as JavaScript, Java or .Net. == Overview of XRX == XRX is a zero translation application architecture that uses XML to store data in the client web browser, on the application server and in the database server. It is because each of these layers uses XML as the same structural data model that XRX applications do not have to translate data structures to and from both object and relational data structures. Because of the lack of need for translation, XRX is considered to have a clean and elegant design. The XRX web application architecture allows developers to focus on the business problem and not the translation problem. XRX benefits from several advances in software technology: === Client Architectural Features === A model–view–controller (MVC) architecture that separates the data from its presentation and business logic. A single element (xf:submission) for all server submissions. This replaces much of the JavaScript code required in most AJAX applications. An advanced event model (XML Events) consistent with W3C standards that frees applications from having to deal with vendor-specific and browser-specific event handling. A Dependency graph that is used to store the dependency structure of the client controllers. This frees the developer from having to manually update either the model or the views when data changes in an application. This allows spreadsheet-like applications to be created on the client with very little effort. A declarative programming style that allows most client XForms applications to be created using a small set of approximately 20 elements. This allows rich client applications to be created without knowledge of JavaScript or other procedural scripting languages. An easy-to-extend system for creating new user interface controls using the EXtensible Bindings Language. This allows developers to add new controls at any time without fear of incompatibilities with W3C standards. === Server Architecture Features === Many native XML databases have built-in REST interfaces making each XQuery inherently a RESTful web service. A functional programming model that promotes side-effect free systems that are easier to debug and easier to run on multiple processors. An easy-to-extend system using XQuery function and modules. === Both Client and Server === Both XRX client and server components support a wide range of XML related standards such as XPath, XML Schema and XML Namespaces. Consistent use of REST interfaces to exchange data between the client and server for all transfers of data including as-you-type data checking and suggest functions. Consistent integration of W3C standards including use of XPath and XML Schema data types. A large library of standard of functions used on both the client and server. == Overall Benefits of XRX == One of the principal benefits of the XRX architecture is that it avoids the requirement to "shred" complex data structures into relational structures and then reconstitute the data back into structures when a record is edited on the client. Another benefits of the XRX Web application architecture is that it avoids most of the problems around the object-relational impedance mismatch. Another advantage is that the client developer does not have to learn JavaScript on the client. == Comparison with Traditional Object/Relational Web Application Architectures == Many traditional web application architectures created in the late 1990 were based on middle object tiers and persistence layers that used tabular data streams and relational database systems. Because each of these layers used different structures to store the models the systems required much additional complexity to translate between layers. == History of XRX == Early examples of using a zero-translation architecture in multi-tier systems can be traced back to the rise of object-oriented databases in the 1990s. See OODBMS History Mark Birbeck suggested that the combination of XForms, XQuery with REST interfaces between the two had many advantages in a meeting to the UK XML User Group in September 2006 . His presentation was one of the first to specifically suggest that the combination of three technologies: XForms and XQuery with REST interfaces would have surprisingly beneficial effects. Mark termed this process "Skimming" but that term did not seem to be contagious. Erik Bruchez of Orbeon spoke at the XML 2007 conference on Boston in December 2007. In his presentation "XForms and the eXist XML database: a perfect couple", Bruchez showed that many people were discovering synergistic benefits of XForms on the client and XQuery on the server. The label for XRX was suggested by a blog posting by Dan McCreary on December 14, 2007. It was in this article that Dan suggested the need for a contagious meme for the ideas behind the XRX architecture. == Generalizations of XRX == Although XRX was originally intended to connote the use of XForms on the client, REST as an interface and XQuery on the server, other proponents of the symmetrical use of XML on the client and server have generalized the term to encompass any XML-centric web client and any server that can store and query XML documents. This use of XRX is generally referred to as "shallow XRX". These generalizations do benefit from a simplified zero-translation architecture but many do not benefit from REST interfaces, XPath for consistent data selection, declarative systems in the client, and functional languages on the server (one of the key aspects of XRX). Use of all three technologies (XForms, REST and XQuery) is referred to as "deep XRX". Although XRX architecture is centred on XForms and XQuery, it does not preclude the use of other technologies that manipulate XML natively, such as XSLT, XProc, and XSL-FO.
Wolfram Mathematica
Wolfram Mathematica (also known as Mathematica) is a software system with built-in libraries for several areas of technical computing that allows machine learning, statistics, symbolic computation, data manipulation, network analysis, time series analysis, NLP, optimization, plotting functions and various types of data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other programming languages. It was conceived by Stephen Wolfram, and is developed by Wolfram Research of Champaign, Illinois. The Wolfram Language is the programming language used in Mathematica. Mathematica 1.0 was released on June 23, 1988 in Champaign, Illinois and Santa Clara, California. Mathematica's Wolfram Language is fundamentally based on Lisp; for example, the Mathematica command Most is identically equal to the Lisp command butlast. == Notebook interface == Mathematica is split into two parts: the kernel and the front end. The kernel interprets expressions (Wolfram Language code) and returns result expressions, which can then be displayed by the front end. The original front end, designed by Theodore Gray in 1988, consists of a notebook interface and allows the creation and editing of notebook documents that can contain code, plaintext, images, and graphics. Code development is also supported through support in a range of standard integrated development environment (IDE) including Eclipse, IntelliJ IDEA, Atom, Vim, Visual Studio Code and Git. The Mathematica Kernel also includes a command line front end. Other interfaces include JMath, based on GNU Readline and WolframScript which runs self-contained Mathematica programs (with arguments) from the UNIX command line. == High-performance computing == Capabilities for high-performance computing were extended with the introduction of packed arrays in version 4 (1999) and sparse matrices (version 5, 2003), and by adopting the GNU Multiple Precision Arithmetic Library to evaluate high-precision arithmetic. Version 5.2 (2005) added automatic multi-threading when computations are performed on multi-core computers. This release included CPU-specific optimized libraries. In addition Mathematica is supported by third party specialist acceleration hardware such as ClearSpeed. In 2002, gridMathematica was introduced to allow user level parallel programming on heterogeneous clusters and multiprocessor systems and in 2008 parallel computing technology was included in all Mathematica licenses including support for grid technology such as Windows HPC Server 2008, Microsoft Compute Cluster Server and Sun Grid. Support for CUDA and OpenCL GPU hardware was added in 2010. == Extensions == As of Version 14, there are 6,602 built-in functions and symbols in the Wolfram Language. Stephen Wolfram announced the launch of the Wolfram Function Repository in June 2019 as a way for the public Wolfram community to contribute functionality to the Wolfram Language. There are currently more than 3000 functions contributed as Resource Functions. In addition to the Wolfram Function Repository, there is a Wolfram Data Repository with computable data and the Wolfram Neural Net Repository for machine learning. Wolfram Mathematica is the basis of the Combinatorica package, which adds discrete mathematics functionality in combinatorics and graph theory to the program. == Connections to other applications, programming languages, and services == Communication with other applications can be done using a protocol called Wolfram Symbolic Transfer Protocol (WSTP). It allows communication between the Wolfram Mathematica kernel and the front end and provides a general interface between the kernel and other applications. Wolfram Research freely distributes a developer kit for linking applications written in the programming language C to the Mathematica kernel through WSTP using J/Link., a Java program that can ask Mathematica to perform computations. Similar functionality is achieved with .NET /Link, but with .NET programs instead of Java programs. Other languages that connect to Mathematica include Haskell, AppleScript, Racket, Visual Basic, Python, and Clojure. Mathematica supports the generation and execution of Modelica models for systems modeling and connects with Wolfram System Modeler. Links are also available to many third-party software packages and APIs. Mathematica can also capture real-time data from a variety of sources and can read and write to public blockchains (Bitcoin, Ethereum, and ARK). It supports import and export of over 220 data, image, video, sound, computer-aided design (CAD), geographic information systems (GIS), document, and biomedical formats. In 2019, support was added for compiling Wolfram Language code to LLVM. Version 12.3 of the Wolfram Language added support for Arduino. == Computable data == Mathematica is also integrated with Wolfram Alpha, an online answer engine that provides additional data, some of which is kept updated in real time, for users who use Mathematica with an internet connection. Some of the data sets include astronomical, chemical, geopolitical, language, biomedical, airplane, and weather data, in addition to mathematical data (such as knots and polyhedra). == Reception == BYTE in 1989 listed Mathematica as among the "Distinction" winners of the BYTE Awards, stating that it "is another breakthrough Macintosh application ... it could enable you to absorb the algebra and calculus that seemed impossible to comprehend from a textbook". Mathematica has been criticized for being closed source. Wolfram Research claims keeping Mathematica closed source is central to its business model and the continuity of the software.
Low-rank approximation
In mathematics, low-rank approximation refers to the process of approximating a given matrix by a matrix of lower rank. More precisely, it is a minimization problem, in which the cost function measures the fit between a given matrix (the data) and an approximating matrix (the optimization variable), subject to a constraint that the approximating matrix has reduced rank. The problem is used for mathematical modeling and data compression. The rank constraint is related to a constraint on the complexity of a model that fits the data. In applications, often there are other constraints on the approximating matrix apart from the rank constraint, e.g., non-negativity and Hankel structure. Low-rank approximation is closely related to numerous other techniques, including principal component analysis, factor analysis, total least squares, latent semantic analysis, orthogonal regression, and dynamic mode decomposition. == Definition == Given structure specification S : R n p → R m × n {\displaystyle {\mathcal {S}}:\mathbb {R} ^{n_{p}}\to \mathbb {R} ^{m\times n}} , vector of structure parameters p ∈ R n p {\displaystyle p\in \mathbb {R} ^{n_{p}}} , norm ‖ ⋅ ‖ {\displaystyle \|\cdot \|} , and desired rank r {\displaystyle r} , minimize over p ^ ‖ p − p ^ ‖ subject to rank ( S ( p ^ ) ) ≤ r . {\displaystyle {\text{minimize}}\quad {\text{over }}{\widehat {p}}\quad \|p-{\widehat {p}}\|\quad {\text{subject to}}\quad \operatorname {rank} {\big (}{\mathcal {S}}({\widehat {p}}){\big )}\leq r.} == Applications == Linear system identification, in which case the approximating matrix is Hankel structured. Machine learning, in which case the approximating matrix is nonlinearly structured. Recommender systems, in which cases the data matrix has missing values and the approximation is categorical. Distance matrix completion, in which case there is a positive definiteness constraint. Natural language processing, in which case the approximation is nonnegative. Computer algebra, in which case the approximation is Sylvester structured. Matrix product states, in which case the approximation is usually rescaled to have fixed Frobenius norm. == Basic low-rank approximation problem == The unstructured problem with fit measured by the Frobenius norm, i.e., minimize over D ^ ‖ D − D ^ ‖ F subject to rank ( D ^ ) ≤ r {\displaystyle {\text{minimize}}\quad {\text{over }}{\widehat {D}}\quad \|D-{\widehat {D}}\|_{\text{F}}\quad {\text{subject to}}\quad \operatorname {rank} {\big (}{\widehat {D}}{\big )}\leq r} has an analytic solution in terms of the singular value decomposition of the data matrix. The result is referred to as the matrix approximation lemma or Eckart–Young–Mirsky theorem. This problem was originally solved by Erhard Schmidt in the infinite dimensional context of integral operators (although his methods easily generalize to arbitrary compact operators on Hilbert spaces) and later rediscovered by C. Eckart and G. Young. L. Mirsky generalized the result to arbitrary unitarily invariant norms. Let D = U Σ V ⊤ ∈ R m × n , m ≥ n {\displaystyle D=U\Sigma V^{\top }\in \mathbb {R} ^{m\times n},\quad m\geq n} be the singular value decomposition of D {\displaystyle D} , where Σ =: diag ( σ 1 , … , σ r ) {\displaystyle \Sigma =:\operatorname {diag} (\sigma _{1},\ldots ,\sigma _{r})} , where r ≤ min { m , n } = n {\displaystyle r\leq \min\{m,n\}=n} , is the m × n {\displaystyle m\times n} rectangular diagonal matrix with r {\displaystyle r} non-zero singular values σ 1 ≥ … ≥ σ r > σ r + 1 = … = σ n = 0 {\displaystyle \sigma _{1}\geq \ldots \geq \sigma _{r}>\sigma _{r+1}=\ldots =\sigma _{n}=0} . For a given k ∈ { 1 , … , r } {\displaystyle k\in \{1,\dots ,r\}} , partition U {\displaystyle U} , Σ {\displaystyle \Sigma } , and V {\displaystyle V} as follows: U =: [ U 1 U 2 ] , Σ =: [ Σ 1 0 0 Σ 2 ] , and V =: [ V 1 V 2 ] , {\displaystyle U=:{\begin{bmatrix}U_{1}&U_{2}\end{bmatrix}},\quad \Sigma =:{\begin{bmatrix}\Sigma _{1}&0\\0&\Sigma _{2}\end{bmatrix}},\quad {\text{and}}\quad V=:{\begin{bmatrix}V_{1}&V_{2}\end{bmatrix}},} where U 1 {\displaystyle U_{1}} is m × k {\displaystyle m\times k} , Σ 1 {\displaystyle \Sigma _{1}} is k × k {\displaystyle k\times k} , and V 1 {\displaystyle V_{1}} is n × k {\displaystyle n\times k} . Then the rank k {\displaystyle k} matrix D ^ ∗ := U 1 Σ 1 V 1 ⊤ , {\displaystyle {\widehat {D}}^{}:=U_{1}\Sigma _{1}V_{1}^{\top },} obtained from the truncated singular value decomposition is such that ‖ D − D ^ ∗ ‖ F = min rank ( D ^ ) ≤ k ‖ D − D ^ ‖ F = σ k + 1 2 + ⋯ + σ r 2 . {\displaystyle \|D-{\widehat {D}}^{}\|_{\text{F}}=\min _{\operatorname {rank} ({\widehat {D}})\leq k}\|D-{\widehat {D}}\|_{\text{F}}={\sqrt {\sigma _{k+1}^{2}+\cdots +\sigma _{r}^{2}}}.} The minimizer D ^ ∗ {\displaystyle {\widehat {D}}^{}} is unique if and only if σ k > σ k + 1 {\displaystyle \sigma _{k}>\sigma _{k+1}} . == Proof of Eckart–Young–Mirsky theorem (for spectral norm) == Let A ∈ R m × n {\displaystyle A\in \mathbb {R} ^{m\times n}} be a real (possibly rectangular) matrix with m ≤ n {\displaystyle m\leq n} . Suppose that A = U Σ V ⊤ {\displaystyle A=U\Sigma V^{\top }} is the singular value decomposition of A {\displaystyle A} . Recall that U {\displaystyle U} and V {\displaystyle V} are orthogonal matrices, and Σ {\displaystyle \Sigma } is an m × n {\displaystyle m\times n} diagonal matrix with entries ( σ 1 , σ 2 , ⋯ , σ m ) {\displaystyle (\sigma _{1},\sigma _{2},\cdots ,\sigma _{m})} such that σ 1 ≥ σ 2 ≥ ⋯ ≥ σ m ≥ 0 {\displaystyle \sigma _{1}\geq \sigma _{2}\geq \cdots \geq \sigma _{m}\geq 0} . We claim that the best rank- k {\displaystyle k} approximation to A {\displaystyle A} in the spectral norm, denoted by ‖ ⋅ ‖ 2 {\displaystyle \|\cdot \|_{2}} , is given by A k := ∑ i = 1 k σ i u i v i ⊤ {\displaystyle A_{k}:=\sum _{i=1}^{k}\sigma _{i}u_{i}v_{i}^{\top }} where u i {\displaystyle u_{i}} and v i {\displaystyle v_{i}} denote the i {\displaystyle i} th column of U {\displaystyle U} and V {\displaystyle V} , respectively. First, note that we have ‖ A − A k ‖ 2 = ‖ ∑ i = 1 n σ i u i v i ⊤ − ∑ i = 1 k σ i u i v i ⊤ ‖ 2 = ‖ ∑ i = k + 1 n σ i u i v i ⊤ ‖ 2 = σ k + 1 {\displaystyle \|A-A_{k}\|_{2}=\left\|\sum _{i=1}^{\color {red}{n}}\sigma _{i}u_{i}v_{i}^{\top }-\sum _{i=1}^{\color {red}{k}}\sigma _{i}u_{i}v_{i}^{\top }\right\|_{2}=\left\|\sum _{i=\color {red}{k+1}}^{n}\sigma _{i}u_{i}v_{i}^{\top }\right\|_{2}=\sigma _{k+1}} Therefore, we need to show that if B k = X Y ⊤ {\displaystyle B_{k}=XY^{\top }} where X {\displaystyle X} and Y {\displaystyle Y} have k {\displaystyle k} columns then ‖ A − A k ‖ 2 = σ k + 1 ≤ ‖ A − B k ‖ 2 {\displaystyle \|A-A_{k}\|_{2}=\sigma _{k+1}\leq \|A-B_{k}\|_{2}} . Since Y {\displaystyle Y} has k {\displaystyle k} columns, then there must be a nontrivial linear combination of the first k + 1 {\displaystyle k+1} columns of V {\displaystyle V} , i.e., w = γ 1 v 1 + ⋯ + γ k + 1 v k + 1 , {\displaystyle w=\gamma _{1}v_{1}+\cdots +\gamma _{k+1}v_{k+1},} such that Y ⊤ w = 0 {\displaystyle Y^{\top }w=0} . Without loss of generality, we can scale w {\displaystyle w} so that ‖ w ‖ 2 = 1 {\displaystyle \|w\|_{2}=1} or (equivalently) γ 1 2 + ⋯ + γ k + 1 2 = 1 {\displaystyle \gamma _{1}^{2}+\cdots +\gamma _{k+1}^{2}=1} . Therefore, ‖ A − B k ‖ 2 2 ≥ ‖ ( A − B k ) w ‖ 2 2 = ‖ A w ‖ 2 2 = γ 1 2 σ 1 2 + ⋯ + γ k + 1 2 σ k + 1 2 ≥ σ k + 1 2 . {\displaystyle \|A-B_{k}\|_{2}^{2}\geq \|(A-B_{k})w\|_{2}^{2}=\|Aw\|_{2}^{2}=\gamma _{1}^{2}\sigma _{1}^{2}+\cdots +\gamma _{k+1}^{2}\sigma _{k+1}^{2}\geq \sigma _{k+1}^{2}.} The result follows by taking the square root of both sides of the above inequality. == Proof of Eckart–Young–Mirsky theorem (for Frobenius norm) == Let A ∈ R m × n {\displaystyle A\in \mathbb {R} ^{m\times n}} be a real (possibly rectangular) matrix with m ≤ n {\displaystyle m\leq n} . Suppose that A = U Σ V ⊤ {\displaystyle A=U\Sigma V^{\top }} is the singular value decomposition of A {\displaystyle A} . We claim that the best rank k {\displaystyle k} approximation to A {\displaystyle A} in the Frobenius norm, denoted by ‖ ⋅ ‖ F {\displaystyle \|\cdot \|_{F}} , is given by A k = ∑ i = 1 k σ i u i v i ⊤ {\displaystyle A_{k}=\sum _{i=1}^{k}\sigma _{i}u_{i}v_{i}^{\top }} where u i {\displaystyle u_{i}} and v i {\displaystyle v_{i}} denote the i {\displaystyle i} th column of U {\displaystyle U} and V {\displaystyle V} , respectively. First, note that we have ‖ A − A k ‖ F 2 = ‖ ∑ i = k + 1 n σ i u i v i ⊤ ‖ F 2 = ∑ i = k + 1 n σ i 2 {\displaystyle \|A-A_{k}\|_{F}^{2}=\left\|\sum _{i=k+1}^{n}\sigma _{i}u_{i}v_{i}^{\top }\right\|_{F}^{2}=\sum _{i=k+1}^{n}\sigma _{i}^{2}} Therefore, we need to show that if B k = X Y ⊤ {\displaystyle B_{k}=XY^{\top }} where X {\displaystyle X} and Y {\displaystyle Y} have k {\displaystyle k} columns then ‖ A − A k ‖ F 2 = ∑ i = k + 1 n σ i 2 ≤ ‖ A − B k ‖ F 2 . {\displaystyle \|A-A_{k}\|_{F}^{2}=\sum _{i=k+1}^{n}\sigma _{i}^{2}\leq \|A-B_{k}\|_{F}^{2}.} By the triangle inequality with the spectral norm
Linguamatics
Linguamatics, headquartered in Cambridge, England, with offices in the United States and UK, is a provider of text mining systems through software licensing and services, primarily for pharmaceutical and healthcare applications. Founded in 2001, the company was purchased by IQVIA in January 2019. == Technology == The company develops enterprise search tools for the life sciences sector. The core natural language processing engine (I2E) uses a federated architecture to incorporate data from 3rd party resources. Initially developed to be used interactively through a graphic user interface, the core software also has an application programming interface that can be used to automate searches. LabKey, Penn Medicine, Atrius Health and Mercy all use Linguamatics software to extract electronic health record data into data warehouses. Linguamatics software is used by 17 of the top 20 global pharmaceutical companies, the US Food and Drug Administration, as well as healthcare providers. == Software community == The core software, "I2E", is used by a number of companies to either extend their own software or to publish their data. Copyright Clearance Center uses I2E to produce searchable indexes of material that would otherwise be unsearchable due to copyright. Thomson Reuters produces Cortellis Informatics Clinical Text Analytics, which depends on I2E to make clinical data accessible and searchable. Pipeline Pilot can integrate I2E as part of a workflow. ChemAxon can be used alongside I2E to allow named entity recognition of chemicals within unstructured data. Data sources include MEDLINE, ClinicalTrials.gov, FDA Drug Labels, PubMed Central, and Patent Abstracts.
Projection-slice theorem
In mathematics, the projection-slice theorem, central slice theorem or Fourier slice theorem in two dimensions states that the results of the following two calculations are equal: Take a two-dimensional function f(r), project (e.g. using the Radon transform) it onto a (one-dimensional) line, and do a Fourier transform of that projection. Take that same function, but do a two-dimensional Fourier transform first, and then slice the function through its origin, parallel to the projection line. In operator terms, if F1 and F2 are the 1- and 2-dimensional Fourier transform operators mentioned above, P1 is the projection operator (which projects a 2-D function onto a 1-D line), S1 is a slice operator (which extracts a 1-D central slice from a function), then F 1 P 1 = S 1 F 2 . {\displaystyle F_{1}P_{1}=S_{1}F_{2}.} This idea can be extended to higher dimensions. This theorem is used, for example, in the analysis of medical CT scans where a "projection" is an x-ray image of an internal organ. The Fourier transforms of these images are seen to be slices through the Fourier transform of the 3-dimensional density of the internal organ, and these slices can be interpolated to build up a complete Fourier transform of that density. The inverse Fourier transform is then used to recover the 3-dimensional density of the object. This technique was first derived by Ronald N. Bracewell in 1956 for a radio-astronomy problem. == The projection-slice theorem in N dimensions == In N dimensions, the projection-slice theorem states that the Fourier transform of the projection of an N-dimensional function f(r) onto an m-dimensional linear submanifold is equal to an m-dimensional slice of the N-dimensional Fourier transform of that function consisting of an m-dimensional linear submanifold through the origin in the Fourier space which is parallel to the projection submanifold. In operator terms: F m P m = S m F N . {\displaystyle F_{m}P_{m}=S_{m}F_{N}.\,} == The generalized Fourier-slice theorem == In addition to generalizing to N dimensions, the projection-slice theorem can be further generalized with an arbitrary change of basis. For convenience of notation, we consider the change of basis to be represented as B, an N-by-N invertible matrix operating on N-dimensional column vectors. Then the generalized Fourier-slice theorem can be stated as F m P m B = S m B − T | B − T | F N {\displaystyle F_{m}P_{m}B=S_{m}{\frac {B^{-T}}{|B^{-T}|}}F_{N}} where B − T = ( B − 1 ) T {\displaystyle B^{-T}=(B^{-1})^{T}} is the transpose of the inverse of the change of basis transform. == Proof in two dimensions == The projection-slice theorem is easily proven for the case of two dimensions. Without loss of generality, we can take the projection line to be the x-axis. There is no loss of generality because if we use a shifted and rotated line, the law still applies. Using a shifted line (in y) gives the same projection and therefore the same 1D Fourier transform results. The rotated function is the Fourier pair of the rotated Fourier transform, for which the theorem again holds. If f(x, y) is a two-dimensional function, then the projection of f(x, y) onto the x axis is p(x) where p ( x ) = ∫ − ∞ ∞ f ( x , y ) d y . {\displaystyle p(x)=\int _{-\infty }^{\infty }f(x,y)\,dy.} The Fourier transform of f ( x , y ) {\displaystyle f(x,y)} is F ( k x , k y ) = ∫ − ∞ ∞ ∫ − ∞ ∞ f ( x , y ) e − 2 π i ( x k x + y k y ) d x d y . {\displaystyle F(k_{x},k_{y})=\int _{-\infty }^{\infty }\int _{-\infty }^{\infty }f(x,y)\,e^{-2\pi i(xk_{x}+yk_{y})}\,dxdy.} The slice is then s ( k x ) {\displaystyle s(k_{x})} s ( k x ) = F ( k x , 0 ) = ∫ − ∞ ∞ ∫ − ∞ ∞ f ( x , y ) e − 2 π i x k x d x d y {\displaystyle s(k_{x})=F(k_{x},0)=\int _{-\infty }^{\infty }\int _{-\infty }^{\infty }f(x,y)\,e^{-2\pi ixk_{x}}\,dxdy} = ∫ − ∞ ∞ [ ∫ − ∞ ∞ f ( x , y ) d y ] e − 2 π i x k x d x {\displaystyle =\int _{-\infty }^{\infty }\left[\int _{-\infty }^{\infty }f(x,y)\,dy\right]\,e^{-2\pi ixk_{x}}dx} = ∫ − ∞ ∞ p ( x ) e − 2 π i x k x d x {\displaystyle =\int _{-\infty }^{\infty }p(x)\,e^{-2\pi ixk_{x}}dx} which is just the Fourier transform of p(x). The proof for higher dimensions is easily generalized from the above example. == The FHA cycle == If the two-dimensional function f(r) is circularly symmetric, it may be represented as f(r), where r = |r|. In this case the projection onto any projection line will be the Abel transform of f(r). The two-dimensional Fourier transform of f(r) will be a circularly symmetric function given by the zeroth-order Hankel transform of f(r), which will therefore also represent any slice through the origin. The projection-slice theorem then states that the Fourier transform of the projection equals the slice or F 1 A 1 = H , {\displaystyle F_{1}A_{1}=H,} where A1 represents the Abel-transform operator, projecting a two-dimensional circularly symmetric function onto a one-dimensional line, F1 represents the 1-D Fourier-transform operator, and H represents the zeroth-order Hankel-transform operator. == Extension to fan beam or cone-beam CT == The projection-slice theorem is suitable for CT image reconstruction with parallel beam projections. It does not directly apply to fanbeam or conebeam CT. The theorem was extended to fan-beam and conebeam CT image reconstruction by Shuang-ren Zhao in 1995.
Types of artificial neural networks
Types of neural networks (NN) include a family of techniques. The simplest types have static components, including number of units, number of layers, unit weights and topology. Dynamic NNs evolve via learning. Some types allow/require learning to be "supervised" by the operator, while others operate independently. Some types operate purely in hardware, while others are purely software and run on general purpose computers. The main types are: Transformers: these use attention to analyze every token in the input stream against every other token in the stream. That technique has enabled neural networks to reach the general public via chatbots, code generators and many other forms. Convolutional neural networks (CNN): a FNN that uses kernels and regularization to evade problems in prior generations of NNs. They are typically used to analyze visual and other two-dimensional data. Generative adversarial networks set networks (of varying structure) against each other, each trying to push the other(s) to produce better results such as winning a game or to deceive the opponent about the authenticity of an input. == Feedforward == In feedforward neural networks the information moves from the input to output directly in every layer. There can be hidden layers with or without cycles/loops to sequence inputs. Feedforward networks can be constructed with various types of units, such as binary McCulloch–Pitts neurons, the simplest of which is the perceptron. Continuous neurons, frequently with sigmoidal activation, are used in the context of backpropagation. == Group method of data handling == The Group Method of Data Handling (GMDH) features fully automatic structural and parametric model optimization. The node activation functions are Kolmogorov–Gabor polynomials that permit additions and multiplications. It uses a deep multilayer perceptron with eight layers. It is a supervised learning network that grows layer by layer, where each layer is trained by regression analysis. Useless items are detected using a validation set, and pruned through regularization. The size and depth of the resulting network depends on the task. == Autoencoder == An autoencoder, autoassociator or Diabolo network is similar to the multilayer perceptron (MLP) – with an input layer, an output layer and one or more hidden layers connecting them. However, the output layer has the same number of units as the input layer. Its purpose is to reconstruct its own inputs (instead of emitting a target value). Therefore, autoencoders are unsupervised learning models. An autoencoder is used for unsupervised learning of efficient codings, typically for the purpose of dimensionality reduction and for learning generative models of data. == Probabilistic == A probabilistic neural network (PNN) is a four-layer feedforward neural network. The layers are Input, hidden pattern, hidden summation, and output. In the PNN algorithm, the parent probability distribution function (PDF) of each class is approximated by a Parzen window and a non-parametric function. Then, using PDF of each class, the class probability of a new input is estimated and Bayes’ rule is employed to allocate it to the class with the highest posterior probability. It was derived from the Bayesian network and a statistical algorithm called Kernel Fisher discriminant analysis. It is used for classification and pattern recognition. == Time delay == A time delay neural network (TDNN) is a feedforward architecture for sequential data that recognizes features independent of sequence position. In order to achieve time-shift invariance, delays are added to the input so that multiple data points (points in time) are analyzed together. It usually forms part of a larger pattern recognition system. It has been implemented using a perceptron network whose connection weights were trained with back propagation (supervised learning). == Convolutional == A convolutional neural network (CNN, or ConvNet or shift invariant or space invariant) is a class of deep network, composed of one or more convolutional layers with fully connected layers (matching those in typical ANNs) on top. It uses tied weights and pooling layers. In particular, max-pooling. It is often structured via Fukushima's convolutional architecture. They are variations of multilayer perceptrons that use minimal preprocessing. This architecture allows CNNs to take advantage of the 2D structure of input data. Its unit connectivity pattern is inspired by the organization of the visual cortex. Units respond to stimuli in a restricted region of space known as the receptive field. Receptive fields partially overlap, over-covering the entire visual field. Unit response can be approximated mathematically by a convolution operation. CNNs are suitable for processing visual and other two-dimensional data. They have shown superior results in both image and speech applications. They can be trained with standard backpropagation. CNNs are easier to train than other regular, deep, feed-forward neural networks and have many fewer parameters to estimate. Capsule Neural Networks (CapsNet) add structures called capsules to a CNN and reuse output from several capsules to form more stable (with respect to various perturbations) representations. Examples of applications in computer vision include DeepDream and robot navigation. They have wide applications in image and video recognition, recommender systems and natural language processing. == Deep stacking network == A deep stacking network (DSN) (deep convex network) is based on a hierarchy of blocks of simplified neural network modules. It was introduced in 2011 by Deng and Yu. It formulates the learning as a convex optimization problem with a closed-form solution, emphasizing the mechanism's similarity to stacked generalization. Each DSN block is a simple module that is easy to train by itself in a supervised fashion without backpropagation for the entire blocks. Each block consists of a simplified multi-layer perceptron (MLP) with a single hidden layer. The hidden layer h has logistic sigmoidal units, and the output layer has linear units. Connections between these layers are represented by weight matrix U; input-to-hidden-layer connections have weight matrix W. Target vectors t form the columns of matrix T, and the input data vectors x form the columns of matrix X. The matrix of hidden units is H = σ ( W T X ) {\displaystyle {\boldsymbol {H}}=\sigma ({\boldsymbol {W}}^{T}{\boldsymbol {X}})} . Modules are trained in order, so lower-layer weights W are known at each stage. The function performs the element-wise logistic sigmoid operation. Each block estimates the same final label class y, and its estimate is concatenated with original input X to form the expanded input for the next block. Thus, the input to the first block contains the original data only, while downstream blocks' input adds the output of preceding blocks. Then learning the upper-layer weight matrix U given other weights in the network can be formulated as a convex optimization problem: min U T f = ‖ U T H − T ‖ F 2 , {\displaystyle \min _{U^{T}}f=\|{\boldsymbol {U}}^{T}{\boldsymbol {H}}-{\boldsymbol {T}}\|_{F}^{2},} which has a closed-form solution. Unlike other deep architectures, such as DBNs, the goal is not to discover the transformed feature representation. The structure of the hierarchy of this kind of architecture makes parallel learning straightforward, as a batch-mode optimization problem. In purely discriminative tasks, DSNs outperform conventional DBNs. === Tensor deep stacking networks === This architecture is a DSN extension. It offers two important improvements: it uses higher-order information from covariance statistics, and it transforms the non-convex problem of a lower-layer to a convex sub-problem of an upper-layer. TDSNs use covariance statistics in a bilinear mapping from each of two distinct sets of hidden units in the same layer to predictions, via a third-order tensor. While parallelization and scalability are not considered seriously in conventional DNNs, all learning for DSNs and TDSNs is done in batch mode, to allow parallelization. Parallelization allows scaling the design to larger (deeper) architectures and data sets. The basic architecture is suitable for diverse tasks such as classification and regression. == Physics-informed == Such a neural network is designed for the numerical solution of mathematical equations, such as differential, integral, delay, fractional and others. As input parameters, PINN accepts variables (spatial, temporal, and others), transmits them through the network block. At the output, it produces an approximate solution and substitutes it into the mathematical model, considering the initial and boundary conditions. If the solution does not satisfy the required accuracy, one uses the backpropagation and rectify the solution. Besides PINN, other architectures have been developed to produce surrogate models for scientific comput