In mathematics and machine learning, the softplus function is f ( x ) = ln ( 1 + e x ) . {\displaystyle f(x)=\ln(1+e^{x}).} It is a smooth approximation (in fact, an analytic function) to the ramp function, which is known as the rectifier or ReLU (rectified linear unit) in machine learning. For large negative x {\displaystyle x} it is ln ( 1 + e x ) = ln ( 1 + ϵ ) ⪆ ln 1 = 0 {\displaystyle \ln(1+e^{x})=\ln(1+\epsilon )\gtrapprox \ln 1=0} , so just above 0, while for large positive x {\displaystyle x} it is ln ( 1 + e x ) ⪆ ln ( e x ) = x {\displaystyle \ln(1+e^{x})\gtrapprox \ln(e^{x})=x} , so just above x {\displaystyle x} . The names softplus and SmoothReLU are used in machine learning. The name "softplus" (2000), by analogy with the earlier softmax (1989) is presumably because it is a smooth (soft) approximation of the positive part of x, which is sometimes denoted with a superscript plus, x + := max ( 0 , x ) {\displaystyle x^{+}:=\max(0,x)} . == Alternative forms == This function can be approximated as: ln ( 1 + e x ) ≈ { ln 2 , x = 0 , x 1 − e − x / ln 2 , x ≠ 0 {\displaystyle \ln \left(1+e^{x}\right)\approx {\begin{cases}\ln 2,&x=0,\\[6pt]{\frac {x}{1-e^{-x/\ln 2}}},&x\neq 0\end{cases}}} By making the change of variables x = y ln ( 2 ) {\displaystyle x=y\ln(2)} , this is equivalent to log 2 ( 1 + 2 y ) ≈ { 1 , y = 0 , y 1 − e − y , y ≠ 0. {\displaystyle \log _{2}(1+2^{y})\approx {\begin{cases}1,&y=0,\\[6pt]{\frac {y}{1-e^{-y}}},&y\neq 0.\end{cases}}} A sharpness parameter k {\displaystyle k} may be included: f ( x ) = ln ( 1 + e k x ) k , f ′ ( x ) = e k x 1 + e k x = 1 1 + e − k x . {\displaystyle f(x)={\frac {\ln(1+e^{kx})}{k}},\qquad \qquad f'(x)={\frac {e^{kx}}{1+e^{kx}}}={\frac {1}{1+e^{-kx}}}.} Additionally, the softplus function is equivalent to the log of the sigmoid function in the following way: − ln ( sigmoid ( − x ) ) = − ln ( 1 1 + e x ) = ln ( 1 + e x ) = softplus ( x ) {\displaystyle -\ln({\text{sigmoid}}(-x))=-\ln \left({\frac {1}{1+e^{x}}}\right)=\ln \left(1+e^{x}\right)={\text{softplus}}(x)} == Related functions == The derivative of softplus is the standard logistic function: f ′ ( x ) = e x 1 + e x = 1 1 + e − x {\displaystyle f'(x)={\frac {e^{x}}{1+e^{x}}}={\frac {1}{1+e^{-x}}}} The logistic function or the sigmoid function is a smooth approximation of the rectifier, the Heaviside step function. === LogSumExp === The multivariable generalization of single-variable softplus is the LogSumExp with the first argument set to zero: L S E 0 + ( x 1 , … , x n ) := LSE ( 0 , x 1 , … , x n ) = ln ( 1 + e x 1 + ⋯ + e x n ) . {\displaystyle \operatorname {LSE_{0}} ^{+}(x_{1},\dots ,x_{n}):=\operatorname {LSE} (0,x_{1},\dots ,x_{n})=\ln(1+e^{x_{1}}+\cdots +e^{x_{n}}).} The LogSumExp function is LSE ( x 1 , … , x n ) = ln ( e x 1 + ⋯ + e x n ) , {\displaystyle \operatorname {LSE} (x_{1},\dots ,x_{n})=\ln(e^{x_{1}}+\cdots +e^{x_{n}}),} and its gradient is the softmax; the softmax with the first argument set to zero is the multivariable generalization of the logistic function. Both LogSumExp and softmax are used in machine learning. === Convex conjugate === The convex conjugate (specifically, the Legendre transformation) of the softplus function is the negative binary entropy function (with base e). This is because (following the definition of the Legendre transformation: the derivatives are inverse functions) the derivative of softplus is the logistic function, whose inverse function is the logit, which is the derivative of negative binary entropy. Softplus can be interpreted as logistic loss (as a positive number), so, by duality, minimizing logistic loss corresponds to maximizing entropy. This justifies the principle of maximum entropy as loss minimization.
Terminology model
A terminology model is a refinement of a concept system. Within a terminology model the concepts (object types) of a specific problem or subject area are defined by subject-matter experts in terms of concept (object type) definitions and definitions of subordinated concepts or characteristics (properties). Besides object types, the terminology model allows defining hierarchical classifications, definitions for object type and property behavior and definition of casual relations. The terminology model is a means for subject-matter experts to express their knowledge about the subject in subject-specific terms. Since the terminology model is structured rather similar to an object-oriented database schema, is can be transformed without loss of information into an object-oriented database schema. Thus, the terminology model is a method for problem analysis on the one side and a mean of defining database schema on the other side. Several terminology models have been developed and published in the field of statistics: Terminology model for classifications Terminology model for statistical variables Reference model for statistical metadata
QF-Test
QF-Test from Quality First Software is a cross-platform software tool for automated testing of programs via the graphical user interface (GUI) test automation). The program is specialized on (Java/Swing, Standard Widget Toolkit (SWT), Eclipse plug-ins and rich client platform (RCP) applications, ULC and JavaFX) cross-web browser test automation of static and dynamic web applications (HTML and web frameworks like Angular, Ext JS, Fluent UI React, Google Web Toolkit (GWT), jQuery UI, jQueryEasyUI Remote Application Platform (RAP), Qooxdoo, RichFaces, Vaadin, React, Smart GWT, Vue.js, ICEfaces and ZK). Version 4.1 added support for macOS and the Apple Safari and Microsoft Edge browsers via the Selenium WebDriver. Representational State Transfer (RESTful) web service testing. From version 5.0, Windows applications can also be tested (classic Win32 applications, .NET framework applications (often developed in C#) based on Windows Presentation Foundation (WPF) or Windows Forms, Windows apps and Universal Windows Platform (UWP) applications using Extensible Application Markup Language (XAML) controls) and modern C++ applications (such as Qt applications). Version 5.3 added support for the Chrome DevTools protocol, which allows browsers to be controlled using CDP drivers. Since then, mobile testing for iOS and Android, accessibility testing of web applications and SmartID, a new approach for more flexible and robust component recognition, have been introduced. Powerful enhancements such as WebAPI testing and AI-assisted validation complement the test automation tool. == Overview == QF-Test (the successor of qftestJUI, available since 2001) enables regression and load testing and runs on Windows, Unix and macOS. It is mainly used commercially by testers, developers or business analysts (modelling, low code approaches) with or without programming knowledge as part of software Quality Assurance. Since December 2008, a webtest add-on is available which allows test automation of browser-based GUIs (such as Internet Explorer, Mozilla Firefox, Google Chrome, Apple Safari, and Microsoft Edge) along with extant Java GUI test functions, which was extended to include JavaFX in July 2014. From 2018, QF-Test version 4.2 can test PDF documents, from 2020 native desktop applications (QF-Test version 5) and in 2022, mobile application testing will be added. The basis for efficient use in test automation is stable component recognition (IDs, logical screen elements, labels, CustomWebResolver, SmartID, ...) with low maintenance effort. == Features == General – QF-Test's capture/replay function enables recording of tests for beginners, while modular programming (modularizing) allows creating large test suites in a concise arrangement. For the advanced user who requires even more control over his application, the tool offers access to internal program structures through the standard scripting languages Jython, the Java implementation of the popular Python language, JavaScript, and Groovy. The tool also offers a batch processing mode, allowing to run tests unattended and then generate XML, HTML and JUnit reports. Thus the tool can be integrated into existing build/test frameworks like Jenkins, Ant or Maven. Another mode is the so-called Daemon mode for distributed test execution. A specific integration with many test management tools exists. There is a test debugger (enabling arbitrary stepping and editing variables at runtime) and a fully automated dependency management that takes care of pre- and postconditions and helps isolating test cases. Data-driven testing with no need for scripting is possible. Web testing: cross-browser on Internet Explorer, Chrome, Firefox, Edge (including Chromium-based), Opera and Safari for static and dynamic websites (HTML5, Ajax, DOM). A headless browser can also be used for testing. QF-Test fully supports frameworks like Angular, React and Vue.js, but also many specific UI toolkits like Smart (GWT), GXT/ExtGWT, ExtJS, ICEfaces, jQuery UI, Kendo UI, PrimeFaces, Qooxdoo, RAP, RichFaces, Vaadin and ZK. Easy integration with Selenium makes it easy to balance development and functional testing. Electron applications can also be tested. Other (e.g., SAP UI5, Siebel Open UI, Salesforce) and future web toolkits can be integrated with little effort. Short-term and individual customisations (CustomWebResolver) are possible via an optimised interface JavaFX, Java Swing, SWT, Eclipse plug-ins and RCP applications and ULC. Support for testing when migrating from JavaSwing or JavaFX to web applications (e.g. via Webswing). Hybrid applications based on multiple technologies are also supported, e.g. applications that integrate HTML content into Java applications using JxBrowser. Windows-based applications (Win32, .NET, Windows Forms, WPF, Windows apps, Qt). Android applications can be tested on real devices and with the Android Studio emulator. iOS applications can also be tested on real devices and with the Xcode Simulator. Testing of PDF documents (document comparisons, checking content, texts, images/graphic objects, layouts, "invisible" or partially hidden objects). QF-Test 9 introduces web accessibility testing to automatically check compliance with WCAG and other standards. QF-Test 10 introduces powerful enhancements for WebAPI testing and AI-assisted validation.
OpenIO
OpenIO offered object storage for a wide range of high-performance applications. OpenIO was founded in 2015 by Laurent Denel (CEO), Jean-François Smigielski (CTO) and five other co-founders; it leveraged open source software, developed since 2006, based on a grid technology that enabled dynamic behaviour and supported heterogenous hardware. In October 2017 OpenIO was completed a $5 million funding rounds. In July 2020 OpenIO had been acquired by OVH and withdrawn from the market to become the core technology of OVHcloud object storage offering. == Software == OpenIO is a software-defined object store that supports S3 and can be deployed on-premises, cloud-hosted or at the edge, on any hardware mix. It has been designed from the beginning for performance and cost-efficiency at any scale, and it has been optimized for Big Data, HPC and AI. OpenIO stores objects within a flat structure within a massively distributed directory with indirections, which allows the data query path to be independent of the number of nodes and the performance not to be affected by the growth of capacity. Servers are organized as a grid of nodes massively distributed, where each node takes part in directory and storage services, which ensures that there is no single point of failure and that new nodes are automatically discovered and immediately available without the need to rebalance data. The software is built on top of a technology that ensures optimal data placement based on real-time metrics and allows the addition or removal of storage devices with automatic performance and load impact optimization. For data protection OpenIO has synchronous and asynchronous replication with multiple copies, and an erasure coding implementation based on Reed-Solomon that can be deployed in one data center or geo-distributed or stretched clusters. The software has a feature that catches all events that occur in the cluster and can pass them up in the stack or to applications running on OpenIO nodes. This enables event-driven computing directly into the storage infrastructure. The open source code is available on Github and it is licensed under AGPL3 for server code and LGPL3 for client code. == Performance == OpenIO claimed in 2019 to have reached 1.372 Tbit/s write speed (171 GB/s) on a cluster of 350 physical machines. The benchmark scenario, conducted under production conditions with standard hardware (commodity servers with 7200 rpm HDDs), consisted in backing up a 38 PB Hadoop datalake via the DistCp command. This level of performance marked, according to analysts, the arrival of a new generation of object storage technologies oriented toward high performance and hyper-scalability.
AIX Toolbox for Linux Applications
The AIX Toolbox for Linux Applications is a collection of GNU tools for IBM AIX. These tools are available for installation using Red Hat's RPM format. == Licensing == Each of these packages includes its own licensing information and while IBM has made the code available to AIX users, the code is provided as is and has not been thoroughly tested. The Toolbox is meant to provide a core set of some of the most common development tools and libraries along with the more popular GNU packages.
Apptek
Applications Technology (AppTek) is a U.S. company headquartered in McLean, Virginia that specializes in artificial intelligence and machine learning for human language technologies. The company provides both managed and professional services for natural language processing (NLP) technologies including automatic speech recognition (ASR), neural machine translation (MT), natural-language understanding (NLU) and neural speech synthesis. AppTek's Head of Science, Prof. Dr. -Ing Hermann Ney, was awarded the IEEE James L. Flanagan Speech and Audio Processing Award in 2019 and the ISCA Medal for Scientific Achievement in 2021 for his work in natural language processing. == History == AppTek was acquired in 1998 by Lernout & Hauspie (at the time a NASDAQ publicly traded company), AppTek organized a management buy-out and went private again in 2001. In 2014, the company sold its hybrid machine translation technology to eBay and has since rebuilt the platform to modern neural-based approaches for machine translation. In 2020, SOSi acquired non-controlling interest in AppTek and became an exclusive reseller of AppTek products for U.S. federal, state, and local government entities.
Biopython
Biopython is an open-source collection of non-commercial Python modules for computational biology and bioinformatics. It makes robust and well-tested code easily accessible to researchers. Python is an object-oriented programming language and is a suitable choice for automation of common tasks. The availability of reusable libraries saves development time and lets researchers focus on addressing scientific questions. Biopython is constantly updated and maintained by a large team of volunteers across the globe. Biopython contains parsers for diverse bioinformatic sequence, alignment, and structure formats. Sequence formats include FASTA, FASTQ, GenBank, and EMBL. Alignment formats include Clustal, BLAST, PHYLIP, and NEXUS. Structural formats include the PDB, which contains the 3D atomic coordinates of the macromolecules. It has provisions to access information from biological databases like NCBI, Expasy, PBD, and BioSQL. This can be used in scripts or incorporated into their software. Biopython contains a standard sequence class, sequence alignment, and motif analysis tools. It also has clustering algorithms, a module for structural biology, and a module for phylogenetics analysis. == History == The development of Biopython began in 1999, and it was first released in July 2000. First "semi-complete" and "semi-stable" release was done in March 2001 and December 2002 respectively. It was developed during a similar time frame and with analogous goals to other projects that added bioinformatics capabilities to their respective programming languages, including BioPerl, BioRuby and BioJava. Early developers on the project included Jeff Chang, Andrew Dalke and Brad Chapman, though over 100 people have made contributions to date. In 2007, a similar Python project, namely PyCogent, was established. The initial scope of Biopython involved accessing, indexing and processing biological sequence files. The retrieved data from common biological databases will then be parsed into a python data structure. While this is still a major focus, over the following years added modules have extended its functionality to cover additional areas of biology. The key challenge in the design of parsers for bioinformatics file formats is the frequency at which the data formats change. This is due to inadequate curation of the structure of the data, and changes in the database contents. This problem is overcome by the application of a standard event-oriented parser design (see Key features and examples). As of version 1.77, Biopython no longer supports Python 2. The current stable release of Biopython version 1.85 was released on 15 January 2025. It only supports Python 3 and the recent releases of Biopython require NumPy (and not Numeric). == Design == Wherever possible, Biopython follows the conventions used by the Python programming language to make it easier for users familiar with Python. For example, Seq and SeqRecord objects can be manipulated via slicing, in a manner similar to Python's strings and lists. It is also designed to be functionally similar to other Bio projects, such as BioPerl. It is organized into modular sub-packages, e.g., Bio.Seq, Bio.Align, Bio.PDB, Bio.Entrez each of them useful in a different bioinformatics domain. It used principles, like encapsulation and polymorphism, notably in classes Seq, SeqRecord, and Bio.PDB.Structure. It can also interoperate with other Python tools (Pandas, Matplotlib and SciPy). Biopython can read and write most common file formats for each of its functional areas, and its license is permissive and compatible with most other software licenses, which allows Biopython to be used in a variety of software projects. == Requirements == Biopython is currently supported and tested with the following Python implementations: Python 3 or PyPy3 NumPy == Key features and examples == === Input and output === Biopython can read and write to a number of common formats. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others. Very large sequence files can exceed a computer's memory resources, so Biopython provides various options for accessing records in large files. They can be loaded entirely into memory in Python data structures, such as lists or dictionaries, providing fast access at the cost of memory usage. Alternatively, the files can be read from disk as needed, with slower performance but lower memory requirements. === Sequences === A core concept in Biopython is the biological sequence, and this is represented by the Seq class. A Biopython Seq object is similar to a Python string in many respects: it supports the Python slice notation, can be concatenated with other sequences and is immutable. This object includes both general string-like and biological sequence-specific methods. It is best to store information about the biological type (DNA, RNA, protein) separately from the sequence, rather than using an explicit alphabet argument. === Sequence annotation === The SeqRecord class describes sequences, along with information such as name, description and features in the form of SeqFeature objects. Each SeqFeature object specifies the type of the feature and its location. Feature types can be ‘gene’, ‘CDS’ (coding sequence), ‘repeat_region’, ‘mobile_element’ or others, and the position of features in the sequence can be exact or approximate. === Accessing online databases === Through the Bio.Entrez module, users of Biopython can download biological data from NCBI databases. Each of the functions provided by the Entrez search engine is available through functions in this module, including searching for and downloading records. === Phylogeny === The Bio.Phylo module provides tools for working with and visualising phylogenetic trees. A variety of file formats are supported for reading and writing, including Newick, NEXUS and phyloXML. Common tree manipulations and traversals are supported via the Tree and Clade objects. Examples include converting and collating tree files, extracting subsets from a tree, changing a tree's root, and analysing branch features such as length or score. Rooted trees can be drawn in ASCII or using matplotlib (see Figure 1), and the Graphviz library can be used to create unrooted layouts (see Figure 2). === Genome diagrams === The GenomeDiagram module provides methods of visualising sequences within Biopython. Sequences can be drawn in a linear or circular form (see Figure 3), and many output formats are supported, including PDF and PNG. Diagrams are created by making tracks and then adding sequence features to those tracks. By looping over a sequence's features and using their attributes to decide if and how they are added to the diagram's tracks, one can exercise much control over the appearance of the final diagram. Cross-links can be drawn between different tracks, allowing one to compare multiple sequences in a single diagram. === Macromolecular structure === The Bio.PDB module can load molecular structures from PDB and mmCIF files, and was added to Biopython in 2003. The Structure object is central to this module, and it organises macromolecular structure in a hierarchical fashion: Structure objects contain Model objects which contain Chain objects which contain Residue objects which contain Atom objects. Disordered residues and atoms get their own classes, DisorderedResidue and DisorderedAtom, that describe their uncertain positions. Using Bio.PDB, one can navigate through individual components of a macromolecular structure file, such as examining each atom in a protein. Common analyses can be carried out, such as measuring distances or angles, comparing residues and calculating residue depth. === Population genetics === The Bio.PopGen module adds support to Biopython for Genepop, a software package for statistical analysis of population genetics. This allows for analyses of Hardy–Weinberg equilibrium, linkage disequilibrium and other features of a population's allele frequencies. This module can also carry out population genetic simulations using coalescent theory with the fastsimcoal2 program. === Wrappers for command line tools === Biopython previously included command-line wrappers for tools such as BLAST, Clustal, EMBOSS, and SAMtools. This option allowed users to run external tool commands from within the code using specialized Biopython classes. However, Bio.Application modules and their wrappers have deprecated and will be removed in future Biopython releases. The main reason for this is the high maintenance burden of updating them with the evolving external tools. The recommended approach is to directly construct and execute command-line tool commands using Python’s built-in subprocess module. This method provides flexibility and removes the dependency on the Biopython wrappers. subprocess is a native Python module useful for running ext