A dendrogram is a diagram representing a tree graph. This diagrammatic representation is frequently used in different contexts: in hierarchical clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses. in computational biology, it shows the clustering of genes or samples, sometimes in the margins of heatmaps. in phylogenetics, it displays the evolutionary relationships among various biological taxa. In this case, the dendrogram is also called a phylogenetic tree. The name dendrogram derives from the two ancient greek words δένδρον (déndron), meaning "tree", and γράμμα (grámma), meaning "drawing, mathematical figure". == Clustering example == For a clustering example, suppose that five taxa ( a {\displaystyle a} to e {\displaystyle e} ) have been clustered by UPGMA based on a matrix of genetic distances. The hierarchical clustering dendrogram would show a column of five nodes representing the initial data (here individual taxa), and the remaining nodes represent the clusters to which the data belong, with the arrows representing the distance (dissimilarity). The distance between merged clusters is monotone, increasing with the level of the merger: the height of each node in the plot is proportional to the value of the intergroup dissimilarity between its two daughters (the nodes on the right representing individual observations all plotted at zero height).
List of performance analysis tools
This is a list of performance analysis tools for use in software development. == General purpose, language independent == The following tools work based on log files that can be generated from various systems. time (Unix) - can be used to determine the run time of a program, separately counting user time vs. system time, and CPU time vs. clock time. timem (Unix) - can be used to determine the wall-clock time, CPU time, and CPU utilization similar to time (Unix) but supports numerous extensions. Supports reporting peak resident set size, major and minor page faults, priority and voluntary context switches via getrusage. Supports sampling procfs on supporting systems to report metrics such as page-based resident set size, virtual memory size, read-bytes, and write-bytes, etc. Supports collecting hardware counters when built with PAPI support. == Multiple languages == The following tools work for multiple languages or binaries. == C and C++ == Arm MAP, a performance profiler supporting Linux platforms. AppDynamics, an application performance management service for C/C++ applications via SDK. AQtime Pro, a performance profiler and memory allocation debugger that can be integrated into Microsoft Visual Studio, and Embarcadero RAD Studio, or can run as a stand-alone application. IBM Rational Purify was a memory debugger allowing performance analysis. Instruments (bundled with Xcode) is used to profile an executable's memory allocations, time usage, filesystem activity, GPU activity etc. Intel Parallel Studio contains Intel VTune Amplifier, which tunes both serial and parallel programs. It also includes Intel Advisor and Intel Inspector. Intel Advisor optimizes vectorization (use of SIMD instructions) and prototypes threading implementations. Intel Inspector detects and debugs races, deadlocks and memory errors. Parasoft Insure++ provides a graphical tool that displays and animates memory allocations in real time to expose memory blowout, fragmentation, overuse, bottlenecks and leaks. Visual Studio Team System Profiler, commercial profiler by Microsoft. == Java == inspectIT is an open-source application performance management (APM) service for monitoring and analyzing software applications, available under the Apache License, Version 2.0 (ALv2). JConsole is the profiler which comes with the Java Development Kit JProfiler JRockit Mission Control, a profiler with low overhead. Netbeans Profiler, a profiler integrated into the NetBeans IDE (internally uses jvisualvm profiler) Plumbr, Java application performance monitoring with automated root cause detection. Links memory leaks, GC inefficiency, slow database and external web service calls, locked threads, and other performance problems to the line in source code that causes them. OverOps, Continuous reliability for the modern software supply chain, automatically detect and deliver root cause automation for all errors. VisualVM is a visual tool integrating several commandline JDK tools and lightweight profiling capabilities. It is bundled with the Java Development Kit since version 6, update 7. == JavaScript == The Firefox web browser's developer tools contain a Performance tool, which gives insight into JavaScript performance of a website. Microsoft Visual Studio AJAX Profiling Extensions is a free profiling tool for JavaScript by Microsoft Research. == .NET == CLR Profiler is a free memory profiler provided by Microsoft for CLR applications. GlowCode is a performance and memory profiler for .NET applications using C# and other .NET languages. It identifies time-intensive functions and detects memory leaks and errors in native, managed and mixed Windows x64 and x86 applications. Visual Studio == PHP == BlackFire.io Dbg Xdebug is a PHP extension which provides debugging and profiling capabilities.
Apps to analyse COVID-19 sounds
Apps to analyse COVID-19 sounds are mobile software applications designed to collect respiratory sounds and aid diagnosis in response to the COVID-19 pandemic. Numerous applications are in development, with different institutions and companies taking various approaches to privacy and data collection. Current efforts are aimed at gathering data. In a later stage, it is possible that sound apps will have the capacity (and ethical approvals) to provide information back to users. In order to develop and train signal analysis approaches, large datasets are required. == History == The COVID-19 outbreak was announced as a global pandemic by the World Health Organization in March 2020 and has affected a growing number of people globally. In this context, advanced artificial intelligence techniques are being considered as tools in aiding our response to global health crisis. Other COVID-19 apps which offer solutions for user tracking have been developed. At the same time a number of approaches which tries to use respiratory sounds and artificial intelligence to understand if the disease can be diagnosed have been proposed. A few studies are available as preprints (i.e. not yet peer-reviewed) documents. == Methodologies == The potential for using speech and sound analysis by artificial intelligence to help in this scenario, by surveying which types of related or contextually significant phenomena can be automatically assessed from speech or sound has been recently overviewed. These include the automatic recognition and monitoring of breathing, dry and wet coughing or sneezing sounds, speech under cold, eating behaviour, sleepiness, or pain. Additionally, the potential use-cases of intelligent speech analysis for COVID-19 diagnosed patients has also been presented. In particular, by analysing speech recordings from these patients, an audio-only-based model to automatically categorise the health state of patients from four aspects, including the severity of illness, sleep quality, fatigue, and anxiety, is constructed. This work shows promise in estimating the severity of illness. Machine learning methods have been explored to recognize and diagnose coughs from different diseases. These included a low complexity, automated recognition and diagnostic tool for screening respiratory infections that utilizes convolutional neural networks (CNNs) to detect cough within environment audio and diagnose three potential illnesses (i.e. bronchitis, bronchiolitis and pertussis) based on their unique cough audio features. A large-scale crowdsourced dataset of respiratory sounds has been collected to aid diagnosis of COVID-19: coughs and breathing sounds are sufficient to distinguish users affected by COVID-19 versus those affected by asthma or healthy controls. Behind these studies is the ambition that automated systems to screen for respiratory diseases based on voice, raw cough or other sound data would have positive medical applications in both clinical and public health arenas. == List of apps to analyse COVID-19 sounds ==
Vujak
VuJak is an early video sampler, a VJ remix and mashup tool created in 1992 by Brian Kane, Lisa Eisenpresser, and Jay Haynes. The original name of the project was Mideo, but it was later changed to VuJak. VuJak was based on MIDI control of video in real-time. It was created with MAX from Opcode Systems, and utilized the newly released QuickTime 1.0 movie object. The first working version of the program was built on a Mac IIfx with 8 megs of ram, and could jump in real-time across a 160 x 120 pixel QuickTime movie via a midi keyboard. Later versions could manipulate full screen video, included the first real-time video scratch feature, had looping, vari-speed, and random play features, and allowed for recording and editing of video sequences within the application. VuJak also had networking capabilities which allowed artists to "jam" in real time across standard phone lines. The first public exhibition of VuJak was at the Digital Hollywood conference in Beverly Hills in 1993, where it was promoted by Timothy Leary. VuJak was featured in Mondo 2000, CBS Evening News, Wired Magazine, Electronic Musician, Billboard Magazine, The Hollywood Reporter, and it was used to create promotional videos for MTV. In 1994, VuJak was a featured interactive exhibition at the Exploratorium in San Francisco. Development of VuJak ceased in 1995.
Single particle analysis
Single particle analysis is a group of related computerized image processing techniques used to analyze images from transmission electron microscopy (TEM). These methods were developed to improve and extend the information obtainable from TEM images of particulate samples, typically proteins or other large biological entities such as viruses. Individual images of stained or unstained particles are very noisy, making interpretation difficult. Combining several digitized images of similar particles together gives an image with stronger and more easily interpretable features. An extension of this technique uses single particle methods to build up a three-dimensional reconstruction of the particle. Using cryo-electron microscopy it has become possible to generate reconstructions with sub-nanometer, near-atomic resolution resolution first in the case of highly symmetric viruses, and now in smaller, asymmetric proteins as well. == Techniques == Single particle analysis can be done on both negatively stained and vitreous ice-embedded transmission electron cryomicroscopy (CryoTEM) samples. Single particle analysis methods are, in general, reliant on the sample being homogeneous, although techniques for dealing with conformational heterogeneity are being developed. Images (micrographs) are taken with an electron microscope using charged-coupled device (CCD) detectors coupled to a phosphorescent layer (in the past, they were instead collected on film and digitized using high-quality scanners). The image processing is carried out using specialized software programs, often run on multi-processor computer clusters. Depending on the sample or the desired results, various steps of two- or three-dimensional processing can be done. === Alignment and classification === Biological samples, and especially samples embedded in thin vitreous ice, are highly radiation sensitive, thus only low electron doses can be used to image the sample. This low dose, as well as variations in the metal stain used (if used) means images have high noise relative to the signal given by the particle being observed. By aligning several similar images to each other so they are in register and then averaging them, an image with higher signal-to-noise ratio can be obtained. As the noise is mostly randomly distributed and the underlying image features constant, by averaging the intensity of each pixel over several images only the constant features are reinforced. Typically, the optimal alignment (a translation and an in-plane rotation) to map one image onto another is calculated by cross-correlation. However, a micrograph often contains particles in multiple different orientations and/or conformations, and so to get more representative image averages, a method is required to group similar particle images together into multiple sets. This is normally carried out using one of several data analysis and image classification algorithms, such as multi-variate statistical analysis and hierarchical ascendant classification, or k-means clustering. Often data sets of tens of thousands of particle images are used, and to reach an optimal solution an iterative procedure of alignment and classification is used, whereby strong image averages produced by classification are used as reference images for a subsequent alignment of the whole data set. === Image filtering === Image filtering (band-pass filtering) is often used to reduce the influence of high and/or low spatial frequency information in the images, which can affect the results of the alignment and classification procedures. This is particularly useful in negative stain images. The algorithms make use of fast Fourier transforms (FFT), often employing Gaussian shaped soft-edged masks in reciprocal space to suppress certain frequency ranges. High-pass filters remove low spatial frequencies (such as ramp or gradient effects), leaving the higher frequencies intact. Low-pass filters remove high spatial frequency features and have a blurring effect on fine details. === Contrast transfer function === Due to the nature of image formation in the electron microscope, bright-field TEM images are obtained using significant underfocus. This, along with features inherent in the microscope's lens system, creates blurring of the collected images visible as a point spread function. The combined effects of the imaging conditions are known as the contrast transfer function (CTF), and can be approximated mathematically as a function in reciprocal space. Specialized image processing techniques such as phase flipping and amplitude correction / Wiener filtering can (at least partially) correct for the CTF, and allow high resolution reconstructions. === Three-dimensional reconstruction === Transmission electron microscopy images are projections of the object showing the distribution of density through the object, similar to medical X-rays. By making use of the projection-slice theorem a three-dimensional reconstruction of the object can be generated by combining many images (2D projections) of the object taken from a range of viewing angles. Proteins in vitreous ice ideally adopt a random distribution of orientations (or viewing angles), allowing a fairly isotropic reconstruction if a large number of particle images are used. This contrasts with electron tomography, where the viewing angles are limited due to the geometry of the sample/imaging set up, giving an anisotropic reconstruction. Filtered back projection is a commonly used method of generating 3D reconstructions in single particle analysis, although many alternative algorithms exist. Before a reconstruction can be made, the orientation of the object in each image needs to be estimated. Several methods have been developed to work out the relative Euler angles of each image. Some are based on common lines (common 1D projections and sinograms), others use iterative projection matching algorithms. The latter works by beginning with a simple, low resolution 3D starting model and compares the experimental images to projections of the model and creates a new 3D to bootstrap towards a solution. Methods are also available for making 3D reconstructions of helical samples (such as tobacco mosaic virus), taking advantage of the inherent helical symmetry. Both real space methods (treating sections of the helix as single particles) and reciprocal space methods (using diffraction patterns) can be used for these samples. === Tilt methods === The specimen stage of the microscope can be tilted (typically along a single axis), allowing the single particle technique known as random conical tilt. An area of the specimen is imaged at both zero and at high angle (~60-70 degrees) tilts, or in the case of the related method of orthogonal tilt reconstruction, +45 and −45 degrees. Pairs of particles corresponding to the same object at two different tilts (tilt pairs) are selected, and by following the parameters used in subsequent alignment and classification steps a three-dimensional reconstruction can be generated relatively easily. This is because the viewing angle (defined as three Euler angles) of each particle is known from the tilt geometry. 3D reconstructions from random conical tilt suffer from missing information resulting from a restricted range of orientations. Known as the missing cone (due to the shape in reciprocal space), this causes distortions in the 3D maps. However, the missing cone problem can often be overcome by combining several tilt reconstructions. Tilt methods are best suited to negatively stained samples, and can be used for particles that adsorb to the carbon support film in preferred orientations. The phenomenon known as charging or beam-induced movement makes collecting high-tilt images of samples in vitreous ice challenging. === Map visualization and fitting === Various software programs are available that allow viewing the 3D maps. These often enable the user to manually dock in protein coordinates (structures from X-ray crystallography, NMR, or a computational model such as one found in the AlphaFold Protein Structure Database) of subunits into the electron density. Several programs can also fit subunits computationally; as of the 2020s using these programs tend to produce better accuracy than manual docking because they can perform labor-intensive tasks such as: The scale of SPA-derived maps depends on knowing the pixel size (angstorms per pixel), which is not always accurate. Programs can automatically correct for this difference by using coordinate data or by using knowledge of chemical bonds. Many proteins are made up of several roughly rigid protein domains linked by flexible parts. Pre-existing coordinate data, whether experimental or computational, may not exactly match the inter-domain positioning of the cyro-EM map. Modern programs can automatically "chop" pre-existing coordinate data into individual domains and fit them in individually. For higher-resolution structures, it is pos
MeeMix
MeeMix Ltd is a company specializing in personalizing media-related content recommendations, discovery and advertising for the telecommunication industry, founded in 2006. On January 1, 2008, MeeMix launched meemix.com, a public personalized internet radio serving as an online testbed for the development of music taste-prediction technologies. Subsequently, MeeMix released in 2009 a line of Business-to-business commercial services intended to personalize media recommendations, discovery and advertising. MeeMix hybrid taste-prediction technology relies on integrating machine learning algorithms, digital signal processing, behavior analysis, metadata analysis and collaborative filtering, and is provided via API web service. In August 2009, MeeMix was announced as Innovator Nominee in the GSM Association’s Mobile Innovation Grand Prix worldwide contest. As of 2013, MeeMix no longer features internet radios on meemix.com. On Sep 28, 2014, meemix.com went offline.
Diia
Diia (Ukrainian: Дія [ˈd⁽ʲ⁾ijɐ] , lit. 'Action'; also an acronym for Держава і Я, Derzhava i Ya, IPA: [derˈʒɑwɐ i ˈjɑ], lit. 'State and Me') is a mobile app, a web portal and a brand of e-governance in Ukraine. Launched in 2020, the Diia app allows Ukrainian citizens to use digital documents on their smartphones instead of physical ones for identification and sharing purposes. The Diia portal allows access to over 130 government services. Eventually, the government plans to make all kinds of state-person interactions available through Diia. Diia was built in partnership with the United States and is poised to be shared with other countries. On the sidelines of the 2023 World Economic Forum in Davos, USAID Administrator Samantha Power said the US hopes to replicate the success of Diia in other countries. == History == Diia was first presented on September 27, 2019, by the Ministry of Digital Transformation of Ukraine as a brand of the State in a Smartphone project. Vice Prime Minister and Minister of Digital Transformation Mykhailo Fedorov announced the creation of a mobile app and a web portal that would unite in a single place all the services provided by the state to citizens and businesses. On February 6, 2020, the mobile app Diia was officially launched. During the presentation, Ukrainian President Volodymyr Zelensky said that 9 million Ukrainians now have access to their driver's license and car registration documents on their phones, while Prime Minister Oleksiy Honcharuk called the implementation of the State in a Smartphone project a priority for the government. In April 2020, the Ukrainian government approved a resolution for experimental usage of digital ID-cards and passports which would be issued to all Ukrainians via the Diia. On October 5, 2020, during the Diia Summit, the government presented a first major update of the app and web portal branded "Diia 2.0". More types of documents were added to the app as well as the ability to share documents with others via a single tap on a push-message. The web portal in turn expanded the number of available services to 27, including the ability to register a private limited company in half an hour. President Zelensky who opened the summit, announced that in 2021 Ukraine will enter the "paper less" mode by prohibiting civil servants from demanding paper documents. By the end of 2020, the app had more than six million users, while the portal had 50 available services. In March 2021, the Ukrainian parliament adopted a bill equating digital identity documents with their physical analogues. Starting on August 23, Ukrainian citizens can use digital ID-cards and passports for all purposes while in Ukraine. According to Minister of Digital Transformation Mykhailo Fedorov, Ukraine will become the first country in the world where digital identity documents are considered legally equivalent to ordinary ones. In September 2024, Diia launched an online marriage registration service, which can be beneficial especially for military personnel who spend much time on the frontline separated from their partners. In October 2024, Diia's online marriage service appeared in Time's Inventions of the 2024 list. In the first month of its operations over 1.1 million Ukrainians tried to make proposals using the technology, and 435 couples got married. == Benefits and challenges == The first and most obvious benefit is the convenience of such a platform. Citizens can have many documents on their smartphones at once, without concern about losing or damaging them. Whenever needed, they can just open an app on their smartphones and show/check the document they need. The idea is that Diia will help cut the bureaucracy associated with public services, which in turn will help fight corruption and increase government savings. Fewer people are needed to be employed in the public sector and fewer human to human interactions are supposed to happen. With the start of the program, already 10% of government employees were reduced, which contributes to hundreds of millions of dollars in savings, but besides this, the initiative also improves the speed, efficiency, and transparency of government services. In addition, the digitalization of the government sector helps to develop the whole IT industry in the country, people become more digitally aware and educated, this affects other sectors as well, increasing the spread of digital infrastructure and expediting the speed of overall digitalization. The UN E-government Development Index, which assesses the capabilities of governments to integrate its functions electronically, such as the use of internet and mobile devices, ranked Ukraine 69th in 193 countries surveyed in 2020. Despite its low ranking in the e-government development index, Ukraine made a big jump on the e-participation index, which they ranked 43rd out of 193 countries from 0.66 in 2018 to 0.81 in 2020 (un.org, 2020), suggesting that the government and its citizens are adapting the IT-based government functions. The main goal of e-government according to Perez-Morote et.al. (2020) is to have accountability and transparency among the countries involved. But to do so, there are several challenges that a country should assess first prior to implementing e-government. In the research written by Heeks (2001), the author identified 2 main challenges that countries face in the development of e-government, first is the strategic challenge which involves the preparedness (e-readiness) of the entire government system for electronic transformation, and second challenge is the tactical challenge where the government must design (e-governance design) a system where it can be understood by every user, it's important that the information that needs to be communicated to the consumers is received clearly. For the first challenge (e-readiness), Ukraine had an internet penetration rate of 76% in 2020 and is expected to grow to 82%, it is important that consumers have the internet access for it to enable the consumers to utilize the service. Another factor is the readiness of its institutional infrastructure, which means that the government has its own organization which is solely focused on implementing the e-government project. In the case of Ukraine, the e-governance team is led by Oleksandr Ryzhenko, and the country's e-governance initiative is even further strengthened by ensuring that the data and legal infrastructure are already prepared. Ukraine has done this by modernizing their legislation that is more appropriate in the digital service, and the data exchange solution used by Ukraine is called Trembita. The human infrastructure is also being updated, as competent individuals must be the one doing the task, hence, EGOV4UKRAINE was launched, this aims to get IT developers for developing a system for administrative services. These efforts by the Ukrainian government did not go unnoticed, and they received an award from the e-Governance Academy as "partner of the year 2017". For the second challenge, which deals with the system design, the success of Ukraine can be seen on the latest data of UNDP, where it shows a high increase in the E-participation index. In 2018, Ukraine ranked 75th it ranked 46th in 2020 (un.org, 2020). Despite visible success, the implementation of the e-government was accompanied by problems. Data leakage became the main one. In May 2020, the data of 26 million driver's licenses appeared in the public domain on the Internet. The Ukrainian government said the Diia app was not linked to a data breach, but it is impossible to say for certain. Any storage of official documents in electronic format is associated with the risk of their leakage. In addition, the Diia application still has data protection issues, as the required protection system has not been implemented. This is also compounded by the country's weak data protection legal regime. In addition, since 2023, Ukrainians are able to register their cars with this app. Issued license plates are not using regional codes, but they are using special codes starting with DI or PD. == Diia City == In May 2020, the government presented Diia City headed by Oleksandr Borniakov, a large-scale project which would establish a virtual model of a free economic zone for representatives of the creative economy. It would provide for special digital residency with a particular taxation regime, intellectual property protection and simplified regulations. Diia City concurrently imposes certain constraints on contracts involving individual entrepreneurs (FOPs). It also offers the benefit of tax rebates. Diia City garners endorsement from the Ukrainian government, believing it will support the country's position in the IT market. As of July 30, 2023, the program had more than 600 residents, including companies like iGama, Avenga, SBRobotiks, and Intellectsoft.