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.

ROCm

ROCm is an Advanced Micro Devices (AMD) software stack for graphics processing unit (GPU) programming. ROCm spans several domains, including general-purpose computing on graphics processing units (GPGPU), high performance computing (HPC), and heterogeneous computing. It offers several programming models: HIP (GPU-kernel-based programming), OpenMP (directive-based programming), and OpenCL. ROCm is free, libre and open-source software (except the GPU firmware blobs), and it is distributed under various licenses. The name initially stood for Radeon Open Compute platform; however, due to Open Compute being a registered trademark, the name no longer functions as an acronym. == Background == The first GPGPU software stack from ATI/AMD was Close to Metal, which became Stream. ROCm was launched around 2016 with the Boltzmann Initiative. ROCm stack builds upon previous AMD GPU stacks; some tools trace back to GPUOpen and others to the Heterogeneous System Architecture (HSA). === Heterogeneous System Architecture Intermediate Language === HSAIL was aimed at producing a middle-level, hardware-agnostic intermediate representation that could be JIT-compiled to the eventual hardware (GPU, FPGA...) using the appropriate finalizer. This approach was dropped for ROCm: now it builds only GPU code, using LLVM, and its AMDGPU backend that was upstreamed, although there is still research on such enhanced modularity with LLVM MLIR. == Programming abilities == ROCm as a stack ranges from the kernel driver to the end-user applications. AMD has introductory videos about AMD GCN hardware, and ROCm programming via its learning portal. One of the best technical introductions about the stack and ROCm/HIP programming, remains, to date, to be found on Reddit. == Hardware support == ROCm is primarily targeted at discrete professional GPUs, but consumer GPUs and APUs of the same architecture as a supported professional GPU are known to work with ROCm. For example, all professional GPUs of the RDNA 2 architecture are officially supported by ROCm 5.x; users report that Consumer RDNA2 units such as the Radeon 6800M APU and the Radeon 6700XT GPU also work. === Professional-grade GPUs === === Consumer-grade GPUs === == Software ecosystem == === Machine learning === Various deep learning frameworks have a ROCm backend: PyTorch TensorFlow ONNX MXNet CuPy MIOpen Caffe Iree (which uses LLVM Multi-Level Intermediate Representation (MLIR)) llama.cpp === Supercomputing === ROCm is gaining significant traction in the top 500. ROCm is used with the Exascale supercomputers El Capitan and Frontier. Some related software is to be found at AMD Infinity hub. === Other acceleration & graphics interoperation === As of version 3.0, Blender can now use HIP compute kernels for its renderer cycles. === Other languages === ==== Julia ==== Julia has the AMDGPU.jl package, which integrates with LLVM and selects components of the ROCm stack. Instead of compiling code through HIP, AMDGPU.jl uses Julia's compiler to generate LLVM IR directly, which is later consumed by LLVM to generate native device code. AMDGPU.jl uses ROCr's HSA implementation to upload native code onto the device and execute it, similar to how HIP loads its own generated device code. AMDGPU.jl also supports integration with ROCm's rocBLAS (for BLAS), rocRAND (for random number generation), and rocFFT (for FFTs). Future integration with rocALUTION, rocSOLVER, MIOpen, and certain other ROCm libraries is planned. === Software distribution === ==== Official ==== Installation instructions are provided for Linux and Windows in the official AMD ROCm documentation. ROCm software is currently spread across several public GitHub repositories. Within the main public meta-repository, there is an XML manifest for each official release: using git-repo, a version control tool built on top of Git, is the recommended way to synchronize with the stack locally. AMD starts distributing containerized applications for ROCm, notably scientific research applications gathered under AMD Infinity Hub. AMD distributes itself packages tailored to various Linux distributions. ==== Third-party ==== There is a growing third-party ecosystem packaging ROCm. Linux distributions are officially packaging (natively) ROCm, with various degrees of advancement: Arch Linux, Gentoo, Debian, Fedora , GNU Guix, and NixOS. There are Spack packages. == Components == There is one kernel-space component, ROCk, and the rest - there is roughly a hundred components in the stack - is made of user-space modules. The unofficial typographic policy is to use: uppercase ROC lowercase following for low-level libraries, i.e. ROCt, and the contrary for user-facing libraries, i.e. rocBLAS. AMD is active developing with the LLVM community, but upstreaming is not instantaneous, and as of January 2022, is still lagging. AMD still officially packages various LLVM forks for parts that are not yet upstreamed – compiler optimizations destined to remain proprietary, debug support, OpenMP offloading, etc. === Low-level === ==== ROCk – Kernel driver ==== ==== ROCm – Device libraries ==== Support libraries implemented as LLVM bitcode. These provide various utilities and functions for math operations, atomics, queries for launch parameters, on-device kernel launch, etc. ==== ROCt – Thunk ==== The thunk is responsible for all the thinking and queuing that goes into the stack. ==== ROCr – Runtime ==== The ROC runtime is a set of APIs/libraries that allows the launch of compute kernels by host applications. It is AMD's implementation of the HSA runtime API. It is different from the ROC Common Language Runtime. ==== ROCm – CompilerSupport ==== ROCm code object manager is in charge of interacting with LLVM intermediate representation. === Mid-level === ==== ROCclr Common Language Runtime ==== The common language runtime is an indirection layer adapting calls to ROCr on Linux and PAL on windows. It used to be able to route between different compilers, like the HSAIL-compiler. It is now being absorbed by the upper indirection layers (HIP and OpenCL). ==== OpenCL ==== ROCm ships its installable client driver (ICD) loader and an OpenCL implementation bundled together. As of January 2022, ROCm 4.5.2 ships OpenCL 2.2, and is lagging behind competition. ==== HIP – Heterogeneous Interface for Portability ==== The AMD implementation for its GPUs is called HIPAMD. There is also a CPU implementation mostly for demonstration purposes. ==== HIPCC ==== HIP builds a `HIPCC` compiler that either wraps Clang and compiles with LLVM open AMDGPU backend, or redirects to the NVIDIA compiler. ==== HIPIFY ==== HIPIFY is a source-to-source compiling tool. It translates CUDA to HIP and reverse, either using a Clang-based tool, or a sed-like Perl script. ==== GPUFORT ==== Like HIPIFY, GPUFORT is a tool compiling source code into other third-generation-language sources, allowing users to migrate from CUDA Fortran to HIP Fortran. It is also in the repertoire of research projects, even more so. === High-level === ROCm high-level libraries are usually consumed directly by application software, such as machine learning frameworks. Most of the following libraries are in the General Matrix Multiply (GEMM) category, which GPU architecture excels at. The majority of these user-facing libraries comes in dual-form: hip for the indirection layer that can route to Nvidia hardware, and roc for the AMD implementation. ==== rocBLAS / hipBLAS ==== rocBLAS and hipBLAS are central in high-level libraries, it is the AMD implementation for Basic Linear Algebra Subprograms. It uses the library Tensile privately. ==== rocSOLVER / hipSOLVER ==== This pair of libraries constitutes the LAPACK implementation for ROCm and is strongly coupled to rocBLAS. === Utilities === ROCm developer tools: Debug, tracer, profiler, System Management Interface, Validation suite, Cluster management. GPUOpen tools: GPU analyzer, memory visualizer... External tools: radeontop (TUI overview) == Comparison with competitors == ROCm competes with other GPU computing stacks: Nvidia CUDA and Intel OneAPI. === Nvidia CUDA === Nvidia's CUDA is closed-source, whereas AMD ROCm is open source. There is open-source software built on top of the closed-source CUDA, for instance RAPIDS. CUDA is able to run on consumer GPUs, whereas ROCm support is mostly offered for professional hardware such as AMD Instinct and AMD Radeon Pro. Nvidia provides a C/C++-centered frontend and its Parallel Thread Execution (PTX) LLVM GPU backend as the Nvidia CUDA Compiler (NVCC). === Intel OneAPI === All the oneAPI corresponding libraries are published on its GitHub Page. ==== Unified Acceleration Foundation (UXL) ==== Unified Acceleration Foundation (UXL) is a new technology consortium that are working on the continuation of the OneAPI initiative, with the goal to create a new open standard accelerator software ecosystem, related open standards and specification projects through Working Groups and Specia

Google matrix

A Google matrix is a particular stochastic matrix that is used by Google's PageRank algorithm. The matrix represents a graph with edges representing links between pages. The PageRank of each page can then be generated iteratively from the Google matrix using the power method. However, in order for the power method to converge, the matrix must be stochastic, irreducible and aperiodic. == Adjacency matrix A and Markov matrix S == In order to generate the Google matrix G, we must first generate an adjacency matrix A which represents the relations between pages or nodes. Assuming there are N pages, we can fill out A by doing the following: A matrix element A i , j {\displaystyle A_{i,j}} is filled with 1 if node j {\displaystyle j} has a link to node i {\displaystyle i} , and 0 otherwise; this is the adjacency matrix of links. A related matrix S corresponding to the transitions in a Markov chain of given network is constructed from A by dividing the elements of column "j" by a number of k j = Σ i = 1 N A i , j {\displaystyle k_{j}=\Sigma _{i=1}^{N}A_{i,j}} where k j {\displaystyle k_{j}} is the total number of outgoing links from node j to all other nodes. The columns having zero matrix elements, corresponding to dangling nodes, are replaced by a constant value 1/N. Such a procedure adds a link from every sink, dangling state a {\displaystyle a} to every other node. Now by the construction the sum of all elements in any column of matrix S is equal to unity. In this way the matrix S is mathematically well defined and it belongs to the class of Markov chains and the class of Perron-Frobenius operators. That makes S suitable for the PageRank algorithm. == Construction of Google matrix G == Then the final Google matrix G can be expressed via S as: G i j = α S i j + ( 1 − α ) 1 N ( 1 ) {\displaystyle G_{ij}=\alpha S_{ij}+(1-\alpha ){\frac {1}{N}}\;\;\;\;\;\;\;\;\;\;\;(1)} By the construction the sum of all non-negative elements inside each matrix column is equal to unity. The numerical coefficient α {\displaystyle \alpha } is known as a damping factor. Usually S is a sparse matrix and for modern directed networks it has only about ten nonzero elements in a line or column, thus only about 10N multiplications are needed to multiply a vector by matrix G. == Examples of Google matrix == An example of the matrix S {\displaystyle S} construction via Eq.(1) within a simple network is given in the article CheiRank. For the actual matrix, Google uses a damping factor α {\displaystyle \alpha } around 0.85. The term ( 1 − α ) {\displaystyle (1-\alpha )} gives a surfer probability to jump randomly on any page. The matrix G {\displaystyle G} belongs to the class of Perron-Frobenius operators of Markov chains. The examples of Google matrix structure are shown in Fig.1 for Wikipedia articles hyperlink network in 2009 at small scale and in Fig.2 for University of Cambridge network in 2006 at large scale. == Spectrum and eigenstates of G matrix == For 0 < α < 1 {\displaystyle 0<\alpha <1} there is only one maximal eigenvalue λ = 1 {\displaystyle \lambda =1} with the corresponding right eigenvector which has non-negative elements P i {\displaystyle P_{i}} which can be viewed as stationary probability distribution. These probabilities ordered by their decreasing values give the PageRank vector P i {\displaystyle P_{i}} with the PageRank K i {\displaystyle K_{i}} used by Google search to rank webpages. Usually one has for the World Wide Web that P ∝ 1 / K β {\displaystyle P\propto 1/K^{\beta }} with β ≈ 0.9 {\displaystyle \beta \approx 0.9} . The number of nodes with a given PageRank value scales as N P ∝ 1 / P ν {\displaystyle N_{P}\propto 1/P^{\nu }} with the exponent ν = 1 + 1 / β ≈ 2.1 {\displaystyle \nu =1+1/\beta \approx 2.1} . The left eigenvector at λ = 1 {\displaystyle \lambda =1} has constant matrix elements. With 0 < α {\displaystyle 0<\alpha } all eigenvalues move as λ i → α λ i {\displaystyle \lambda _{i}\rightarrow \alpha \lambda _{i}} except the maximal eigenvalue λ = 1 {\displaystyle \lambda =1} , which remains unchanged. The PageRank vector varies with α {\displaystyle \alpha } but other eigenvectors with λ i < 1 {\displaystyle \lambda _{i}<1} remain unchanged due to their orthogonality to the constant left vector at λ = 1 {\displaystyle \lambda =1} . The gap between λ = 1 {\displaystyle \lambda =1} and other eigenvalue being 1 − α ≈ 0.15 {\displaystyle 1-\alpha \approx 0.15} gives a rapid convergence of a random initial vector to the PageRank approximately after 50 multiplications on G {\displaystyle G} matrix. At α = 1 {\displaystyle \alpha =1} the matrix G {\displaystyle G} has generally many degenerate eigenvalues λ = 1 {\displaystyle \lambda =1} (see e.g. [6]). Examples of the eigenvalue spectrum of the Google matrix of various directed networks is shown in Fig.3 from and Fig.4 from. The Google matrix can be also constructed for the Ulam networks generated by the Ulam method [8] for dynamical maps. The spectral properties of such matrices are discussed in [9,10,11,12,13,15]. In a number of cases the spectrum is described by the fractal Weyl law [10,12]. The Google matrix can be constructed also for other directed networks, e.g. for the procedure call network of the Linux Kernel software introduced in [15]. In this case the spectrum of λ {\displaystyle \lambda } is described by the fractal Weyl law with the fractal dimension d ≈ 1.3 {\displaystyle d\approx 1.3} (see Fig.5 from ). Numerical analysis shows that the eigenstates of matrix G {\displaystyle G} are localized (see Fig.6 from ). Arnoldi iteration method allows to compute many eigenvalues and eigenvectors for matrices of rather large size [13]. Other examples of G {\displaystyle G} matrix include the Google matrix of brain [17] and business process management [18], see also. Applications of Google matrix analysis to DNA sequences is described in [20]. Such a Google matrix approach allows also to analyze entanglement of cultures via ranking of multilingual Wikipedia articles abouts persons [21] == Historical notes == The Google matrix with damping factor was described by Sergey Brin and Larry Page in 1998 [22], see also articles on PageRank history [23], [24].

Richard Zemel

Richard Stanley Zemel (born 1963) is a Canadian-American computer scientist and professor at Columbia University, Department of Computer Science, and a leading figure in the field of machine learning and computer vision. Zemel studied the history of science at Harvard University and obtained his B.A. in 1984. He continued his study at the Department of Computer Science of the University of Toronto under the supervision of Geoffrey Hinton. He obtained his M.Sc. and Ph.D. both in computer science in 1989 and 1994, respectively.

Is an AI Logo Maker Worth It in 2026?

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Super-resolution optical fluctuation imaging

Super-resolution optical fluctuation imaging (SOFI) is a post-processing method for the calculation of super-resolved images from recorded image time series that is based on the temporal correlations of independently fluctuating fluorescent emitters. SOFI has been developed for super-resolution of biological specimen that are labelled with independently fluctuating fluorescent emitters (organic dyes, fluorescent proteins). In comparison to other super-resolution microscopy techniques such as STORM or PALM that rely on single-molecule localization and hence only allow one active molecule per diffraction-limited area (DLA) and timepoint, SOFI does not necessitate a controlled photoswitching and/ or photoactivation as well as long imaging times. Nevertheless, it still requires fluorophores that are cycling through two distinguishable states, either real on-/off-states or states with different fluorescence intensities. In mathematical terms SOFI-imaging relies on the calculation of cumulants, for what two distinguishable ways exist. For one thing an image can be calculated via auto-cumulants that by definition only rely on the information of each pixel itself, and for another thing an improved method utilizes the information of different pixels via the calculation of cross-cumulants. Both methods can increase the final image resolution significantly although the cumulant calculation has its limitations. Actually SOFI is able to increase the resolution in all three dimensions. == Principle == Likewise to other super-resolution methods SOFI is based on recording an image time series on a CCD- or CMOS camera. In contrary to other methods the recorded time series can be substantially shorter, since a precise localization of emitters is not required and therefore a larger quantity of activated fluorophores per diffraction-limited area is allowed. The pixel values of a SOFI-image of the n-th order are calculated from the values of the pixel time series in the form of a n-th order cumulant, whereas the final value assigned to a pixel can be imagined as the integral over a correlation function. The finally assigned pixel value intensities are a measure of the brightness and correlation of the fluorescence signal. Mathematically, the n-th order cumulant is related to the n-th order correlation function, but exhibits some advantages concerning the resulting resolution of the image. Since in SOFI several emitters per DLA are allowed, the photon count at each pixel results from the superposition of the signals of all activated nearby emitters. The cumulant calculation now filters the signal and leaves only highly correlated fluctuations. This provides a contrast enhancement and therefore a background reduction for good measure. As it is implied in the figure on the left the fluorescence source distribution: ∑ k = 1 N δ ( r → − r → k ) ⋅ ε k ⋅ s k ( t ) {\displaystyle \sum _{k=1}^{N}\delta ({\vec {r}}-{\vec {r}}_{k})\cdot \varepsilon _{k}\cdot s_{k}(t)} is convolved with the system's point spread function (PSF) U(r). Hence the fluorescence signal at time t and position r → {\displaystyle {\vec {r}}} is given by F ( r → , t ) = ∑ k = 1 N U ( r → − r → k ) ⋅ ε k ⋅ s k ( t ) . {\displaystyle F({\vec {r}},t)=\sum _{k=1}^{N}U({\vec {r}}-{\vec {r}}_{k})\cdot \varepsilon _{k}\cdot s_{k}(t).} Within the above equations N is the amount of emitters, located at the positions r → k {\displaystyle {\vec {r}}_{k}} with a time-dependent molecular brightness ε k ⋅ s k {\displaystyle \varepsilon _{k}\cdot s_{k}} where ε k {\displaystyle \varepsilon _{k}} is a variable for the constant molecular brightness and s k ( t ) {\displaystyle s_{k}(t)} is a time-dependent fluctuation function. The molecular brightness is just the average fluorescence count-rate divided by the number of molecules within a specific region. For simplification it has to be assumed that the sample is in a stationary equilibrium and therefore the fluorescence signal can be expressed as a zero-mean fluctuation: δ F ( r → , t ) = F ( r → , t ) − ⟨ F ( r → , t ) ⟩ t {\displaystyle \delta F({\vec {r}},t)=F({\vec {r}},t)-\langle F({\vec {r}},t)\rangle _{t}} where ⟨ ⋯ ⟩ t {\displaystyle \langle \cdots \rangle _{t}} denotes time-averaging. The auto-correlation here e.g. the second-order can then be described deductively as follows for a certain time-lag τ {\displaystyle \tau } : δ F ( r → , t ) = ⟨ δ F ( r → , t + τ ) ⋅ δ F ( r → , t ) ⟩ t {\displaystyle \delta F({\vec {r}},t)=\langle \delta F({\vec {r}},t+\tau )\cdot \delta F({\vec {r}},t)\rangle _{t}} From these equations it follows that the PSF of the optical system has to be taken to the power of the order of the correlation. Thus in a second-order correlation the PSF would be reduced along all dimensions by a factor of 2 {\displaystyle {\sqrt {2}}} . As a result, the resolution of the SOFI-images increases according to this factor. === Cumulants versus correlations === Using only the simple correlation function for a reassignment of pixel values, would ascribe to the independency of fluctuations of the emitters in time in a way that no cross-correlation terms would contribute to the new pixel value. Calculations of higher-order correlation functions would suffer from lower-order correlations for what reason it is superior to calculate cumulants, since all lower-order correlation terms vanish. == Cumulant-calculation == === Auto-cumulants === For computational reasons it is convenient to set all time-lags in higher-order cumulants to zero so that a general expression for the n-th order auto-cumulant can be found: A C n ( r → , τ 1 … n − 1 = 0 ) = ∑ k = 1 N U n ( r → − r → k ) ε k n w k ( 0 ) {\displaystyle AC_{n}({\vec {r}},\tau _{1\ldots n-1}=0)=\sum _{k=1}^{N}U^{n}({\vec {r}}-{\vec {r}}_{k})\varepsilon _{k}^{n}w_{k}(0)} w k {\displaystyle w_{k}} is a specific correlation based weighting function influenced by the order of the cumulant and mainly depending on the fluctuation properties of the emitters. Albeit there is no fundamental limitation in calculating very high orders of cumulants and thereby shrinking the FWHM of the PSF there are practical limitations according to the weighting of the values assigned to the final image. Emitters with a higher molecular brightness will show a strong increase in terms of the pixel cumulant value assigned at higher-orders as well as this performance can be expected from a diverse appearance of fluctuations of different emitters. A wide intensity range of the resulting image can therefore be expected and as a result dim emitters can get masked by bright emitters in higher-order images:. The calculation of auto-cumulants can be realized in a very attractive way in a mathematical sense. The n-th order cumulant can be calculated with a basic recursion from moments K n ( r → ) = μ n ( r → ) − ∑ i = 1 n − 1 ( n − 1 i ) K n − i ( r → ) μ i ( r → ) {\displaystyle K_{n}({\vec {r}})=\mu _{n}({\vec {r}})-\sum _{i=1}^{n-1}{\begin{pmatrix}n-1\\i\end{pmatrix}}K_{n-i}({\vec {r}})\mu _{i}({\vec {r}})} where K is a cumulant of the index's order, likewise μ {\displaystyle \mu } represents the moments. The term within the brackets indicates a binomial coefficient. This way of computation is straightforward in comparison with calculating cumulants with standard formulas. It allows for the calculation of cumulants with only little time of computing and is, as it is well implemented, even suitable for the calculation of high-order cumulants on large images. === Cross-cumulants === In a more advanced approach cross-cumulants are calculated by taking the information of several pixels into account. Cross-cumulants can be described as follows: C C n ( r → , τ 1 … n − 1 = 0 ) = ∏ j < l n U ( r → j − r → l n ) ⋅ ∑ i = 1 N U n ( r → i − ∑ k n r → k n ) ε i n w i ( 0 ) {\displaystyle CC_{n}({\vec {r}},\tau _{1\ldots n-1}=0)=\prod _{j

Baum–Welch algorithm

In electrical engineering, statistical computing and bioinformatics, the Baum–Welch algorithm is a special case of the expectation–maximization algorithm used to find the unknown parameters of a hidden Markov model (HMM). It makes use of the forward-backward algorithm to compute the statistics for the expectation step. The Baum–Welch algorithm, the primary method for inference in hidden Markov models, is numerically unstable due to its recursive calculation of joint probabilities. As the number of variables grows, these joint probabilities become increasingly small, leading to the forward recursions rapidly approaching values below machine precision. == History == The Baum–Welch algorithm was named after its inventors Leonard E. Baum and Lloyd R. Welch. The algorithm and the Hidden Markov models were first described in a series of articles by Baum and his peers at the IDA Center for Communications Research, Princeton in the late 1960s and early 1970s. One of the first major applications of HMMs was to the field of speech processing. In the 1980s, HMMs were emerging as a useful tool in the analysis of biological systems and information, and in particular genetic information. They have since become an important tool in the probabilistic modeling of genomic sequences. == Description == A hidden Markov model describes the joint probability of a collection of "hidden" and observed discrete random variables. It relies on the assumption that the i-th hidden variable given the (i − 1)-th hidden variable is independent of previous hidden variables, and the current observation variables depend only on the current hidden state. The Baum–Welch algorithm uses the well known EM algorithm to find the maximum likelihood estimate of the parameters of a hidden Markov model given a set of observed feature vectors. Let X t {\displaystyle X_{t}} be a discrete hidden random variable with N {\displaystyle N} possible values (i.e. We assume there are N {\displaystyle N} states in total). We assume the P ( X t ∣ X t − 1 ) {\displaystyle P(X_{t}\mid X_{t-1})} is independent of time t {\displaystyle t} , which leads to the definition of the time-independent stochastic transition matrix A = { a i j } = P ( X t = j ∣ X t − 1 = i ) . {\displaystyle A=\{a_{ij}\}=P(X_{t}=j\mid X_{t-1}=i).} The initial state distribution (i.e. when t = 1 {\displaystyle t=1} ) is given by π i = P ( X 1 = i ) . {\displaystyle \pi _{i}=P(X_{1}=i).} The observation variables Y t {\displaystyle Y_{t}} can take one of K {\displaystyle K} possible values. We also assume the observation given the "hidden" state is time independent. The probability of a certain observation y i {\displaystyle y_{i}} at time t {\displaystyle t} for state X t = j {\displaystyle X_{t}=j} is given by b j ( y i ) = P ( Y t = y i ∣ X t = j ) . {\displaystyle b_{j}(y_{i})=P(Y_{t}=y_{i}\mid X_{t}=j).} Taking into account all the possible values of Y t {\displaystyle Y_{t}} and X t {\displaystyle X_{t}} , we obtain the N × K {\displaystyle N\times K} matrix B = { b j ( y i ) } {\displaystyle B=\{b_{j}(y_{i})\}} where b j {\displaystyle b_{j}} belongs to all the possible states and y i {\displaystyle y_{i}} belongs to all the observations. An observation sequence is given by Y = ( Y 1 = y 1 , Y 2 = y 2 , … , Y T = y T ) {\displaystyle Y=(Y_{1}=y_{1},Y_{2}=y_{2},\ldots ,Y_{T}=y_{T})} . Thus we can describe a hidden Markov chain by θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} . The Baum–Welch algorithm finds a local maximum for θ ∗ = a r g m a x θ ⁡ P ( Y ∣ θ ) {\displaystyle \theta ^{}=\operatorname {arg\,max} _{\theta }P(Y\mid \theta )} (i.e. the HMM parameters θ {\displaystyle \theta } that maximize the probability of the observation). === Algorithm === Set θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} with random initial conditions. They can also be set using prior information about the parameters if it is available; this can speed up the algorithm and also steer it toward the desired local maximum. ==== Forward procedure ==== Let α i ( t ) = P ( Y 1 = y 1 , … , Y t = y t , X t = i ∣ θ ) {\displaystyle \alpha _{i}(t)=P(Y_{1}=y_{1},\ldots ,Y_{t}=y_{t},X_{t}=i\mid \theta )} , the probability of seeing the observations y 1 , y 2 , … , y t {\displaystyle y_{1},y_{2},\ldots ,y_{t}} and being in state i {\displaystyle i} at time t {\displaystyle t} . This is found recursively: α i ( 1 ) = π i b i ( y 1 ) , {\displaystyle \alpha _{i}(1)=\pi _{i}b_{i}(y_{1}),} α i ( t + 1 ) = b i ( y t + 1 ) ∑ j = 1 N α j ( t ) a j i . {\displaystyle \alpha _{i}(t+1)=b_{i}(y_{t+1})\sum _{j=1}^{N}\alpha _{j}(t)a_{ji}.} Since this series converges exponentially to zero, the algorithm will numerically underflow for longer sequences. However, this can be avoided in a slightly modified algorithm by scaling α {\displaystyle \alpha } in the forward and β {\displaystyle \beta } in the backward procedure below. ==== Backward procedure ==== Let β i ( t ) = P ( Y t + 1 = y t + 1 , … , Y T = y T ∣ X t = i , θ ) {\displaystyle \beta _{i}(t)=P(Y_{t+1}=y_{t+1},\ldots ,Y_{T}=y_{T}\mid X_{t}=i,\theta )} that is the probability of the ending partial sequence y t + 1 , … , y T {\displaystyle y_{t+1},\ldots ,y_{T}} given starting state i {\displaystyle i} at time t {\displaystyle t} . We calculate β i ( t ) {\displaystyle \beta _{i}(t)} as, β i ( T ) = 1 , {\displaystyle \beta _{i}(T)=1,} β i ( t ) = ∑ j = 1 N β j ( t + 1 ) a i j b j ( y t + 1 ) . {\displaystyle \beta _{i}(t)=\sum _{j=1}^{N}\beta _{j}(t+1)a_{ij}b_{j}(y_{t+1}).} ==== Update ==== We can now calculate the temporary variables, according to Bayes' theorem: γ i ( t ) = P ( X t = i ∣ Y , θ ) = P ( X t = i , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) β i ( t ) ∑ j = 1 N α j ( t ) β j ( t ) , {\displaystyle \gamma _{i}(t)=P(X_{t}=i\mid Y,\theta )={\frac {P(X_{t}=i,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)\beta _{i}(t)}{\sum _{j=1}^{N}\alpha _{j}(t)\beta _{j}(t)}},} which is the probability of being in state i {\displaystyle i} at time t {\displaystyle t} given the observed sequence Y {\displaystyle Y} and the parameters θ {\displaystyle \theta } ξ i j ( t ) = P ( X t = i , X t + 1 = j ∣ Y , θ ) = P ( X t = i , X t + 1 = j , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) a i j β j ( t + 1 ) b j ( y t + 1 ) ∑ k = 1 N ∑ w = 1 N α k ( t ) a k w β w ( t + 1 ) b w ( y t + 1 ) , {\displaystyle \xi _{ij}(t)=P(X_{t}=i,X_{t+1}=j\mid Y,\theta )={\frac {P(X_{t}=i,X_{t+1}=j,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)a_{ij}\beta _{j}(t+1)b_{j}(y_{t+1})}{\sum _{k=1}^{N}\sum _{w=1}^{N}\alpha _{k}(t)a_{kw}\beta _{w}(t+1)b_{w}(y_{t+1})}},} which is the probability of being in state i {\displaystyle i} and j {\displaystyle j} at times t {\displaystyle t} and t + 1 {\displaystyle t+1} respectively given the observed sequence Y {\displaystyle Y} and parameters θ {\displaystyle \theta } . The denominators of γ i ( t ) {\displaystyle \gamma _{i}(t)} and ξ i j ( t ) {\displaystyle \xi _{ij}(t)} are the same ; they represent the probability of making the observation Y {\displaystyle Y} given the parameters θ {\displaystyle \theta } . The parameters of the hidden Markov model θ {\displaystyle \theta } can now be updated: π i ∗ = γ i ( 1 ) , {\displaystyle \pi _{i}^{}=\gamma _{i}(1),} which is the expected frequency spent in state i {\displaystyle i} at time 1 {\displaystyle 1} . a i j ∗ = ∑ t = 1 T − 1 ξ i j ( t ) ∑ t = 1 T − 1 γ i ( t ) , {\displaystyle a_{ij}^{}={\frac {\sum _{t=1}^{T-1}\xi _{ij}(t)}{\sum _{t=1}^{T-1}\gamma _{i}(t)}},} which is the expected number of transitions from state i to state j compared to the expected total number of transitions starting in state i, including from state i to itself. The number of transitions starting in state i is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 T 1 y t = v k γ i ( t ) ∑ t = 1 T γ i ( t ) , {\displaystyle b_{i}^{}(v_{k})={\frac {\sum _{t=1}^{T}1_{y_{t}=v_{k}}\gamma _{i}(t)}{\sum _{t=1}^{T}\gamma _{i}(t)}},} where 1 y t = v k = { 1 if y t = v k , 0 otherwise {\displaystyle 1_{y_{t}=v_{k}}={\begin{cases}1&{\text{if }}y_{t}=v_{k},\\0&{\text{otherwise}}\end{cases}}} is an indicator function, and b i ∗ ( v k ) {\displaystyle b_{i}^{}(v_{k})} is the expected number of times the output observations have been equal to v k {\displaystyle v_{k}} while in state i {\displaystyle i} over the expected total number of times in state i {\displaystyle i} . These steps are now repeated iteratively until a desired level of convergence. Note: It is possible to over-fit a particular data set. That is, P ( Y ∣ θ final ) > P ( Y ∣ θ true ) {\displaystyle P(Y\mid \theta _{\text{final}})>P(Y\mid \theta _{\text{true}})} . The algorithm also does not guarantee a global maximum. ==== Multiple sequences ==== The algorithm described thus far assumes a single observed sequence Y = y 1 , … , y T {\displaystyle Y=y_{1},\ldots ,y_{T}} . However, in many situations, there are several sequences observed: Y 1 ,