Persistent Homology
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Persistent Homology
:''See homology for an introduction to the notation.'' Persistent homology is a method for computing topological features of a space at different spatial resolutions. More persistent features are detected over a wide range of spatial scales and are deemed more likely to represent true features of the underlying space rather than artifacts of sampling, noise, or particular choice of parameters. To find the persistent homology of a space, the space must first be represented as a simplicial complex. A distance function on the underlying space corresponds to a filtration of the simplicial complex, that is a nested sequence of increasing subsets. Definition Formally, consider a real-valued function on a simplicial complex f:K \rightarrow \mathbb that is non-decreasing on increasing sequences of faces, so f(\sigma) \leq f(\tau) whenever \sigma is a face of \tau in K. Then for every a \in \mathbb the sublevel set K_a=f^((-\infty, a]) is a subcomplex of ''K'', and the ordering of th ...
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Homology (mathematics)
In mathematics, homology is a general way of associating a sequence of algebraic objects, such as abelian groups or modules, with other mathematical objects such as topological spaces. Homology groups were originally defined in algebraic topology. Similar constructions are available in a wide variety of other contexts, such as abstract algebra, groups, Lie algebras, Galois theory, and algebraic geometry. The original motivation for defining homology groups was the observation that two shapes can be distinguished by examining their holes. For instance, a circle is not a disk because the circle has a hole through it while the disk is solid, and the ordinary sphere is not a circle because the sphere encloses a two-dimensional hole while the circle encloses a one-dimensional hole. However, because a hole is "not there", it is not immediately obvious how to define a hole or how to distinguish different kinds of holes. Homology was originally a rigorous mathematical method for defi ...
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Matlab
MATLAB (an abbreviation of "MATrix LABoratory") is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages. Although MATLAB is intended primarily for numeric computing, an optional toolbox uses the MuPAD symbolic engine allowing access to symbolic computing abilities. An additional package, Simulink, adds graphical multi-domain simulation and model-based design for dynamic and embedded systems. As of 2020, MATLAB has more than 4 million users worldwide. They come from various backgrounds of engineering, science, and economics. History Origins MATLAB was invented by mathematician and computer programmer Cleve Moler. The idea for MATLAB was based on his 1960s PhD thesis. Moler became a math professor at the University of New Mexico and starte ...
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Computational Topology
Algorithmic topology, or computational topology, is a subfield of topology with an overlap with areas of computer science, in particular, computational geometry and computational complexity theory. A primary concern of algorithmic topology, as its name suggests, is to develop efficient algorithms for solving problems that arise naturally in fields such as computational geometry, graphics, robotics, structural biology and chemistry, using methods from computable topology. Major algorithms by subject area Algorithmic 3-manifold theory A large family of algorithms concerning 3-manifolds revolve around normal surface theory, which is a phrase that encompasses several techniques to turn problems in 3-manifold theory into integer linear programming problems. * ''Rubinstein and Thompson's 3-sphere recognition algorithm''. This is an algorithm that takes as input a triangulated 3-manifold and determines whether or not the manifold is homeomorphic to the 3-sphere. It has exponential ru ...
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Topological Data Analysis
In applied mathematics, topological based data analysis (TDA) is an approach to the analysis of datasets using techniques from topology. Extraction of information from datasets that are high-dimensional, incomplete and noisy is generally challenging. TDA provides a general framework to analyze such data in a manner that is insensitive to the particular metric chosen and provides dimensionality reduction and robustness to noise. Beyond this, it inherits functoriality, a fundamental concept of modern mathematics, from its topological nature, which allows it to adapt to new mathematical tools. The initial motivation is to study the shape of data. TDA has combined algebraic topology and other tools from pure mathematics to allow mathematically rigorous study of "shape". The main tool is persistent homology, an adaptation of homology to point cloud data. Persistent homology has been applied to many types of data across many fields. Moreover, its mathematical foundation is also of theore ...
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MIT License
The MIT License is a permissive free software license originating at the Massachusetts Institute of Technology (MIT) in the late 1980s. As a permissive license, it puts only very limited restriction on reuse and has, therefore, high license compatibility. Unlike copyleft software licenses, the MIT License also permits reuse within proprietary software, provided that all copies of the software or its substantial portions include a copy of the terms of the MIT License and also a copyright notice. , the MIT License was the most popular software license found in one analysis, continuing from reports in 2015 that the MIT License was the most popular software license on GitHub. Notable projects that use the MIT License include the X Window System, Ruby on Rails, Nim, Node.js, Lua, and jQuery. Notable companies using the MIT License include Microsoft ( .NET), Google ( Angular), and Meta (React). License terms The MIT License has the identifier MIT in the SPDX License List. It is ...
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Julia (programming Language)
Julia is a high-level, dynamic programming language. Its features are well suited for numerical analysis and computational science. Distinctive aspects of Julia's design include a type system with parametric polymorphism in a dynamic programming language; with multiple dispatch as its core programming paradigm. Julia supports concurrent, (composable) parallel and distributed computing (with or without using MPI or the built-in corresponding to "OpenMP-style" threads), and direct calling of C and Fortran libraries without glue code. Julia uses a just-in-time (JIT) compiler that is referred to as "just- ahead-of-time" (JAOT) in the Julia community, as Julia compiles all code (by default) to machine code before running it. Julia is garbage-collected, uses eager evaluation, and includes efficient libraries for floating-point calculations, linear algebra, random number generation, and regular expression matching. Many libraries are available, including some (e.g., for fast Fo ...
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R (programming Language)
R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. Users have created packages to augment the functions of the R language. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages used in data mining. R ranks 12th in the TIOBE index, a measure of programming language popularity, in which the language peaked in 8th place in August 2020. The official R software environment is an open-source free software environment within the GNU package, available under the GNU General Public License. It is written primarily in C, Fortran, and R itself (partially self-hosting). Precompiled executables are provided for various operating systems. R ...
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GPLv3
The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the four freedoms to run, study, share, and modify the software. The license was the first copyleft for general use and was originally written by the founder of the Free Software Foundation (FSF), Richard Stallman, for the GNU Project. The license grants the recipients of a computer program the rights of the Free Software Definition. These GPL series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. It is more restrictive than the Lesser General Public License and even further distinct from the more widely used permissive software licenses BSD, MIT, and Apache. Historically, the GPL license family has been one of the most popular software licenses in the free and open-source software domain. Prominent free software programs licensed under the GPL include the Linux kernel an ...
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MIT License
The MIT License is a permissive free software license originating at the Massachusetts Institute of Technology (MIT) in the late 1980s. As a permissive license, it puts only very limited restriction on reuse and has, therefore, high license compatibility. Unlike copyleft software licenses, the MIT License also permits reuse within proprietary software, provided that all copies of the software or its substantial portions include a copy of the terms of the MIT License and also a copyright notice. , the MIT License was the most popular software license found in one analysis, continuing from reports in 2015 that the MIT License was the most popular software license on GitHub. Notable projects that use the MIT License include the X Window System, Ruby on Rails, Nim, Node.js, Lua, and jQuery. Notable companies using the MIT License include Microsoft ( .NET), Google ( Angular), and Meta (React). License terms The MIT License has the identifier MIT in the SPDX License List. It is ...
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Python (programming Language)
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC programming language and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ranks as ...
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BSD Licenses
BSD licenses are a family of permissive free software licenses, imposing minimal restrictions on the use and distribution of covered software. This is in contrast to copyleft licenses, which have share-alike requirements. The original BSD license was used for its namesake, the Berkeley Software Distribution (BSD), a Unix-like operating system. The original version has since been revised, and its descendants are referred to as modified BSD licenses. BSD is both a license and a class of license (generally referred to as BSD-like). The modified BSD license (in wide use today) is very similar to the license originally used for the BSD version of Unix. The BSD license is a simple license that merely requires that all code retain the BSD license notice if redistributed in source code format, or reproduce the notice if redistributed in binary format. The BSD license (unlike some other licenses e.g. GPL) does not require that source code be distributed at all. Terms In addition to ...
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Java (programming Language)
Java is a high-level, class-based, object-oriented programming language that is designed to have as few implementation dependencies as possible. It is a general-purpose programming language intended to let programmers ''write once, run anywhere'' ( WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as reflection and runtime code modification) that are typically not available in traditional compiled languages. , Java was one of the most popular programming languages in use according to GitHub, particularly for client–server web applications, with a reported 9 million developers. Java was originally developed ...
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