The Brain Imaging Data Structure (BIDS) is a standard for organizing, annotating, and describing data collected during neuroimaging experiments. It is based on a formalized file and directory structure and metadata files (based on JSON and TSV) with controlled vocabulary. This standard has been adopted by a multitude of labs around the world as well as databases such as OpenNeuro, SchizConnect, Developing Human Connectome Project, and FCP-INDI, and is seeing uptake in an increasing number of studies. While originally specified for MRI data, BIDS has been extended to several other imaging modalities such as MEG, EEG, and intracranial EEG (see also BIDS Extension Proposals). == History == The project is a community-driven effort. BIDS, originally OBIDS (Open Brain Imaging Data Structure), was initiated during an INCF sponsored data sharing working group meeting (January 2015) at Stanford University. It was subsequently spearheaded and maintained by Chris Gorgolewski. Since October 2019, the project is headed by a Steering Group and maintained by a separate team of maintainers, the Maintainers Group, according to a governance document that was approved of by the BIDS community in a vote. BIDS has advanced under the direction and effort of contributors, the community of researchers that appreciate the value of standardizing neuroimaging data to facilitate sharing and analysis. == BIDS Extension Proposals == BIDS can be extended in a backwards compatible way and is evolving over time. This is accomplished through BIDS Extension Proposals (BEPs), which are community-driven processes following agreed-upon guidelines. A full list of finalized BEPs and BEPs in progress can be found on the BIDS website
Desktop Window Manager
Desktop Window Manager (DWM, previously Desktop Compositing Engine or DCE in builds of pre-reset Windows Longhorn) is the compositing window manager in Microsoft Windows since Windows Vista that enables the use of hardware acceleration to render the graphical user interface of Windows. It was originally created to enable portions of the new "Windows Aero" user experience, which allowed for effects such as transparency, 3D window switching and more. It is also included with Windows Server 2008, but requires the "Desktop Experience" feature and compatible graphics drivers to be installed. == Architecture == The Desktop Window Manager is a compositing window manager, meaning that each program has a buffer that it writes data to; DWM then composites each program's buffer into a final image. By comparison, the stacking window manager in Windows XP and earlier (and also Windows Vista and Windows 7 with Windows Aero disabled) comprises a single display buffer to which all programs write. DWM works in different ways depending on the operating system (Windows 7 or Windows Vista) and on the version of the graphics drivers it uses (WDDM 1.0 or 1.1). Under Windows 7 and with WDDM 1.1 drivers, DWM only writes the program's buffer to the video RAM, even if it is a graphics device interface (GDI) program. This is because Windows 7 supports (limited) hardware acceleration for GDI and in doing so does not need to keep a copy of the buffer in system RAM so that the CPU can write to it. Because the compositor has access to the graphics of all applications, it easily allows visual effects that string together visuals from multiple applications, such as transparency. DWM uses DirectX to perform the function of compositing and rendering in the GPU, freeing the CPU of the task of managing the rendering from the off-screen buffers to the display. However, it does not affect applications painting to the off-screen buffers – depending on the technologies used for that, this might still be CPU-bound. DWM-agnostic rendering techniques like GDI are redirected to the buffers by rendering the user interface (UI) as bitmaps. DWM-aware rendering technologies like WPF directly make the internal data structures available in a DWM-compatible format. The window contents in the buffers are then converted to DirectX textures. The desktop itself is a full-screen Direct3D surface, with windows being represented as a mesh consisting of two adjacent (and mutually inverted) triangles, which are transformed to represent a 2D rectangle. The texture, representing the UI chrome, is then mapped onto these rectangles. Window transitions are implemented as transformations of the meshes, using shader programs. With Windows Vista, the transitions are limited to the set of built-in shaders that implement the transformations. Greg Schechter, a developer at Microsoft has suggested that this might be opened up for developers and users to plug in their own effects in a future release. DWM only maps the primary desktop object as a 3D surface; other desktop objects, including virtual desktops as well as the secure desktop used by User Account Control are not. Because all applications render to an off-screen buffer, they can be read off the buffer embedded in other applications as well. Since the off-screen buffer is constantly updated by the application, the embedded rendering will be a dynamic representation of the application window and not a static rendering. This is how the live thumbnail previews and Windows Flip work in Windows Vista and Windows 7. DWM exposes a public API that allows applications to access these thumbnail representations. The size of the thumbnail is not fixed; applications can request the thumbnails at any size - smaller than the original window, at the same size or even larger - and DWM will scale them properly before returning. Aero Flip does not use the public thumbnail APIs as they do not allow for directly accessing the Direct3D textures. Instead, Aero Flip is implemented directly in the DWM engine. The Desktop Window Manager uses Media Integration Layer (MIL), the unmanaged compositor which it shares with Windows Presentation Foundation, to represent the windows as composition nodes in a composition tree. The composition tree represents the desktop and all the windows hosted in it, which are then rendered by MIL from the back of the scene to the front. Since all the windows contribute to the final image, the color of a resultant pixel can be decided by more than one window. This is used to implement effects such as per-pixel transparency. DWM allows custom shaders to be invoked to control how pixels from multiple applications are used to create the displayed pixel. The DWM includes built-in Pixel Shader 2.0 programs which compute the color of a pixel in a window by averaging the color of the pixel as determined by the window behind it and its neighboring pixels. These shaders are used by DWM to achieve the blur effect in the window borders of windows managed by DWM, and optionally for the areas where it is requested by the application. Since MIL provides a retained mode graphics system by caching the composition trees, the job of repainting and refreshing the screen when windows are moved is handled by DWM and MIL, freeing the application of the responsibility. The background data is already in the composition tree and the off-screen buffers and is directly used to render the background. In pre-Vista Windows OSs, background applications had to be requested to re-render themselves by sending them the WM_PAINT message. DWM uses double-buffered graphics to prevent flickering and tearing when moving windows. The compositing engine uses optimizations such as culling to improve performance, as well as not redrawing areas that have not changed. Because the compositor is multi-monitor aware, DWM natively supports this too. During full-screen applications, such as games, DWM does not perform window compositing and therefore performance will not appreciably decrease. On Windows 8 and Windows Server 2012, DWM is used at all times and cannot be disabled, due to the new "start screen experience" implemented. Since the DWM process is usually required to run at all times on Windows 8, users experiencing an issue with the process are seeing memory usage decrease after a system reboot. This is often the first step in a long list of troubleshooting tasks that can help. It is possible to prevent DWM from restarting temporarily in Windows 8, which causes the desktop to turn black, the taskbar grey, and break the start screen/modern apps, but desktop apps will continue to function and appear just like Windows 7 and Vista's Basic theme, based on the single-buffer renderer used by XP. They also use Windows 8's centered title bar, visible within Windows PreInstallation Environment. Starting up Windows without DWM will not work because the default lock screen requires DWM unlike the fallback lockscreen that appears as a command line interface program when Windows.UI.Logon.dll isn't present on Windows versions such as 1507 and later, so it can only be done on the fly, and does not have any practical purposes. Starting with Windows 10, disabling DWM in such a way will cause the entire compositing engine to break, even traditional desktop apps, due to Universal App implementations in the taskbar and new start menu. Windows can still be partially usable without the presence of DWM but requires Sihost.exe to not be present due to it relying on DWM. Most of the applications in Windows 11 require DWM to render UI elements and transparency, Windows 11's new task manager requires dwm to render menus unlike the fallback -d version. Unlike its predecessors, Windows 8 supports basic display adapters through Windows Advanced Rasterization Platform (WARP), which uses software rendering and the CPU to render the interface rather than the graphics card. This allows DWM to function without compatible drivers, but not at the same level of performance as with a normal graphics card. DWM on Windows 8 also adds support for stereoscopic 3D. == Redirection == For rendering techniques that are not DWM-aware, output must be redirected to the DWM buffers. With Windows, either GDI or DirectX can be used for rendering. To make these two work with DWM, redirection techniques for both are provided. With GDI, which is the most used UI rendering technique in Microsoft Windows, each application window is notified when it or a part of it comes in view and it is the job of the application to render itself. Without DWM, the rendering rasterizes the UI in a buffer in video memory, from where it is rendered to the screen. Under DWM, GDI calls are redirected to use the Canonical Display Driver (cdd.dll), a software renderer. A buffer equal to the size of the window is allocated in system memory and CDD.DLL outputs to this buffer rather than the video memory. Another buffer is allocated in the video memory to represent t
BookCorpus
BookCorpus (also sometimes referred to as the Toronto Book Corpus) is a dataset consisting of the text of around 7,000 self-published books scraped from the indie ebook distribution website Smashwords. It was the main corpus used to train the initial GPT model by OpenAI, and has been used as training data for other early large language models including Google's BERT. The dataset consists of around 985 million words, and the books that comprise it span a range of genres, including romance, science fiction, and fantasy. The corpus was introduced in a 2015 paper by researchers from the University of Toronto and MIT titled "Aligning Books and Movies: Towards Story-like Visual Explanations by Watching Movies and Reading Books". The authors described it as consisting of "free books written by yet unpublished authors," yet this is factually incorrect. These books were published by self-published ("indie") authors who priced them at free; the books were downloaded without the consent or permission of Smashwords or Smashwords authors and in violation of the Smashwords Terms of Service. The dataset was initially hosted on a University of Toronto webpage. An official version of the original dataset is no longer publicly available, though at least one substitute, BookCorpusOpen, has been created. Though not documented in the original 2015 paper, the site from which the corpus's books were scraped is now known to be Smashwords.
XGBoost
XGBoost (eXtreme Gradient Boosting) is an open-source software library which provides a regularizing gradient boosting framework for C++, Java, Python, R, Julia, Perl, and Scala. It works on Linux, Microsoft Windows, and macOS. From the project description, it aims to provide a "Scalable, Portable and Distributed Gradient Boosting (GBM, GBRT, GBDT) Library". It runs on a single machine, as well as the distributed processing frameworks Apache Hadoop, Apache Spark, Apache Flink, and Dask. XGBoost gained much popularity and attention in the mid-2010s as the algorithm of choice for many winning teams of machine learning competitions. == History == XGBoost initially started as a research project by Tianqi Chen as part of the Distributed (Deep) Machine Learning Community (DMLC) group at the University of Washington. Initially, it began as a terminal application which could be configured using a libsvm configuration file. It became well known in the ML competition circles after its use in the winning solution of the Higgs Machine Learning Challenge. Soon after, the Python and R packages were built, and XGBoost now has package implementations for Java, Scala, Julia, Perl, and other languages. This brought the library to more developers and contributed to its popularity among the Kaggle community, where it has been used for a large number of competitions. It was soon integrated with a number of other packages making it easier to use in their respective communities. It has now been integrated with scikit-learn for Python users and with the caret package for R users. It can also be integrated into Data Flow frameworks like Apache Spark, Apache Hadoop, and Apache Flink using the abstracted Rabit and XGBoost4J. XGBoost is also available on OpenCL for FPGAs. An efficient, scalable implementation of XGBoost has been published by Tianqi Chen and Carlos Guestrin. While the XGBoost model often achieves higher accuracy than a single decision tree, it sacrifices the intrinsic interpretability of decision trees. For example, following the path that a decision tree takes to make its decision is trivial and self-explained, but following the paths of hundreds or thousands of trees is much harder. == Features == Salient features of XGBoost which make it different from other gradient boosting algorithms include: Clever penalization of trees A proportional shrinking of leaf nodes Newton Boosting Extra randomization parameter Implementation on single, distributed systems and out-of-core computation Automatic feature selection Theoretically justified weighted quantile sketching for efficient computation Parallel tree structure boosting with sparsity Efficient cacheable block structure for decision tree training == The algorithm == XGBoost works as Newton–Raphson in function space unlike gradient boosting that works as gradient descent in function space, a second order Taylor approximation is used in the loss function to make the connection to Newton–Raphson method. A generic unregularized XGBoost algorithm is: == Parameters == XGBoost has parameters which can be specified to affect how it functions and performs. Some parameters include: Learning rate (also known as the "step size" or “"shrinkage"), it is a number between 0 and 1 (default is 0.3), which determines the rate the algorithm learns from each iteration. n_estimators, sets the number of trees to be built in the ensemble, where more trees generally increases the complexity of the model, but can lead to overfitting with too many trees. Gamma (also known as Lagrange multiplier or the minimum loss reduction parameter), controls the minimum amount of loss reduction required to make a further split on a leaf node of the tree. The default in XGBoost is 0 . max_depth, represents how deeply each tree in the boosting process can grow during training, where the default is 6. == Awards == John Chambers Award (2016) High Energy Physics meets Machine Learning award (HEP meets ML) (2016)
Artificial development
Artificial development, also known as artificial embryogeny or machine intelligence or computational development, is an area of computer science and engineering concerned with computational models motivated by genotype–phenotype mappings in biological systems. Artificial development is often considered a sub-field of evolutionary computation, although the principles of artificial development have also been used within stand-alone computational models. Within evolutionary computation, the need for artificial development techniques was motivated by the perceived lack of scalability and evolvability of direct solution encodings (Tufte, 2008). Artificial development entails indirect solution encoding. Rather than describing a solution directly, an indirect encoding describes (either explicitly or implicitly) the process by which a solution is constructed. Often, but not always, these indirect encodings are based upon biological principles of development such as morphogen gradients, cell division and cellular differentiation (e.g. Doursat 2008), gene regulatory networks (e.g. Guo et al., 2009), degeneracy (Whitacre et al., 2010), grammatical evolution (de Salabert et al., 2006), or analogous computational processes such as re-writing, iteration, and time. The influences of interaction with the environment, spatiality and physical constraints on differentiated multi-cellular development have been investigated more recently (e.g. Knabe et al. 2008). Artificial development approaches have been applied to a number of computational and design problems, including electronic circuit design (Miller and Banzhaf 2003), robotic controllers (e.g. Taylor 2004), and the design of physical structures (e.g. Hornby 2004).
Glyph (data visualization)
In the context of data visualization, a glyph is any marker, such as an arrow or similar marking, used to specify part of a visualization. This is a representation to visualize data where the data set is presented as a collection of visual objects. These visual objects are collectively called a glyph. It helps visualizing data relation in data analysis, statistics, etc. by using any custom notation. In the context of data visualization, a glyph is the visual representation of a piece of data where the attributes of a graphical entity are dictated by one or more attributes of a data record. == Constructing glyphs == Glyph construction can be a complex process when there are many dimensions to be represented in the visualization. Maguire et al proposed a taxonomy based approach to glyph-design that uses a tree to guide the visual encodings used to representation various data items. Duffy et al created perhaps one of the most complex glyph representations with their representation of sperm movement.
Grammatical evolution
Grammatical evolution (GE) is a genetic programming (GP) technique (or approach) from evolutionary computation pioneered by Conor Ryan, JJ Collins and Michael O'Neill in 1998 at the BDS Group in the University of Limerick. As in any other GP approach, the objective is to find an executable program, program fragment, or function, which will achieve a good fitness value for a given objective function. In most published work on GP, a LISP-style tree-structured expression is directly manipulated, whereas GE applies genetic operators to an integer string, subsequently mapped to a program (or similar) through the use of a grammar, which is typically expressed in Backus–Naur form. One of the benefits of GE is that this mapping simplifies the application of search to different programming languages and other structures. == Problem addressed == In type-free, conventional Koza-style GP, the function set must meet the requirement of closure: all functions must be capable of accepting as their arguments the output of all other functions in the function set. Usually, this is implemented by dealing with a single data-type such as double-precision floating point. While modern Genetic Programming frameworks support typing, such type-systems have limitations that Grammatical Evolution does not suffer from. == GE's solution == GE offers a solution to the single-type limitation by evolving solutions according to a user-specified grammar (usually a grammar in Backus-Naur form). Therefore, the search space can be restricted, and domain knowledge of the problem can be incorporated. The inspiration for this approach comes from a desire to separate the "genotype" from the "phenotype": in GP, the objects the search algorithm operates on and what the fitness evaluation function interprets are one and the same. In contrast, GE's "genotypes" are ordered lists of integers which code for selecting rules from the provided context-free grammar. The phenotype, however, is the same as in Koza-style GP: a tree-like structure that is evaluated recursively. This model is more in line with how genetics work in nature, where there is a separation between an organism's genotype and the final expression of phenotype in proteins, etc. Separating genotype and phenotype allows a modular approach. In particular, the search portion of the GE paradigm needn't be carried out by any one particular algorithm or method. Observe that the objects GE performs search on are the same as those used in genetic algorithms. This means, in principle, that any existing genetic algorithm package, such as the popular GAlib, can be used to carry out the search, and a developer implementing a GE system need only worry about carrying out the mapping from list of integers to program tree. It is also in principle possible to perform the search using some other method, such as particle swarm optimization (see the remark below); the modular nature of GE creates many opportunities for hybrids as the problem of interest to be solved dictates. Brabazon and O'Neill have successfully applied GE to predicting corporate bankruptcy, forecasting stock indices, bond credit ratings, and other financial applications. GE has also been used with a classic predator-prey model to explore the impact of parameters such as predator efficiency, niche number, and random mutations on ecological stability. It is possible to structure a GE grammar that for a given function/terminal set is equivalent to genetic programming. == Criticism == Despite its successes, GE has been the subject of some criticism. One issue is that as a result of its mapping operation, GE's genetic operators do not achieve high locality which is a highly regarded property of genetic operators in evolutionary algorithms. == Variants == Although GE was originally described in terms of using an Evolutionary Algorithm, specifically, a Genetic Algorithm, other variants exist. For example, GE researchers have experimented with using particle swarm optimization to carry out the searching instead of genetic algorithms with results comparable to that of normal GE; this is referred to as a "grammatical swarm"; using only the basic PSO model it has been found that PSO is probably equally capable of carrying out the search process in GE as simple genetic algorithms are. (Although PSO is normally a floating-point search paradigm, it can be discretized, e.g., by simply rounding each vector to the nearest integer, for use with GE.) Yet another possible variation that has been experimented with in the literature is attempting to encode semantic information in the grammar in order to further bias the search process. Other work showed that, with biased grammars that leverage domain knowledge, even random search can be used to drive GE. == Related work == GE was originally a combination of the linear representation as used by the Genetic Algorithm for Developing Software (GADS) and Backus Naur Form grammars, which were originally used in tree-based GP by Wong and Leung in 1995 and Whigham in 1996. Other related work noted in the original GE paper was that of Frederic Gruau, who used a conceptually similar "embryonic" approach, as well as that of Keller and Banzhaf, which similarly used linear genomes. == Implementations == There are several implementations of GE. These include the following.