Spatial Principal Component Analysis (sPCA) is a multivariate statistical technique that complements the traditional Principal Component Analysis (PCA) by incorporating spatial information into the analysis of genetic variation. While traditional PCA can be used to find spatial patterns, it focuses on reducing data dimensionality by identifying uncorrelated principal components that capture maximum variance, thus often lacking power to identify non-trivial spatial genetic patterns. By accounting for spatial autocorrelation, sPCA is able to uncover spatial patterns in the data and find the spatial structure of datasets where observations are either geographically or topologically linked. This statistical power improvement allows the investigation of cryptic spatial patterns of genetic variability otherwise overlooked. sPCA has been applied in various fields, including geography, ecology and genetics. == History == sPCA was introduced in 2008 by Thibaut Jombart, Sébastien Devillard, Anne-Béatrice Dufour, and D. Pontier as a spatially explicit method to investigate the spatial pattern of genetic variation among individuals or populations. In 2017, Valeria Montano and Thibaut Jombart published an alternative non-parametric test to evaluate the significance of global and local spatial genetic patterns with improved statistical power. == Details == sPCA modifies the PCA framework by integrating spatial weights, typically in the form of connectivity matrices or spatial adjacency graphs. It identifies principal components (PCs) that maximize both genentic variance and spatial autocorreation, as measured by Moran's I. These weights represent relationships between observations based on geographic distance or other spatial criteria. The method decomposes variance into two components: Global structures, correspond to positive autocorrelation, that is, reflect broad-scale spatial patterns where similar values cluster over large regions. Local structures, correspond to negative autocorrelation, that is, capture fine-scale spatial variations or localized patterns. The core of sPCA relies on the eigenanalysis of a spatially weighted covariance or correlation matrix. The spatial weight matrix can be constructed using techniques such as Delaunay triangulation, nearest-neighbor graphs, or distance-based criteria. Applications of sPCA should be used only as an explorative tool. == Applications == sPCA has been widely used in many fields, including: Ecology: To find spatial patterns in species distributions and environmental gradients. Genetics: Population structure and gene flow analysis while allowing for spatial autocorrelation considerations. Biogeography: To identify historical dispersal routes, and barriers to gene flow, providing insights into species distribution patterns and evolutionary history. == Software/Source Code == sPCA implementations are available in R in adegenet and ntbox . These tools facilitate the application of sPCA by providing functions for constructing spatial weight matrices, performing eigenanalysis, and obtaining spatial principal components in an easy-to-read form.
Gollum browser
Gollum browser is a discontinued web browser for accessing Wikipedia. Since 2017, Gollum is no longer accessible online. Gollum is designed to browse Wikipedia in an easier way than directly using the web browser. Links external to Wikipedia are opened in the user's regular browser. Gollum is opened from a regular browser and makes a window that puts the Wikipedia search bar on the toolbar. Gollum was created by Harald Hanek in 2005 using PHP and Ajax. According to one blogger, Gollum provides a way to bypass censorship of Wikipedia in China. == Languages == Though the website is available only in English and German, Gollum's GUI is available in more than 32 languages and can browse nearly 50 Wikipedia editions. === Gollum's GUI === === Browsable Wikipedia editions ===
Hall circles
Hall circles (also known as M-circles and N-circles) are a graphical tool in control theory used to obtain values of a closed-loop transfer function from the Nyquist plot (or the Nichols plot) of the associated open-loop transfer function. Hall circles have been introduced in control theory by Albert C. Hall in his thesis. == Construction == Consider a closed-loop linear control system with open-loop transfer function given by transfer function G ( s ) {\displaystyle G(s)} and with a unit gain in the feedback loop. The closed-loop transfer function is given by T ( s ) = G ( s ) 1 + G ( s ) {\textstyle T(s)={\frac {G(s)}{1+G(s)}}} . To check the stability of T(s), it is possible to use the Nyquist stability criterion with the Nyquist plot of the open-loop transfer function G(s). Note, however, that the Nyquist plot of G(s) does not give the actual values of T(s). To get this information from the G(s)-plane, Hall proposed to construct the locus of points in the G(s)-plane such that T(s) has constant magnitude and also the locus of points in the G(s)-plane such that T(s) has constant phase angle. Given a positive real value M representing a fixed magnitude, and denoting G(s) by z, the points satisfying M = | T ( s ) | = | G ( s ) | | 1 + G ( s ) | = | z | | 1 + z | {\displaystyle M=|T(s)|={\frac {|G(s)|}{|1+G(s)|}}={\frac {|z|}{|1+z|}}} are given by the points z in the G(s)-plane such that the ratio of the distance between z and 0 and the distance between z and -1 is equal to M. The points z satisfying this locus condition are circles of Apollonius, and this locus is known in the context of control systems as M-circles. Given a positive real value N representing a phase angle, the points satisfying N = arg [ G ( s ) 1 + G ( s ) ] = arg [ G ( s ) ] − arg [ 1 + G ( s ) ] = arg [ z ] − arg [ 1 + z ] {\displaystyle N=\arg \left[{\frac {G(s)}{1+G(s)}}\right]=\arg[G(s)]-\arg[1+G(s)]=\arg[z]-\arg[1+z]} are given by the points z in the G(s)-plane such that the angle between -1 and z and the angle between 0 and z is constant. In other words, the angle opposed to the line segment between -1 and 0 must be constant. This implies that the points z satisfying this locus condition are arcs of circles, and this locus is known in the context of control systems as N-circles. == Usage == To use the Hall circles, a plot of M and N circles is done over the Nyquist plot of the open-loop transfer function. The points of the intersection between these graphics give the corresponding value of the closed-loop transfer function. Hall circles are also used with the Nichols plot and in this setting, are also known as Nichols chart. Rather than overlaying directly the Hall circles over the Nichols plot, the points of the circles are transferred to a new coordinate system where the ordinate is given by 20 log 10 ( | G ( s ) | ) {\displaystyle 20\log _{10}(|G(s)|)} and the abscissa is given by arg ( G ( s ) ) {\displaystyle \arg(G(s))} . The advantage of using Nichols chart is that adjusting the gain of the open loop transfer function directly reflects in up and down translation of the Nichols plot in the chart.
Ontology for Biomedical Investigations
The Ontology for Biomedical Investigations (OBI) is an open-access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, the materials used, the data generated and the type of analysis performed on it. The project is being developed as part of the OBO Foundry and as such adheres to all the principles therein such as orthogonal coverage (i.e. clear delineation from other foundry member ontologies) and the use of a common formal language. In OBI the common formal language used is the Web Ontology Language (OWL). As of March 2008, a pre-release version of the ontology was made available at the project's SVN repository. == Scope == The Ontology for Biomedical Investigations (OBI) addresses the need for controlled vocabularies to support integration and joint ("cross-omics") analysis of experimental data, a need originally identified in the transcriptomics domain by the FGED Society, which developed the MGED Ontology as an annotation resource for microarray data.Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al. (November 2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology. 25 (11): 1251–5. doi:10.1038/nbt1346. PMC 2814061. PMID 17989687. OBI uses the basic formal ontology upper-level ontology as a means of describing general entities that do not belong to a specific problem domain. As such, all OBI classes are a subclass of some BFO class. The ontology has the scope of modeling all biomedical investigations and as such contains ontology terms for aspects such as: biological material – for example blood plasma instrument (and parts of an instrument therein) – for example DNA microarray, centrifuge information content – such as an image or a digital information entity such as an electronic medical record design and execution of an investigation (and individual experiments therein) – for example study design, electrophoresis material separation data transformation (incorporating aspects such as data normalization and data analysis) – for example principal components analysis dimensionality reduction, mean calculation Less 'concrete' aspects such as the role a given entity may play in a particular scenario (for example the role of a chemical compound in an experiment) and the function of an entity (for example the digestive function of the stomach to nutriate the body) are also covered in the ontology. == OBI consortium == The MGED Ontology was originally identified in the transcriptomics domain by the FGED Society and was developed to address the needs of data integration. Following a mutual decision to collaborate, this effort later became a wider collaboration between groups such as FGED, PSI and MSI in response to the needs of areas such as transcriptomics, proteomics and metabolomics and the FuGO (Functional Genomics Investigation Ontology) was created. This later became the OBI covering the wider scope of all biomedical investigations. As an international, cross-domain initiative, the OBI consortium draws upon a pool of experts from a variety of fields, not limited to biology. The current list of OBI consortium members is available at the OBI consortium website. The consortium is made up of a coordinating committee which is a combination of two subgroups, the Community Representative (those representing a particular biomedical community) and the Core Developers (ontology developers who may or may not be members of any single community). Separate to the coordinating committee is the Developers Working Group which consists of developers within the communities collaborating in the development of OBI at the discretion of current OBI Consortium members. == Papers on OBI ==
Applied Information Science in Economics
The Applied Information Science in Economics (Russian: Прикладная информатика в Экономике) or Applied Computer Science in Economics is a professional qualification generally awarded in Russian Federation. The degree inherited from the U.S.S.R. education system also known as Specialist degree. The degree is awarded after five years of full-time study and includes several internships, course-works, thesis writing and defense. The degree has similarities with German Magister Artium or Diplom degree. However, due to the Bologna Process number of such degrees are declining. Degree focuses on applying mathematical methods in economics involving maximum information technology. It is very close to applied mathematics, but includes also major part of computer science. == List of specialty codes in the education system == 080801 - Applied computer science in economics 351400 - Applied computer science == Fields of activity == Organization and management; Project design; Experimental research; Marketing; Consulting; Operational and Maintenance. == Major == Information Science and Programming. High Level Methods of Information Science and Programming. Information Technologies in Economics. Computer Systems, Networks and Telecommunications Services. Operational Environments, Systems and Shells. Architecture and Design of Information Systems for Companies. Data Bases. Information security. Information Management. Imitative Simulation.
Learning curve (machine learning)
In machine learning (ML), a learning curve (or training curve) is a graphical representation that shows how a model's performance on a training set (and usually a validation set) changes with the number of training iterations (epochs) or the amount of training data. Typically, the number of training epochs or training set size is plotted on the x-axis, and the value of the loss function (and possibly some other metric such as the cross-validation score) on the y-axis. Synonyms include error curve, experience curve, improvement curve and generalization curve. More abstractly, learning curves plot the difference between learning effort and predictive performance, where "learning effort" usually means the number of training samples, and "predictive performance" means accuracy on testing samples. Learning curves have many useful purposes in ML, including: choosing model parameters during design, adjusting optimization to improve convergence, and diagnosing problems such as overfitting (or underfitting). Learning curves can also be tools for determining how much a model benefits from adding more training data, and whether the model suffers more from a variance error or a bias error. If both the validation score and the training score converge to a certain value, then the model will no longer significantly benefit from more training data. == Formal definition == When creating a function to approximate the distribution of some data, it is necessary to define a loss function L ( f θ ( X ) , Y ) {\displaystyle L(f_{\theta }(X),Y)} to measure how good the model output is (e.g., accuracy for classification tasks or mean squared error for regression). We then define an optimization process which finds model parameters θ {\displaystyle \theta } such that L ( f θ ( X ) , Y ) {\displaystyle L(f_{\theta }(X),Y)} is minimized, referred to as θ ∗ {\displaystyle \theta ^{}} . === Training curve for amount of data === If the training data is { x 1 , x 2 , … , x n } , { y 1 , y 2 , … y n } {\displaystyle \{x_{1},x_{2},\dots ,x_{n}\},\{y_{1},y_{2},\dots y_{n}\}} and the validation data is { x 1 ′ , x 2 ′ , … x m ′ } , { y 1 ′ , y 2 ′ , … y m ′ } {\displaystyle \{x_{1}',x_{2}',\dots x_{m}'\},\{y_{1}',y_{2}',\dots y_{m}'\}} , a learning curve is the plot of the two curves i ↦ L ( f θ ∗ ( X i , Y i ) ( X i ) , Y i ) {\displaystyle i\mapsto L(f_{\theta ^{}(X_{i},Y_{i})}(X_{i}),Y_{i})} i ↦ L ( f θ ∗ ( X i , Y i ) ( X i ′ ) , Y i ′ ) {\displaystyle i\mapsto L(f_{\theta ^{}(X_{i},Y_{i})}(X_{i}'),Y_{i}')} where X i = { x 1 , x 2 , … x i } {\displaystyle X_{i}=\{x_{1},x_{2},\dots x_{i}\}} === Training curve for number of iterations === Many optimization algorithms are iterative, repeating the same step (such as backpropagation) until the process converges to an optimal value. Gradient descent is one such algorithm. If θ i ∗ {\displaystyle \theta _{i}^{}} is the approximation of the optimal θ {\displaystyle \theta } after i {\displaystyle i} steps, a learning curve is the plot of i ↦ L ( f θ i ∗ ( X , Y ) ( X ) , Y ) {\displaystyle i\mapsto L(f_{\theta _{i}^{}(X,Y)}(X),Y)} i ↦ L ( f θ i ∗ ( X , Y ) ( X ′ ) , Y ′ ) {\displaystyle i\mapsto L(f_{\theta _{i}^{}(X,Y)}(X'),Y')}
Knuth–Plass line-breaking algorithm
The Knuth–Plass algorithm is a line-breaking algorithm designed for use in Donald Knuth's typesetting program TeX. It integrates the problems of text justification and hyphenation into a single algorithm by using a discrete dynamic programming method to minimize a loss function that attempts to quantify the aesthetic qualities desired in the finished output. The algorithm works by dividing the text into a stream of three kinds of objects: boxes, which are non-resizable chunks of content, glue, which are flexible, resizeable elements, and penalties, which represent places where breaking is undesirable (or, if negative, desirable). The loss function, known as "badness", is defined in terms of the deformation of the glue elements, and any extra penalties incurred through line breaking. Making hyphenation decisions follows naturally from the algorithm, but the choice of possible hyphenation points within words, and optionally their preference weighting, must be performed first, and that information inserted into the text stream in advance. Knuth and Plass' original algorithm does not include page breaking, but may be modified to interface with a pagination algorithm, such as the algorithm designed by Plass in his PhD thesis. Typically, the cost function for this technique should be modified so that it does not count the space left on the final line of a paragraph; this modification allows a paragraph to end in the middle of a line without penalty. The same technique can also be extended to take into account other factors such as the number of lines or costs for hyphenating long words. == Computational complexity == A naive brute-force exhaustive search for the minimum badness by trying every possible combination of breakpoints would take an impractical O ( 2 n ) {\displaystyle O(2^{n})} time. The classic Knuth-Plass dynamic programming approach to solving the minimization problem is a worst-case O ( n 2 ) {\displaystyle O(n^{2})} algorithm but usually runs much faster, in close to linear time. Solving for the Knuth-Plass optimum can be shown to be a special case of the convex least-weight subsequence problem, which can be solved in O ( n ) {\displaystyle O(n)} time. Methods to do this include the SMAWK algorithm. == Simple example of minimum raggedness metric == For the input text AAA BB CC DDDDD with line width 6, a greedy algorithm that puts as many words on a line as possible while preserving order before moving to the next line, would produce: ------ Line width: 6 AAA BB Remaining space: 0 CC Remaining space: 4 DDDDD Remaining space: 1 The sum of squared space left over by this method is 0 2 + 4 2 + 1 2 = 17 {\displaystyle 0^{2}+4^{2}+1^{2}=17} . However, the optimal solution achieves the smaller sum 3 2 + 1 2 + 1 2 = 11 {\displaystyle 3^{2}+1^{2}+1^{2}=11} : ------ Line width: 6 AAA Remaining space: 3 BB CC Remaining space: 1 DDDDD Remaining space: 1 The difference here is that the first line is broken before BB instead of after it, yielding a better right margin and a lower cost 11.