Spatial embedding

Spatial embedding is one of feature learning techniques used in spatial analysis where points, lines, polygons or other spatial data types. representing geographic locations are mapped to vectors of real numbers. Conceptually it involves a mathematical embedding from a space with many dimensions per geographic object to a continuous vector space with a much lower dimension. Such embedding methods allow complex spatial data to be used in neural networks and have been shown to improve performance in spatial analysis tasks == Embedded data types == Geographic data can take many forms: text, images, graphs, trajectories, polygons. Depending on the task, there may be a need to combine multimodal data from different sources. The next section describes examples of different types of data and their uses. === Text === Geolocated posts on social media can be used to acquire a library of documents bound to a given place that can be later transformed to embedded vectors using word embedding techniques. === Image === Satellites and aircraft collect digital spatial data acquired from remotely sensed images which can be used in machine learning. They are sometimes hard to analyse using basic image analysis methods and convolutional neural networks can be used to acquire an embedding of images bound to a given geographical object or a region. === Point === A single point of interest (POI) can be assigned multiple features that can be used in machine learning. These could be demographic, transportation, meteorological, or economic data, for example. When embedding single points, it is common to consider the entire set of available points as nodes in a graph. === Line / multiline === Among other things, motion trajectories are represented as lines (multilines). Individual trajectories are embedded taking into account travel time, distances and also features of points visited along the way. Embedding of trajectories allows to improve performance of such tasks as clustering and also categorization. === Polygon === The geographic areas analyzed in machine learning are defined by both administrative boundaries and top-down division into grids of regular shapes such as rectangles, for example. Both types are represented as polygons and, like points, can be assigned different demographic, transportation, or economic features. A polygon can also have features related to the size of the area or shape it represents. === Graph === An example domain where graph representation is used is the street layout in a city, where vertices can be intersections and edges can be roads. The vertices can also be destination points like public transport stops or important points in the city, and the edges represent the flow between them. Embedding graphs or single vertices allows to improve accuracy of analysis methods in which the treated geographical domain can be represented as a network. == Usage == POI recommendation - generating personalized point of interest recommendations based on user preferences. Next/future location prediction - prediction of the next location a person will go to based on their historical trajectory. Zone functions classification - based on different mobility of people or POI distribution a function of a given area in a city can be predicted. Crime prediction - estimation of crime rate in different regions of a city. Local event detection - studying spatio-temporal changes in embeddings can provide valuable information in detection of local event occurring in specific location. Regional mobility popularity prediction - analysis of mobility can show patterns in popularity of different regions in a city. Shape matching - finding a similar shape of given polygon, for example finding building with the same shape as input building. Travel time estimation - predicting estimated travel time given current traffic conditions and special occurring events. Time estimation for on-demand food delivery - estimation of delivery time when placing an order through the website. == Temporal aspect == Some of the data analyzed has a timestamp associated with it. In some cases of data analysis this information is omitted and in others it is used to divide the set into groups. The most common division is the separation of weekdays from weekends or division into hours of the day. This is particularly important in the analysis of mobility data, because the characteristics of mobility during the week and at different times of the day are very different from each other. Another area in which time division into, for example, individual months can be used is in the analysis of tourism of a given region. In order to take such a split into account, embedding methods treat the time stamp specifically or separate versions of the model are developed for different subgroups of the analyzed set.

Lessac Technologies

Lessac Technologies, Inc. (LTI) is an American firm which develops voice synthesis software, licenses technology and sells synthesized novels as MP3 files. The firm currently has seven patents granted and three more pending for its automated methods of converting digital text into human-sounding speech, more accurately recognizing human speech and outputting the text representing the words and phrases of said speech, along with recognizing the speaker's emotional state. The LTI technology is partly based on the work of the late Arthur Lessac, a Professor of Theater at the State University of New York and the creator of Lessac Kinesensic Training, and LTI has licensed exclusive rights to exploit Arthur Lessac's copyrighted works in the fields of speech synthesis and speech recognition. Based on the view that music is speech and speech is music, Lessac's work and books focused on body and speech energies and how they go together. Arthur Lessac's textual annotation system, which was originally developed to assist actors, singers, and orators in marking up scripts to prepare for performance, is adapted in LTI's speech synthesis system as the basic representation of the speech to be synthesized (Lessemes), in contrast to many other systems which use a phonetic representation. LTI's software has two major components: (1) a linguistic front-end that converts plain text to a sequence of prosodic and phonosensory graphic symbols (Lessemes) based on Arthur Lessac's annotation system, which specify the speech units to be synthesized; (2) a signal-processing back-end that takes the Lessemes as acoustic data and produces human-sounding synthesized speech as output, using unit selection and concatenation. LTI's text-to-speech system came in second in the world-wide Blizzard Challenge 2011 and 2012. The first-place team in 2011 also employed LTI's "front-end" technology, but with its own back-end. The Blizzard Challenge, conducted by the Language Technologies Institute of Carnegie Mellon University, was devised as a way to evaluate speech synthesis techniques by having different research groups build voices from the same voice-actor recordings, and comparing the results through listening tests. LTI was founded in 2000 by H. Donald Wilson (chairman), a lawyer, LexisNexis entrepreneur and business associate of Arthur Lessac; and Gary A. Marple (chief inventor), after Marple suggested that Arthur Lessac's kinesensic voice training might be applicable to computational linguistics. After Wilson's death in 2006, his nephew John Reichenbach became the firm's CEO.

Local tangent space alignment

Local tangent space alignment (LTSA) is a method for manifold learning, which can efficiently learn a nonlinear embedding into low-dimensional coordinates from high-dimensional data, and can also reconstruct high-dimensional coordinates from embedding coordinates. It is based on the intuition that when a manifold is correctly unfolded, all of the tangent hyperplanes to the manifold will become aligned. It begins by computing the k-nearest neighbors of every point. It computes the tangent space at every point by computing the d-first principal components in each local neighborhood. It then optimizes to find an embedding that aligns the tangent spaces, but it ignores the label information conveyed by data samples, and thus can not be used for classification directly.

T-distributed stochastic neighbor embedding

t-distributed stochastic neighbor embedding (t-SNE) is a statistical method for visualizing high-dimensional data by giving each datapoint a location in a two or three-dimensional map. It is based on Stochastic Neighbor Embedding originally developed by Geoffrey Hinton and Sam Roweis, where Laurens van der Maaten and Hinton proposed the t-distributed variant. It is a nonlinear dimensionality reduction technique for embedding high-dimensional data for visualization in a low-dimensional space of two or three dimensions. Specifically, it models each high-dimensional object by a two- or three-dimensional point in such a way that similar objects are modeled by nearby points and dissimilar objects are modeled by distant points with high probability. The t-SNE algorithm comprises two main stages. First, t-SNE constructs a probability distribution over pairs of high-dimensional objects in such a way that similar objects are assigned a higher probability while dissimilar points are assigned a lower probability. Second, t-SNE defines a similar probability distribution over the points in the low-dimensional map, and it minimizes the Kullback–Leibler divergence (KL divergence) between the two distributions with respect to the locations of the points in the map. While the original algorithm uses the Euclidean distance between objects as the base of its similarity metric, this can be changed as appropriate. A Riemannian variant is UMAP. t-SNE has been used for visualization in a wide range of applications, including genomics, computer security research, natural language processing, music analysis, cancer research, bioinformatics, geological domain interpretation, and biomedical signal processing. For a data set with n {\displaystyle n} elements, t-SNE runs in O ( n 2 ) {\displaystyle O(n^{2})} time and requires O ( n 2 ) {\displaystyle O(n^{2})} space. == Details == Given a set of N {\displaystyle N} high-dimensional objects x 1 , … , x N {\displaystyle \mathbf {x} _{1},\dots ,\mathbf {x} _{N}} , t-SNE first computes probabilities p i j {\displaystyle p_{ij}} that are proportional to the similarity of objects x i {\displaystyle \mathbf {x} _{i}} and x j {\displaystyle \mathbf {x} _{j}} , as follows. For i ≠ j {\displaystyle i\neq j} , define p j ∣ i = exp ⁡ ( − ‖ x i − x j ‖ 2 / 2 σ i 2 ) ∑ k ≠ i exp ⁡ ( − ‖ x i − x k ‖ 2 / 2 σ i 2 ) {\displaystyle p_{j\mid i}={\frac {\exp(-\lVert \mathbf {x} _{i}-\mathbf {x} _{j}\rVert ^{2}/2\sigma _{i}^{2})}{\sum _{k\neq i}\exp(-\lVert \mathbf {x} _{i}-\mathbf {x} _{k}\rVert ^{2}/2\sigma _{i}^{2})}}} and set p i ∣ i = 0 {\displaystyle p_{i\mid i}=0} . Note the above denominator ensures ∑ j p j ∣ i = 1 {\displaystyle \sum _{j}p_{j\mid i}=1} for all i {\displaystyle i} . As van der Maaten and Hinton explained: "The similarity of datapoint x j {\displaystyle x_{j}} to datapoint x i {\displaystyle x_{i}} is the conditional probability, p j | i {\displaystyle p_{j|i}} , that x i {\displaystyle x_{i}} would pick x j {\displaystyle x_{j}} as its neighbor if neighbors were picked in proportion to their probability density under a Gaussian centered at x i {\displaystyle x_{i}} ." Now define p i j = p j ∣ i + p i ∣ j 2 N {\displaystyle p_{ij}={\frac {p_{j\mid i}+p_{i\mid j}}{2N}}} This is motivated because p i {\displaystyle p_{i}} and p j {\displaystyle p_{j}} from the N samples are estimated as 1/N, so the conditional probability can be written as p i ∣ j = N p i j {\displaystyle p_{i\mid j}=Np_{ij}} and p j ∣ i = N p j i {\displaystyle p_{j\mid i}=Np_{ji}} . Since p i j = p j i {\displaystyle p_{ij}=p_{ji}} , you can obtain previous formula. Also note that p i i = 0 {\displaystyle p_{ii}=0} and ∑ i , j p i j = 1 {\displaystyle \sum _{i,j}p_{ij}=1} . The bandwidth of the Gaussian kernels σ i {\displaystyle \sigma _{i}} is set in such a way that the entropy of the conditional distribution equals a predefined entropy using the bisection method. As a result, the bandwidth is adapted to the density of the data: smaller values of σ i {\displaystyle \sigma _{i}} are used in denser parts of the data space. The entropy increases with the perplexity of this distribution P i {\displaystyle P_{i}} ; this relation is seen as P e r p ( P i ) = 2 H ( P i ) {\displaystyle Perp(P_{i})=2^{H(P_{i})}} where H ( P i ) {\displaystyle H(P_{i})} is the Shannon entropy H ( P i ) = − ∑ j p j | i log 2 ⁡ p j | i . {\displaystyle H(P_{i})=-\sum _{j}p_{j|i}\log _{2}p_{j|i}.} The perplexity is a hand-chosen parameter of t-SNE, and as the authors state, "perplexity can be interpreted as a smooth measure of the effective number of neighbors. The performance of SNE is fairly robust to changes in the perplexity, and typical values are between 5 and 50.". Since the Gaussian kernel uses the Euclidean distance ‖ x i − x j ‖ {\displaystyle \lVert x_{i}-x_{j}\rVert } , it is affected by the curse of dimensionality, and in high dimensional data when distances lose the ability to discriminate, the p i j {\displaystyle p_{ij}} become too similar (asymptotically, they would converge to a constant). It has been proposed to adjust the distances with a power transform, based on the intrinsic dimension of each point, to alleviate this. t-SNE aims to learn a d {\displaystyle d} -dimensional map y 1 , … , y N {\displaystyle \mathbf {y} _{1},\dots ,\mathbf {y} _{N}} (with y i ∈ R d {\displaystyle \mathbf {y} _{i}\in \mathbb {R} ^{d}} and d {\displaystyle d} typically chosen as 2 or 3) that reflects the similarities p i j {\displaystyle p_{ij}} as well as possible. To this end, it measures similarities q i j {\displaystyle q_{ij}} between two points in the map y i {\displaystyle \mathbf {y} _{i}} and y j {\displaystyle \mathbf {y} _{j}} , using a very similar approach. Specifically, for i ≠ j {\displaystyle i\neq j} , define q i j {\displaystyle q_{ij}} as q i j = ( 1 + ‖ y i − y j ‖ 2 ) − 1 ∑ k ∑ l ≠ k ( 1 + ‖ y k − y l ‖ 2 ) − 1 {\displaystyle q_{ij}={\frac {(1+\lVert \mathbf {y} _{i}-\mathbf {y} _{j}\rVert ^{2})^{-1}}{\sum _{k}\sum _{l\neq k}(1+\lVert \mathbf {y} _{k}-\mathbf {y} _{l}\rVert ^{2})^{-1}}}} and set q i i = 0 {\displaystyle q_{ii}=0} . Herein a heavy-tailed Student t-distribution (with one-degree of freedom, which is the same as a Cauchy distribution) is used to measure similarities between low-dimensional points in order to allow dissimilar objects to be modeled far apart in the map. The locations of the points y i {\displaystyle \mathbf {y} _{i}} in the map are determined by minimizing the (non-symmetric) Kullback–Leibler divergence of the distribution P {\displaystyle P} from the distribution Q {\displaystyle Q} , that is: K L ( P ∥ Q ) = ∑ i ≠ j p i j log ⁡ p i j q i j {\displaystyle \mathrm {KL} \left(P\parallel Q\right)=\sum _{i\neq j}p_{ij}\log {\frac {p_{ij}}{q_{ij}}}} The minimization of the Kullback–Leibler divergence with respect to the points y i {\displaystyle \mathbf {y} _{i}} is performed using gradient descent. The result of this optimization is a map that reflects the similarities between the high-dimensional inputs. == Output == While t-SNE plots often seem to display clusters, the visual clusters can be strongly influenced by the chosen parameterization (especially the perplexity) and so a good understanding of the parameters for t-SNE is needed. Such "clusters" can be shown to even appear in structured data with no clear clustering, and so may be false findings. Similarly, the size of clusters produced by t-SNE is not informative, and neither is the distance between clusters. Thus, interactive exploration may be needed to choose parameters and validate results. It has been shown that t-SNE can often recover well-separated clusters, and with special parameter choices, approximates a simple form of spectral clustering. == Software == A C++ implementation of Barnes-Hut is available on the github account of one of the original authors. The R package Rtsne implements t-SNE in R. ELKI contains tSNE, also with Barnes-Hut approximation scikit-learn, a popular machine learning library in Python implements t-SNE with both exact solutions and the Barnes-Hut approximation. Tensorboard, the visualization kit associated with TensorFlow, also implements t-SNE (online version) The Julia package TSne implements t-SNE

Elastic net regularization

In statistics and, in particular, in the fitting of linear or logistic regression models, the elastic net is a regularized regression method that linearly combines the L1 and L2 penalties of the lasso and ridge methods. Nevertheless, elastic net regularization is typically more accurate than both methods with regard to reconstruction. == Specification == The elastic net method overcomes the limitations of the LASSO (least absolute shrinkage and selection operator) method which uses a penalty function based on ‖ β ‖ 1 = ∑ j = 1 p | β j | . {\displaystyle \|\beta \|_{1}=\textstyle \sum _{j=1}^{p}|\beta _{j}|.} Use of this penalty function has several limitations. For example, in the "large p, small n" case (high-dimensional data with few examples), the LASSO selects at most n variables before it saturates. Also if there is a group of highly correlated variables, then the LASSO tends to select one variable from a group and ignore the others. To overcome these limitations, the elastic net adds a quadratic part ( ‖ β ‖ 2 {\displaystyle \|\beta \|^{2}} ) to the penalty, which when used alone is ridge regression (known also as Tikhonov regularization). The estimates from the elastic net method are defined by β ^ ≡ argmin β ( ‖ y − X β ‖ 2 + λ 2 ‖ β ‖ 2 + λ 1 ‖ β ‖ 1 ) . {\displaystyle {\hat {\beta }}\equiv {\underset {\beta }{\operatorname {argmin} }}(\|y-X\beta \|^{2}+\lambda _{2}\|\beta \|^{2}+\lambda _{1}\|\beta \|_{1}).} The quadratic penalty term makes the loss function strongly convex, and it therefore has a unique minimum. The elastic net method includes the LASSO and ridge regression: in other words, each of them is a special case where λ 1 = λ , λ 2 = 0 {\displaystyle \lambda _{1}=\lambda ,\lambda _{2}=0} or λ 1 = 0 , λ 2 = λ {\displaystyle \lambda _{1}=0,\lambda _{2}=\lambda } . Meanwhile, the naive version of elastic net method finds an estimator in a two-stage procedure : first for each fixed λ 2 {\displaystyle \lambda _{2}} it finds the ridge regression coefficients, and then does a LASSO type shrinkage. This kind of estimation incurs a double amount of shrinkage, which leads to increased bias and poor predictions. To improve the prediction performance, sometimes the coefficients of the naive version of elastic net is rescaled by multiplying the estimated coefficients by ( 1 + λ 2 ) {\displaystyle (1+\lambda _{2})} . Examples of where the elastic net method has been applied are: Support vector machine Metric learning Portfolio optimization Cancer prognosis == Reduction to support vector machine == It was proven in 2014 that the elastic net can be reduced to the linear support vector machine. A similar reduction was previously proven for the LASSO in 2014. The authors showed that for every instance of the elastic net, an artificial binary classification problem can be constructed such that the hyper-plane solution of a linear support vector machine (SVM) is identical to the solution β {\displaystyle \beta } (after re-scaling). The reduction immediately enables the use of highly optimized SVM solvers for elastic net problems. It also enables the use of GPU acceleration, which is often already used for large-scale SVM solvers. The reduction is a simple transformation of the original data and regularization constants X ∈ R n × p , y ∈ R n , λ 1 ≥ 0 , λ 2 ≥ 0 {\displaystyle X\in {\mathbb {R} }^{n\times p},y\in {\mathbb {R} }^{n},\lambda _{1}\geq 0,\lambda _{2}\geq 0} into new artificial data instances and a regularization constant that specify a binary classification problem and the SVM regularization constant X 2 ∈ R 2 p × n , y 2 ∈ { − 1 , 1 } 2 p , C ≥ 0. {\displaystyle X_{2}\in {\mathbb {R} }^{2p\times n},y_{2}\in \{-1,1\}^{2p},C\geq 0.} Here, y 2 {\displaystyle y_{2}} consists of binary labels − 1 , 1 {\displaystyle {-1,1}} . When 2 p > n {\displaystyle 2p>n} it is typically faster to solve the linear SVM in the primal, whereas otherwise the dual formulation is faster. Some authors have referred to the transformation as Support Vector Elastic Net (SVEN), and provided the following MATLAB pseudo-code: == Software == "Glmnet: Lasso and elastic-net regularized generalized linear models" is a software which is implemented as an R source package and as a MATLAB toolbox. This includes fast algorithms for estimation of generalized linear models with ℓ1 (the lasso), ℓ2 (ridge regression) and mixtures of the two penalties (the elastic net) using cyclical coordinate descent, computed along a regularization path. JMP Pro 11 includes elastic net regularization, using the Generalized Regression personality with Fit Model. "pensim: Simulation of high-dimensional data and parallelized repeated penalized regression" implements an alternate, parallelised "2D" tuning method of the ℓ parameters, a method claimed to result in improved prediction accuracy. scikit-learn includes linear regression and logistic regression with elastic net regularization. SVEN, a Matlab implementation of Support Vector Elastic Net. This solver reduces the Elastic Net problem to an instance of SVM binary classification and uses a Matlab SVM solver to find the solution. Because SVM is easily parallelizable, the code can be faster than Glmnet on modern hardware. SpaSM, a Matlab implementation of sparse regression, classification and principal component analysis, including elastic net regularized regression. Apache Spark provides support for Elastic Net Regression in its MLlib machine learning library. The method is available as a parameter of the more general LinearRegression class. SAS (software) The SAS procedure Glmselect and SAS Viya procedure Regselect support the use of elastic net regularization for model selection.

Amira (software)

Amira (ah-MEER-ah) is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo. == Overview == Amira is an extendable software system for scientific visualization, data analysis, and presentation of 3D and 4D data. It is used by researchers and engineers in academia and industry. It is a tool for processing, analysis and visualization of data from various modalities; e.g. micro-CT, PET, Ultrasound. It is used in many fields, such as microscopy in biology and materials science, molecular biology, quantum physics, astrophysics, computational fluid dynamics (CFD), finite element modeling (FEM), non-destructive testing (NDT), and many more. One of the key features, besides data visualization, is Amira's set of tools for image segmentation and geometry reconstruction. This allows the user to mark (or segment) structures and regions of interest in 3D image volumes using automatic, semi-automatic, and manual tools. The segmentation can then be used for a variety of subsequent tasks, such as volumetric analysis, density analysis, shape analysis, or the generation of 3D computer models for visualization, numerical simulations, or rapid prototyping or 3D printing. Other key Amira features are multi-planar and volume visualization, image registration, filament tracing, cell separation and analysis, tetrahedral mesh generation, fiber-tracking from diffusion tensor imaging (DTI) data, skeletonization, spatial graph analysis, and stereoscopic rendering of 3D data over multiple displays and immersive virtual reality environments, including CAVEs. As a commercial product Amira requires the purchase of a license or an academic subscription. A time-limited, but full-featured evaluation version is available for download free of charge. == History == === 1993–1998: Research software === Amira's roots go back to 1993 and the Department for Scientific Visualization, headed by Hans-Christian Hege at the Zuse Institute Berlin (ZIB). The ZIB is a research institute for mathematics and informatics. The Scientific Visualization department's mission is to help solve computationally and scientifically challenging tasks in medicine, biology, engineering and materials science. For this purpose, it develops algorithms and software for 2D, 3D, and 4D data visualization and visually supported exploration and analysis. At that time, the young visualization group at the ZIB had experience with the extendable, data flow-oriented visualization environments apE, IRIS Explorer, and Advanced Visualization Studio (AVS), but was not satisfied with these products' interactivity, flexibility, and ease-of-use for non-computer scientists. Therefore, the development of a new software system was started in a research project within a medically oriented, multi-disciplinary collaborative research center. Based on experiences that Tobias Höllerer had gained in late 1993 with the new graphics library IRIS Inventor, it was decided to utilize that library. The development of the medical planning system was performed by Detlev Stalling, who later became the chief software architect of Amira. The new software was called "HyperPlan", highlighting its initial target application – a planning system for hyperthermia cancer treatment. The system was being developed on Silicon Graphics (SGI) computers, which at the time were the standard workstations used for high-end graphics computing. The software was based on libraries such as OpenGL (originally IRIS GL), Open Inventor (originally IRIS Inventor), and the graphical user interface libraries X11, Motif (software), and ViewKit. In 1998, X11/Motif/Viewkit were replaced by the Qt toolkit. The HyperPlan framework served as the base for more and more projects at the ZIB and was used by a growing number of researchers in collaborating institutions. The projects included applications in medical image computing, medical visualization, neurobiology, confocal microscopy, flow visualization, molecular analytics and computational astrophysics. === 1998–today: Commercially supported product === The growing number of users of the system started to exceed the capacities that ZIB could spare for software distribution and support, as ZIB's primary mission was algorithmic research. Therefore, the spin-off company Indeed – Visual Concepts GmbH was founded by Hans-Christian Hege, Detlev Stalling, and Malte Westerhoff. In Feb 1998 the HyperPlan software was given the new, application-neutral name "Amira". This name is not an acronym, but was chosen for being pronounceable in different languages and providing a suitable connotation, namely "to look at" or "to wonder at", from the Latin verb "admirare" (to admire), which reflects a basic situation in data visualization. A major re-design of the software was undertaken by Detlev Stalling and Malte Westerhoff in order to make it a commercially supportable product and to make it available on non-SGI computers as well. In March 1999, the first version of the commercial Amira was exhibited at the CeBIT tradeshow in Hannover, Germany on SGI IRIX and Hewlett-Packard UniX (HP-UX) booths. Versions for Linux and Microsoft Windows followed within the following twelve months. Later Mac OS X support was added. Indeed – Visual Concepts GmbH selected the Bordeaux, France and San Diego, United States based company TGS, Inc. as the worldwide distributor for Amira and completed five major releases (up to version 3.1) in the subsequent four years. In 2003 both Indeed – Visual Concepts GmbH, as well as TGS, Inc. were acquired by Massachusetts-based Mercury Computer Systems, Inc. (NASDAQ:MRCY) and became part of Mercury's newly formed life sciences business unit, later branded Visage Imaging. In 2009, Mercury Computer Systems, Inc. spun off Visage Imaging again and sold it to Melbourne, Australia based Promedicus Ltd (ASX:PME), a leading provider of radiology information systems and medical IT solutions. During this time, Amira continued to be developed in Berlin, Germany and in close collaboration with the ZIB, still headed by the original creators of Amira. TGS, located in Bordeaux, France was sold by Mercury Computer systems to a French investor and renamed to Visualization Sciences Group (VSG). VSG continued the work on a complementary product named Avizo, based on the same source code but customized for material sciences. In August 2012, FEI, to that date the largest OEM reseller of Amira, purchased VSG and the Amira business from Promedicus. This brought the two software sisters Amira and Avizo back into one hand. In August 2013, Visualization Sciences Group (VSG) became a business unit of FEI. In 2016 FEI has been bought by Thermo Fisher Scientific and became part of its Materials & Structural Analysis division in early 2017. Amira and Avizo are still being marketed as two different products; Amira for life sciences and Avizo for materials science, but the development efforts are now joined once again. In the meantime, the number of scientific articles using the Amira / Avizo software, is in the order of 10 thousands. == Amira options == === Microscopy option === Specific readers for microscopy data Image deconvolution Exploration of 3D imagery obtained from virtually any microscope Extraction and editing of filament networks from microscopy images === DICOM reader === Import of clinical and preclinical data in DICOM format === Mesh option === Generation of 3D finite element (FE) meshes from segmented image data Support for many state-of-the-art FE solver formats High-quality visualization of simulation mesh-based results, using scalar, vector, and tensor field display modules === Skeletonization option === Reconstruction and analysis of neural and vascular networks Visualization of skeletonized networks Length and diameter quantification of network segments Ordering of segments in a tree graph Skeletonization of very large image stacks === Molecular option === Advanced tools for the visualization of molecule models Hardware-accelerated volume rendering Powerful molecule editor Specific tools for complex molecular visualization === Developer option === Creation of new custom components for visualizing or data processing Implementation of new file readers or writers C++ programming language Development wizard for getting started quickly === Neuro option === Medical image analysis for DTI and brain perfusion Fiber tracking supporting several stream-line based algorithms Fiber separation into fiber bundles based on user defined source and destination regions Computation of tensor fields, diffusion weighted maps Eigenvalue decomposition of tensor fields Computation of mean transit time, cerebral blood flow, and cerebral blood volume === VR option === Visualization of data on large tiled displays

Correlation clustering

Clustering is the problem of partitioning data points into groups based on similarity or dissimilarity. Correlation clustering is a clustering framework in which a set of objects is partitioned into clusters based on pairwise similarity and dissimilarity information, without requiring the number of clusters to be specified in advance. == Description of the problem == In machine learning, correlation clustering (also known as cluster editing) considers settings in which pairwise similarity or dissimilarity relationships between objects are known. A standard formulation models the input as an unweighted complete graph G = ( V , E ) {\displaystyle G=(V,E)} , where each edge is labeled either + {\displaystyle +} or − {\displaystyle -} (that is, the graph is a signed graph), indicating whether the corresponding endpoints are similar or dissimilar. The goal is to find a clustering (that is, a partition of V {\displaystyle V} ) that either maximizes the number of agreements—the sum of positive edges whose endpoints lie in the same cluster and negative edges whose endpoints lie in different clusters—or minimizes the number of disagreements—the sum of positive edges whose endpoints are separated and negative edges whose endpoints lie in the same cluster. Unlike other clustering methods such as k-means, correlation clustering does not require choosing the number of clusters k {\displaystyle k} in advance. It is not always possible to find a clustering with zero disagreements. For example, consider a triangle graph containing two positive edges and one negative edge. In this case, every clustering incurs at least one disagreement. Such configurations are referred to in the literature as bad triangles. From a computational perspective, optimizing the correlation clustering objective is challenging. The (decision version of the) problem is NP-complete. A large body of subsequent work has developed approximation algorithms for correlation clustering under various assumptions, including complete or general graphs and unweighted or weighted graphs, for both minimization and maximization objectives. This problem is considered one of the fundamental combinatorial optimization problems, and many algorithmic techniques have been developed to address it. The problem has also been studied extensively across multiple disciplines. A comprehensive literature review of early correlation clustering research is provided by Wahid and Hassini. == Formal Definitions == Let G = ( V , E ) {\displaystyle G=(V,E)} be a graph with nodes V {\displaystyle V} and edges E {\displaystyle E} . A clustering of G {\displaystyle G} is a partition of its node set Π = { π 1 , … , π k } {\displaystyle \Pi =\{\pi _{1},\dots ,\pi _{k}\}} with V = π 1 ∪ ⋯ ∪ π k {\displaystyle V=\pi _{1}\cup \dots \cup \pi _{k}} and π i ∩ π j = ∅ {\displaystyle \pi _{i}\cap \pi _{j}=\emptyset } for i ≠ j {\displaystyle i\neq j} . For a given clustering Π {\displaystyle \Pi } , let δ ( Π ) = { { u , v } ∈ E ∣ { u , v } ⊈ π ∀ π ∈ Π } {\displaystyle \delta (\Pi )=\{\{u,v\}\in E\mid \{u,v\}\not \subseteq \pi \;\forall \pi \in \Pi \}} denote the subset of edges of G {\displaystyle G} whose endpoints are in different subsets of the clustering Π {\displaystyle \Pi } . Now, let w : E → R ≥ 0 {\displaystyle w\colon E\to \mathbb {R} _{\geq 0}} be a function that assigns a non-negative weight to each edge of the graph and let E = E + ∪ E − {\displaystyle E=E^{+}\cup E^{-}} be a partition of the edges into attractive ( E + {\displaystyle E^{+}} ) and repulsive ( E − {\displaystyle E^{-}} ) edges; that is, the edges are signed. The minimum disagreement correlation clustering problem is the following optimization problem: minimize Π ∑ e ∈ E + ∩ δ ( Π ) w e + ∑ e ∈ E − ∖ δ ( Π ) w e . {\displaystyle {\begin{aligned}&{\underset {\Pi }{\operatorname {minimize} }}&&\sum _{e\in E^{+}\cap \delta (\Pi )}w_{e}+\sum _{e\in E^{-}\setminus \delta (\Pi )}w_{e}\;.\end{aligned}}} Here, the set E + ∩ δ ( Π ) {\displaystyle E^{+}\cap \delta (\Pi )} contains the attractive edges whose endpoints are in different components with respect to the clustering Π {\displaystyle \Pi } and the set E − ∖ δ ( Π ) {\displaystyle E^{-}\setminus \delta (\Pi )} contains the repulsive edges whose endpoints are in the same component with respect to the clustering Π {\displaystyle \Pi } . Together these two sets contain all edges that disagree with the clustering Π {\displaystyle \Pi } . Similarly to the minimum disagreement correlation clustering problem, the maximum agreement correlation clustering problem is defined as maximize Π ∑ e ∈ E + ∖ δ ( Π ) w e + ∑ e ∈ E − ∩ δ ( Π ) w e . {\displaystyle {\begin{aligned}&{\underset {\Pi }{\operatorname {maximize} }}&&\sum _{e\in E^{+}\setminus \delta (\Pi )}w_{e}+\sum _{e\in E^{-}\cap \delta (\Pi )}w_{e}\;.\end{aligned}}} Here, the set E + ∖ δ ( Π ) {\displaystyle E^{+}\setminus \delta (\Pi )} contains the attractive edges whose endpoints are in the same component with respect to the clustering Π {\displaystyle \Pi } and the set E − ∩ δ ( Π ) {\displaystyle E^{-}\cap \delta (\Pi )} contains the repulsive edges whose endpoints are in different components with respect to the clustering Π {\displaystyle \Pi } . Together these two sets contain all edges that agree with the clustering Π {\displaystyle \Pi } . Instead of formulating the correlation clustering problem in terms of non-negative edge weights and a partition of the edges into attractive and repulsive edges the problem is also formulated in terms of positive and negative edge costs without partitioning the set of edges explicitly. For given weights w : E → R ≥ 0 {\displaystyle w\colon E\to \mathbb {R} _{\geq 0}} and a given partition E = E + ∪ E − {\displaystyle E=E^{+}\cup E^{-}} of the edges into attractive and repulsive edges, the edge costs can be defined by c e = { w e if e ∈ E + − w e if e ∈ E − {\displaystyle {\begin{aligned}c_{e}={\begin{cases}\;\;w_{e}&{\text{if }}e\in E^{+}\\-w_{e}&{\text{if }}e\in E^{-}\end{cases}}\end{aligned}}} for all e ∈ E {\displaystyle e\in E} . An edge whose endpoints are in different clusters is said to be cut. The set δ ( Π ) {\displaystyle \delta (\Pi )} of all edges that are cut is often called a multicut of G {\displaystyle G} . The minimum cost multicut problem is the problem of finding a clustering Π {\displaystyle \Pi } of G {\displaystyle G} such that the sum of the costs of the edges whose endpoints are in different clusters is minimal: minimize Π ∑ e ∈ δ ( Π ) c e . {\displaystyle {\begin{aligned}&{\underset {\Pi }{\operatorname {minimize} }}&&\sum _{e\in \delta (\Pi )}c_{e}\;.\end{aligned}}} Similar to the minimum cost multicut problem, coalition structure generation in weighted graph games is the problem of finding a clustering such that the sum of the costs of the edges that are not cut is maximal: maximize Π ∑ e ∈ E ∖ δ ( Π ) c e . {\displaystyle {\begin{aligned}&{\underset {\Pi }{\operatorname {maximize} }}&&\sum _{e\in E\setminus \delta (\Pi )}c_{e}\;.\end{aligned}}} This formulation is also known as the clique partitioning problem. It can be shown that all four problems that are formulated above are equivalent. This means that a clustering that is optimal with respect to any of the four objectives is optimal for all of the four objectives. == Algorithms == If the graph admits a clustering with zero disagreements, then deleting all negative edges and computing the connected components of the remaining graph yields an optimal clustering. A necessary and sufficient condition for the existence of such a clustering was given by Davis: no cycle in the graph may contain exactly one negative edge. Bansal et al. discuss the NP-completeness proof and also present both a constant factor approximation algorithm and polynomial-time approximation scheme to find the clusters in this setting. Ailon et al. propose a randomized 3-approximation algorithm for the same problem. CC-Pivot(G=(V,E+,E−)) Pick random pivot i ∈ V Set C = { i } {\displaystyle C=\{i\}} , V'=Ø For all j ∈ V, j ≠ i; If (i,j) ∈ E+ then Add j to C Else (If (i,j) ∈ E−) Add j to V' Let G' be the subgraph induced by V' Return clustering C,CC-Pivot(G') The authors show that the above algorithm is a 3-approximation algorithm for correlation clustering. The best polynomial-time approximation algorithm known at the moment for this problem achieves a ~2.06 approximation by rounding a linear program, as shown by Chawla, Makarychev, Schramm, and Yaroslavtsev. Karpinski and Schudy proved existence of a polynomial time approximation scheme (PTAS) for that problem on complete graphs and fixed number of clusters. == Optimal number of clusters == In 2011, it was shown by Bagon and Galun that the optimization of the correlation clustering functional is closely related to well known discrete optimization methods. In their work they proposed a probabilistic analysis of the underlying implicit model that allows the correlation clustering functional to estimate the