We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels---the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out---instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data.
Also important from Viola and Isenberg's discussion @cite_39 is their concept of , which are traversed in scale space. We also connect the DNA representations at different scales, facilitating a smooth transition between them. In creating this axis of abstraction, we focus primarily on changes of Viola and Isenberg's geometric axis, but without a geometric interpolation of different representations. Instead, we use visual embedding of one scale in another one.
@cite_39
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Disentangling factors of variation has always been a challenging problem in representation learning. Existing algorithms suffer from many limitations, such as unpredictable disentangling factors, bad quality of generated images from encodings, lack of identity information, etc. In this paper, we proposed a supervised algorithm called DNA-GAN trying to disentangle different attributes of images. The latent representations of images are DNA-like, in which each individual piece represents an independent factor of variation. By annihilating the recessive piece and swapping a certain piece of two latent representations, we obtain another two different representations which could be decoded into images. In order to obtain realistic images and also disentangled representations, we introduced the discriminator for adversarial training. Experiments on Multi-PIE and CelebA datasets demonstrate the effectiveness of our method and the advantage of overcoming limitations existing in other methods. Natural DNA can encode complexity on an enormous scale. Researchers are attempting to achieve the same representational efficiency in computers by implementing developmental encodings, i.e. encodings that map the genotype to the phenotype through a process of growth from a small starting point to a mature form. A major challenge in in this effort is to find the right level of abstraction of biological development to capture its essential properties without introducing unnecessary inefficiencies. In this paper, a novel abstraction of natural development, called Compositional Pattern Producing Networks (CPPNs), is proposed. Unlike currently accepted abstractions such as iterative rewrite systems and cellular growth simulations, CPPNs map to the phenotype without local interaction, that is, each individual component of the phenotype is determined independently of every other component. Results produced with CPPNs through interactive evolution of two-dimensional images show that such an encoding can nevertheless produce structural motifs often attributed to more conventional developmental abstractions, suggesting that local interaction may not be essential to the desirable properties of natural encoding in the way that is usually assumed. In this work, we move beyond the traditional complex-valued representations, introducing more expressive hypercomplex representations to model entities and relations for knowledge graph embeddings. More specifically, quaternion embeddings, hypercomplex-valued embeddings with three imaginary components, are utilized to represent entities. Relations are modelled as rotations in the quaternion space. The advantages of the proposed approach are: (1) Latent inter-dependencies (between all components) are aptly captured with Hamilton product, encouraging a more compact interaction between entities and relations; (2) Quaternions enable expressive rotation in four-dimensional space and have more degree of freedom than rotation in complex plane; (3) The proposed framework is a generalization of ComplEx on hypercomplex space while offering better geometrical interpretations, concurrently satisfying the key desiderata of relational representation learning (i.e., modeling symmetry, anti-symmetry and inversion). Experimental results demonstrate that our method achieves state-of-the-art performance on four well-established knowledge graph completion benchmarks. In computer vision, the one-parameter family of images obtained from the Laplacian-of-a-Gaussian-filtered version of the image, parameterized by the width of the Gaussian, has proved to be a useful data structure for the extraction of feature data. In particular, the zero crossings of this so-called scale-space data are associated with edges and have been proposed by D. Marr (1982) and others as the basis of a representation of the image data. The question arises as to whether the representation is complete and stable. The authors survey some of the studies and results related to these questions as well as several studies that attempt reconstructions based on this or related representations. They formulate a novel method for reconstruction from zero crossings in scale space that is based on minimizing equation error, and they present results showing that the reconstruction is possible but can be unstable. They further show that the method applies when gradient data along the zero crossings are included in the representation, and they demonstrate empirically that the reconstruction is then stable. > We present the H3 layout technique for drawing large directed graphs as node-link diagrams in 3D hyperbolic space. We can lay out much larger structures than can be handled using traditional techniques for drawing general graphs because we assume a hierarchical nature of the data. We impose a hierarchy on the graph by using domain-specific knowledge to find an appropriate spanning tree. Links which are not part of the spanning tree do not influence the layout but can be selectively drawn by user request. The volume of hyperbolic 3-space increases exponentially, as opposed to the familiar geometric increase of euclidean 3-space. We exploit this exponential amount of room by computing the layout according to the hyperbolic metric. We optimize the cone tree layout algorithm for 3D hyperbolic space by placing children on a hemisphere around the cone mouth instead of on its perimeter. Hyperbolic navigation affords a Focus+Context view of the structure with minimal visual clutter. We have successfully laid out hierarchies of over 20,000 nodes. Our implementation accommodates navigation through graphs too large to be rendered interactively by allowing the user to explicitly prune or expand subtrees. This paper describes a generalized axiomatic scale-space theory that makes it possible to derive the notions of linear scale-space, affine Gaussian scale-space and linear spatio-temporal scale-space using a similar set of assumptions (scale-space axioms). The notion of non-enhancement of local extrema is generalized from previous application over discrete and rotationally symmetric kernels to continuous and more general non-isotropic kernels over both spatial and spatio-temporal image domains. It is shown how a complete classification can be given of the linear (Gaussian) scale-space concepts that satisfy these conditions on isotropic spatial, non-isotropic spatial and spatio-temporal domains, which results in a general taxonomy of Gaussian scale-spaces for continuous image data. The resulting theory allows filter shapes to be tuned from specific context information and provides a theoretical foundation for the recently exploited mechanisms of shape adaptation and velocity adaptation, with highly useful applications in computer vision. It is also shown how time-causal spatio-temporal scale-spaces can be derived from similar assumptions. The mathematical structure of these scale-spaces is analyzed in detail concerning transformation properties over space and time, the temporal cascade structure they satisfy over time as well as properties of the resulting multi-scale spatio-temporal derivative operators. It is also shown how temporal derivatives with respect to transformed time can be defined, leading to the formulation of a novel analogue of scale normalized derivatives for time-causal scale-spaces. The kernels generated from these two types of theories have interesting relations to biological vision. We show how filter kernels generated from the Gaussian spatio-temporal scale-space as well as the time-causal spatio-temporal scale-space relate to spatio-temporal receptive field profiles registered from mammalian vision. Specifically, we show that there are close analogies to space-time separable cells in the LGN as well as to both space-time separable and non-separable cells in the striate cortex. We do also present a set of plausible models for complex cells using extended quasi-quadrature measures expressed in terms of scale normalized spatio-temporal derivatives. The theories presented as well as their relations to biological vision show that it is possible to describe a general set of Gaussian and or time-causal scale-spaces using a unified framework, which generalizes and complements previously presented scale-space formulations in this area. We introduce a novel projection-based visualization method for high-dimensional data sets by combining concepts from MDS and the geometry of the hyperbolic spaces. This approach hyperbolic multi-dimensional scaling (H-MDS) is a synthesis of two important concepts for explorative data analysis and visualization: (i) multi-dimensional scaling uses proximity or pair distance data to generate a low-dimensional, spatial presentation of the data; (ii) previous work on the "hyperbolic tree browser" demonstrated the extraordinary advantages for an interactive display of graph-like data in the two-dimensional hyperbolic space (H2).In the new approach, H-MDS maps proximity data directly into the H2. This removes the restriction to "quasihierarchical", graph-based data--a major limitation of (ii). Since a suitable distance function can convert all kinds of data to proximity (or distance-based) data, this type of data can be considered the most general.We review important properties of the hyperbolic space and, in particular, the circular Poincare model of the H2. It enables effective human-computer interaction: by mouse dragging the "focus", the user can navigate in the data without loosing the context. In H2 the "fish-eye" behavior originates not simply by a non-linear view transformation but rather by extraordinary, non-Euclidean properties of the H2. Especially, the exponential growth of length and area of the underlying space makes the H2 a prime target for mapping hierarchical and (now also) high-dimensional data.Several high-dimensional mapping examples including synthetic and real-world data are presented. Since high-dimensional data produce "ring"-shaped displays, we present methods to enhance the display by modulating the dissimilarity contrast. This is demonstrated for an application for unstructured text: i.e., by using multiple film critiques from news:rec.art.movies.reviews and www.imdb.com, each movie is placed within the H2--creating a "space of movies" for interactive exploration. Many real-world domains can be represented as large node-link graphs: backbone Internet routers connect with 70,000 other hosts, mid-sized Web servers handle between 20,000 and 200,000 hyperlinked documents, and dictionaries contain millions of words defined in terms of each other. Computational manipulation of such large graphs is common, but previous tools for graph visualization have been limited to datasets of a few thousand nodes. Visual depictions of graphs and networks are external representations that exploit human visual processing to reduce the cognitive load of many tasks that require understanding of global or local structure. We assert that the two key advantages of computer-based systems for information visualization over traditional paper-based visual exposition are interactivity and scalability. We also argue that designing visualization software by taking the characteristics of a target user's task domain into account leads to systems that are more effective and scale to larger datasets than previous work. This thesis contains a detailed analysis of three specialized systems for the interactive exploration of large graphs, relating the intended tasks to the spatial layout and visual encoding choices. We present two novel algorithms for specialized layout and drawing that use quite different visual metaphors. The H3 system for visualizing the hyperlink structures of web sites scales to datasets of over 100,000 nodes by using a carefully chosen spanning tree as the layout backbone, 3D hyperbolic geometry for a Focus+Context view, and provides a fluid interactive experience through guaranteed frame rate drawing. The Constellation system features a highly specialized 2D layout intended to spatially encode domain-specific information for computational linguists checking the plausibility of a large semantic network created from dictionaries. The Planet Multicast system for displaying the tunnel topology of the Internet's multicast backbone provides a literal 3D geographic layout of arcs on a globe to help MBone maintainers find misconfigured long-distance tunnels. Each of these three systems provides a very different view of the graph structure, and we evaluate their efficacy for the intended task. We generalize these findings in our analysis of the importance of interactivity and specialization for graph visualization systems that are effective and scalable. This paper presents work in progress on a new technique for visu- alising and manipulating large hierarchies. The information slices approach compactly visualises hierarchical structures using a series of semi-circular discs. The technique is described in the context of our early experience with a prototype file system visualiser based on information slices. Over the last few years, the emerging field of information visuali- sation has resulted in a numerous techniques for helping visualise and make sense of large information spaces (10). Among these are several techniques for visualising and interacting with large hierar- chies which go beyond the traditional approach taken in 2d scrolling browsers such as the Windows Explorer. Treemaps (6, 9) are space-filling visualisations of hierarchies based on successive horizontal and vertical subdivision of screen rectangles. The area of each rectangle is proportional to some at- tribute of the underlying hierarchy such as the (total) size of each subtree. Xdu (4) is a utility for the X window system which displays a graphical disk usage for Unix file systems. Rectangles are stacked from left to right as the directory tree is descended. The current di- rectory is represented by the leftmost rectangle, which is the entire height of the window. Subdirectories are represented by neighbour- ing rectangles in the next column, whose height are proportional to the size of each subdirectory. The hyperbolic browser (7) uses a focus and context technique based on hyperbolic geometry. A hierarchy is laid out uniformly on the hyperbolic plane and then mapped to the unit disc for display on screen. Nodes in the centre of the disc are largest and nodes are assigned progressively less space towards the perimeter of the disc. Cheops (3) is based on multiple re-use of overlaid triangles in the display. Working top-down, the selection of a node (triangle) at a particular level designates that node's children are to be represented The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap layout consensus approach to assembly. This paper describes a view-based method for recognizing 3D objects from 2D images. We employ an aspect-graph structure, where the aspects are not based on the singularities of visual mapping but are instead formed using a notion of shape similarity between views. Specifically, the viewing sphere is endowed with a metric of dis-similarity for each pair of views and the problem of aspect generation is viewed as a “segmentation” of the viewing sphere into homogeneous regions. The viewing sphere is sampled at regular (5 degree) intervals and the similarity metric is used in an iterative procedure to combine views into aspects with a prototype representing each aspect. This is done in a “region-growing” regime which stands in contrast to the usual “edge detection” styles to computing the aspect graph. The aspect growth is constrained such that two aspects of an object remain distinct under the given similarity metric. Once the database of 3D objects is organized as a set of aspects, and prototypes for these aspects for each object, unknown views of database objects are compared with the prototypes and the results are ordered by similarity. We use two similarity metrics for shape, one based on curve matching and the other based on matching shock graphs, which for a database of 64 objects and unknown views of objects from the database give a recall rate of (90.3 , 74.2 , 59.7 ) and (95.2 , 69.0 , 57.5 ), respectively, for the top three matchess cumulative recall rate based on the top three matches is 98 and 100 , respectively. The result of indexing unknown views of objects not in the database also produce intuitive matches. We also develop a hierarchical indexing scheme to prune unlikely objects at an early stage to improve the efficiency of indexing, resulting in savings of 35 at the top level and of 55 at the next level, cumulatively. Abstract We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support interactive exploration within large structural biology assemblies up to the size of bacterial cells. We describe fundamental rendering techniques as well as approaches for element instantiation, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field. We introduce several techniques for sampling and visualizing the latent spaces of generative models. Replacing linear interpolation with spherical linear interpolation prevents diverging from a model's prior distribution and produces sharper samples. J-Diagrams and MINE grids are introduced as visualizations of manifolds created by analogies and nearest neighbors. We demonstrate two new techniques for deriving attribute vectors: bias-corrected vectors with data replication and synthetic vectors with data augmentation. Binary classification using attribute vectors is presented as a technique supporting quantitative analysis of the latent space. Most techniques are intended to be independent of model type and examples are shown on both Variational Autoencoders and Generative Adversarial Networks. An operation preceding most human DNA analyses is read mapping, which aligns millions of short sequences (called reads) to a reference genome. This step involves an enormous amount of computation (evaluating edit distances for millions upon billions of sequence pairs) and thus needs to be outsourced to low-cost commercial clouds. This asks for scalable techniques to protect sensitive DNA information, a demand that cannot be met by any existing techniques (e.g., homomorphic encryption, secure multiparty computation). In this paper, we report a new step towards secure and scalable read mapping on the hybrid cloud, which includes both the public commercial cloud and the private cloud within an organization. Inspired by the famous “seed-and-extend” method, our approach strategically splits a mapping task: the public cloud seeks exact matches between the keyed hash values of short read substrings (called seeds) and those of reference sequences to roughly position reads on the genome; the private cloud extends the seeds from these positions to find right alignments. Our novel seed-combination technique further moves most workload of this task to the public cloud. The new approach is found to work effectively against known inference attacks, and also easily scale to millions of reads. Representations that are invariant to translation, scale and other transformations, can considerably reduce the sample complexity of learning, allowing recognition of new object classes from very few examples|a hallmark of human recognition. Empirical estimates of one-dimensional projections of the distribution induced by a group of ane transformations are proven to represent a unique and invariant signature associated with an image. We show how projections yielding invariant signatures for future images can be learned automatically, and updated continuously, during unsupervised visual experience. A module performing ltering and pooling, like simple and complex cells as proposed by Hubel and Wiesel, can compute such estimates. Under this view, a pooling stage estimates a one-dimensional probability distribution. Invariance from observations through a restricted window is equivalent to a sparsity property w.r.t. to a transformation, which yields templates that are a) Gabor for optimal simultaneous invariance to translation and scale or b) very specic for complex, class-dependent transformations such as rotation in depth of faces. Hierarchical architectures consisting of this basic Hubel-Wiesel module inherit its properties of invariance, stability, and discriminability while capturing the compositional organization of the visual world in terms of wholes and parts, and are invariant to complex transformations that may only be locally ane. The theory applies to several existing deep learning convolutional architectures for image and speech recognition. It also suggests that the main computational goal of the ventral stream of visual cortex is to provide a hierarchical representation of new objects images which is invariant to transformations, stable, and discriminative for recognition|and that this representation may be continuously learned in an unsupervised way during development and natural visual experience. Large scale visual understanding is challenging, as it requires a model to handle the widely-spread and imbalanced distribution of triples. In real-world scenarios with large numbers of objects and relations, some are seen very commonly while others are barely seen. We develop a new relationship detection model that embeds objects and relations into two vector spaces where both discriminative capability and semantic affinity are preserved. We learn both a visual and a semantic module that map features from the two modalities into a shared space, where matched pairs of features have to discriminate against those unmatched, but also maintain close distances to semantically similar ones. Benefiting from that, our model can achieve superior performance even when the visual entity categories scale up to more than 80,000, with extremely skewed class distribution. We demonstrate the efficacy of our model on a large and imbalanced benchmark based of Visual Genome that comprises 53,000+ objects and 29,000+ relations, a scale at which no previous work has ever been evaluated at. We show superiority of our model over carefully designed baselines on the original Visual Genome dataset with 80,000+ categories. We also show state-of-the-art performance on the VRD dataset and the scene graph dataset which is a subset of Visual Genome with 200 categories. Preface Introduction Molecular Biology Mathematics, Statistics, and Computer Science Some Molecular Biology DNA and Proteins The Central Dogma The Genetic Code Transfer RNA and Protein Sequences Genes Are Not Simple Biological Chemistry Restriction Maps Introduction Graphs Interval Graphs Measuring Fragment Sizes Multiple Maps Double Digest Problem Classifying Multiple Solutions Algorithms for DDP Algorithms and Complexity DDP is N P-Complete Approaches to DDP Simulated Annealing: TSP and DDP Mapping with Real Data Cloning and Clone Libraries A Finite Number of Random Clones Libraries by Complete Digestion Libraries by Partial Digestion Genomes per Microgram Physical Genome Maps: Oceans, Islands, and Anchors Mapping by Fingerprinting Mapping by Anchoring An Overview of Clone Overlap Putting It Together Sequence Assembly Shotgun Sequencing Sequencing by Hybridization Shotgun Sequencing Revisited Databases and Rapid Sequence Analysis DNA and Protein Sequence Databases A Tree Representation of a Sequence Hashing a Sequence Repeats in a Sequence Sequence Comparison by Hashing Sequence Comparison with at most l Mismatches Sequence Comparison by Statistical Content Dynamic Programming Alignment of Two Sequences The Number of Alignments Shortest and Longest Paths in a Network Global Distance Alignment Global Similarity Alignment Fitting One Sequence into Another Local Alignment and Clumps Linear Space Algorithms Tracebacks Inversions Map Alignment Parametric Sequence Comparisons Multiple Sequence Alignment The Cystic Fibrosis Gene Dynamic Programming in r-Dimensions Weighted-Average Sequences Profile Analysis Alignment by Hidden Markov Models Consensus Word Analysis Probability and Statistics for Sequence Alignment Global Alignment Local Alignment Extreme Value Distributions The Chein-Stein Method Poisson Approximation and Long Matches Sequence Alignment with Scores Probability and Statistics for Sequence Patterns A Central Limit Theorem Nonoverlapping Pattern Counts Poisson Approximation Site Distributions RNA Secondary Structure Combinatorics Minimum Free-energy Structures Consensus folding Trees and Sequences Trees Distance Parsimony Maximum Likelihood Trees Sources and Perspectives Molecular Biology Physical Maps and Clone Libraries Sequence Assembly Sequence Comparisons Probability and Statistics RNA Secondary Structure Trees and Sequences References Problem Solutions and Hints Mathematical Notation Algorithm Index Author Index Subject Index Indyk and Sidiropoulos (2007) proved that any orientable graph of genus @math can be probabilistically embedded into a graph of genus @math with constant distortion. Viewing a graph of genus @math as embedded on the surface of a sphere with @math handles attached, Indyk and Sidiropoulos' method gives an embedding into a distribution over planar graphs with distortion @math , by iteratively removing the handles. By removing all @math handles at once, we present a probabilistic embedding with distortion @math for both orientable and non-orientable graphs. Our result is obtained by showing that the nimum-cut graph of Erickson and Har Peled (2004) has low dilation, and then randomly cutting this graph out of the surface using the Peeling Lemma of Lee and Sidiropoulos (2009). We introduce a novel kernel that upgrades the Weisfeiler-Lehman and other graph kernels to effectively exploit high-dimensional and continuous vertex attributes. Graphs are first decomposed into subgraphs. Vertices of the subgraphs are then compared by a kernel that combines the similarity of their labels and the similarity of their structural role, using a suitable vertex invariant. By changing this invariant we obtain a family of graph kernels which includes generalizations of Weisfeiler-Lehman, NSPDK, and propagation kernels. We demonstrate empirically that these kernels obtain state-of-the-art results on relational data sets. The nearestor near-neighbor query problems arise in a large variety of database applications, usually in the context of similarity searching. Of late, there has been increasing interest in building search index structures for performing similarity search over high-dimensional data, e.g., image databases, document collections, time-series databases, and genome databases. Unfortunately, all known techniques for solving this problem fall prey to the of dimensionality." That is, the data structures scale poorly with data dimensionality; in fact, if the number of dimensions exceeds 10 to 20, searching in k-d trees and related structures involves the inspection of a large fraction of the database, thereby doing no better than brute-force linear search. It has been suggested that since the selection of features and the choice of a distance metric in typical applications is rather heuristic, determining an approximate nearest neighbor should su ce for most practical purposes. In this paper, we examine a novel scheme for approximate similarity search based on hashing. The basic idea is to hash the points Supported by NAVY N00014-96-1-1221 grant and NSF Grant IIS-9811904. Supported by Stanford Graduate Fellowship and NSF NYI Award CCR-9357849. Supported by ARO MURI Grant DAAH04-96-1-0007, NSF Grant IIS-9811904, and NSF Young Investigator Award CCR9357849, with matching funds from IBM, Mitsubishi, Schlumberger Foundation, Shell Foundation, and Xerox Corporation. Permission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage, the VLDB copyright notice and the title of the publication and its date appear, and notice is given that copying is by permission of the Very Large Data Base Endowment. To copy otherwise, or to republish, requires a fee and or special permission from the Endowment. Proceedings of the 25th VLDB Conference, Edinburgh, Scotland, 1999. from the database so as to ensure that the probability of collision is much higher for objects that are close to each other than for those that are far apart. We provide experimental evidence that our method gives signi cant improvement in running time over other methods for searching in highdimensional spaces based on hierarchical tree decomposition. Experimental results also indicate that our scheme scales well even for a relatively large number of dimensions (more than 50).