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. >