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.
On a high level, our work relates to the use of abstraction in creating effective visual representations, , the use of . Viola and Isenberg @cite_39 describe this concept as a process, which removes detail when transitioning from a lower-level to a higher-level representation, yet which preserves the overall concept. While they attribute the removed detail to natural variation, noise, etc.'' in the investigated multi-scale representation we actually deal with a different data scenario: DNA assemblies at different levels of scale. We thus technically do not deal with a concept-preserving transformation'' @cite_39 , but with a process in which the underlying representational concept (or parts of it) can change. Nonetheless, their view of abstraction as an interactive process that allows viewers to relate one representation (at one scale) to another one (at a different scale) is essential to our work.
@cite_39
1650052828 2560971156 2786897815 2890964348
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. Abstract Visualizing high-dimensional labeled data on a two-dimensional plane can quickly result in visual clutter and information overload. To address this problem, the data usually needs to be structured, so that only parts of it are displayed at a time. We present a hierarchy-based approach that projects labeled data on different levels of detail on a two-dimensional plane, whilst keeping the user׳s cognitive load between the level changes as low as possible. The approach consists of three steps: First, the data is hierarchically clustered; second, the user can determine levels of detail; third, the levels of detail are visualized one at a time on a two-dimensional plane. Animations make transitions between the levels of detail traceable, while the exploration on each level is supported by several interaction techniques, including halos, a darts view, and a magic lens. We demonstrate the applicability and usefulness of the approach with use cases from the patent domain and a question-and-answer website. In addition, we conducted a qualitative evaluation to assess the usefulness and comprehensibility of our approach. The seemingly infinite diversity of the natural world arises from a relatively small set of coherent rules, such as the laws of physics or chemistry. We conjecture that these rules give rise to regularities that can be discovered through primarily unsupervised experiences and represented as abstract concepts. If such representations are compositional and hierarchical, they can be recombined into an exponentially large set of new concepts. This paper describes SCAN (Symbol-Concept Association Network), a new framework for learning such abstractions in the visual domain. SCAN learns concepts through fast symbol association, grounding them in disentangled visual primitives that are discovered in an unsupervised manner. Unlike state of the art multimodal generative model baselines, our approach requires very few pairings between symbols and images and makes no assumptions about the form of symbol representations. Once trained, SCAN is capable of multimodal bi-directional inference, generating a diverse set of image samples from symbolic descriptions and vice versa. It also allows for traversal and manipulation of the implicit hierarchy of visual concepts through symbolic instructions and learnt logical recombination operations. Such manipulations enable SCAN to break away from its training data distribution and imagine novel visual concepts through symbolically instructed recombination of previously learnt concepts. 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.