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.
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This paper introduces U-relations, a succinct and purely relational representation system for uncertain databases. U-relations support attribute-level uncertainty using vertical partitioning. If we consider positive relational algebra extended by an operation for computing possible answers, a query on the logical level can be translated into, and evaluated as, a single relational algebra query on the U-relational representation. The translation scheme essentially preserves the size of the query in terms of number of operations and, in particular, number of joins. Standard techniques employed in off-the-shelf relational database management systems are effective for optimizing and processing queries on U-relations. In our experiments we show that query evaluation on U-relations scales to large amounts of data with high degrees of uncertainty. The future of robots, as our companions is dependent on their ability to understand, interpret and represent the environment in a human compatible manner. Towards this aim, this work attempts to create a hierarchical probabilistic concept-oriented representation of space, based on objects. Specifically, it details efforts taken towards learning and generating concepts and attempts to classify places using the concepts gleaned. Several algorithms, from naive ones using only object category presence to more sophisticated ones using both objects and relationships, are proposed. Both learning and inference use the information encoded in the underlying representation-objects and relative spatial information between them. The approaches are based on learning from exemplars, clustering and the use of Bayesian network classifiers. The approaches are generative. Further, even though they are based on learning from exemplars, they are not ontology specific; i.e. they do not assume the use of any particular ontology. The presented algorithms rely on a robots inherent high-level feature extraction capability (object recognition and structural element extraction) capability to actually form concept models and infer them. Thus, this report presents methods that could enable a robot to to link sensory information to increasingly abstract concepts (spatial constructs). Such a conceptualization and the representation that results thereof would enable robots to be more cognizant of their surroundings and yet, compatible to us. Experiments on conceptualization and place classification are reported. Thus, the theme of this work is-conceptualization and classification for representation and spatial cognition. Abstract In which order can a product be assembled or disassembled? How many hands are required? How many degrees of freedom? What parts should be withdrawn to allow the removal of a specified subassembly? To answer such questions automatically, important theoretical issues in geometric reasoning must be addressed. This paper investigates the planning of assembly algorithms specifying (dis) assembly operations on the components of a product and the ordering of these operations. It also presents measures to evaluate the complexity of these algorithms and techniques to estimate the inherent complexity of a product. The central concept underlying these planning and complexity evaluation techniques is that of a “non-directional blocking graph”, a qualitative representation of the internal structure of an assembly product. This representation describes the combinatorial set of parts interactions in polynomial space. It is obtained by identifying physical criticalities where geometric interferences among parts change. It is generated from an input geometric description of the product. The main application considered in the paper is the creation of smart environments to help designers create products that are easier to manufacture and service. Other possible applications include planning for rapid prototyping and autonomous robots. 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.