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
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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. Abstract To support our reasoning abilities perception must recover environmental regularities—e.g., rigidity, “objectness,” axes of symmetry—for later use by cognition. To create a theory of how our perceptual apparatus can produce meaningful cognitive primitives from an array of image intensities we require a representation whose elements may be lawfully related to important physical regularities, and that correctly describes the perceptual organization people impose on the stimulus. Unfortunately, the representations that are currently available were originally developed for other purposes (e.g., physics, engineering) and have so far proven unsuitable for the problems of perception or common-sense reasoning. In answer to this problem we present a representation that has proven competent to accurately describe an extensive variety of natural forms (e.g., people, mountains, clouds, trees), as well as man-made forms, in a succinct and natural manner. The approach taken in this representational system is to describe scene structure at a scale that is similar to our naive perceptual notion of “a part,” by use of descriptions that reflect a possible formative history of the object, e.g., how the object might have been constructed from lumps of clay. For this representation to be useful it must be possible to recover such descriptions from image data; we show that the primitive elements of such descriptions may be recovered in an overconstrained and therefore reliable manner. We believe that this descriptive system makes an important contribution towards solving current problems in perceiving and reasoning about natural forms by allowing us to construct accurate descriptions that are extremely compact and that capture people's intuitive notions about the part structure of three-dimensional forms. Recent work on mid-level visual representations aims to capture information at the level of complexity higher than typical "visual words", but lower than full-blown semantic objects. Several approaches [5,6,12,23] have been proposed to discover mid-level visual elements, that are both 1) representative, i.e., frequently occurring within a visual dataset, and 2) visually discriminative. However, the current approaches are rather ad hoc and difficult to analyze and evaluate. In this work, we pose visual element discovery as discriminative mode seeking, drawing connections to the the well-known and well-studied mean-shift algorithm [2, 1, 4, 8]. Given a weakly-labeled image collection, our method discovers visually-coherent patch clusters that are maximally discriminative with respect to the labels. One advantage of our formulation is that it requires only a single pass through the data. We also propose the Purity-Coverage plot as a principled way of experimentally analyzing and evaluating different visual discovery approaches, and compare our method against prior work on the Paris Street View dataset of [5]. We also evaluate our method on the task of scene classification, demonstrating state-of-the-art performance on the MIT Scene-67 dataset. Understanding, reasoning, and manipulating semantic concepts of images have been a fundamental research problem for decades. Previous work mainly focused on direct manipulation on natural image manifold through color strokes, key-points, textures, and holes-to-fill. In this work, we present a novel hierarchical framework for semantic image manipulation. Key to our hierarchical framework is that we employ a structured semantic layout as our intermediate representation for manipulation. Initialized with coarse-level bounding boxes, our structure generator first creates pixel-wise semantic layout capturing the object shape, object-object interactions, and object-scene relations. Then our image generator fills in the pixel-level textures guided by the semantic layout. Such framework allows a user to manipulate images at object-level by adding, removing, and moving one bounding box at a time. Experimental evaluations demonstrate the advantages of the hierarchical manipulation framework over existing image generation and context hole-filing models, both qualitatively and quantitatively. Benefits of the hierarchical framework are further demonstrated in applications such as semantic object manipulation, interactive image editing, and data-driven image manipulation. The paper presents an approach for shape analysis based on predicate abstraction. Using a predicate base that involves reachability relations between program variables pointing into the heap, we are able to analyze functional properties of programs with destructive heap updates, such as list reversal and various in-place list sorts. The approach allows verification of both safety and liveness properties. The abstraction we use does not require any abstract representation of the heap nodes (e.g. abstract shapes), only reachability relations between the program variables. The computation of the abstract transition relation is precise and automatic yet does not require the use of a theorem prover. Instead, we use a small model theorem to identify a truncated (small) finite-state version of the program whose abstraction is identical to the abstraction of the unbounded-heap version of the same program. The abstraction of the finite-state version is then computed by BDD techniques. For proving liveness properties, we augment the original system by a well-founded ranking function, which is abstracted together with the system. Well-foundedness is then abstracted into strong fairness (compassion). We show that, for a restricted class of programs that still includes many interesting cases, the small model theorem can be applied to this joint abstraction. Independently of the application to shape-analysis examples, we demonstrate the utility of the ranking abstraction method and its advantages over the direct use of ranking functions in a deductive verification of the same property. Most existing zero-shot learning approaches exploit transfer learning via an intermediate-level semantic representation such as visual attributes or semantic word vectors. Such a semantic representation is shared between an annotated auxiliary dataset and a target dataset with no annotation. A projection from a low-level feature space to the semantic space is learned from the auxiliary dataset and is applied without adaptation to the target dataset. In this paper we identify an inherent limitation with this approach. That is, due to having disjoint and potentially unrelated classes, the projection functions learned from the auxiliary dataset domain are biased when applied directly to the target dataset domain. We call this problem the projection domain shift problem and propose a novel framework, transductive multi-view embedding, to solve it. It is ‘transductive’ in that unlabelled target data points are explored for projection adaptation, and ‘multi-view’ in that both low-level feature (view) and multiple semantic representations (views) are embedded to rectify the projection shift. We demonstrate through extensive experiments that our framework (1) rectifies the projection shift between the auxiliary and target domains, (2) exploits the complementarity of multiple semantic representations, (3) achieves state-of-the-art recognition results on image and video benchmark datasets, and (4) enables novel cross-view annotation tasks. We present a transformation-grounded image generation network for novel 3D view synthesis from a single image. Our approach first explicitly infers the parts of the geometry visible both in the input and novel views and then casts the remaining synthesis problem as image completion. Specifically, we both predict a flow to move the pixels from the input to the novel view along with a novel visibility map that helps deal with occulsion disocculsion. Next, conditioned on those intermediate results, we hallucinate (infer) parts of the object invisible in the input image. In addition to the new network structure, training with a combination of adversarial and perceptual loss results in a reduction in common artifacts of novel view synthesis such as distortions and holes, while successfully generating high frequency details and preserving visual aspects of the input image. We evaluate our approach on a wide range of synthetic and real examples. Both qualitative and quantitative results show our method achieves significantly better results compared to existing methods. Despite the importance of image representations such as histograms of oriented gradients and deep Convolutional Neural Networks (CNN), our theoretical understanding of them remains limited. Aiming at filling this gap, we investigate three key mathematical properties of representations: equivariance, invariance, and equivalence. Equivariance studies how transformations of the input image are encoded by the representation, invariance being a special case where a transformation has no effect. Equivalence studies whether two representations, for example two different parametrisations of a CNN, capture the same visual information or not. A number of methods to establish these properties empirically are proposed, including introducing transformation and stitching layers in CNNs. These methods are then applied to popular representations to reveal insightful aspects of their structure, including clarifying at which layers in a CNN certain geometric invariances are achieved. While the focus of the paper is theoretical, direct applications to structured-output regression are demonstrated too. Despite the importance of image representations such as histograms of oriented gradients and deep Convolutional Neural Networks (CNN), our theoretical understanding of them remains limited. Aiming at filling this gap, we investigate three key mathematical properties of representations: equivariance, invariance, and equivalence. Equivariance studies how transformations of the input image are encoded by the representation, invariance being a special case where a transformation has no effect. Equivalence studies whether two representations, for example two different parametrisations of a CNN, capture the same visual information or not. A number of methods to establish these properties empirically are proposed, including introducing transformation and stitching layers in CNNs. These methods are then applied to popular representations to reveal insightful aspects of their structure, including clarifying at which layers in a CNN certain geometric invariances are achieved. While the focus of the paper is theoretical, direct applications to structured-output regression are demonstrated too. Though a large body of computer vision research has investigated developing generic semantic representations, efforts towards developing a similar representation for 3D has been limited. In this paper, we learn a generic 3D representation through solving a set of foundational proxy 3D tasks: object-centric camera pose estimation and wide baseline feature matching. Our method is based upon the premise that by providing supervision over a set of carefully selected foundational tasks, generalization to novel tasks and abstraction capabilities can be achieved. We empirically show that the internal representation of a multi-task ConvNet trained to solve the above core problems generalizes to novel 3D tasks (e.g., scene layout estimation, object pose estimation, surface normal estimation) without the need for fine-tuning and shows traits of abstraction abilities (e.g., cross modality pose estimation). Human free-hand sketches have been studied in various contexts including sketch recognition, synthesis and fine-grained sketch-based image retrieval (FG-SBIR). A fundamental challenge for sketch analysis is to deal with drastically different human drawing styles, particularly in terms of abstraction level. In this work, we propose the first stroke-level sketch abstraction model based on the insight of sketch abstraction as a process of trading off between the recognizability of a sketch and the number of strokes used to draw it. Concretely, we train a model for abstract sketch generation through reinforcement learning of a stroke removal policy that learns to predict which strokes can be safely removed without affecting recognizability. We show that our abstraction model can be used for various sketch analysis tasks including: (1) modeling stroke saliency and understanding the decision of sketch recognition models, (2) synthesizing sketches of variable abstraction for a given category, or reference object instance in a photo, and (3) training a FG-SBIR model with photos only, bypassing the expensive photo-sketch pair collection step. We propose a new technique for visual attribute transfer across images that may have very different appearance but have perceptually similar semantic structure. By visual attribute transfer, we mean transfer of visual information (such as color, tone, texture, and style) from one image to another. For example, one image could be that of a painting or a sketch while the other is a photo of a real scene, and both depict the same type of scene. Our technique finds semantically-meaningful dense correspondences between two input images. To accomplish this, it adapts the notion of "image analogy" [ 2001] with features extracted from a Deep Convolutional Neutral Network for matching; we call our technique deep image analogy. A coarse-to-fine strategy is used to compute the nearest-neighbor field for generating the results. We validate the effectiveness of our proposed method in a variety of cases, including style texture transfer, color style swap, sketch painting to photo, and time lapse. We explore the concept of abstraction as it is used in visualization, with the ultimate goal of understanding and formally defining it. Researchers so far have used the concept of abstraction largely by intuition without a precise meaning. This lack of specificity left questions on the characteristics of abstraction, its variants, its control, or its ultimate potential for visualization and, in particular, illustrative visualization mostly unanswered. In this paper we thus provide a first formalization of the abstraction concept and discuss how this formalization affects the application of abstraction in a variety of visualization scenarios. Based on this discussion, we derive a number of open questions still waiting to be answered, thus formulating a research agenda for the use of abstraction for the visual representation and exploration of data. This paper, therefore, is intended to provide a contribution to the discussion of the theoretical foundations of our field, rather than attempting to provide a completed and final theory. The recent advances in deep neural networks have convincingly demonstrated high capability in learning vision models on large datasets. Nevertheless, collecting expert labeled datasets especially with pixel-level annotations is an extremely expensive process. An appealing alternative is to render synthetic data (e.g., computer games) and generate ground truth automatically. However, simply applying the models learnt on synthetic images may lead to high generalization error on real images due to domain shift. In this paper, we facilitate this issue from the perspectives of both visual appearance-level and representation-level domain adaptation. The former adapts source-domain images to appear as if drawn from the "style" in the target domain and the latter attempts to learn domain-invariant representations. Specifically, we present Fully Convolutional Adaptation Networks (FCAN), a novel deep architecture for semantic segmentation which combines Appearance Adaptation Networks (AAN) and Representation Adaptation Networks (RAN). AAN learns a transformation from one domain to the other in the pixel space and RAN is optimized in an adversarial learning manner to maximally fool the domain discriminator with the learnt source and target representations. Extensive experiments are conducted on the transfer from GTA5 (game videos) to Cityscapes (urban street scenes) on semantic segmentation and our proposal achieves superior results when comparing to state-of-the-art unsupervised adaptation techniques. More remarkably, we obtain a new record: mIoU of 47.5 on BDDS (drive-cam videos) in an unsupervised setting. The recent advances in deep neural networks have convincingly demonstrated high capability in learning vision models on large datasets. Nevertheless, collecting expert labeled datasets especially with pixel-level annotations is an extremely expensive process. An appealing alternative is to render synthetic data (e.g., computer games) and generate ground truth automatically. However, simply applying the models learnt on synthetic images may lead to high generalization error on real images due to domain shift. In this paper, we facilitate this issue from the perspectives of both visual appearance-level and representation-level domain adaptation. The former adapts source-domain images to appear as if drawn from the "style" in the target domain and the latter attempts to learn domain-invariant representations. Specifically, we present Fully Convolutional Adaptation Networks (FCAN), a novel deep architecture for semantic segmentation which combines Appearance Adaptation Networks (AAN) and Representation Adaptation Networks (RAN). AAN learns a transformation from one domain to the other in the pixel space and RAN is optimized in an adversarial learning manner to maximally fool the domain discriminator with the learnt source and target representations. Extensive experiments are conducted on the transfer from GTA5 (game videos) to Cityscapes (urban street scenes) on semantic segmentation and our proposal achieves superior results when comparing to state-of-the-art unsupervised adaptation techniques. More remarkably, we obtain a new record: mIoU of 47.5 on BDDS (drive-cam videos) in an unsupervised setting. Multi-scale representations are motivated by the scale invariant properties of natural images. While many low level statistical measures, such as the local mean and variance of intensity, behave in a scale invariant manner, there are many higher order deviations from scale invariance where zero-crossings merge and disappear. Such scale variant behavior is important information to represent because it is not easily predicted from lower resolution data. A scale variant image pyramid is a representation that separates this information from the more redundant and predictable scale invariant information. We consider the problem of constructing abstract representations for planning in high-dimensional, continuous environments. We assume an agent equipped with a collection of high-level actions, and construct representations provably capable of evaluating plans composed of sequences of those actions. @PARASPLIT We first consider the deterministic planning case, and show that the relevant computation involves set operations performed over sets of states. We define the specific collection of sets that is necessary and sufficient for planning, and use them to construct a grounded abstract symbolic representation that is provably suitable for deterministic planning. The resulting representation can be expressed in PDDL, a canonical high-level planning domain language; we construct such a representation for the Playroom domain and solve it in milliseconds using an off-the-shelf planner. @PARASPLIT We then consider probabilistic planning, which we show requires generalizing from sets of states to distributions over states. We identify the specific distributions required for planning, and use them to construct a grounded abstract symbolic representation that correctly estimates the expected reward and probability of success of any plan. In addition, we show that learning the relevant probability distributions corresponds to specific instances of probabilistic density estimation and probabilistic classification. We construct an agent that autonomously learns the correct abstract representation of a computer game domain, and rapidly solves it. @PARASPLIT Finally, we apply these techniques to create a physical robot system that autonomously learns its own symbolic representation of a mobile manipulation task directly from sensorimotor data---point clouds, map locations, and joint angles---and then plans using that representation. Together, these results establish a principled link between high-level actions and abstract representations, a concrete theoretical foundation for constructing abstract representations with provable properties, and a practical mechanism for autonomously learning abstract high-level representations.