DimSUM: Dimension and Scale Unifying Map for Visual Abstraction of DNA Origami Structures

We present a novel visualization concept for DNA origami structures that integrates a multitude of representations into a Dimension and Scale Unifying Map (DimSUM). This novel abstraction map provides means to analyze, smoothly transition between, and interact with many visual representations of the DNA origami structures in an effective way that was not possible before. DNA origami structures are nanoscale objects, which are challenging to model in silico. In our holistic approach we seamlessly combine three‐dimensional realistic shape models, two‐dimensional diagrammatic representations, and ordered alignments in one‐dimensional arrangements, with semantic transitions across many scales. To navigate through this large, two‐dimensional abstraction map we highlight locations that users frequently visit for certain tasks and datasets. Particularly interesting viewpoints can be explicitly saved to optimize the workflow. We have developed DimSUM together with domain scientists specialized in DNA nanotechnology. In the paper we discuss our design decisions for both the visualization and the interaction techniques. We demonstrate two practical use cases in which our approach increases the specialists’ understanding and improves their effectiveness in the analysis. Finally, we discuss the implications of our concept for the use of controlled abstraction in visualization in general.     

Legal stories and the process of proof

In this paper, we continue our research on a hybrid narrative-argumentative approach to evidential reasoning in the law by showing the interaction between factual reasoning (providing a proof for ‘what happened’ in a case) and legal reasoning (making a decision based on the proof). First we extend the hybrid theory by making the connection with reasoning towards legal consequences. We then emphasise the role of legal stories (as opposed to the factual stories of the hybrid theory). Legal stories provide a coherent, holistic legal perspective on a case. They steer what needs to be proven but are also selected on the basis of what can be proven. We show how these legal stories can be used to model a shift of the legal perspective on a case, and we discuss how gaps in a legal story can be filled using a factual story (i.e. the process of reasoning with circumstantial evidence). Our model is illustrated by a discussion of the Dutch Wamel murder case.     

Visualization of variability and configuration options

When designing, constructing, and maintaining diverse and variable software systems, a key challenge is the complexity of systems. A potential approach to tackle this challenge are techniques from variability management and product line engineering to handle the diversity and variability. A key asset in variability management is a variability model, which explicitly specifies the commonalities and variability of a system and the constraints between variants. However, handling variability and configurations remains a challenge due to the complexity on a cognitive level as human engineers reach their limits in identifying, understanding, and using all relevant details. In this paper we address this issue by providing concepts for interactive visual tool support for the configuration of systems with the help of feature models. We discuss relevant principles from the area of information visualization and their application to the domain of feature model configuration. We discuss techniques for interactive configuration support based on a reasoning engine, which, e.g., ensures the validity of configurations. We illustrate our findings by a concrete tool solution called S2T2 Configurator.     

利用问题求解理论来研究交互式复杂信息的可视分析行为

面对大数据的挑战,力图将人的推理能力和计算系统的数据处理能力相结合的交 互式可视分析研究变得愈发重要。然而目前仍缺乏有效的认知理论来指导面向复杂信息的可视 分析系统的设计,诸如意义构建等现有的理论框架通常着眼于分析行为的外在特征,未能对此 类行为的内在认知机理进行深入研究。因此提出将问题求解作为一种理论框架来解释交互可视 分析行为的基本认知活动,并建议从非良构问题的角度来描述可视分析过程中用户所面临的主 要挑战,还从问题表征及问题求解策略等角度分析了可视分析系统对分析行为的影响。本研究 在理论上,将认知心理学领域的问题求解理论引入到交互可视分析行为的研究中,该方法对设 计面向复杂信息分析的其他类型交互系统也有启示作用;在实践层面上,从问题求解的支持角 度探索了可视分析系统的设计和评估问题。     

The shaping of information by visual metaphors

The nature of an information visualization can be considered to lie in the visual metaphors it uses to structure information. The process of understanding a visualization therefore involves an interaction between these external visual metaphors and the user's internal knowledge representations. To investigate this claim, we conducted an experiment to test the effects of visual metaphor and verbal metaphor on the understanding of tree visualizations. Participants answered simple data comprehension questions while viewing either a treemap or a node-link diagram. Questions were worded to reflect a verbal metaphor that was either compatible or incompatible with the visualization a participant was using. The results suggest that the visual metaphor indeed affects how a user derives information from a visualization. Additionally, we found that the degree to which a user is affected by the metaphor is strongly correlated with the user's ability to answer task questions correctly. These findings are a first step towards illuminating how visual metaphors shape user understanding, and have significant implications for the evaluation, application, and theory of visualization.     

习题内外表示异质融合的知识追踪模型

现有知识追踪研究大多使用习题蕴涵的知识点等内隐信息或历史交互数据等外显信息建模习题表示,没有注意到内外信息的异质性特征,缺乏对习题内外信息的异质融合。针对上述问题,提出了融合内外异质信息的知识追踪模型。首先,基于知识点等内隐信息,计算历史知识点与当前知识点之间的相关程度,刻画历史知识点对当前知识点的影响,建模习题的内隐表示;其次,基于交互数据等外显信息,计算历史习题与当前习题之间的相关程度,获取历史习题对当前习题的影响,建模习题的外显表示;再次,基于上述习题的内外表示,使用通道注意力机制融合得到习题的内外异质表示,从而预测学习者的作答表现。为了验证提出模型的性能和有效性,选取了四个相关的基线模型,在三个真实数据集上进行了对比实验。实验结果表明：在性能方面,提出的模型在多个评价指标上均取得较好的效果;在有效性方面,消融实验证明了提出的模型可以更好地根据内外信息建模习题表示;在应用方面,设计智慧学习环境证明了提出的模型在实际教学场景中的可用性。     

Beyond Mind: How Brains Make up Artificial Cognitive Systems

What I call semiotic brains are brains that make up a series of signs and that are engaged in making or manifesting or reacting to a series of signs: through this semiotic activity they are at the same time engaged in “being minds” and so in thinking intelligently. An important effect of this semiotic activity of brains is a continuous process of disembodiment of mind that exhibits a new cognitive perspective on the mechanisms underling the semiotic emergence of meaning processes. Indeed at the roots of sophisticated thinking abilities there is a process of disembodiment of mind that presents a new cognitive perspective on the role of external models, representations, and various semiotic materials. Taking advantage of Turing’s comparison between “unorganized” brains and “logical” and “practical” machines” this paper illustrates the centrality to cognition of the disembodiment of mind from the point of view of the interplay between internal and external representations, both mimetic and creative. The last part of the paper describes the concept of mimetic mind I have introduced to shed new cognitive and philosophical light on the role of computational modeling and on the decline of the so-called Cartesian computationalism.     

Embodied cognition of information visualization: Human–computer interaction with six degrees of freedom in movement of an information space

Mental healthcare has been identified as one of the major social and economic challenges that society will face in the coming decades. In this paper, we explore the potential of technology to improve people’s access to and engagement in, as well as the effectiveness and affordability of, mental healthcare services while interacting with computers. Information visualization plays a crucial role in people’s interaction with computers. Specifically, information visualization represents data or concepts graphically and helps people construct cognitive maps i.e., mental representations of the information space. Well-designed information visualization methods enable users to employ their mental capabilities to manipulate an information space and perceive it based on good mental health. According to the latest study of mental capability, movement will guide insight in problem solving situations. Movement in the 3D world is a crucial part of our mental capability, but traditional information visualization approaches fail to consider it. In an attempt to fill this research gap, we propose a new information visualization method that integrates a user’s visual perception and his/her ergonomic perception. Specifically, the approach enables users to manipulate an information space to follow the behavior of human movement in the 3D world with six degrees of freedom. Users can move an information space along the x-, y-, and z-axes as well as rotate it-giving six degrees of freedom. Manipulating the information space in this way provides users with a more comprehensive understanding of the space, and integrates their visual capability and ergonomic perception so that they can fully utilize their mental capabilities.     

Abducing chances in hybrid humans as decision makers

As a matter of fact, humans continuously delegate and distribute cognitive functions to the environment to lessen their limits. They build models, representations, and other various mediating structures that are considered to aid thought. In doing these, humans are engaged in a process of cognitive niche construction. In this sense, I argue that a cognitive niche emerges from a network of continuous interplays between individuals and the environment, in which people alter and modify the environment by mimetically externalizing fleeting thoughts, private ideas, etc. into external supports. Through mimetic activities, humans create external semiotic anchors that are the result of a process in which concepts, ideas, and thoughts are projected onto external structures. Once concepts and thoughts are externalized and projected, new chances and ways of inferring come up from the blend. For cognitive niche construction may also contribute to make available a great portion of chances - in terms of information and knowledge - that otherwise would remain simply unexpressed or unreachable. The central part of the paper will illustrate that “abduction” - or reasoning to explanatory hypotheses - is also central to understanding some features of the problem of action and decision-making. Abduction prompts action and plays a key role in decision-making, like Peirce teaches: the neurological perspective depicted in this paper also increases knowledge about the distinction between thought and motor action, seeing both aspects as fruit of brain activity. We can say that thought possesses an essential “motor” component reflected in brain action but not in actual movement. On the basis of this analysis, I can further illustrate some problems related to the role of abducting chances in decision-making, both in deliberate and in unconscious cases.     

Mining the Semantic Web

In the Semantic Web vision of the World Wide Web, content will not only be accessible to humans but will also be available in machine interpretable form as ontological knowledge bases. Ontological knowledge bases enable formal querying and reasoning and, consequently, a main research focus has been the investigation of how deductive reasoning can be utilized in ontological representations to enable more advanced applications. However, purely logic methods have not yet proven to be very effective for several reasons: First, there still is the unsolved problem of scalability of reasoning to Web scale. Second, logical reasoning has problems with uncertain information, which is abundant on Semantic Web data due to its distributed and heterogeneous nature. Third, the construction of ontological knowledge bases suitable for advanced reasoning techniques is complex, which ultimately results in a lack of such expressive real-world data sets with large amounts of instance data. From another perspective, the more expressive structured representations open up new opportunities for data mining, knowledge extraction and machine learning techniques. If moving towards the idea that part of the knowledge already lies in the data, inductive methods appear promising, in particular since inductive methods can inherently handle noisy, inconsistent, uncertain and missing data. While there has been broad coverage of inducing concept structures from less structured sources (text, Web pages), like in ontology learning, given the problems mentioned above, we focus on new methods for dealing with Semantic Web knowledge bases, relying on statistical inference on their standard representations. We argue that machine learning research has to offer a wide variety of methods applicable to different expressivity levels of Semantic Web knowledge bases: ranging from weakly expressive but widely available knowledge bases in RDF to highly expressive first-order knowledge bases, this paper surveys statistical approaches to mining the Semantic Web. We specifically cover similarity and distance-based methods, kernel machines, multivariate prediction models, relational graphical models and first-order probabilistic learning approaches and discuss their applicability to Semantic Web representations. Finally we present selected experiments which were conducted on Semantic Web mining tasks for some of the algorithms presented before. This is intended to show the breadth and general potential of this exiting new research and application area for data mining.     

A General Illumination Model for Molecular Visualization

Several visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom‐based representations are the Space‐filling, the Solvent Excluded Surface, the Balls‐and‐Sticks, and the Licorice models. While each of these representations has its individual benefits, when applied to large‐scale models spatial arrangements can be difficult to interpret when employing current visualization techniques. In the past it has been shown that global illumination techniques improve the perception of molecular visualizations; unfortunately existing approaches are tailored towards a single visual representation. We propose a general illumination model for molecular visualization that is valid for different representations. With our illumination model, it becomes possible, for the first time, to achieve consistent illumination among all atom‐based molecular representations. The proposed model can be further evaluated in real‐time, as it employs an analytical solution to simulate diffuse light interactions between objects. To be able to derive such a solution for the rather complicated and diverse visual representations, we propose the use of regression analysis together with adapted parameter sampling strategies as well as shape parametrization guided sampling, which are applied to the geometric building blocks of the targeted visual representations. We will discuss the proposed sampling strategies, the derived illumination model, and demonstrate its capabilities when visualizing several dynamic molecules.     

融合语义信息的矩阵分解词向量学习模型

词向量在自然语言处理中起着重要的作用,近年来受到越来越多研究者的关注。然而,传统词向量学习方法往往依赖于大量未经标注的文本语料库,却忽略了单词的语义信息如单词间的语义关系。为了充分利用已有领域知识库（包含丰富的词语义信息）,文中提出一种融合语义信息的词向量学习方法（KbEMF）,该方法在矩阵分解学习词向量的模型上加入领域知识约束项,使得拥有强语义关系的词对获得的词向量相对近似。在实际数据上进行的单词类比推理任务和单词相似度量任务结果表明,KbEMF比已有模型具有明显的性能提升。     

Linking perception and action through motivation and affect

Research into cognitive architectures is described within a framework spanning major issues in artificial intelligence and cognitive science. Earlier work on motivation is extended with a cognitive model of reasoning which, together with an affective mechanism, enables consistent decision-making across a variety of cognitive and reactive processes. Cognition involves the control of behaviour within both external and internal environments. The control of behaviour is vital to an autonomous system as it acts to further its goals. Except in the most spartan of environments, the potential available information and associated combinatorics in a perception, cognition, and action sequence can tax even the most powerful agents. The affect magnitude concept solves some problems with BDI models, and allows for adaptive decision-making over a number of tasks in different domains. The cognitive and affective components are brought together using motivational constructs. The generic cognitive model can adapt to different environments and tasks as it makes use of motivational models to direct reactive and situated processes.     

Thinking with external representations

Why do people create extra representations to help them make sense of situations, diagrams, illustrations, instructions and problems? The obvious explanation—external representations save internal memory and computation—is only part of the story. I discuss seven ways external representations enhance cognitive power: they change the cost structure of the inferential landscape; they provide a structure that can serve as a shareable object of thought; they create persistent referents; they facilitate re-representation; they are often a more natural representation of structure than mental representations; they facilitate the computation of more explicit encoding of information; they enable the construction of arbitrarily complex structure; and they lower the cost of controlling thought—they help coordinate thought. Jointly, these functions allow people to think more powerfully with external representations than without. They allow us to think the previously unthinkable.     

Detail-In-Context Visualization for Satellite Imagery

We use the complex logarithm as a transformation for the visualization and navigation of highly complex satellite and aerial imagery. The resulting depictions show details and context with greatly different scales in one seamless image while avoiding local distortions. We motivate our approach by showing its relations to the ordinary perspective views and classical map projections. We discuss how to organize and process the huge amount of imagery in realtime using modern graphics hardware with an extended clipmapping technique. Finally, we provide details and experiences concerning the interpretation of and interaction with the resulting representations.     

Benefitting InfoVis with visual difficulties

Many well-cited theories for visualization design state that a visual representation should be optimized for quick and immediate interpretation by a user. Distracting elements like decorative "chartjunk" or extraneous information are avoided so as not to slow comprehension. Yet several recent studies in visualization research provide evidence that non-efficient visual elements may benefit comprehension and recall on the part of users. Similarly, findings from studies related to learning from visual displays in various subfields of psychology suggest that introducing cognitive difficulties to visualization interaction can improve a user's understanding of important information. In this paper, we synthesize empirical results from cross-disciplinary research on visual information representations, providing a counterpoint to efficiency-based design theory with guidelines that describe how visual difficulties can be introduced to benefit comprehension and recall. We identify conditions under which the application of visual difficulties is appropriate based on underlying factors in visualization interaction like active processing and engagement. We characterize effective graph design as a trade-off between efficiency and learning difficulties in order to provide Information Visualization (InfoVis) researchers and practitioners with a framework for organizing explorations of graphs for which comprehension and recall are crucial. We identify implications of this view for the design and evaluation of information visualizations.     

DaisyViz: A model-based user interface toolkit for interactive information visualization systems

While information visualization technologies have transformed our life and work, designing information visualization systems still faces challenges. Non-expert users or end-users need toolkits that allow for rapid design and prototyping, along with supporting unified data structures suitable for different data types (e.g., tree, network, temporal, and multi-dimensional data), various visualization, interaction tasks. To address these issues, we designed DaisyViz, a model-based user interface toolkit, which enables end-users to rapidly develop domain-specific information visualization applications without traditional programming. DaisyViz is based on a user interface model for information (UIMI), which includes three declarative models: data model, visualization model, and control model. In the development process, a user first constructs a UIMI with interactive visual tools. The results of the UIMI are then parsed to generate a prototype system automatically. In this paper, we discuss the concept of UIMI, describe the architecture of DaisyViz, and show how to use DaisyViz to build an information visualization system. We also present a usability study of DaisyViz we conducted. Our findings indicate DaisyViz is an effective toolkit to help end-users build interactive information visualization systems.