We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.
@cite_16 explore the use of visual causal vectors to indicate causal relationships between data elements, and Bartram and Yao @cite_43 utilize animated causal overlays in order to highlight causal flows and to indicate the relative strength of the causal effect. @cite_20 also find that the use of animation is superior in terms of both accuracy and speed in comparison to static representations for facilitating comprehension of complex causal relations.
@cite_43 @cite_16 @cite_20
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We address the problem of visually detecting causal events and fitting them together into a coherent story of the action witnessed by the camera. We show that this can be done by reasoning about the motions and collisions of surfaces, using high-level causal constraints derived from psychological studies of infant visual behavior. These constraints are naive forms of basic physical laws governing substantiality, contiguity, momentum, and acceleration. We describe two implementations. One system parses instructional videos, extracting plans of action and key frames suitable for storyboarding. Since learning will play a role in making such systems robust, we introduce a new framework for higher-order hidden Markov models and demonstrate its use in a second system that segments stereo video into actions in near real-time. Rather than attempt accurate low-level vision, both systems use high-level causal analysis to integrate fast but sloppy pixel-based representations over time. The output is suitable for summary, indexing, and automated editing. Michotte's theory of ampliation suggests that causal relationships are perceived by objects animated under appropriate spatiotemporal conditions. We extend the theory of ampliation and propose that the immediate perception of complex causal relations is also dependent on a set of structural and temporal rules. We designed animated representations, based on Michotte's rules, for showing complex causal relationships or causal semantics. In this paper we describe a set of animations for showing semantics such as causal amplification, causal strength, causal dampening, and causal multiplicity. In a two part study we compared the effectiveness of both the static and animated representations. The first study (N=44) asked participants to recall passages that were previously displayed using both types of representations. Participants were 8 more accurate in recalling causal semantics when they were presented using animations instead of static graphs. In the second study (N=112) we evaluated the intuitiveness of the representations. Our results showed that while users were as accurate with the static graphs as with the animations, they were 9 faster in matching the correct causal statements in the animated condition. Overall our results show that animated diagrams that are designed based on perceptual rules such as those proposed by Michotte have the potential to facilitate comprehension of complex causal relations. Most approaches to representing causality, such as the common causal graph, require a separate and static view, but in many cases it is useful to add the dimension of causality to the context of an existing visualization. Building on research from perceptual psychology that shows the perception of causality is a low-level visual event derived from certain types of motion, we are investigating how to add animated causal representations, called visual causal vectors, onto other visualizations. We refer to these as causal overlays. Our initial experimental results show this approach has great potential but that extra cues are needed to elicit the perception of causality when the motions are overlaid on other graphical objects. In this paper we describe the approach and report on a study that examined two issues of this technique: how to accurately convey the causal flow and how to represent the strength of the causal effect. The discovery of causal relationships from purely observational data is a fundamental problem in science. The most elementary form of such a causal discovery problem is to decide whether X causes Y or, alternatively, Y causes X, given joint observations of two variables X,Y. An example is to decide whether altitude causes temperature, or vice versa, given only joint measurements of both variables. Even under the simplifying assumptions of no confounding, no feedback loops, and no selection bias, such bivariate causal discovery problems are challenging. Nevertheless, several approaches for addressing those problems have been proposed in recent years. We review two families of such methods: methods based on Additive Noise Models (ANMs) and Information Geometric Causal Inference (IGCI). We present the benchmark CAUSEEFFECTPAIRS that consists of data for 100 different causee ffect pairs selected from 37 data sets from various domains (e.g., meteorology, biology, medicine, engineering, economy, etc.) and motivate our decisions regarding the "ground truth" causal directions of all pairs. We evaluate the performance of several bivariate causal discovery methods on these real-world benchmark data and in addition on artificially simulated data. Our empirical results on real-world data indicate that certain methods are indeed able to distinguish cause from effect using only purely observational data, although more benchmark data would be needed to obtain statistically significant conclusions. One of the best performing methods overall is the method based on Additive Noise Models that has originally been proposed by (2009), which obtains an accuracy of 63 ± 10 and an AUC of 0.74 ± 0.05 on the real-world benchmark. As the main theoretical contribution of this work we prove the consistency of that method.