Dimensionality Reduction (DR) is a core building block in visualizing multidimensional data. For DR techniques to be useful in exploratory data analysis, they need to be adapted to human needs and domain-specific problems, ideally, interactively, and on-the-fly. Many visual analytics systems have already demonstrated the benefits of tightly integrating DR with interactive visualizations. Nevertheless, a general, structured understanding of this integration is missing. To address this, we systematically studied the visual analytics and visualization literature to investigate how analysts interact with automatic DR techniques. The results reveal seven common interaction scenarios that are amenable to interactive control such as specifying algorithmic constraints, selecting relevant features, or choosing among several DR algorithms. We investigate specific implementations of visual analysis systems integrating DR, and analyze ways that other machine learning methods have been combined with DR. Summarizing the results in a “human in the loop” process model provides a general lens for the evaluation of visual interactive DR systems. We apply the proposed model to study and classify several systems previously described in the literature, and to derive future research opportunities.
Significance: Gene transcription is a highly regulated dynamic process. Delays in transcription have important consequences on dynamics of gene expression and consequently on downstream biological function. We model temporal dynamics of transcription using genome-wide time course data measuring transcriptional activity and mRNA concentration. We find a significant number of genes exhibit a long RNA processing delay between transcription termination and mRNA production. These long processing delays are more common for short genes, which would otherwise be expected to transcribe most rapidly. The distribution of intronic reads suggests that these delays are required for splicing to be completed. Understanding such delays is essential for understanding how a rapid cellular response is regulated.
1 July 2001 in IEEE Transactions on Neural Networks
We introduce a method for deriving a metric, locally based on the Fisher information matrix, into the data space. A self-organizing map (SOM) is computed in the new metric to explore financial statements of enterprises. The metric measures local distances in terms of changes in the distribution of an auxiliary random variable that reflects what is important in the data. In this paper the variable indicates bankruptcy within the next few years. The conditional density of the auxiliary variable is first estimated, and the change in the estimate resulting from local displacements in the primary data space is measured using the Fisher information matrix. When a self-organizing map is computed in the new metric it still visualizes the data space in a topology-preserving fashion, but represents the (local) directions in which the probability of bankruptcy changes the most.
Exploratory search requires the system to assist the user in comprehending the information space and expressing evolving search intents for iterative exploration and retrieval of information. We introduce interactive intent modeling, a technique that models a user’s evolving search intents and visualizes them as keywords for interaction. The user can provide feedback on the keywords, from which the system learns and visualizes an improved intent estimate and retrieves information. We report experiments comparing variants of a system implementing interactive intent modeling to a control system. Data comprising search logs, interaction logs, essay answers, and questionnaires indicate significant improvements in task performance, information retrieval performance over the session, information comprehension performance, and user experience. The improvements in retrieval effectiveness can be attributed to the intent modeling and the effect on users’ task performance, breadth of information comprehension, and user experience are shown to be dependent on a richer visualization. Our results demonstrate the utility of combining interactive modeling of search intentions with interactive visualization of the models that can benefit both directing the exploratory search process and making sense of the information space. Our findings can help design personalized systems that support exploratory information seeking and discovery of novel information.