explorase: Multivariate Exploratory Analysis and Visualization for Systems Biology

The datasets being produced by high-throughput biological experiments, such as microarrays, have forced biologists to turn to sophisticated statistical analysis and visualization tools in order to understand their data. We address the particular need for an open-source exploratory data analysis tool that applies numerical methods in coordination with interactive graphics to the analysis of experimental data. The software package, known as explorase, provides a graphical user interface (GUI) on top of the R platform for statistical computing and the GGobi software for multivariate interactive graphics. The GUI is designed for use by biologists, many of whom are unfamiliar with the R language. It displays metadata about experimental design and biological entities in tables that are sortable and filterable. There are menu shortcuts to the analysis methods implemented in R, including graphical interfaces to linear modeling tools. The GUI is linked to data plots in GGobi through a brush tool that simultaneously colors rows in the entity information table and points in the GGobi plots.

Interactive visual exploration of a large spatio-temporal dataset: Reflections on a geovisualization mashup

Exploratory visual analysis is useful for the preliminary investigation of large structured, multifaceted spatio-temporal datasets. This process requires the selection and aggregation of records by time, space and attribute, the ability to transform data and the flexibility to apply appropriate visual encodings and interactions. We propose an approach inspired by geographical 'mashups' in which freely-available functionality and data are loosely but flexibly combined using de facto exchange standards. Our case study combines MySQL, PHP and the LandSerf GIS to allow Google Earth to be used for visual synthesis and interaction with encodings described in KML. This approach is applied to the exploration of a log of 1.42 million requests made of a mobile directory service. Novel combinations of interaction and visual encoding are developed including spatial 'tag clouds', 'tag maps', 'data dials' and multi-scale density surfaces. Four aspects of the approach are informally evaluated: the visual encodings employed, their success in the visual exploration of the clataset, the specific tools used and the 'rnashup' approach. Preliminary findings will be beneficial to others considering using mashups for visualization. The specific techniques developed may be more widely applied to offer insights into the structure of multifarious spatio-temporal data of the type explored here

ICE: An Interactive Configuration Explorer for High Dimensional Categorical Parameter Spaces

There are many applications where users seek to explore the impact of the settings of several categorical variables with respect to one dependent numerical variable. For example, a computer systems analyst might want to study how the type of file system or storage device affects system performance. A usual choice is the method of Parallel Sets designed to visualize multivariate categorical variables. However, we found that the magnitude of the parameter impacts on the numerical variable cannot be easily observed here. We also attempted a dimension reduction approach based on Multiple Correspondence Analysis but found that the SVD-generated 2D layout resulted in a loss of information. We hence propose a novel approach, the Interactive Configuration Explorer (ICE), which directly addresses the need of analysts to learn how the dependent numerical variable is affected by the parameter settings given multiple optimization objectives. No information is lost as ICE shows the complete distribution and statistics of the dependent variable in context with each categorical variable. Analysts can interactively filter the variables to optimize for certain goals such as achieving a system with maximum performance, low variance, etc. Our system was developed in tight collaboration with a group of systems performance researchers and its final effectiveness was evaluated with expert interviews, a comparative user study, and two case studies.Comment: 10 pages, Published by IEEE at VIS 2019 (Vancouver, BC, Canada

Measuring Data Abstraction Quality in Multiresolution Visualizations

Data abstraction techniques are widely used in multiresolution visualization systems to reduce visual clutter and facilitate analysis from overview to detail. However, analysts are usually unaware of how well the abstracted data represent the original dataset, which can impact the reliability of results gleaned from the abstractions. In this thesis, we define three types of data abstraction quality measures for computing the degree to which the abstraction conveys the original dataset: the Histogram Difference Measure, the Nearest Neighbor Measure and Statistical Measure. They have been integrated within XmdvTool, a public-domain multiresolution visualization system for multivariate data analysis that supports sampling as well as clustering to simplify data. Several interactive operations are provided, including adjusting the data abstraction level, changing selected regions, and setting the acceptable data abstraction quality level. Conducting these operations, analysts can select an optimal data abstraction level. We did an evaluation to check how well the data abstraction measures conform to the data abstraction quality perceived by users. We adjusted the data abstraction measures based on the results of the evaluation. We also experimented on the measures with different distance methods and different computing mechanisms, in order to find the optimal variation from many variations of each type of measure. Finally, we developed two case studies to demonstrate how analysts can compare different abstraction methods using the measures to see how well relative data density and outliers are maintained, and then select an abstraction method that meets the requirement of their analytic tasks

Interactive Search and Exploration in Online Discussion Forums Using Multimodal Embeddings

In this paper we present a novel interactive multimodal learning system, which facilitates search and exploration in large networks of social multimedia users. It allows the analyst to identify and select users of interest, and to find similar users in an interactive learning setting. Our approach is based on novel multimodal representations of users, words and concepts, which we simultaneously learn by deploying a general-purpose neural embedding model. We show these representations to be useful not only for categorizing users, but also for automatically generating user and community profiles. Inspired by traditional summarization approaches, we create the profiles by selecting diverse and representative content from all available modalities, i.e. the text, image and user modality. The usefulness of the approach is evaluated using artificial actors, which simulate user behavior in a relevance feedback scenario. Multiple experiments were conducted in order to evaluate the quality of our multimodal representations, to compare different embedding strategies, and to determine the importance of different modalities. We demonstrate the capabilities of the proposed approach on two different multimedia collections originating from the violent online extremism forum Stormfront and the microblogging platform Twitter, which are particularly interesting due to the high semantic level of the discussions they feature

BioIMAX : a Web2.0 approach to visual data mining in bioimage data

Loyek C. BioIMAX : a Web2.0 approach to visual data mining in bioimage data. Bielefeld: Universität Bielefeld; 2012

STV-based Video Feature Processing for Action Recognition

In comparison to still image-based processes, video features can provide rich and intuitive information about dynamic events occurred over a period of time, such as human actions, crowd behaviours, and other subject pattern changes. Although substantial progresses have been made in the last decade on image processing and seen its successful applications in face matching and object recognition, video-based event detection still remains one of the most difficult challenges in computer vision research due to its complex continuous or discrete input signals, arbitrary dynamic feature definitions, and the often ambiguous analytical methods. In this paper, a Spatio-Temporal Volume (STV) and region intersection (RI) based 3D shape-matching method has been proposed to facilitate the definition and recognition of human actions recorded in videos. The distinctive characteristics and the performance gain of the devised approach stemmed from a coefficient factor-boosted 3D region intersection and matching mechanism developed in this research. This paper also reported the investigation into techniques for efficient STV data filtering to reduce the amount of voxels (volumetric-pixels) that need to be processed in each operational cycle in the implemented system. The encouraging features and improvements on the operational performance registered in the experiments have been discussed at the end