Persistent Homology Guided Force-Directed Graph Layouts

Graphs are commonly used to encode relationships among entities, yet their abstractness makes them difficult to analyze. Node-link diagrams are popular for drawing graphs, and force-directed layouts provide a flexible method for node arrangements that use local relationships in an attempt to reveal the global shape of the graph. However, clutter and overlap of unrelated structures can lead to confusing graph visualizations. This paper leverages the persistent homology features of an undirected graph as derived information for interactive manipulation of force-directed layouts. We first discuss how to efficiently extract 0-dimensional persistent homology features from both weighted and unweighted undirected graphs. We then introduce the interactive persistence barcode used to manipulate the force-directed graph layout. In particular, the user adds and removes contracting and repulsing forces generated by the persistent homology features, eventually selecting the set of persistent homology features that most improve the layout. Finally, we demonstrate the utility of our approach across a variety of synthetic and real datasets

Mapper on Graphs for Network Visualization

Networks are an exceedingly popular type of data for representing relationships between individuals, businesses, proteins, brain regions, telecommunication endpoints, etc. Network or graph visualization provides an intuitive way to explore the node-link structures of network data for instant sense-making. However, naive node-link diagrams can fail to convey insights regarding network structures, even for moderately sized data of a few hundred nodes. We propose to apply the mapper construction--a popular tool in topological data analysis--to graph visualization, which provides a strong theoretical basis for summarizing network data while preserving their core structures. We develop a variation of the mapper construction targeting weighted, undirected graphs, called mapper on graphs, which generates property-preserving summaries of graphs. We provide a software tool that enables interactive explorations of such summaries and demonstrates the effectiveness of our method for synthetic and real-world data. The mapper on graphs approach we propose represents a new class of techniques that leverages tools from topological data analysis in addressing challenges in graph visualization

TDANetVis: Suggesting temporal resolutions for graph visualization using zigzag persistent homology

Temporal graphs are commonly used to represent complex systems and track the evolution of their constituents over time. Visualizing these graphs is crucial as it allows one to quickly identify anomalies, trends, patterns, and other properties leading to better decision-making. In this context, the to-be-adopted temporal resolution is crucial in constructing and analyzing the layout visually. The choice of a resolution is critical, e.g., when dealing with temporally sparse graphs. In such cases, changing the temporal resolution by grouping events (i.e., edges) from consecutive timestamps, a technique known as timeslicing, can aid in the analysis and reveal patterns that might not be discernible otherwise. However, choosing a suitable temporal resolution is not trivial. In this paper, we propose TDANetVis, a methodology that suggests temporal resolutions potentially relevant for analyzing a given graph, i.e., resolutions that lead to substantial topological changes in the graph structure. To achieve this goal, TDANetVis leverages zigzag persistent homology, a well-established technique from Topological Data Analysis (TDA). To enhance visual graph analysis, TDANetVis also incorporates the colored barcode, a novel timeline-based visualization built on the persistence barcodes commonly used in TDA. We demonstrate the usefulness and effectiveness of TDANetVis through a usage scenario and a user study involving 27 participants.Comment: This document contains the main article and supplementary material. For associated code and software, see https://github.com/raphaeltinarrage/TDANetVi

Computational Approaches To Anti-Toxin Therapies And Biomarker Identification

This work describes the fundamental study of two bacterial toxins with computational methods, the rational design of a potent inhibitor using molecular dynamics, as well as the development of two bioinformatic methods for mining genomic data. Clostridium difficile is an opportunistic bacillus which produces two large glucosylating toxins. These toxins, TcdA and TcdB cause severe intestinal damage. As Clostridium difficile harbors considerable antibiotic resistance, one treatment strategy is to prevent the tissue damage that the toxins cause. The catalytic glucosyltransferase domain of TcdA and TcdB was studied using molecular dynamics in the presence of both a protein-protein binding partner and several substrates. These experiments were combined with lead optimization techniques to create a potent irreversible inhibitor which protects 95% of cells in vitro. Dynamics studies on a TcdB cysteine protease domain were performed to an allosteric communication pathway. Comparative analysis of the static and dynamic properties of the TcdA and TcdB glucosyltransferase domains were carried out to determine the basis for the differential lethality of these toxins. Large scale biological data is readily available in the post-genomic era, but it can be difficult to effectively use that data. Two bioinformatics methods were developed to process whole-genome data. Software was developed to return all genes containing a motif in single genome. This provides a list of genes which may be within the same regulatory network or targeted by a specific DNA binding factor. A second bioinformatic method was created to link the data from genome-wide association studies (GWAS) to specific genes. GWAS studies are frequently subjected to statistical analysis, but mutations are rarely investigated structurally. HyDn-SNP-S allows a researcher to find mutations in a gene that correlate to a GWAS studied phenotype. Across human DNA polymerases, this resulted in strongly predictive haplotypes for breast and prostate cancer. Molecular dynamics applied to DNA Polymerase Lambda suggested a structural explanation for the decrease in polymerase fidelity with that mutant. When applied to Histone Deacetylases, mutations were found that alter substrate binding, and post-translational modification

Supporting Methodology Transfer in Visualization Research with Literature-Based Discovery and Visual Text Analytics

[ES] La creciente especialización de la ciencia está motivando la rápida fragmentación de disciplinas bien establecidas en comunidades interdisciplinares. Esta descom- posición se puede observar en un tipo de investigación en visualización conocida como investigación de visualización dirigida por el problema. En ella, equipos de expertos en visualización y un dominio concreto, colaboran en un área específica de conocimiento como pueden ser las humanidades digitales, la bioinformática, la seguridad informática o las ciencias del deporte. Esta tesis propone una serie de métodos inspirados en avances recientes en el análisis automático de textos y la rep- resentación del conocimiento para promover la adecuada comunicación y transferen- cia de conocimiento entre estas comunidades. Los métodos obtenidos se combinaron en una interfaz de análisis visual de textos orientada al descubrimiento científico, GlassViz, que fue diseñada con estos objetivos en mente. La herramienta se probó por primera vez en el dominio de las humanidades digitales para explorar un corpus masivo de artículos de visualización de propósito general. GlassViz fue adaptada en un estudio posterior para que soportase diferentes fuentes de datos representativas de estas comunidades, mostrando evidencia de que el enfoque propuesto también es una alternativa válida para abordar el problema de la fragmentación en la investigación en visualización