ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining

Background New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed. Results We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges according to associated data values. We demonstrated the advantages of these new capabilities through three biological network visualization case studies: human disease association network, drug-target interaction network and protein-peptide mapping network. Conclusion The architectural design of ProteoLens makes it suitable for bioinformatics expert data analysts who are experienced with relational database management to perform large-scale integrated network visual explorations. ProteoLens is a promising visual analytic platform that will facilitate knowledge discoveries in future network and systems biology studies

Review of: Australian Rock Art: A New Synthesis

Rock-art studies have now come of age, and are among the most fertile explorations of expressive culture. Through an interdisciplinary approach to its study, we have expanded our knowledge into the realms of aesthetics, belief systems, and social structures. Australian rock an is particularly significant, since it is a visual expression that has been practiced by contemporary as well as prehistoric Aboriginals. Robert Layton\u27s most recent book -his new synthesis of Australian rock art- is an ambitious and successful analysis of Aboriginal rock art from across the continent

Ibie’ka (Ideographs): Developing Visual Signs for Expressing Contemporary Niger Delta in an Era of Petroleum Oil Exploitation

Visual signs (ideographs) are artistic codified expressions that promote social and cultural integration. They are normally based on popular conventions which over a period of time become generally accepted. In pre-western literate Africa, apart from oral communication, visual codes were employed within social groups. The impact of such codifications were usually entrenched in socio-religious and cultural rubrics. In modern society, much of such knowledge systems have become lost to western literate types. The adverse effect of such transference is noticeable in near total alienation of popular visual arts codifications and their appreciation. Persons now rely solely on the written text for communication. Whereas it is important that artistic visualizations should promote and preserve indigenous aesthetics wherein knowledge systems that promote such exists. It is from this perspective that Ibie’ka signs, inspired by rigorous studio explorations as expressed in the researcher’s Niger Delta Visuals (NDV) present new possibilities for indigenous communication that espouses conditions of human challenges related to exploitative tendencies of oil exploration in the Niger delta. Based on studio exploratory approach, Ibie’ka signs add to a repertoire of new expressive sinology that aptly promotes indigenous knowledge system in contemporary Africa.Key words: Ibie’ka, signs, petroleum oil, exploitation

Progressive growing of self-organized hierarchical representations for exploration

Designing agent that can autonomously discover and learn a diversity of structures and skills in unknown changing environments is key for lifelong machine learning. A central challenge is how to learn incrementally representations in order to progressively build a map of the discovered structures and re-use it to further explore. To address this challenge, we identify and target several key functionalities. First, we aim to build lasting representations and avoid catastrophic forgetting throughout the exploration process. Secondly we aim to learn a diversity of representations allowing to discover a "diversity of diversity" of structures (and associated skills) in complex high-dimensional environments. Thirdly, we target representations that can structure the agent discoveries in a coarse-to-fine manner. Finally, we target the reuse of such representations to drive exploration toward an "interesting" type of diversity, for instance leveraging human guidance. Current approaches in state representation learning rely generally on monolithic architectures which do not enable all these functionalities. Therefore, we present a novel technique to progressively construct a Hierarchy of Observation Latent Models for Exploration Stratification, called HOLMES. This technique couples the use of a dynamic modular model architecture for representation learning with intrinsically-motivated goal exploration processes (IMGEPs). The paper shows results in the domain of automated discovery of diverse self-organized patterns, considering as testbed the experimental framework from Reinke et al. (2019)

Speculative practices : utilizing InfoVis to explore untapped literary collections

Funding: Canadian Social Sciences and Humanities Research CouncilIn this paper we exemplify how information visualization supports speculative thinking, hypotheses testing, and preliminary interpretation processes as part of literary research. While InfoVis has become a buzz topic in the digital humanities, skepticism remains about how effectively it integrates into and expands on traditional humanities research approaches. From an InfoVis perspective, we lack case studies that show the specific design challenges that make literary studies and humanities research at large a unique application area for information visualization. We examine these questions through our case study of the Speculative W@nderverse, a visualization tool that was designed to enable the analysis and exploration of an untapped literary collection consisting of thousands of science fiction short stories. We present the results of two empirical studies that involved general-interest readers and literary scholars who used the evolving visualization prototype as part of their research for over a year. Our findings suggest a design space for visualizing literary collections that is defined by (1) their academic and public relevance, (2) the tension between qualitative vs. quantitative methods of interpretation, (3) result- vs. process-driven approaches to InfoVis, and (4) the unique material and visual qualities of cultural collections. Through the Speculative W@nderverse we demonstrate how visualization can bridge these sometimes contradictory perspectives by cultivating curiosity and providing entry points into literary collections while, at the same time, supporting multiple aspects of humanities research processes.PostprintPeer reviewe

Experiential Role of Artefacts in Cooperative Design

The role of material artefacts in supporting distributed and co-located work practices has been well acknowledged within the HCI and CSCW research. In this paper, we show that in addition to their ecological, coordinative and organizational support, artefacts also play an ‘experiential’ role. In this case, artefacts not only improve efficiency or have a purely functional role (e.g. allowing people to complete tasks quickly), but the presence and manifestations of these artefacts bring quality and richness to people’s performance and help in making better sense of their everyday lives. In a domain like industrial design, such artefacts play an important role for supporting creativity and innovation. Based on our prolonged ethnographic fieldwork on understanding cooperative design practices of industrial design students and researchers, we describe several experiential practices that are supported by mundane artefacts like sketches, drawings, physical models and explorative prototypes – used and developed in designers’ everyday work. Our main intention to carry out this kind of research is to develop technologies to support designers’ everyday practices. We believe that with the emergence of ubiquitous computing, there is a growing need to focus on personal, emotional and social side of people’s everyday experiences. By focusing on the experiential practices of designers, we can provide a holistic view in the design of new interactive technologies

Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

Comics, robots, fashion and programming: outlining the concept of actDresses

This paper concerns the design of physical languages for controlling and programming robotic consumer products. For this purpose we explore basic theories of semiotics represented in the two separate fields of comics and fashion, and how these could be used as resources in the development of new physical languages. Based on these theories, the design concept of actDresses is defined, and supplemented by three example scenarios of how the concept can be used for controlling, programming, and predicting the behaviour of robotic systems

Walter J. Ong, S.J.: A retrospective

Communication Research Trends usually charts current communication research, introducing its readers to recent developments across the range of inquiry into communication. This issue, however, takes a different tack, looking back on the writings of Walter J. Ong, S.J., who died at the age of 90 in August 2003. Ong spent his scholarly career at Saint Louis University, where he served as University Professor of Humanities, the William E. Haren Professor of English, and Professor of Humanities in Psychiatry at the Saint Louis University School of Medicine. In a career that spanned 60 years, Ong published 16 books, 245 articles, and 108 reviews. In addition, he edited a number of works and gave interviews that further explored his wide-ranging interests. Readers interested in a full bibliography of Ong’s works should refer to the web site prepared by Professor Betty Youngkin at the University of Dayton, at http://homepages.udayton.edu/~youngkin/biblio.htm. From the perspective of an interest in connections among many areas of human knowledge over such a long career, he explored a whole gamut of activities by careful observations of the threads that run through western culture and by insightful analysis of what he observed. Communication forms one of those many threads in the West—perhaps the dominant one—and so it occupies a similar place in Ong’s work. The tapestry Ong weaves has, bit by bit, influenced thinking about communication as well as research. And so, Communication Research Trends looks back on the writings of Walter Ong, S.J