A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

Ideation as an intellectual information acquisition and use context: Investigating game designers’ information-based ideation behavior

Human Information Behavior (HIB) research commonly examines behavior in the context of why information is acquired and how it will be used, but usually at the level of the work or everyday-life tasks the information will support. HIB has not been examined in detail at the broader contextual level of intellectual purpose (i.e. the higher-order conceptual tasks the information was acquired to support). Examination at this level can enhance holistic understanding of HIB as a ‘means to an intellectual end’ and inform the design of digital information environments that support information interaction for specific intellectual purposes. We investigate information-based ideation (IBI) as a specific intellectual information acquisition and use context by conducting Critical Incident-style interviews with ten game designers, focusing on how they interact with information to generate and develop creative design ideas. Our findings give rise to a framework of their ideation-focused HIB, which systems designers can leverage to reason about how best to support certain behaviors to drive design ideation. These findings emphasize the importance of intellectual purpose as a driver for acquisition and desired outcome of use

Learning Visual Features from Snapshots for Web Search

When applying learning to rank algorithms to Web search, a large number of features are usually designed to capture the relevance signals. Most of these features are computed based on the extracted textual elements, link analysis, and user logs. However, Web pages are not solely linked texts, but have structured layout organizing a large variety of elements in different styles. Such layout itself can convey useful visual information, indicating the relevance of a Web page. For example, the query-independent layout (i.e., raw page layout) can help identify the page quality, while the query-dependent layout (i.e., page rendered with matched query words) can further tell rich structural information (e.g., size, position and proximity) of the matching signals. However, such visual information of layout has been seldom utilized in Web search in the past. In this work, we propose to learn rich visual features automatically from the layout of Web pages (i.e., Web page snapshots) for relevance ranking. Both query-independent and query-dependent snapshots are considered as the new inputs. We then propose a novel visual perception model inspired by human's visual search behaviors on page viewing to extract the visual features. This model can be learned end-to-end together with traditional human-crafted features. We also show that such visual features can be efficiently acquired in the online setting with an extended inverted indexing scheme. Experiments on benchmark collections demonstrate that learning visual features from Web page snapshots can significantly improve the performance of relevance ranking in ad-hoc Web retrieval tasks.Comment: CIKM 201

ToScA North America (6 – 8 June 2017, The University of Texas, Austin, TX) Program

ToScA North America will address key areas of science, including Multi-modal Imaging, Geosciences, Forensics, Increasing Contrast, Educational Outreach, Data, Materials Science and Medical and Biological Science.University of Texas High-Resolution X-ray CT Facility (UTCT); Jackson School of Geosciences, The University of Texas at Austin; Natural History Museum (London); Royal Microscopical Society (Oxford, UK)Geological Science

Physical Primitive Decomposition

Objects are made of parts, each with distinct geometry, physics, functionality, and affordances. Developing such a distributed, physical, interpretable representation of objects will facilitate intelligent agents to better explore and interact with the world. In this paper, we study physical primitive decomposition---understanding an object through its components, each with physical and geometric attributes. As annotated data for object parts and physics are rare, we propose a novel formulation that learns physical primitives by explaining both an object's appearance and its behaviors in physical events. Our model performs well on block towers and tools in both synthetic and real scenarios; we also demonstrate that visual and physical observations often provide complementary signals. We further present ablation and behavioral studies to better understand our model and contrast it with human performance.Comment: ECCV 2018. Project page: http://ppd.csail.mit.edu

Sequential Prediction of Social Media Popularity with Deep Temporal Context Networks

Prediction of popularity has profound impact for social media, since it offers opportunities to reveal individual preference and public attention from evolutionary social systems. Previous research, although achieves promising results, neglects one distinctive characteristic of social data, i.e., sequentiality. For example, the popularity of online content is generated over time with sequential post streams of social media. To investigate the sequential prediction of popularity, we propose a novel prediction framework called Deep Temporal Context Networks (DTCN) by incorporating both temporal context and temporal attention into account. Our DTCN contains three main components, from embedding, learning to predicting. With a joint embedding network, we obtain a unified deep representation of multi-modal user-post data in a common embedding space. Then, based on the embedded data sequence over time, temporal context learning attempts to recurrently learn two adaptive temporal contexts for sequential popularity. Finally, a novel temporal attention is designed to predict new popularity (the popularity of a new user-post pair) with temporal coherence across multiple time-scales. Experiments on our released image dataset with about 600K Flickr photos demonstrate that DTCN outperforms state-of-the-art deep prediction algorithms, with an average of 21.51% relative performance improvement in the popularity prediction (Spearman Ranking Correlation).Comment: accepted in IJCAI-1

Searching Data: A Review of Observational Data Retrieval Practices in Selected Disciplines

A cross-disciplinary examination of the user behaviours involved in seeking and evaluating data is surprisingly absent from the research data discussion. This review explores the data retrieval literature to identify commonalities in how users search for and evaluate observational research data. Two analytical frameworks rooted in information retrieval and science technology studies are used to identify key similarities in practices as a first step toward developing a model describing data retrieval