Barry Smith an sich

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński

Referent tracking for corporate memories

For corporate memory and enterprise ontology systems to be maximally useful, they must be freed from certain barriers placed around them by traditional knowledge management paradigms. This means, above all, that they must mirror more faithfully those portions of reality which are salient to the workings of the enterprise, including the changes that occur with the passage of time. The purpose of this chapter is to demonstrate how theories based on philosophical realism can contribute to this objective. We discuss how realism-based ontologies (capturing what is generic) combined with referent tracking (capturing what is specific) can play a key role in building the robust and useful corporate memories of the future

Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research

Improving average ranking precision in user searches for biomedical research datasets

Availability of research datasets is keystone for health and life science study reproducibility and scientific progress. Due to the heterogeneity and complexity of these data, a main challenge to be overcome by research data management systems is to provide users with the best answers for their search queries. In the context of the 2016 bioCADDIE Dataset Retrieval Challenge, we investigate a novel ranking pipeline to improve the search of datasets used in biomedical experiments. Our system comprises a query expansion model based on word embeddings, a similarity measure algorithm that takes into consideration the relevance of the query terms, and a dataset categorisation method that boosts the rank of datasets matching query constraints. The system was evaluated using a corpus with 800k datasets and 21 annotated user queries. Our system provides competitive results when compared to the other challenge participants. In the official run, it achieved the highest infAP among the participants, being +22.3% higher than the median infAP of the participant's best submissions. Overall, it is ranked at top 2 if an aggregated metric using the best official measures per participant is considered. The query expansion method showed positive impact on the system's performance increasing our baseline up to +5.0% and +3.4% for the infAP and infNDCG metrics, respectively. Our similarity measure algorithm seems to be robust, in particular compared to Divergence From Randomness framework, having smaller performance variations under different training conditions. Finally, the result categorization did not have significant impact on the system's performance. We believe that our solution could be used to enhance biomedical dataset management systems. In particular, the use of data driven query expansion methods could be an alternative to the complexity of biomedical terminologies

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

Fully Automatic and Real-Time Catheter Segmentation in X-Ray Fluoroscopy

Augmenting X-ray imaging with 3D roadmap to improve guidance is a common strategy. Such approaches benefit from automated analysis of the X-ray images, such as the automatic detection and tracking of instruments. In this paper, we propose a real-time method to segment the catheter and guidewire in 2D X-ray fluoroscopic sequences. The method is based on deep convolutional neural networks. The network takes as input the current image and the three previous ones, and segments the catheter and guidewire in the current image. Subsequently, a centerline model of the catheter is constructed from the segmented image. A small set of annotated data combined with data augmentation is used to train the network. We trained the method on images from 182 X-ray sequences from 23 different interventions. On a testing set with images of 55 X-ray sequences from 5 other interventions, a median centerline distance error of 0.2 mm and a median tip distance error of 0.9 mm was obtained. The segmentation of the instruments in 2D X-ray sequences is performed in a real-time fully-automatic manner.Comment: Accepted to MICCAI 201