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arXiv 2024年

作者： Yadav, Dipendra Strauß, Tobias Yordanova, Kristina University of Rostock Department of Computer Science and Electrical Engineering Institute of Visual & Analytic Computing Mobile Multimedia Information Systems Albert-Einstein-Str. 22 Rostock18059 Germany

Natural language processing has seen exponential growth since deep learning has been used for various tasks. Deep learning has replaced the old rule-based methods by providing better performance on almost all the tasks in NLP, as deep learning basically looks into the hidden patterns and structures in the data which were sometimes not detected and at other-times overlooked by the rule-based systems. The research and development in NLP have been however focused on some handful languages of the world given their financial importance and a huge number of speakers. This has left out most of the other languages unexplored. The other reason for the lack of research in these languages is the unavailability of properly annotated and the required amount of datasets which is very important for training deep learning neural networks. The situation looks grim. When we look at the world language tree, thankfully we see that most of the unexplored languages have other well-explored languages nearby which basically means that both the languages are kind of similar. So if we could somehow adapt research and development from one language to another, it could be really helpful for both the languages. The goal of this thesis work is to explore transfer learning for the task of Part-of-speech(POS) tagging between Hindi and Nepali languages which are part of the Indo-Aryan language family with very high similarity. We have tried to explore the possibility of jointly training a model for the task of POS tagging in both Hindi and Nepali language and see if it helps in improving the performance of the model. We also try to explore if multitask learning in the Hindi language can be helpful for the task of POS tagging with auxiliary tasks of the gender tagging and singularity/plurality tagging. The deep learning architecture used for this work is BLSTM-CNN-CRF. The model is trained with monolingual word embeddings, vector mapped embeddings, and also with jointly trained Hindi-Nepali word emb

关键词： Embeddings

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visual analytics for Early Detection of Retinal Diseases

arXiv

引用

arXiv 2022年

作者： Röhlig, Martin Stachs, Oliver Schumann, Heidrun Visual and Analytic Computing University of Rostock Germany Department of Ophthalmology Rostock University Medical Center Germany

Advances in optical coherence tomography (OCT) have enabled noninvasive imaging of substructures of the human retina with high spatial resolution. OCT examinations are now a standard procedure in clinics and an integral part of ophthalmic research. The interpretation of the OCT helps ophthalmologists understand the impact of various retinal and systemic diseases on the structure of the retina in a way not previously possible. In the early stages of retinal diseases, however, the identification and analysis of small and localized substructural changes in the retina remains a challenge. We present an overview of novel visual analytics approaches for the interactive exploration of early retinal changes in single and multiple patients, the comparison of the changes with normative data, and automated quantification and measurement of diagnosis-relevant information. We developed these approaches in close collaboration with ophthalmology researchers and industry experts from a leading OCT device manufacturer. As a result, they not only significantly reduced the time and effort required for OCT data analysis, especially in the context of cross-sectional studies, but have also led to several new discoveries published in biomedical journals. © 2022, CC BY.

关键词： visualization

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Comparing the Effect of Code Optimizations on Simulation Runtime Across Synchronous Cellular Automata Models of HIV

Comparing the Effect of Code Optimizations on Simulation Run...

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2021 Winter Simulation Conference, WSC 2021

作者： Li, Junjiang Giabbanelli, Philippe J. Koster, Till Miami University Department of Computer Science Software Engineering OH45056 United States Institute for Visual and Analytic Computing University of Rostock Rostock18059 Germany

ISBN: (纸本)9781665433112

Models developed by domain experts occasionally struggle to achieve a sufficient execution speed. Improving performances requires expertise in parallel and distributed simulations, hardware, or time to profile performances to identify bottlenecks. However, end-users in biological simulations of the Human Immunodeficiency Virus (HIV) have repeatedly demonstrated that these resources are either not available or not sought, resulting in models that are developed through user-friendly languages and platforms, then used on workstations. This situation becomes problematic when performances cannot cope with the salient characteristics of the phenomenon that is modeled, as is the case with cellular automata (CA) models of HIV. In this paper, we optimize the Python code of CA models of HIV to scale the number of cells handled by a simulation on a workstation commonly available to end-users. We demonstrate this scalability via five HIV CA models and compare these results to assess how modeling choices can impact runtime. © 2021 IEEE.

关键词： Viruses

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LEARNING SURROGATE EQUATIONS FOR THE ANALYSIS OF AN AGENT-BASED CANCER MODEL

arXiv

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arXiv 2025年

作者： Burrage, Kevin Burrage, Pamela Kreikemeyer, Justin N. Uhrmacher, Adelinde M. Weerasinghe, Hasitha N. School of Mathematical Sciences Queensland University of Technology BrisbaneQLD Australia Department of Computer Science University of Oxford United Kingdom Modelling and Simulation Institute for Visual and Analytic Computing Faculty of Informatics and Electrical Engineering University of Rostock Rostock Germany

In this paper, we adapt a two species agent-based cancer model that describes the interaction between cancer cells and healthy cells on a uniform grid to include the interaction with a third species – namely immune cells. We run six different scenarios to explore the competition between cancer and immune cells and the initial concentration of the immune cells on cancer dynamics. We then use coupled equation learning to construct a population-based reaction model for each scenario. We show how they can be unified into a single surrogate population-based reaction model, whose underlying three coupled ordinary differential equations are much easier to analyse than the original agent-based model. As an example, by finding the single steady state of the cancer concentration, we are able to find a linear relationship between this concentration and the initial concentration of the immune cells. This then enables us to estimate suitable values for the competition and initial concentration to reduce the cancer substantially without performing additional complex and expensive simulations from an agent-based stochastic model. The work shows the importance of performing equation learning from agent-based stochastic data for gaining key insights about the behaviour of complex cellular dynamics. © 2025, CC BY.

关键词： Lung cancer

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Human activity recognition using attribute-based neural networks and context information

arXiv

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arXiv 2021年

作者： Lüdtke, Stefan Rueda, Fernando Moya Ahmed, Waqas Fink, Gernot A. Kirste, Thomas Institute of Visual & Analytic Computing University of Rostock Germany Department of Computer Science TU Dortmund University Germany

We consider human activity recognition (HAR) from wearable sensor data in manual-work processes, like warehouse order-picking. Such structured domains can often be partitioned into distinct process steps, e.g., packaging or transporting. Each process step can have a different prior distribution over activity classes, e.g., standing or walking, and different system dynamics. Here, we show how such context information can be integrated systematically into a deep neural network-based HAR system. Specifically, we propose a hybrid architecture that combines a deep neural network—that estimates high-level movement descriptors, attributes, from the raw-sensor data—and a shallow classifier, which predicts activity classes from the estimated attributes and (optional) context information, like the currently executed process step. We empirically show that our proposed architecture increases HAR performance, compared to state-of-the-art methods. Additionally, we show that HAR performance can be further increased when information about process steps is incorporated, even when that information is only partially correct. © 2021, CC BY.

关键词： Deep neural networks

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The Language of Infographics: Toward Understanding Conceptual Metaphor Use in Scientific Storytelling

arXiv

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arXiv 2024年

作者： Pokojná, Hana Isenberg, Tobias Bruckner, Stefan Kozlíková, Barbora Garrison, Laura Visitlab Faculty of Informatics Masaryk University Czech Republic Inria Université Paris-Saclay CNRS Inria LISN France The Institute for Visual and Analytic Computing University of Rostock Germany Visitlab Faculty of Informatics Masaryk University Czech Republic The Department of Informatics Mohn Medical Imaging and Visualization Centre Department of Radiology Haukeland University Hospital University of Bergen Norway

We apply an approach from cognitive linguistics by mapping Conceptual Metaphor Theory (CMT) to the visualization domain to address patterns of visual conceptual metaphors that are often used in science infographics. Metaphors play an essential part in visual communication and are frequently employed to explain complex concepts. However, their use is often based on intuition, rather than following a formal process. At present, we lack tools and language for understanding and describing metaphor use in visualization to the extent where taxonomy and grammar could guide the creation of visual components, e.g., infographics. Our classification of the visual conceptual mappings within scientific representations is based on the breakdown of visual components in existing scientific infographics. We demonstrate the development of this mapping through a detailed analysis of data collected from four domains (biomedicine, climate, space, and anthropology) that represent a diverse range of visual conceptual metaphors used in the visual communication of science. This work allows us to identify patterns of visual conceptual metaphor use within the domains, resolve ambiguities about why specific conceptual metaphors are used, and develop a better overall understanding of visual metaphor use in scientific infographics. Our analysis shows that ontological and orientational conceptual metaphors are the most widely applied to translate complex scientific concepts. To support our findings we developed a visual exploratory tool based on the collected database that places the individual infographics on a spatio-temporal scale and illustrates the breakdown of visual conceptual metaphors. © 2024, CC BY.

关键词： visualization

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Automatic reuse, adaption, and execution of simulation experiments via provenance patterns

arXiv

引用

arXiv 2021年

作者： Wilsdorf, Pia Wolpers, Anja Hilton, Jason Haack, Fiete Uhrmacher, Adelinde M. Institute for Visual and Analytic Computing University of Rostock Germany Department of Social Statistics and Demography University of Southampton United Kingdom

Simulation experiments are typically conducted repeatedly during the model development process, for example, to re-validate if a behavioral property still holds after several model changes. Approaches for automatically reusing and generating simulation experiments can support modelers in conducting simulation studies in a more systematic and effective manner. They rely on explicit experiment specifications and, so far, on user interaction for initiating the reuse. Thereby, they are constrained to support the reuse of simulation experiments in a specific setting. Our approach now goes one step further by automatically identifying and adapting the experiments to be reused for a variety of scenarios. To achieve this, we exploit provenance graphs of simulation studies, which provide valuable information about the previous modeling and experimenting activities, and contain meta-information about the different entities that were used or produced during the simulation study. We define provenance patterns and associate them with a semantics, which allows us to interpret the different activities, and construct transformation rules for provenance graphs. Our approach is implemented in a Reuse and Adapt framework for Simulation Experiments (RASE) which can interface with various modeling and simulation tools. In the case studies, we demonstrate the utility of our framework for a) the repeated sensitivity analysis of an agent-based model of migration routes, and b) the cross-validation of two models of a cell signaling pathway. Copyright © 2021, The Authors. All rights reserved.

关键词： Sensitivity analysis

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Artifact Abstract: Kitchen Task Assessment Dataset for Measuring Errors due to Cognitive Impairments

Artifact Abstract: Kitchen Task Assessment Dataset for Measu...

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IEEE International Conference on Pervasive computing and Communications (PerCom)

作者： Kristina Yordanova Albert Hein Thomas Kirste Department of Visual and Analytic Computing University of Rostock Rostock Germany

ISBN: (数字)9781728146577

ISBN: (纸本)9781728146584

This document provides guidelines to using the data in the kitchen task assessment dataset. This dataset contains normal behaviour as well as erroneous behaviour due to dementia. The dataset including annotation, sensor data and synchronisation scripts is publicly available and can be downloaded from the Library of the University of Rostock [4] , download link https://***/10.18453/rosdok_id00002605 . The video data is accessible on request. If you are interested in the video data, please, contact Peter Eschholz at ***( at )***.

关键词： Cognitive Decline Error measure Dataset video data KITCHEN Normal behavior Libraries handicrafts Artifacts

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Studying the Influence of Cell Culture Medium Composition on Ciliary Length with Detectcilia: An R Package for Automated Detection and Length Measurement of Primary Cilia

SSRN

引用

SSRN 2023年

作者： Budde, Kai Krueger, Simone Sehlke, Clemens Lemcke, Heiko Jonitz-Heincke, Anika David, Robert Bader, Rainer Uhrmacher, Adelinde M. Institute for Visual and Analytic Computing University of Rostock Rostock18051 Germany Research Laboratory for Biomechanics and Implant Technology Department of Orthopedics Rostock University Medical Center Rostock18057 Germany Reference and Translation Center for Cardiac Stem Cell Therapy Department of Cardiac Surgery Rostock University Medical Center Rostock18057 Germany Department of Life Light and Matter Interdisciplinary Faculty University of Rostock Rostock18051 Germany

Background and objective: The primary cilium is a cellular protrusion found on most mammalian cell types. This structure is involved in various cell signaling pathways, functioning as a cellular antenna. Therefore, the length of the primary cilium influences its functionality. To investigate the impact of physical or chemical stimuli on the ciliary length, this value is to be determined easily and ***: To automatically and reproducibly detect and measure primary cilia, we have implemented an open-source R package called detectCilia. As a case study, we compare the influence of four different cell culture media compositions on the lengths of primary cilia of human chondrocytes. These media compositions include i) Insulin-Transferrin-Selenium (ITS), ii) ITS and Dexamethasone (Dexa), iii) ITS, Dexa, Insulin-like Growth Factor 1 (IGF-1), and Transforming Growth Factor β⁠1 (TGF-β⁠1), or iv) Fetal Bovine Serum (FBS). The automated detection and length measurement results of detectCilia are also compared with the results of two similar tools: ACDC and ***: Our package provides similar results as the manual evaluation of primary cilia. A comparison with ACDC and CiliaQ shows different advantages of all three tools, which makes detectCilia a valuable addition. In our automatic analysis of our case study, we find that the medium composition has an impact on the ciliary length. The cultivation with ITS and Dexa has led to the longest primary ***: detectCilia is able to automatically and reproducibly detect and measure primary cilia in confocal microscopy images without the need for elaborated user interaction. © 2023, The Authors. All rights reserved.

关键词： Insulin

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Simulation Studies of Social Systems – Telling the Story Based on Provenance Patterns

TechRxiv

引用

TechRxiv 2022年

作者： Reinhardt, Oliver Prike, Toby Hinsch, Martin Bijak, Jakub Wilsdorf, Pia Uhrmacher, Adelinde M. Institute for Visual and Analytic Computing University of Rostock Germany School of Psychological Science University of Western Australia Australia MRC/CSO Social and Public Health Sciences Unit University of Glasgow United Kingdom Department of Social Statistics and Demography University of Southampton United Kingdom

Social simulation studies are complex. They typically combine various sources of data and hypotheses, that are integrated by intertwined processes of model building, simulation experiment execution, and analysis. Various documentation approaches exist to support the transparency and traceability of complex social simulation studies. In particular, provenance patterns can be used to capture central activities and entities of a simulation study. Entities can include, simulation models, experiments, or research questions, and activities – model building, calibration, validation, and analysis. The exploitation of provenance standards enables information on sources and activities, which contribute to the generation of an entity, to be queryable and computationally accessible. In this study, we refine the provenance pattern-based approach to address specific challenges of social agent-based simulation studies. Specifically, we focus on the activities and entities involved in collecting and analyzing primary data about human decisions, and the collection and quality assessment of secondary data. We illustrate the potential of this approach by applying it to central activities and results of the Bayesian Agent-Based Population Studies project and by presenting its implementation in a web-based tool. © 2022, CC BY.

关键词： Model buildings

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