Preface

DAMSS-2018 is the jubilee 10th international workshop on data analysis methods for software systems, organized in Druskininkai, Lithuania, at the end of the year. The same place and the same time every year. Ten years passed from the first workshop. History of the workshop starts from 2009 with 16 presentations. The idea of such workshop came up at the Institute of Mathematics and Informatics. Lithuanian Academy of Sciences and the Lithuanian Computer Society supported this idea. This idea got approval both in the Lithuanian research community and abroad. The number of this year presentations is 81. The number of registered participants is 113 from 13 countries. In 2010, the Institute of Mathematics and Informatics became a member of Vilnius University, the largest university of Lithuania. In 2017, the institute changes its name into the Institute of Data Science and Digital Technologies. This name reflects recent activities of the institute. The renewed institute has eight research groups: Cognitive Computing, Image and Signal Analysis, Cyber-Social Systems Engineering, Statistics and Probability, Global Optimization, Intelligent Technologies, Education Systems, Blockchain Technologies. The main goal of the workshop is to introduce the research undertaken at Lithuanian and foreign universities in the fields of data science and software engineering. Annual organization of the workshop allows the fast interchanging of new ideas among the research community. Even 11 companies supported the workshop this year. This means that the topics of the workshop are actual for business, too. Topics of the workshop cover big data, bioinformatics, data science, blockchain technologies, deep learning, digital technologies, high-performance computing, visualization methods for multidimensional data, machine learning, medical informatics, ontological engineering, optimization in data science, business rules, and software engineering. Seeking to facilitate relations between science and business, a special session and panel discussion is organized this year about topical business problems that may be solved together with the research community. This book gives an overview of all presentations of DAMSS-2018.DAMSS-2018 is the jubilee 10th international workshop on data analysis methods for software systems, organized in Druskininkai, Lithuania, at the end of the year. The same place and the same time every year. Ten years passed from the first workshop. History of the workshop starts from 2009 with 16 presentations. The idea of such workshop came up at the Institute of Mathematics and Informatics. Lithuanian Academy of Sciences and the Lithuanian Computer Society supported this idea. This idea got approval both in the Lithuanian research community and abroad. The number of this year presentations is 81. The number of registered participants is 113 from 13 countries. In 2010, the Institute of Mathematics and Informatics became a member of Vilnius University, the largest university of Lithuania. In 2017, the institute changes its name into the Institute of Data Science and Digital Technologies. This name reflects recent activities of the institute. The renewed institute has eight research groups: Cognitive Computing, Image and Signal Analysis, Cyber-Social Systems Engineering, Statistics and Probability, Global Optimization, Intelligent Technologies, Education Systems, Blockchain Technologies. The main goal of the workshop is to introduce the research undertaken at Lithuanian and foreign universities in the fields of data science and software engineering. Annual organization of the workshop allows the fast interchanging of new ideas among the research community. Even 11 companies supported the workshop this year. This means that the topics of the workshop are actual for business, too. Topics of the workshop cover big data, bioinformatics, data science, blockchain technologies, deep learning, digital technologies, high-performance computing, visualization methods for multidimensional data, machine learning, medical informatics, ontological engineering, optimization in data science, business rules, and software engineering. Seeking to facilitate relations between science and business, a special session and panel discussion is organized this year about topical business problems that may be solved together with the research community. This book gives an overview of all presentations of DAMSS-2018

The Affordances of Place: Digital Agency and the Lived Spaces of Information

International audienceAffordances provide a useful frame for understanding how users interact with devices, but applications of the term to digital devices must take into account that human agents operate within a material environment that is distinct from the digital environment in which these devices operate. A more restrictive approach to affordances would focus on the agency of digital devices distinct from the agency of human users. Location-aware mobile devices provide a particularly compelling example of the complex interplay of agents and agencies, and how “augmented affordances†give rise to a lived space of information for human users

A Video-Based Augmented Reality System for Human-in-the-Loop Muscle Strength Assessment of Juvenile Dermatomyositis

As the most common idiopathic inflammatory myopathy in children, juvenile dermatomyositis (JDM) is characterized by skin rashes and muscle weakness. The childhood myositis assessment scale (CMAS) is commonly used to measure the degree of muscle involvement for diagnosis or rehabilitation monitoring. On the one hand, human diagnosis is not scalable and may be subject to personal bias. On the other hand, automatic action quality assessment (AQA) algorithms cannot guarantee 100% accuracy, making them not suitable for biomedical applications. As a solution, we propose a video-based augmented reality system for human-in-the-loop muscle strength assessment of children with JDM. We first propose an AQA algorithm for muscle strength assessment of JDM using contrastive regression trained by a JDM dataset. Our core insight is to visualize the AQA results as a virtual character facilitated by a 3D animation dataset, so that users can compare the real-world patient and the virtual character to understand and verify the AQA results. To allow effective comparisons, we propose a video-based augmented reality system. Given a feed, we adapt computer vision algorithms for scene understanding, evaluate the optimal way of augmenting the virtual character into the scene, and highlight important parts for effective human verification. The experimental results confirm the effectiveness of our AQA algorithm, and the results of the user study demonstrate that humans can more accurately and quickly assess the muscle strength of children using our system

Deep neural networks in the cloud: Review, applications, challenges and research directions

Deep neural networks (DNNs) are currently being deployed as machine learning technology in a wide range of important real-world applications. DNNs consist of a huge number of parameters that require millions of floating-point operations (FLOPs) to be executed both in learning and prediction modes. A more effective method is to implement DNNs in a cloud computing system equipped with centralized servers and data storage sub-systems with high-speed and high-performance computing capabilities. This paper presents an up-to-date survey on current state-of-the-art deployed DNNs for cloud computing. Various DNN complexities associated with different architectures are presented and discussed alongside the necessities of using cloud computing. We also present an extensive overview of different cloud computing platforms for the deployment of DNNs and discuss them in detail. Moreover, DNN applications already deployed in cloud computing systems are reviewed to demonstrate the advantages of using cloud computing for DNNs. The paper emphasizes the challenges of deploying DNNs in cloud computing systems and provides guidance on enhancing current and new deployments.The EGIA project (KK-2022/00119The Consolidated Research Group MATHMODE (IT1456-22

A review on machine learning approaches and trends in drug discovery

Abstract: Drug discovery aims at finding new compounds with specific chemical properties for the treatment of diseases. In the last years, the approach used in this search presents an important component in computer science with the skyrocketing of machine learning techniques due to its democratization. With the objectives set by the Precision Medicine initiative and the new challenges generated, it is necessary to establish robust, standard and reproducible computational methodologies to achieve the objectives set. Currently, predictive models based on Machine Learning have gained great importance in the step prior to preclinical studies. This stage manages to drastically reduce costs and research times in the discovery of new drugs. This review article focuses on how these new methodologies are being used in recent years of research. Analyzing the state of the art in this field will give us an idea of where cheminformatics will be developed in the short term, the limitations it presents and the positive results it has achieved. This review will focus mainly on the methods used to model the molecular data, as well as the biological problems addressed and the Machine Learning algorithms used for drug discovery in recent years.Instituto de Salud Carlos III; PI17/01826Instituto de Salud Carlos III; PI17/01561Xunta de Galicia; Ref. ED431D 2017/16Xunta de Galicia; Ref. ED431D 2017/23Xunta de Galicia; Ref. ED431C 2018/4

Integrative bioinformatics and graph-based methods for predicting adverse effects of developmental drugs

Adverse drug effects are complex phenomena that involve the interplay between drug molecules and their protein targets at various levels of biological organisation, from molecular to organismal. Many factors are known to contribute toward the safety profile of a drug, including the chemical properties of the drug molecule itself, the biological properties of drug targets and other proteins that are involved in pharmacodynamics and pharmacokinetics aspects of drug action, and the characteristics of the intended patient population. A multitude of scattered publicly available resources exist that cover these important aspects of drug activity. These include manually curated biological databases, high-throughput experimental results from gene expression and human genetics resources as well as drug labels and registered clinical trial records. This thesis proposes an integrated analysis of these disparate sources of information to help bridge the gap between the molecular and the clinical aspects of drug action. For example, to address the commonly held assumption that narrowly expressed proteins make safer drug targets, an integrative data-driven analysis was conducted to systematically investigate the relationship between the tissue expression profile of drug targets and the organs affected by clinically observed adverse drug reactions. Similarly, human genetics data were used extensively throughout the thesis to compare adverse symptoms induced by drug molecules with the phenotypes associated with the genes encoding their target proteins. One of the main outcomes of this thesis was the generation of a large knowledge graph, which incorporates diverse molecular and phenotypic data in a structured network format. To leverage the integrated information, two graph-based machine learning methods were developed to predict a wide range of adverse drug effects caused by approved and developmental therapies

Systems Modeling to Predict Mechano-Chemo Interactions In Cardiac Fibrosis

Cardiac fibrosis poses a central challenge in preventing heart failure for patients who have suffered a cardiac injury such as myocardial infarction or aortic valve stenosis. This chronic condition is characterized by a reduction in contractile function through combined hypertrophy and excessive scar formation, and although currently prescribed therapeutics targeting hypertrophy have shown improvements in patient outcomes, pathological fibrosis remains a leading cause of reduced cardiac function for patients long-term. Cardiac fibroblasts play a key role in regulating scar formation during heart failure progression, and interacting biochemical and biomechanical cues within the myocardium guide the activation of fibroblasts and expression of extracellular matrix proteins. While targeted experimental studies of fibroblast activation have elucidated the roles of individual pathways in fibroblast activation, intracellular crosstalk between mechanotransduction and chemotransduction pathways from multiple biochemical cues has largely confounded efforts to control overall cell behavior within the myocardial environment. Computational networks of intracellular signaling can account for complex interactions between signaling pathways and provide a promising approach for identifying influential mechanisms mediating cell behavior. The overarching goal of this dissertation is to improve our understanding of complex signaling in fibroblasts by investigating the role of mechano-chemo interactions in cardiac fibroblast-mediated fibrosis using a combination of experimental studies and systems-level computational models. Firstly, using an in vitro screen of cardiac fibroblast-secreted proteins in response to combinations of biochemical stimuli and mechanical tension, we found that tension modulated cell sensitivity towards biochemical stimuli, thereby altering cell behavior based on the mechanical context. Secondly, using a curated model of fibroblast intracellular signaling, we expanded model topology to include robust mechanotransduction pathways, improved accuracy of model predictions compared to independent experimental studies, and identified mechanically dependent mechanisms-of- ction and mechano-adaptive drug candidates in a post-infarction scenario. Lastly, using an inferred network of fibroblast transcriptional regulation and model fitting to patient-specific data, we showed the utility of model-based approaches in identifying influential pathways underlying fibrotic protein expression during aortic valve stenosis and predicting patient-specific responses to pharmacological intervention. Our work suggests that computational-based approaches can generate insight into influential mechanisms among complex systems, and such tools may be promising for further therapeutic development and precision medicine