Proceedings of the 2020 Joint Workshop of Fraunhofer IOSB and Institute for Anthropomatics, Vision and Fusion Laboratory

In 2020 fand der jährliche Workshop des Faunhofer IOSB und the Lehrstuhls für interaktive Echtzeitsysteme statt. Vom 27. bis zum 31. Juli trugen die Doktorranden der beiden Institute über den Stand ihrer Forschung vor in Themen wie KI, maschinellen Lernen, computer vision, usage control, Metrologie vor. Die Ergebnisse dieser Vorträge sind in diesem Band als technische Berichte gesammelt

Supervised learning for detection of duplicates in genomic sequence databases

Motivation First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases. Results We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from metadata, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material

Reducing the labeling effort for entity resolution using distant supervision and active learning

Entity resolution is the task of identifying records in one or more data sources which refer to the same real-world object. It is often treated as a supervised binary classification task in which a labeled set of matching and non-matching record pairs is used for training a machine learning model. Acquiring labeled data for training machine learning models is expensive and time-consuming, as it typically involves one or more human annotators who need to manually inspect and label the data. It is thus considered a major limitation of supervised entity resolution methods. In this thesis, we research two approaches, relying on distant supervision and active learning, for reducing the labeling effort involved in constructing training sets for entity resolution tasks with different profiling characteristics. Our first approach investigates the utility of semantic annotations found in HTML pages as a source of distant supervision. We profile the adoption growth of semantic annotations over multiple years and focus on product-related schema.org annotations. We develop a pipeline for cleansing and grouping semantically annotated offers describing the same products, thus creating the WDC Product Corpus, the largest publicly available training set for entity resolution. The high predictive performance of entity resolution models trained on offer pairs from the WDC Product Corpus clearly demonstrates the usefulness of semantic annotations as distant supervision for product-related entity resolution tasks. Our second approach focuses on active learning techniques, which have been widely used for reducing the labeling effort for entity resolution in related work. Yet, we identify two research gaps: the inefficient initialization of active learning and the lack of active learning methods tailored to multi-source entity resolution. We address the first research gap by developing an unsupervised method for initializing and further assisting the complete active learning workflow. Compared to active learning baselines that use random sampling or transfer learning for initialization, our method guarantees high anytime performance within a limited labeling budget for tasks with different profiling characteristics. We address the second research gap by developing ALMSER, the first active learning method which uses signals inherent to multi-source entity resolution tasks for query selection and model training. Our evaluation results indicate that exploiting such signals for query selection alone has a varying effect on model performance across different multi-source entity resolution tasks. We further investigate this finding by analyzing the impact of the profiling characteristics of multi-source entity resolution tasks on the performance of active learning methods which use different signals for query selection

The Effect of Data Curation on the Accuracy of Quantitative Structure-Activity Relationship Models

In the 33 years since the first public release of GenBank, and the 15 years since the publication of the first pilot assembly of the human genome, drug discovery has been awash in a tsunami of data. But it has only been within the past decade that medicinal chemists and chemical biologists have had access to the same sorts of large-scale, public-access databases as bioinformaticians and molecular biologists have had for so long. The release of this data has sparked a renewed interest in computational methods for rational drug design, but questions have arisen recently about the accuracy and quality of this data. The same question has arisen in other scientific disciplines, but it has a particular urgency to practitioners of Quantitative Structure-Activity Relationship (QSAR) modeling. By its nature QSAR modeling depends on both activity data and chemical structures. While activities are usually expressed as numerical scalar values, a form ubiquitous throughout the sciences, chemical structures (especially that must be interpretable as such by computer software) are stored in a variety of specialized formats which are much less common and mostly ignored outside of cheminformatics and related fields. While previous research has determined that a 5% error rate in data being used for modeling can cause a QSAR model to be non-predictive and useless for its intended purpose, and workflows have been proposed which reduce the effect of inconsistent chemical structure representations on model accuracy, a fundamental question remains: “how accurate are the structure and activity data freely available to researchers?” To this end, we have undertaken two surveys of data quality, one focusing on chemical structure information in Internet resources and a second examining the uncertainty associated with compounds reported in the medicinal chemistry literature as abstracted in ChEMBL. The results of these studies have informed the creation of an improved workflow for the curation of structure-activity data which is intended to identify problematic data points in raw data extracted from databases so that an expert human curator can examine the underlying literature and resolve discrepancies between reported values. This workflow was in turn applied to the creation of two QSAR models that were used to implement a virtual screen seeking molecules capable of binding to both the serotonergic reuptake transporter and the alpha2a adrenergic receptor. While no suitable compounds were identified in the initial screening process, regions of chemical space that may yield truly novel alpha 2a receptor ligands have been identified. These regions can be targeted in future efforts. Basing data curation workflows on manual processes by human curators is not particularly viable, as humans have a tendency to introduce errors by inattention even as they identify and repair other problems. Computers cannot effectively curate data either. While they are highly accurate when programmed properly, they lack human creativity and insight that would allow them to determine which data points represent truly inaccurate information. In order to effectively curate data, humans and computers must both be incorporated into a workflow that harnesses their strengths and limits their liabilities.Doctor of Philosoph

Virtual Reality Games for Motor Rehabilitation

This paper presents a fuzzy logic based method to track user satisfaction without the need for devices to monitor users physiological conditions. User satisfaction is the key to any product’s acceptance; computer applications and video games provide a unique opportunity to provide a tailored environment for each user to better suit their needs. We have implemented a non-adaptive fuzzy logic model of emotion, based on the emotional component of the Fuzzy Logic Adaptive Model of Emotion (FLAME) proposed by El-Nasr, to estimate player emotion in UnrealTournament 2004. In this paper we describe the implementation of this system and present the results of one of several play tests. Our research contradicts the current literature that suggests physiological measurements are needed. We show that it is possible to use a software only method to estimate user emotion

Applied Metaheuristic Computing

For decades, Applied Metaheuristic Computing (AMC) has been a prevailing optimization technique for tackling perplexing engineering and business problems, such as scheduling, routing, ordering, bin packing, assignment, facility layout planning, among others. This is partly because the classic exact methods are constrained with prior assumptions, and partly due to the heuristics being problem-dependent and lacking generalization. AMC, on the contrary, guides the course of low-level heuristics to search beyond the local optimality, which impairs the capability of traditional computation methods. This topic series has collected quality papers proposing cutting-edge methodology and innovative applications which drive the advances of AMC

ICSEA 2021: the sixteenth international conference on software engineering advances

The Sixteenth International Conference on Software Engineering Advances (ICSEA 2021), held on October 3 - 7, 2021 in Barcelona, Spain, continued a series of events covering a broad spectrum of software-related topics. The conference covered fundamentals on designing, implementing, testing, validating and maintaining various kinds of software. The tracks treated the topics from theory to practice, in terms of methodologies, design, implementation, testing, use cases, tools, and lessons learnt. The conference topics covered classical and advanced methodologies, open source, agile software, as well as software deployment and software economics and education. The conference had the following tracks: Advances in fundamentals for software development Advanced mechanisms for software development Advanced design tools for developing software Software engineering for service computing (SOA and Cloud) Advanced facilities for accessing software Software performance Software security, privacy, safeness Advances in software testing Specialized software advanced applications Web Accessibility Open source software Agile and Lean approaches in software engineering Software deployment and maintenance Software engineering techniques, metrics, and formalisms Software economics, adoption, and education Business technology Improving productivity in research on software engineering Trends and achievements Similar to the previous edition, this event continued to be very competitive in its selection process and very well perceived by the international software engineering community. As such, it is attracting excellent contributions and active participation from all over the world. We were very pleased to receive a large amount of top quality contributions. We take here the opportunity to warmly thank all the members of the ICSEA 2021 technical program committee as well as the numerous reviewers. The creation of such a broad and high quality conference program would not have been possible without their involvement. We also kindly thank all the authors that dedicated much of their time and efforts to contribute to the ICSEA 2021. We truly believe that thanks to all these efforts, the final conference program consists of top quality contributions. This event could also not have been a reality without the support of many individuals, organizations and sponsors. We also gratefully thank the members of the ICSEA 2021 organizing committee for their help in handling the logistics and for their work that is making this professional meeting a success. We hope the ICSEA 2021 was a successful international forum for the exchange of ideas and results between academia and industry and to promote further progress in software engineering research