004 Datenverarbeitung; Informatik
Refine
Has Fulltext
- yes (127)
Is part of the Bibliography
- yes (127)
Year of publication
Document Type
- Journal article (127) (remove)
Keywords
- virtual reality (15)
- machine learning (5)
- augmented reality (4)
- human-computer interaction (4)
- crowdsensing (3)
- database (3)
- deep learning (3)
- immersion (3)
- mHealth (3)
- neural networks (3)
Institute
- Institut für Informatik (78)
- Theodor-Boveri-Institut für Biowissenschaften (27)
- Institut Mensch - Computer - Medien (15)
- Institut für Klinische Epidemiologie und Biometrie (7)
- Center for Computational and Theoretical Biology (4)
- Medizinische Klinik und Poliklinik II (3)
- Institut für Funktionsmaterialien und Biofabrikation (2)
- Institut für Pharmazie und Lebensmittelchemie (2)
- Institut für Psychologie (2)
- Deutsches Zentrum für Herzinsuffizienz (DZHI) (1)
Sonstige beteiligte Institutionen
In this paper we study connectivity augmentation problems. Given a connected graph G with some desirable property, we want to make G 2-vertex connected (or 2-edge connected) by adding edges such that the resulting graph keeps the property. The aim is to add as few edges as possible. The property that we consider is planarity, both in an abstract graph-theoretic and in a geometric setting, where vertices correspond to points in the plane and edges to straight-line segments.
We show that it is NP-hard to nd a minimum-cardinality augmentation that makes a planar graph 2-edge connected. For making a planar graph 2-vertex connected this was known. We further show that both problems are hard in the geometric setting, even when restricted to trees. The problems remain hard for higher degrees of connectivity. On the other hand we give polynomial-time algorithms for the special case of convex geometric graphs.
We also study the following related problem. Given a planar (plane geometric) graph G, two vertices s and t of G, and an integer c, how many edges have to be added to G such that G is still planar (plane geometric) and contains c edge- (or vertex-) disjoint s{t paths? For the planar case we give a linear-time algorithm for c = 2. For the plane geometric case we give optimal worst-case bounds for c = 2; for c = 3 we characterize the cases that have a solution.
Background:
Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.
Methodology/Principal Findings:
Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.
Conclusions/Significance:
Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.
Einleitung:
Multiple-Choice-Klausuren spielen immer noch eine herausragende Rolle für fakultätsinterne medizinische Prüfungen. Neben inhaltlichen Arbeiten stellt sich die Frage, wie die technische Abwicklung optimiert werden kann. Für Dozenten in der Medizin gibt es zunehmend drei Optionen zur Durchführung von MC-Klausuren: Papierklausuren mit oder ohne Computerunterstützung oder vollständig elektronische Klausuren. Kritische Faktoren sind der Aufwand für die Formatierung der Klausur, der logistische Aufwand bei der Klausurdurchführung, die Qualität, Schnelligkeit und der Aufwand der Klausurkorrektur, die Bereitstellung der Dokumente für die Einsichtnahme, und die statistische Analyse der Klausurergebnisse.
Methoden:
An der Universität Würzburg wird seit drei Semestern ein Computerprogramm zur Eingabe und Formatierung der MC-Fragen in medizinischen und anderen Papierklausuren verwendet und optimiert, mit dem im Wintersemester (WS) 2009/2010 elf, im Sommersemester (SS) 2010 zwölf und im WS 2010/11 dreizehn medizinische Klausuren erstellt und anschließend die eingescannten Antwortblätter automatisch ausgewertet wurden. In den letzten beiden Semestern wurden die Aufwände protokolliert.
Ergebnisse:
Der Aufwand der Formatierung und der Auswertung einschl. nachträglicher Anpassung der Auswertung einer Durchschnittsklausur mit ca. 140 Teilnehmern und ca. 35 Fragen ist von 5-7 Stunden für Klausuren ohne Komplikation im WS 2009/2010 über ca. 2 Stunden im SS 2010 auf ca. 1,5 Stunden im WS 2010/11 gefallen. Einschließlich der Klausuren mit Komplikationen bei der Auswertung betrug die durchschnittliche Zeit im SS 2010 ca. 3 Stunden und im WS 10/11 ca. 2,67 Stunden pro Klausur.
Diskussion:
Für konventionelle Multiple-Choice-Klausuren bietet die computergestützte Formatierung und Auswertung von Papierklausuren einen beträchtlichen Zeitvorteil für die Dozenten im Vergleich zur manuellen Korrektur von Papierklausuren und benötigt im Vergleich zu rein elektronischen Klausuren eine deutlich einfachere technische Infrastruktur und weniger Personal bei der Klausurdurchführung.
This article is about a measurement analysis based approach to help software practitioners in managing the additional level complexities and variabilities in software product line applications. The architecture of the proposed approach i.e. ZAC is designed and implemented to perform preprocessesed source code analysis, calculate traditional and product line metrics and visualize results in two and three dimensional diagrams. Experiments using real time data sets are performed which concluded with the results that the ZAC can be very helpful for the software practitioners in understanding the overall structure and complexity of product line applications. Moreover the obtained results prove strong positive correlation between calculated traditional and product line measures.
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays
(2010)
Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see “Additional Files” section) and at: http://www.alice-dsl.net/evgeniy. vainshtein/ICEP/
Background: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Results: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Conclusions: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.
Background
Colorectal cancer is a leading cause of cancer-related deaths worldwide. The best method to prevent CRC is a colonoscopy. However, not all colon polyps have the risk of becoming cancerous. Therefore, polyps are classified using different classification systems. After the classification, further treatment and procedures are based on the classification of the polyp. Nevertheless, classification is not easy. Therefore, we suggest two novel automated classifications system assisting gastroenterologists in classifying polyps based on the NICE and Paris classification.
Methods
We build two classification systems. One is classifying polyps based on their shape (Paris). The other classifies polyps based on their texture and surface patterns (NICE). A two-step process for the Paris classification is introduced: First, detecting and cropping the polyp on the image, and secondly, classifying the polyp based on the cropped area with a transformer network. For the NICE classification, we design a few-shot learning algorithm based on the Deep Metric Learning approach. The algorithm creates an embedding space for polyps, which allows classification from a few examples to account for the data scarcity of NICE annotated images in our database.
Results
For the Paris classification, we achieve an accuracy of 89.35 %, surpassing all papers in the literature and establishing a new state-of-the-art and baseline accuracy for other publications on a public data set. For the NICE classification, we achieve a competitive accuracy of 81.13 % and demonstrate thereby the viability of the few-shot learning paradigm in polyp classification in data-scarce environments. Additionally, we show different ablations of the algorithms. Finally, we further elaborate on the explainability of the system by showing heat maps of the neural network explaining neural activations.
Conclusion
Overall we introduce two polyp classification systems to assist gastroenterologists. We achieve state-of-the-art performance in the Paris classification and demonstrate the viability of the few-shot learning paradigm in the NICE classification, addressing the prevalent data scarcity issues faced in medical machine learning.