On the Effect of Inter-observer Variability for a Reliable Estimation of Uncertainty of Medical Image Segmentation

Uncertainty estimation methods are expected to improve the understanding and quality of computer-assisted methods used in medical applications (e.g., neurosurgical interventions, radiotherapy planning), where automated medical image segmentation is crucial. In supervised machine learning, a common practice to generate ground truth label data is to merge observer annotations. However, as many medical image tasks show a high inter-observer variability resulting from factors such as image quality, different levels of user expertise and domain knowledge, little is known as to how inter-observer variability and commonly used fusion methods affect the estimation of uncertainty of automated image segmentation. In this paper we analyze the effect of common image label fusion techniques on uncertainty estimation, and propose to learn the uncertainty among observers. The results highlight the negative effect of fusion methods applied in deep learning, to obtain reliable estimates of segmentation uncertainty. Additionally, we show that the learned observers' uncertainty can be combined with current standard Monte Carlo dropout Bayesian neural networks to characterize uncertainty of model's parameters.Comment: Appears in Medical Image Computing and Computer Assisted Interventions (MICCAI), 201

Définition d'un tableau de bord pour le Service de la santé publique du canton de Neuchâtel

[...] L'Etat se doit d'imposer aux institutions des objectifs de qualité corollairement aux objectifs financiers. La préparation et la négociation des contrats de prestations ainsi que du cadre budgétaire et le contrôle du respect des éléments y relatifs devient une tâche primordiale de l'Etat. C'est par ce biais qu'il garde un certain contrôle sur les objectifs des institutions. Dès lors, pour ne pas recréer les conditions-cadres que l'on veut justement changer, à savoir le manque d'incitation à la bonne gestion, l'État doit se doter d'instruments de surveillance capables de mettre en évidence suffisamment tôt une éventuelle dérive financière, de manière à permettre la prise de mesures adéquates. Il doit également surveiller l'activité des institutions et en mesurer les effets au sein de la population (qualité des soins, accessibilité, etc.). Cette surveillance nécessite la collecte de données épidémiologiques et elle s'exerce grâce à la création de tableaux de bord composés d'indicateurs pertinents. [...] [Auteur, p. 20]]]> Total Quality Management ; Health Services Administration ; Benchmarking ; Delivery of Health Care fre https://serval.unil.ch/resource/serval:BIB_D88A9140E37E.P001/REF.pdf http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_D88A9140E37E0 info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_D88A9140E37E0 info:eu-repo/semantics/openAccess Copying allowed only for non-profit organizations https://serval.unil.ch/disclaimer application/pdf oai:serval.unil.ch:BIB_D88C6DA8E404 2022-05-07T01:28:04Z openaire documents urnserval <oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"> https://serval.unil.ch/notice/serval:BIB_D88C6DA8E404 Strategien nachhaltiger Bevölkerungsinformation : eine Analyse der Stop-Aids-Präventionskampagnen des Bundesamtes für Gesundheit unter besonderer Berücksichtigung des Social Marketing Stemmle, Dietler Cattacin, Sandro Losa, Stefano Schleiter, Susanne info:eu-repo/semantics/book book 2003 <![CDATA[Die vorliegende Studie hatte zum Ziel, die Erfahrungen der 15-jährigen Stop-Aids-Kampagnen im Hinblick auf deren Fortführung zu analysieren. Dabei wurden über einen Methodenmix Daten und Informationen erhoben und trianguliert. Vier studienspezifische Fragestellungen zur zukünftigen Ausrichtung der Kampagnen wurden beantwortet. 1. Wurden die Ziele der Stop-Aids-Kampagnen erreicht und wie müssen diese, falls überhaupt, in Zukunft angepasst werden? 2. Haben sich die Botschaften bisheriger Stop-Aids-Kampagnen bewährt und wie sind diese weiter zu entwickeln? 3. Hat sich die bisherige Form der Realisierung der Stop-Aids-Kampagnen bewährt und wie ist diese weiter zu gestalten? 4. Hat sich die bisherige Organisation der Stop-Aids-Kampagnen bewährt und wie soll diese in Zukunft konzipiert sein? Die Studie kommt zum Schluss, dass es einer Erneuerung sowie Vertiefung der Positionierung der Stop-Aids-Kampagnen in der Gesamtbevölkerung bedarf, damit sie auch in Zukunft wirksam bleiben und Erfolg haben. La but de la présente étude était d’analyser les résultats de la campagne Stop-Sida, menée depuis 15 ans, en vue de son développement. Pour ce faire, nous avons opté pour une combinaison de méthodes et la triangulation d’informations. Quatre questions pour la future orientation des campagnes étaient au centre de l’analyse. 1. Les buts de la campagne Stop-Sida ont-ils été atteints et comment, si non, doivent-ils être adaptés ? 2. Les messages des campagnes menées jusqu’à présent se sont-ils confirmés et comment devraient-ils être développés à l'avenir ? 3. La manière de réaliser les campagnes Stop-Sida s’est-elle confirmée et doit-elle être reconduite ? 4. L’organisation des campagnes Stop-Sida s’est-elle avérée adéquate et comment devrait-on procéder à l'avenir ? D'une manière générale et pour conclure, nous pouvons affirmer qu’un renouvellement et un développement de la campagne Stop-Sida, destinée à la population, sont indispensables pour que celle-ci continue à porter ses fruits

Understanding co-expressed gene sets by identifying regulators and modeling genomic elements

Genomic researchers commonly study complex phenotypes by identifying experimentally derived sets of functionally related genes with similar transcriptional profiles. These gene sets are then frequently subjected to statistical tests of association relating them to previously characterized gene sets from literature and public databases. However, few tools exist examining the non-coding, regulatory sequence of gene sets for evidence of a shared regulatory signature that may signal the involvement of important DNA-binding proteins called transcription factors (TFs). Here, we proposed and developed new computational methods for identifying major regulatory features of co-expressed gene sets that incorporate TF-DNA binding specificities (“motifs”) with other important features such as sequence conservation and chromatin structure. We additionally demonstrated a novel approach for discovering regulatory signatures that are shared across gene sets from multiple experimental conditions or tissues. Given the co-expressed genes of a particular cell type, we also attempted to annotate their specific regulatory sequences (“enhancers”) by constructing models of enhancer activity that incorporate the expression and binding specificities of the relevant transcription factors. We first developed and tested these models in well-characterized cell types, and then evaluated the extent to which these models were applicable using only minimal experimental evidence to poorly characterized systems without known transcriptional regulators and functional enhancers. Finally, we developed a network-based algorithm for examining novel gene sets that integrates many diverse types of biological evidences and relationships to better discover functionally related genes. This novel approach processed a comprehensive, heterogeneous network of biological knowledge and ranked genes and molecular properties represented in the network for their relevance to the given set of co-expressed genes

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF-DNA binding specificities (\u27motifs\u27). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF-DNA binding. We demonstrate that predicted binding profiles and expression patterns of hundreds of TFs are sufficient to identify major regulators of approximately 200 spatiotemporal expression domains in the Drosophila embryo. We are then able to learn reliable statistical models of enhancer activity for over 70 expression domains and apply those models to annotate domain specific enhancers genome-wide. Throughout this work, we apply our motif and accessibility based approach to comprehensively characterize the regulatory network of fruitfly embryonic development and show that the accuracy of our computational method compares favorably to approaches that rely on data from many experimental assays. Acids Research

Characteristics of Lesser Spotted Woodpeckers Dendrocopos minor on irruptive autumn movement along the coast of southern Norway

The Lesser Spotted Woodpecker Dendrocopos minor is a facultative autumn migrant in Fennoscandia, but there is little published information about its migratory ecology. Analysing data from 26 years (1990–2015) of trapping at Lista Bird Observatory, southern Norway, we found that autumn migration varied in relation to sex and age in this species. Annual numbers of trapped birds fluctuated between 0 and 19 but there was no significant temporal trend in the numbers of birds trapped. However, the numbers were positively correlated with similar data from Falsterbo Bird Observatory in southern Sweden. Thus, the annual fluctuation of Lesser Spotted Woodpeckers at Lista probably reflects the situation across larger parts of the southern Scandinavian Peninsula. In total, 96% of the birds trapped at Lista (n = 136) were in their first calendar year, showing clear evidence for differential migration in the species. There was no sex bias in the material but the median arrival date was about 14 days earlier in males than in females. Wing length increased over the season in both sexes, although the explanatory value of this seasonal progression was low. Also, body mass was higher in males than in females and increased with date of trapping when body size (wing length) was controlled for. Our findings comply with the hypothesis that annual fluctuation in the number of migrating Lesser Spotted Woodpeckers is caused by varying breeding success in the source population(s), mediated by intra-specific competition (the competitive release hypothesis)