Parea: multi-view ensemble clustering for cancer subtype discovery

Multi-view clustering methods are essential for the stratification of patients into sub-groups of similar molecular characteristics. In recent years, a wide range of methods has been developed for this purpose. However, due to the high diversity of cancer-related data, a single method may not perform sufficiently well in all cases. We present Parea, a multi-view hierarchical ensemble clustering approach for disease subtype discovery. We demonstrate its performance on several machine learning benchmark datasets. We apply and validate our methodology on real-world multi-view cancer patient data. Parea outperforms the current state-of-the-art on six out of seven analysed cancer types. We have integrated the Parea method into our developed Python package Pyrea (https://github.com/mdbloice/Pyrea), which enables the effortless and flexible design of ensemble workflows while incorporating a wide range of fusion and clustering algorithms

A New Method for Morphometric Analysis of Tissue Distribution of Mobile Cells in Relation to Immobile Tissue Structures

The distribution of cells in stained tissue sections provides information that may be analyzed by means of morphometric computation. We developed an algorithm for automated analysis for the purpose of answering questions pertaining to the relative densities of wandering cells in the vicinity of comparatively immobile tissue structures such as vessels or tumors. As an example, we present the analysis of distribution of CD56-positive cells and of CXCR3-positive cells (relative densities of peri-vascular versus non-vascular cell populations) in relation to the endothelium of capillaries and venules of human parietal decidua tissue of first trimester pregnancy. In addition, the distibution of CD56-positive cells (mostly uterine NK cells) in relation to spiral arteries is analyzed. The image analysis is based on microphotographs of two-color immunohistological stainings. Discrete distances (10–50 µm) from the fixed structures were chosen for the purpose of definining the extent of neighborhood areas. For the sake of better comparison of cell distributions at different overall cell densities a model of random distribution of “cells” in relation to neighborhood areas and rest decidua of a specific sample was built. In the chosen instances, we found increased perivascular density of CD56-positive cells and of CXCR3-positive cells. In contrast, no accumulation of CD56-positive cells was found in the neighborhood of spiral arteries

Amino-acid PET versus MRI guided re-irradiation in patients with recurrent glioblastoma multiforme (GLIAA) – protocol of a randomized phase II trial (NOA 10/ARO 2013-1)

Background: The higher specificity of amino-acid positron emission tomography (AA-PET) in the diagnosis of gliomas, as well as in the differentiation between recurrence and treatment-related alterations, in comparison to contrast enhancement in T1-weighted MRI was demonstrated in many studies and is the rationale for their implementation into radiation oncology treatment planning. Several clinical trials have demonstrated the significant differences between AA-PET and standard MRI concerning the definition of the gross tumor volume (GTV). A small single-center non-randomized prospective study in patients with recurrent high grade gliomas treated with stereotactic fractionated radiotherapy (SFRT) showed a significant improvement in survival when AA-PET was integrated in target volume delineation, in comparison to patients treated based on CT/MRI alone. Methods: This protocol describes a prospective, open label, randomized, multi-center phase II trial designed to test if radiotherapy target volume delineation based on FET-PET leads to improvement in progression free survival (PFS) in patients with recurrent glioblastoma (GBM) treated with re-irradiation, compared to target volume delineation based on T1Gd-MRI. The target sample size is 200 randomized patients with a 1:1 allocation ratio to both arms. The primary endpoint (PFS) is determined by serial MRI scans, supplemented by AA-PET-scans and/or biopsy/surgery if suspicious of progression. Secondary endpoints include overall survival (OS), locally controlled survival (time to local progression or death), volumetric assessment of GTV delineated by either method, topography of progression in relation to MRIor PET-derived target volumes, rate of long term survivors (> 1 year), localization of necrosis after re-irradiation, quality of life (QoL) assessed by the EORTC QLQ-C15 PAL questionnaire, evaluation of safety of FET-application in AA-PET imaging and toxicity of re-irradiation. Discussion: This is a protocol of a randomized phase II trial designed to test a new strategy of radiotherapy target volume delineation for improving the outcome of patients with recurrent GBM. Moreover, the trial will help to develop a standardized methodology for the integration of AA-PET and other imaging biomarkers in radiation treatment planning. Trial registration: The GLIAA trial is registered with ClinicalTrials.gov (NCT01252459, registration date 02.12.2010), German Clinical Trials Registry (DRKS00000634, registration date 10.10.2014), and European Clinical Trials Database (EudraCT-No. 2012-001121-27, registration date 27.02.2012)

Additive and Generalized Additive Models

This paper is the attempt to summarize the state of art in additive and generalized additive models (GAM). The emphasis is on approaches and numerical procedures which have emerged since the monograph of Hastie and Tibshirani (1990) although reconsidering certain aspects of their work. Apart from GAM, vector GAM (VGAM), alternating conditional expectations (ACE), and additivity and variance stabilization (AVAS) are discussed. Last but not least there are software hints for all these models

Legitimierende und delegitimierende Einflüsse auf die Regierungspopularität

Ziel der vorliegenden Arbeit ist es, an Hand von Regierungspopularitätsdaten eines politisch homogenen Zeitraumes, namentlich jenes der sozial-liberalen Koalition in der Bundesrepublik Deutschland (BRD), Regierungshandeln und andere damit in Verbindung stehende politische Aktivitäten im Hinblick auf ihren Legitimationswert zu untersuchen

Legitimierende und delegitimierende Einfluesse auf die Regierungspopularitaet: e. Interventionsanalyse d. Regierungspopularitaet d. sozial-liberalen Koalition in d. Bundesrepublik Deutschland in d. Jahren 1970 -1981

Available from Bibliothek des Instituts fuer Weltwirtschaft, ZBW, Duesternbrook Weg 120, D-24105 Kiel C 138315 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

An Iterative Projection Algorithm and Some Simulation Results

. An iterative projection method for large linear equation systems is described. It has favourable properties with respect to many statistical applications. A major advantage is that convergence can be established without restrictions on the system matrix. Hence diagonal dominance or regularity are not required. The reason why this numerical method has not been much used in computational statistics is its slow convergence behaviour. In this paper we introduce a relaxation concept and the optimal choice of the relaxation parameter, even for nearly singular systems, is studied in a simulation experiment. Keywords. Iterative projections, lack of diagonal dominance, linear equation systems, non-parametrics, regression, relaxation, regression fitting, singularity, simulations, time series fitting 1 Introduction The estimation of many parametric, non- as well as semiparametric statistical models involves the solution of large linear equation systems. Up to now iterative procedures like Jac..

Additive and generalized additive models: a survey

SIGLEAvailable from Bibliothek des Instituts fuer Weltwirtschaft, ZBW, Duesternbrook Weg 120, D-24105 Kiel W 1190 (97) / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekDEGerman