EURECCA colorectal: multidisciplinary mission statement on better care for patients with colon and rectal cancer in Europe

Background: Care for patients with colon and rectal cancer has improved in the last twenty years however still considerable variation exists in cancer management and outcome between European countries. Therefore, EURECCA, which is the acronym of European Registration of cancer care, is aiming at defining core treatment strategies and developing a European audit structure in order to improve the quality of care for all patients with colon and rectal cancer. In December 2012 the first multidisciplinary consensus conference about colon and rectum was held looking for multidisciplinary consensus. The expert panel consisted of representatives of European scientific organisations involved in cancer care of patients with colon and rectal cancer and representatives of national colorectal registries. Methods: The expert panel had delegates of the European Society of Surgical Oncology (ESSO), European Society for Radiotherapy & Oncology (ESTRO), European Society of Pathology (ESP), European Society for Medical Oncology (ESMO), European Society of Radiology (ESR), European Society of Coloproctology (ESCP), European CanCer Organisation (ECCO), European Oncology Nursing Society (EONS) and the European Colorectal Cancer Patient Organisation (EuropaColon), as well as delegates from national registries or audits. Experts commented and voted on the two web-based online voting rounds before the meeting (between 4th and 25th October and between the 20th November and 3rd December 2012) as well as one online round after the meeting (4th-20th March 2013) and were invited to lecture on the subjects during the meeting (13th-15th December 2012). The sentences in the consensus document were available during the meeting and a televoting round during the conference by all participants was performed. All sentences that were voted on are available on the EURECCA website www.canceraudit.eu. The consensus document was divided in sections describing evidence based algorithms of diagnostics, pathology, surgery, medical oncology, radiotherapy, and follow-up where applicable for treatment of colon cancer, rectal cancer and stage IV separately. Consensus was achieved using the Delphi method. Results: The total number of the voted sentences was 465. All chapters were voted on by at least 75% of the experts. Of the 465 sentences, 84% achieved large consensus, 6% achieved moderate consensus, and 7% resulted in minimum consensus. Only 3% was disagreed by more than 50% of the members. Conclusions: It is feasible to achieve European Consensus on key diagnostic and treatment issues using the Delphi method. This consensus embodies the expertise of professionals from all disciplines involved in the care for patients with colon and rectal cancer. Diagnostic and treatment algorithms were developed to implement the current evidence and to define core treatment guidance for multidisciplinary team management of colon and rectal cancer throughout Europe.

Could machine learning improve the prediction of pelvic nodal status of prostate cancer patients? Preliminary results of a pilot study.

We tested and compared performances of Roach formula, Partin tables and of three Machine Learning (ML) based algorithms based on decision trees in identifying N+ prostate cancer (PC). 1,555 cN0 and 50 cN+ PC were analyzed. Results were also verified on an independent population of 204 operated cN0 patients, with a known pN status (187 pN0, 17 pN1 patients). ML performed better, also when tested on the surgical population, with accuracy, specificity, and sensitivity ranging between 48-86%, 35-91%, and 17-79%, respectively. ML potentially allows better prediction of the nodal status of PC, potentially allowing a better tailoring of pelvic irradiation.

Anonymizing Graphs: Measuring Quality for Clustering

Peer-reviewed

Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Spectral Retinal Images Reconstruction

While red-green-blue (RGB) image of retina has quite limited information, retinal multispectral images provide both spatial and spectral information which could enhance the capability of exploring the eye-related problems in their early stages. In this thesis, two learning-based algorithms for reconstructing of spectral retinal images from the RGB images are developed by a two-step manner. First, related previous techniques are reviewed and studied. Then, the most suitable methods are enhanced and combined to have new algorithms for the reconstruction of spectral retinal images. The proposed approaches are based on radial basis function network to learn a mapping from tristimulus colour space to multi-spectral space. The resemblance level of reproduced spectral images and original images is estimated using spectral distance metrics spectral angle mapper, spectral correlation mapper, and spectral information divergence, which show a promising result from the suggested algorithms.

De novo transcriptome assembly and annotation of the isopod Idotea balthica

The Baltic Sea is a unique environment that contains unique genetic populations. In order to study these populations on a genetic level basic molecular research is needed. The aim of this thesis was to provide a basic genetic resource for population genomic studies by de novo assembling a transcriptome for the Baltic Sea isopod Idotea balthica. RNA was extracted from a whole single adult male isopod and sequenced using Illumina (125bp PE) RNA-Seq. The reads were preprocessed using FASTQC for quality control, TRIMMOMATIC for trimming, and RCORRECTOR for error correction. The preprocessed reads were then assembled with TRINITY, a de Bruijn graph-based assembler, using different k-mer sizes. The different assemblies were combined and clustered using CD-HIT. The assemblies were evaluated using TRANSRATE for quality and filtering, BUSCO for completeness, and TRANSDECODER for annotation potential. The 25-mer assembly was annotated using PANNZER (protein annotation with z-score) and BLASTX. The 25-mer assembly represents the best first draft assembly since it contains the most information. However, this assembly shows high levels of polymorphism, which currently cannot be differentiated as paralogs or allelic variants. Furthermore, this assembly is incomplete, which could be improved by sampling additional developmental stages.

Modeling Metal Protein Complexes from Experimental Extended X-ray Absorption Fine Structure using Computational Intelligence

Experimental Extended X-ray Absorption Fine Structure (EXAFS) spectra carry information about the chemical structure of metal protein complexes. However, pre- dicting the structure of such complexes from EXAFS spectra is not a simple task. Currently methods such as Monte Carlo optimization or simulated annealing are used in structure refinement of EXAFS. These methods have proven somewhat successful in structure refinement but have not been successful in finding the global minima. Multiple population based algorithms, including a genetic algorithm, a restarting ge- netic algorithm, differential evolution, and particle swarm optimization, are studied for their effectiveness in structure refinement of EXAFS. The oxygen-evolving com- plex in S1 is used as a benchmark for comparing the algorithms. These algorithms were successful in finding new atomic structures that produced improved calculated EXAFS spectra over atomic structures previously found.

Moranapho : apprentissage non supervisé de la morphologie d'une langue par généralisation de relations analogiques

Récemment, nous avons pu observer un intérêt grandissant pour l'application de l'analogie formelle à l'analyse morphologique. L'intérêt premier de ce concept repose sur ses parallèles avec le processus mental impliqué dans la création de nouveaux termes basée sur les relations morphologiques préexistantes de la langue. Toutefois, l'utilisation de ce concept reste tout de même marginale due notamment à son coût de calcul élevé.Dans ce document, nous présenterons le système à base de graphe Moranapho fondé sur l'analogie formelle. Nous démontrerons par notre participation au Morpho Challenge 2009 (Kurimo:10) et nos expériences subséquentes, que la qualité des analyses obtenues par ce système rivalise avec l'état de l'art. Nous analyserons aussi l'influence de certaines de ses composantes sur la qualité des analyses morphologiques produites. Nous appuierons les conclusions tirées de nos analyses sur des théories bien établies dans le domaine de la linguistique. Ceci nous permet donc de fournir certaines prédictions sur les succès et les échecs de notre système, lorsqu'appliqué à d'autres langues que celles testées au cours de nos expériences.

Mures : Un système de recommandation de musique

Pendant la dernière décennie nous avons vu une transformation incroyable du monde de la musique qui est passé des cassettes et disques compacts à la musique numérique en ligne. Avec l'explosion de la musique numérique, nous avons besoin de systèmes de recommandation de musique pour choisir les chansons susceptibles d’être appréciés à partir de ces énormes bases de données en ligne ou personnelles. Actuellement, la plupart des systèmes de recommandation de musique utilisent l’algorithme de filtrage collaboratif ou celui du filtrage à base de contenu. Dans ce mémoire, nous proposons un algorithme hybride et original qui combine le filtrage collaboratif avec le filtrage basé sur étiquetage, amélioré par la technique de filtrage basée sur le contexte d’utilisation afin de produire de meilleures recommandations. Notre approche suppose que les préférences de l'utilisateur changent selon le contexte d'utilisation. Par exemple, un utilisateur écoute un genre de musique en conduisant vers son travail, un autre type en voyageant avec la famille en vacances, un autre pendant une soirée romantique ou aux fêtes. De plus, si la sélection a été générée pour plus d'un utilisateur (voyage en famille, fête) le système proposera des chansons en fonction des préférences de tous ces utilisateurs. L'objectif principal de notre système est de recommander à l'utilisateur de la musique à partir de sa collection personnelle ou à partir de la collection du système, les nouveautés et les prochains concerts. Un autre objectif de notre système sera de collecter des données provenant de sources extérieures, en s'appuyant sur des techniques de crawling et sur les flux RSS pour offrir des informations reliées à la musique tels que: les nouveautés, les prochains concerts, les paroles et les artistes similaires. Nous essayerons d’unifier des ensembles de données disponibles gratuitement sur le Web tels que les habitudes d’écoute de Last.fm, la base de données de la musique de MusicBrainz et les étiquettes des MusicStrands afin d'obtenir des identificateurs uniques pour les chansons, les albums et les artistes.

Development of Hierarchical Clustering Techniques for Gridded Data from Mixed Data Sequences

Knowledge discovery in databases is the non-trivial process of identifying valid, novel potentially useful and ultimately understandable patterns from data. The term Data mining refers to the process which does the exploratory analysis on the data and builds some model on the data. To infer patterns from data, data mining involves different approaches like association rule mining, classification techniques or clustering techniques. Among the many data mining techniques, clustering plays a major role, since it helps to group the related data for assessing properties and drawing conclusions. Most of the clustering algorithms act on a dataset with uniform format, since the similarity or dissimilarity between the data points is a significant factor in finding out the clusters. If a dataset consists of mixed attributes, i.e. a combination of numerical and categorical variables, a preferred approach is to convert different formats into a uniform format. The research study explores the various techniques to convert the mixed data sets to a numerical equivalent, so as to make it equipped for applying the statistical and similar algorithms. The results of clustering mixed category data after conversion to numeric data type have been demonstrated using a crime data set. The thesis also proposes an extension to the well known algorithm for handling mixed data types, to deal with data sets having only categorical data. The proposed conversion has been validated on a data set corresponding to breast cancer. Moreover, another issue with the clustering process is the visualization of output. Different geometric techniques like scatter plot, or projection plots are available, but none of the techniques display the result projecting the whole database but rather demonstrate attribute-pair wise analysis

Capturing Emergent Semantics from Social Annotation Systems

The ongoing growth of the World Wide Web, catalyzed by the increasing possibility of ubiquitous access via a variety of devices, continues to strengthen its role as our prevalent information and commmunication medium. However, although tools like search engines facilitate retrieval, the task of finally making sense of Web content is still often left to human interpretation. The vision of supporting both humans and machines in such knowledge-based activities led to the development of different systems which allow to structure Web resources by metadata annotations. Interestingly, two major approaches which gained a considerable amount of attention are addressing the problem from nearly opposite directions: On the one hand, the idea of the Semantic Web suggests to formalize the knowledge within a particular domain by means of the "top-down" approach of defining ontologies. On the other hand, Social Annotation Systems as part of the so-called Web 2.0 movement implement a "bottom-up" style of categorization using arbitrary keywords. Experience as well as research in the characteristics of both systems has shown that their strengths and weaknesses seem to be inverse: While Social Annotation suffers from problems like, e. g., ambiguity or lack or precision, ontologies were especially designed to eliminate those. On the contrary, the latter suffer from a knowledge acquisition bottleneck, which is successfully overcome by the large user populations of Social Annotation Systems. Instead of being regarded as competing paradigms, the obvious potential synergies from a combination of both motivated approaches to "bridge the gap" between them. These were fostered by the evidence of emergent semantics, i. e., the self-organized evolution of implicit conceptual structures, within Social Annotation data. While several techniques to exploit the emergent patterns were proposed, a systematic analysis - especially regarding paradigms from the field of ontology learning - is still largely missing. This also includes a deeper understanding of the circumstances which affect the evolution processes. This work aims to address this gap by providing an in-depth study of methods and influencing factors to capture emergent semantics from Social Annotation Systems. We focus hereby on the acquisition of lexical semantics from the underlying networks of keywords, users and resources. Structured along different ontology learning tasks, we use a methodology of semantic grounding to characterize and evaluate the semantic relations captured by different methods. In all cases, our studies are based on datasets from several Social Annotation Systems. Specifically, we first analyze semantic relatedness among keywords, and identify measures which detect different notions of relatedness. These constitute the input of concept learning algorithms, which focus then on the discovery of synonymous and ambiguous keywords. Hereby, we assess the usefulness of various clustering techniques. As a prerequisite to induce hierarchical relationships, our next step is to study measures which quantify the level of generality of a particular keyword. We find that comparatively simple measures can approximate the generality information encoded in reference taxonomies. These insights are used to inform the final task, namely the creation of concept hierarchies. For this purpose, generality-based algorithms exhibit advantages compared to clustering approaches. In order to complement the identification of suitable methods to capture semantic structures, we analyze as a next step several factors which influence their emergence. Empirical evidence is provided that the amount of available data plays a crucial role for determining keyword meanings. From a different perspective, we examine pragmatic aspects by considering different annotation patterns among users. Based on a broad distinction between "categorizers" and "describers", we find that the latter produce more accurate results. This suggests a causal link between pragmatic and semantic aspects of keyword annotation. As a special kind of usage pattern, we then have a look at system abuse and spam. While observing a mixed picture, we suggest that an individual decision should be taken instead of disregarding spammers as a matter of principle. Finally, we discuss a set of applications which operationalize the results of our studies for enhancing both Social Annotation and semantic systems. These comprise on the one hand tools which foster the emergence of semantics, and on the one hand applications which exploit the socially induced relations to improve, e. g., searching, browsing, or user profiling facilities. In summary, the contributions of this work highlight viable methods and crucial aspects for designing enhanced knowledge-based services of a Social Semantic Web.

The Kineticist's Workbench: Combining Symbolic and Numerical Methods in the Simulation of Chemical Reaction Mechanisms

The Kineticist's Workbench is a program that simulates chemical reaction mechanisms by predicting, generating, and interpreting numerical data. Prior to simulation, it analyzes a given mechanism to predict that mechanism's behavior; it then simulates the mechanism numerically; and afterward, it interprets and summarizes the data it has generated. In performing these tasks, the Workbench uses a variety of techniques: graph- theoretic algorithms (for analyzing mechanisms), traditional numerical simulation methods, and algorithms that examine simulation results and reinterpret them in qualitative terms. The Workbench thus serves as a prototype for a new class of scientific computational tools---tools that provide symbiotic collaborations between qualitative and quantitative methods.

Towards Direct Policy Search Reinforcement Learning for Robot Control

This paper proposes a high-level reinforcement learning (RL) control system for solving the action selection problem of an autonomous robot. Although the dominant approach, when using RL, has been to apply value function based algorithms, the system here detailed is characterized by the use of direct policy search methods. Rather than approximating a value function, these methodologies approximate a policy using an independent function approximator with its own parameters, trying to maximize the future expected reward. The policy based algorithm presented in this paper is used for learning the internal state/action mapping of a behavior. In this preliminary work, we demonstrate its feasibility with simulated experiments using the underwater robot GARBI in a target reaching task

TU Graz: Course: 707.000 Web Science and Web Technology: Lecture 6: Network Evolution and Process

In this class, we will discuss the nature of network evolution and some selected network processes. We will discuss graph generation algorithms that generate networks with different interesting characteristics. Optional : The Structure and Function of Complex Networks (chapter 8), M.E.J. Newman, SIAM Review 45 167--256 (2003); Optional: Emergence of Scaling in Random Networks, A.L. Barabasi and R. Albert, Science 286, 509 (1999)