• Efforts towards accessible and reliable bioinformatics 

      Kalaš, Matúš (Doctoral thesis, 2015-11-19)
      The aim of the presented work was contributing to making scientific computing more accessible, reliable, and thus more efficient for researchers, primarily computational biologists and molecular biologists. Many approaches ...
    • Elastic Grid Resources using Cloud Technologies 

      Carlsen, Joachim Christoffer (Master thesis, 2014-06-02)
      A Large Ion Collider Experiment (ALICE) is one of four experiments at the Large Hadron Collider (LHC) at CERN. The detectors in the ALICE experiment produce data at a rate of 4 GB/s after being filtered and compressed ...
    • The EMBRACE web service collection 

      Pettifer, Steve; Ison, Jon; Kalaš, Matúš; Thorne, David; McDermott, Philip; Jonassen, Inge; Ali, Liaquat; Fernandez, Jose M; Rodriguez, Jose M; Pisano, David G; Blanchet, Christophe; Uludag, Mahmut; Rice, Peter; Bartaseviciute, Edita; Rapacki, Kristoffer; Hekkelman, Maarten; Sand, Olivier; Stockinger, Heinz; Clegg, Andrew B; Bongcam-Rudloff, Eric; Salzemann, Jean; Breton, Vincent; Attwood, Teresa K; Cameron, Graham; Vriend, Gert (Peer reviewed; Journal article, 2010-05-10)
      The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web ...
    • Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks 

      Antila, Hanne S.; Kav, Batuhan; Miettinen, Markus Sakari; Martinez-Seara, Hector; Jungwirth, Pavel; Ollila, O. H. Samuli (Journal article; Peer reviewed, 2022)
      Molecular simulations of biological membranes and proxies thereof are entering a new era characterized by several key aspects. Progress starts with the realization that the outcome of the simulations can only be as good ...
    • Employing Deep Learning for Fish Recognition 

      Reithaug, Adrian (Master thesis, 2018-08-21)
      Underwater imagery processing is in high demand, but the unrestricted environment makes it difficult to develop methods for analyzing it. Not only is obtaining a dataset for a single species difficult, but there are reported ...
    • Encoding and decoding of several optimal rank metric codes 

      Kadir, Wrya Karim Kadir; Li, Chunlei; Zullo, Ferdinando (Journal article; Peer reviewed, 2022)
      This paper presents encoding and decoding algorithms for several families of optimal rank metric codes whose codes are in restricted forms of symmetric, alternating and Hermitian matrices. First, we show the evaluation ...
    • Energy-scale Aware Feature Extraction for Flow Visualization 

      Pobitzer, Armin; Tutkun, Murat; Anreassen, Øyvind; Fuchs, Raphael; Peikert, Ronald; Hauser, Helwig (Peer reviewed; Journal article, 2011)
      In the visualization of flow simulation data, feature detectors often tend to result in overly rich response, making some sort of filtering or simplification necessary to convey meaningful images. In this paper we present ...
    • Enhancing Content Management in DPG 

      Pino Arevalo, Ana Gabriela (Master thesis, 2013-11-20)
      This thesis analyzes the usability aspects of PCE and implements a new Single Page Application that attempts to solve this issues
    • An Ensemble Feature Selection Framework Integrating Stability 

      Zhang, Xiaokang; Jonassen, Inge (Chapter; Peer reviewed, 2019)
      Ensemble feature selection has drawn more and more attention in recent years. There are mainly two strategies for ensemble feature selection, namely data perturbation and function perturbation. Data perturbation performs ...
    • Enumerating minimal connected dominating sets in graphs of bounded chordality 

      Golovach, Petr; Heggernes, Pinar; Kratsch, Dieter (Peer reviewed; Journal article, 2015)
      Listing, generating or enumerating objects of specified type is one of the principal tasks in algorithmics. In graph algorithms one often enumerates vertex subsets satisfying a certain property. We study the enumeration ...
    • eQTLs as causal instruments for the reconstruction of hormone linked gene networks 

      Bankier, Sean Alexander; Michoel, Tom (Journal article; Peer reviewed, 2022)
      Hormones act within in highly dynamic systems and much of the phenotypic response to variation in hormone levels is mediated by changes in gene expression. The increase in the number and power of large genetic association ...
    • Error Detection and Correction for Symmetric and Asymmetric Channels 

      Naydenova, Irina Petkova (Doctoral thesis, 2007-08-27)
      When a message is sent over a channel errors can occur due to noise during the transmission. So it is very important to know the error correction and detection capability of the code, which is used to encode the message. ...
    • ETH Tight Algorithms for Geometric Intersection Graphs: Now in Polynomial Space 

      Fomin, Fedor; Golovach, Petr; Inamdar, Tanmay Nitin; Saurabh, Saket (Journal article; Peer reviewed, 2021)
      De Berg et al. in [SICOMP 2020] gave an algorithmic framework for subexponential algorithms on geometric graphs with tight (up to ETH) running times. This framework is based on dynamic programming on graphs of weighted ...
    • ETH-Tight Algorithms for Finding Surfaces in Simplicial Complexes of Bounded Treewidth 

      Black, Mitchell; Blaser, Nello; Nayyeri, Amir; Vågset, Erlend Raa (Journal article; Peer reviewed, 2022)
      Given a simplicial complex with n simplices, we consider the Connected Subsurface Recognition (c-SR) problem of finding a subcomplex that is homeomorphic to a given connected surface with a fixed boundary. We also study ...
    • ETH-tight algorithms for long path and cycle on unit disk graphs 

      Fomin, Fedor; Lokshtanov, Daniel; Panolan, Fahad; Saurabh, Saket; Zehavi, Meirav (Journal article; Peer reviewed, 2020)
      We present an algorithm for the extensively studied Long Path and Long Cycle problems on unit disk graphs that runs in time 2O(√k)(n + m). Under the Exponential Time Hypothesis, Long Path and Long Cycle on unit disk graphs ...
    • Evolution and developmental system drift in the endoderm gene regulatory network of Caenorhabditis and other nematodes 

      Ewe, Chee Kiang; Torres Cleuren, Yamila Nicole; Rothman, Joel H (Journal article; Peer reviewed, 2020)
      Developmental gene regulatory networks (GRNs) underpin metazoan embryogenesis and have undergone substantial modification to generate the tremendous variety of animal forms present on Earth today. The nematode Caenorhabditis ...
    • Exact algorithms for MAX-2SAT and MAX-3SAT via multidimensional matrix multiplication 

      Petkevich, Yevgheni (Master thesis, 2015-06-01)
      In this thesis it is showed how an \(O(n^{4-\epsilon})\) algorithm for the cube multiplication problem (that is defined in the thesis) would imply a faster than naive \(O^{*}(2^{n(1-\frac{\epsilon}{4})})\) algorithm for ...
    • Exact algorithms for treewidth and minimum fill-in 

      Fomin, Fedor; Todinca, Ioan; Kratsch, Dieter; Villanger, Yngve (Journal article, 2006)
    • Exact and approximate digraph bandwidth 

      Jain, Pallavi; Kanesh, Lawqueen; Lochet, William; Saurabh, Saket; Sharma, Roohani (Journal article; Peer reviewed, 2019)
      In this paper, we introduce a directed variant of the classical Bandwidth problem and study it from the view-point of moderately exponential time algorithms, both exactly and approximately. Motivated by the definitions of ...
    • Exact Exponential Algorithms for Clustering Problems 

      Fomin, Fedor; Golovach, Petr; Inamdar, Tanmay Nitin; Purohit, Nidhi; Saurabh, Saket (Journal article; Peer reviewed, 2022)
      In this paper we initiate a systematic study of exact algorithms for some of the well known clustering problems, namely k-MEDIAN and k-MEANS. In k-MEDIAN, the input consists of a set X of n points belonging to a metric ...