Analysing next generation sequencing data often involves the use of a sequence aligner to map the sequenced reads against a reference. The output of this process is the basis of many downstream analyses and its qualit...
详细信息
ISBN:
(纸本)9783319787220;9783319787237
Analysing next generation sequencing data often involves the use of a sequence aligner to map the sequenced reads against a reference. The output of this process is the basis of many downstream analyses and its quality thus critical. Many different alignment tools exist, each with a multitude of options, creating a vast amount of possibilities to align sequences. Choosing the correct aligner and options for a specific dataset is complex, and yet it can have a major impact on the quality of the data analysis. We propose a new approach in which we combine the output of multiple sequence aligners to create an improved sequence alignment files. Our novel approach can be used to either increase the sensitivity or the specificity of the alignment process. The software is freely available for non-commercial usage at http://***/.
The technology-driven gig-platform sector has emerged as a new source of employment generation both globally as well domestically. This recent transformation in the labour market is reshaping the nature of labour prac...
详细信息
Many ubiquitous computing systems and applications, including mobile learning ones, can make use of personalization procedures in order to support and improve universal usability. In our previous work, we have created...
详细信息
ISBN:
(纸本)9783642027093
Many ubiquitous computing systems and applications, including mobile learning ones, can make use of personalization procedures in order to support and improve universal usability. In our previous work, we have created a GUI menu model for mobile device applications, where personalization capabilities are primarily derived from the use of adaptable and adaptive techniques. In this paper we analyze from a theoretical point of view the efficiency of the two adaptation approaches and related algorithms. A task simulation framework has been developed for comparison of static and automatically adapted menus in the mobile application environment. Algorithm functionality is evaluated according to adaptivity effects provided in various mend configurations and within several classes of randomly generated navigation tasks. Simulation results thus obtained support the usage of adaptivity, which provides a valuable improvement in navigation efficiency within menu-based mobile interfaces.
One of the main challenges in algorithmics in general, and in Memetic Computing, in particular, is the automatic design of search algorithms. A recent advance in this direction (in terms of continuous problems) is the...
详细信息
ISBN:
(纸本)9781479944910
One of the main challenges in algorithmics in general, and in Memetic Computing, in particular, is the automatic design of search algorithms. A recent advance in this direction (in terms of continuous problems) is the development of a software prototype that builds up an algorithm based upon a problem analysis of its separability. This prototype has been called the Separability Prototype for Automatic Memes (SPAM). This article modifies the SPAM by incorporating within it an adaptive model used in hyper-heuristics for tackling optimization problems. This model, namely Adaptive Operator Selection (AOS), rewards at run time the most promising heuristics/memes so that they are more likely to be used in the following stages of the search process. The resulting framework, here referred to as SPAM-AOS, has been tested on various benchmark problems and compared with modern algorithms representing the-state-of-the-art of search for continuous problems. Numerical results show that the proposed SPAM-AOS is a promising framework that outperforms the original SPAM and other modern algorithms. Most importantly, this study shows how certain areas of Memetic Computing and Hyper-heuristics are very closely related topics and it also shows that their combination can lead to the development of powerful algorithmic frameworks.
Component-graphs are defined as the generalization of component-trees to images taking their values in partially ordered sets. Similarly to component-trees, component-graphs are a lossless image model, and can allow f...
详细信息
ISBN:
(纸本)9783319572406;9783319572390
Component-graphs are defined as the generalization of component-trees to images taking their values in partially ordered sets. Similarly to component-trees, component-graphs are a lossless image model, and can allow for the development of various image processing approaches (antiextensive filtering, segmentation by node selection). However, component-graphs are not trees, but directed acyclic graphs. This induces a structural complexity associated to a higher combinatorial cost. These properties make the handling of component-graphs a non-trivial task. We propose a preliminary discussion on a new way of building and manipulating component-graphs, with the purpose of reaching reasonable space and time costs. Tackling these complexity issues is indeed required for actually involving component-graphs in efficient image processing approaches.
algorithmics is a crucial step in programming learning processes. It helps learners to propose a better writing and understanding of solutions without worrying about programming language syntactic complexity. Once alg...
详细信息
ISBN:
(纸本)9783030499327;9783030499310
algorithmics is a crucial step in programming learning processes. It helps learners to propose a better writing and understanding of solutions without worrying about programming language syntactic complexity. Once algorithm is clearly established, the next step is to translate it into a given programming language. When writing programs, syntax errors are common mainly due to the multiplicity of programming languages and strict syntactic rules. We propose in this work a web and mobile interface to automatically generate, from algorithms based on Pseudocode ontology, the corresponding codes in several programming languages such as C, Pascal and Python.
We start by studying the class of $k$- degenerate graphs which are often used to model sparse real-world graphs. We focus on enumeration questions for these graphs. That is, we try and provide algorithms which must ou...
详细信息
We start by studying the class of $k$- degenerate graphs which are often used to model sparse real-world graphs. We focus on enumeration questions for these graphs. That is, we try and provide algorithms which must output, without duplication, all the occurrences of some input subgraph. We investigate the questions of finding all cycles of some given size and all maximal cliques in the graph. Our two contributions are a worst-case output size optimal algorithm for fixed-size cycle enumeration and an output sensitive algorithm for maximal clique enumeration for this restricted class of graphs. In a second part we consider graphs in a distributed manner. We investigate questions related to finding matchings of the network, when no assumption is made on the initial state of the system. These algorithms are often referred to as self- stabilizing. Our two main contributions are an algorithm returning an approximation of the maximum matching and a new algorithm for maximal matching when communication simulates message passing. Finally, we introduce and investigate some special families of polytopes, namely primitive zonotopes, which can be described as the Minkowski sum of short primitive vectors. We highlight connections with the largest possible diameter of the convex hull of a set of points in dimension d whose coordinates are integers between 0 and k. Our main contributions are new lower bounds for this diameter question as well as descriptions of small instances of these objects.
The most compelling ideas in systems are abstractions such as virtual memory, sockets, or packet scheduling. algorithmics is the servant of abstraction, allowing system performance to approach that of the underlying h...
详细信息
ISBN:
(纸本)9781450328364
The most compelling ideas in systems are abstractions such as virtual memory, sockets, or packet scheduling. algorithmics is the servant of abstraction, allowing system performance to approach that of the underlying hardware, sometimes by using efficient algorithms but often by simply leveraging other aspects of the system. I will survey the trajectory of network algorithmics starting with a focus on speed and scale in the 1990s to measurement and security in the 2000s. While doing so, I will reflect on my experiences in choosing problems and conducting research. I will conclude by describing my passion for the emerging field of network verification and its confluence with programming language *** Varghese worked at DEC designing DECNET protocols before obtaining his Ph.D. in 1992 from MIT. He worked from 1993-1999 at Washington University and from 1999 to 2012 at UCSD, both as professor of computer science. He joined Microsoft Research as a Principal Researcher in 2012. He won the ONR Young Investigator Award in 1996, and was elected to be a Fellow of the Association for Computing Machinery (ACM) in 2002. He helped design the 40 Gbps forwarding engine for Procket Networks, subsequently acquired by Cisco Systems. His book "Network algorithmics" was published in December 2004 by Morgan-Kaufman. He co-founded NetSift Inc. in May 2004. NetSift was acquired by Cisco in 2005. He was the 2014 winner of the IEEE Koji Kobayashi Computers and Communications Award
暂无评论