Learning to merge search results for efficient Distributed Information Retrieval

Merging search results from different servers is a major problem in Distributed Information Retrieval. We used Regression-SVM and Ranking-SVM which would learn a function that merges results based on information that is readily available: i.e. the ranks, titles, summaries and URLs contained in the results pages. By not downloading additional information, such as the full document, we decrease bandwidth usage. CORI and Round Robin merging were used as our baselines; surprisingly, our results show that the SVM-methods do not improve over those baselines

Extreme Scale De Novo Metagenome Assembly

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big shared memory machines and cannot handle contemporary metagenome datasets that exceed Terabytes in size. In this paper, we introduce the MetaHipMer pipeline, a high-quality and high-performance metagenome assembler that employs an iterative de Bruijn graph approach. MetaHipMer leverages a specialized scaffolding algorithm that produces long scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is end-to-end parallelized using the Unified Parallel C language and therefore can run seamlessly on shared and distributed-memory systems. Experimental results show that MetaHipMer matches or outperforms the state-of-the-art tools in terms of accuracy. Moreover, MetaHipMer scales efficiently to large concurrencies and is able to assemble previously intractable grand challenge metagenomes. We demonstrate the unprecedented capability of MetaHipMer by computing the first full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion reads - size 2.6 TBytes.Comment: Accepted to SC1

Simulation of vector boson plus many jet final states at the high luminosity LHC

We present a novel event generation framework for the efficient simulation of vector boson plus multi-jet backgrounds at the high-luminosity LHC and at possible future hadron colliders. MPI parallelization of parton-level and particle-level event generation and storage of parton-level event information using the HDF5 data format allow us to obtain leading-order merged Monte-Carlo predictions with up to nine jets in the final state. The parton-level event samples generated in this manner correspond to an integrated luminosity of 3ab-1 and are made publicly available for future phenomenological studies.Comment: 10 pages, 8 figures, 5 table

Updating collection representations for federated search

To facilitate the search for relevant information across a set of online distributed collections, a federated information retrieval system typically represents each collection, centrally, by a set of vocabularies or sampled documents. Accurate retrieval is therefore related to how precise each representation reflects the underlying content stored in that collection. As collections evolve over time, collection representations should also be updated to reflect any change, however, a current solution has not yet been proposed. In this study we examine both the implications of out-of-date representation sets on retrieval accuracy, as well as proposing three different policies for managing necessary updates. Each policy is evaluated on a testbed of forty-four dynamic collections over an eight-week period. Our findings show that out-of-date representations significantly degrade performance overtime, however, adopting a suitable update policy can minimise this problem

Multiple Retrieval Models and Regression Models for Prior Art Search

This paper presents the system called PATATRAS (PATent and Article Tracking, Retrieval and AnalysiS) realized for the IP track of CLEF 2009. Our approach presents three main characteristics: 1. The usage of multiple retrieval models (KL, Okapi) and term index definitions (lemma, phrase, concept) for the three languages considered in the present track (English, French, German) producing ten different sets of ranked results. 2. The merging of the different results based on multiple regression models using an additional validation set created from the patent collection. 3. The exploitation of patent metadata and of the citation structures for creating restricted initial working sets of patents and for producing a final re-ranking regression model. As we exploit specific metadata of the patent documents and the citation relations only at the creation of initial working sets and during the final post ranking step, our architecture remains generic and easy to extend