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Search Results: 1 - 10 of 5641 matches for " Giovanni Manzini "
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Lower bounds for sparse matrix vector multiplication on hypercubic networks
Giovanni Manzini
Discrete Mathematics & Theoretical Computer Science , 1998,
Abstract: In this paper we consider the problem of computing on a local memory machine the product y = Ax,where A is a random n×n sparse matrix with Θ(n) nonzero elements. To study the average case communication cost of this problem, we introduce four different probability measures on the set of sparse matrices. We prove that on most local memory machines with p processors, this computation requires Ω((n/p) log p) time on the average. We prove that the same lower bound also holds, in the worst case, for matrices with only 2n or 3n nonzero elements.
Rigorous drift-diffusion asymptotics of a high-field quantum transport equation
Chiara Manzini,Giovanni Frosali
Mathematics , 2006,
Abstract: The asymptotic analysis of a linear high-field Wigner-BGK equation is developped by a modified Chapman-Enskog procedure. By an expansion of the unknown Wigner function in powers of the Knudsen number $\epsilon$, evolution equations are derived for the terms of zeroth and first order in $\epsilon$. In particular, it is obtained a quantum drift-diffusion equation for the position density, which is corrected by field-dependent terms of order $\epsilon$. Well-posedness and regularity of the approximate problems are established, and it is proved that the difference between exact and asymptotic solutions is of order $\epsilon ^2$, uniformly in time and for arbitrary initial data.
Lightweight Data Indexing and Compression in External Memory
Paolo Ferragina,Travis Gagie,Giovanni Manzini
Computer Science , 2009,
Abstract: In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use only ${n}$ bits of disk working space while all previous approaches use $\Th{n \log n}$ bits of disk working space. Moreover, our algorithms access disk data only via sequential scans, thus they take full advantage of modern disk features that make sequential disk accesses much faster than random accesses. We also present a scan-based algorithm for inverting the BWT that uses $\Th{n}$ bits of working space, and a lightweight {\em internal-memory} algorithm for computing the BWT which is the fastest in the literature when the available working space is $\os{n}$ bits. Finally, we prove {\em lower} bounds on the complexity of computing and inverting the BWT via sequential scans in terms of the classic product: internal-memory space $\times$ number of passes over the disk data.
Compressed Spaced Suffix Arrays
Travis Gagie,Giovanni Manzini,Daniel Valenzuela
Computer Science , 2013,
Abstract: Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data structure, either a hash table or a spaced suffix array (SSA). In this paper we show how to compress SSAs relative to normal suffix arrays (SAs) and still support fast random access to them. We first prove a theoretical upper bound on the space needed to store an SSA when we already have the SA. We then present experiments indicating that our approach works even better in practice.
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment
Paolo Ferragina, Raffaele Giancarlo, Valentina Greco, Giovanni Manzini, Gabriel Valiente
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-252
Abstract: We experimentally test the USM methodology by using 25 compressors, all three of its known approximations and six data sets of relevance to Molecular Biology. This offers the first systematic and quantitative experimental assessment of this methodology, that naturally complements the many theoretical and the preliminary experimental results available. Moreover, we compare the USM methodology both with methods based on alignments and not. We may group our experiments into two sets. The first one, performed via ROC (Receiver Operating Curve) analysis, aims at assessing the intrinsic ability of the methodology to discriminate and classify biological sequences and structures. A second set of experiments aims at assessing how well two commonly available classification algorithms, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and NJ (Neighbor Joining), can use the methodology to perform their task, their performance being evaluated against gold standards and with the use of well known statistical indexes, i.e., the F-measure and the partition distance. Based on the experiments, several conclusions can be drawn and, from them, novel valuable guidelines for the use of USM on biological data. The main ones are reported next.UCD and NCD are indistinguishable, i.e., they yield nearly the same values of the statistical indexes we have used, accross experiments and data sets, while CD is almost always worse than both. UPGMA seems to yield better classification results with respect to NJ, i.e., better values of the statistical indexes (10% difference or above), on a substantial fraction of experiments, compressors and USM approximation choices. The compression program PPMd, based on PPM (Prediction by Partial Matching), for generic data and Gencompress for DNA, are the best performers among the compression algorithms we have used, although the difference in performance, as measured by statistical indexes, between them and the other algorithms depends critically on the
A Decision-Support System for the Car Pooling Problem  [PDF]
Riccardo Manzini, Arrigo Pareschi
Journal of Transportation Technologies (JTTs) , 2012, DOI: 10.4236/jtts.2012.22011
Abstract: The continuous increase of human mobility combined with a relevant use of private vehicles contributes to increase the ill effects of vehicle externalities on the environment, e.g. high levels of air pollution, toxic emissions, noise pollution, and on the quality of life, e.g. parking problem, traffic congestion, and increase in the number of crashes and accidents. Transport demand management plays a very critical role in achieving greenhouse gas emission reduction targets. This study demonstrates that car pooling (CP) is an effective strategy to reduce transport volumes, transportation costs and related hill externalities in agreement with EU programs of emissions reduction targets. This paper presents an original approach to solve the CP problem. It is based on hierarchical clustering models, which have been adopted by an original decision support system (DSS). The DSS helps mobility managers to generate the pools and to design feasible paths for shared vehicles. A significant case studies and obtained results by the application of the proposed models are illustrated. They demonstrate the effectiveness of the approach and the supporting decisions tool.
Relative Select
Christina Boucher,Alexander Bowe,Travis Gagie,Giovanni Manzini,Jouni Sirén
Computer Science , 2015,
Abstract: Motivated by the problem of storing coloured de Bruijn graphs, we show how, if we can already support fast select queries on one string, then we can store a little extra information and support fairly fast select queries on a similar string.
Reusing an FM-index
Djamal Belazzougui,Travis Gagie,Simon Gog,Giovanni Manzini,Jouni Sirén
Computer Science , 2014,
Abstract: Intuitively, if two strings $S_1$ and $S_2$ are sufficiently similar and we already have an FM-index for $S_1$ then, by storing a little extra information, we should be able to reuse parts of that index in an FM-index for $S_2$. We formalize this intuition and show that it can lead to significant space savings in practice, as well as to some interesting theoretical problems.
Manzini,Jorge Luis;
Acta bioethica , 2005, DOI: 10.4067/S1726-569X2005000200009
Abstract: this paper pretends to draw a brief review upon the ethical aspects of a prescription at a "micro" level, that is of the therapeutic relationship based on the georgetown "theory of principles" and on the technical aspects of a correct prescription according to the lex artis, sustained on the so-called "evidence based medicine" and on the who's requests and publications. it then turns to the subject of the medical prescription as a problem of public health. it stops at its social impact and at the undue pressures that doctors must suffer in order to prescribe, especially those coming from the pharmaceutical industry. it also offers a juridical framework focused on the human rights' international law. universal access to medication should be reached -understood as a social good of fundamental importance- in order to attain the right to sanitary assistance. several ethical justifications that hold up this right are taken into account, especially rawls' theory of justice
Manzini,Jorge Luis;
Acta bioethica , 2000, DOI: 10.4067/S1726-569X2000000200010
Abstract: this paper consists in a particularised analysis of the declaration of helsinki, revised at the 52nd wma general assembly at edinburgh in october 2000. the framework was as follows: 1) an introduction to the subject 2) a general consideration about formal and substantial aspects of the changes 3) a detailed analysis of every modified article, be it a change or an addition; and the comparison, when appropiate, between the spanish and the english versions of the declaration. this plan was developed by means of xxv "commentaries" interpolated along the transcription of the declaration, as was available from the wma website, http://www.wma.net/s/helsinki.html, on november 28, 2000. the phrases and paragraphs analysed are identified by means of different printing characters for the modified and new pieces, and the english version. the analysis was made from a bioethical perspective, especially regarding human rights concerns, as well as considering the scientific issues of medical research, including the viewpoint of evidence based medicine. conclusions: 1) all of the amendments strengthen the declaration, advocating for higher respect for the human rights of research subjects. 2) a further revision of the formal aspects (language) of the spanish version would be advisable, because of its many punctual weaknesses and ambiguities, as compared with the english version
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