arXiv subjects

Alexandre P. Francisco

Publications and source records attributed to Alexandre P. Francisco.

26 records · Page 2Linked to original sources

arXiv2019

VeilGraph: Streaming Graph Approximations

Graphs are found in a plethora of domains, including online social networks, the World Wide Web and the study of epidemics, to name a few. With the advent of greater volumes of information and the need for continuously updated results under temporal constraints, it is necessary to explore novel approaches that further enable performance improvements. In the scope of stream processing over graphs, we research the trade-offs between result accuracy and the speedup of approximate computation techniques. We see this as a natural path towards these performance improvements. Herein we present \name, through which we conducted our research. We showcase an innovative model for approximate graph processing, implemented in \texttt{Apache Flink}. We analyze our model and evaluate it with the case study of the PageRank algorithm \cite{pageRank}, perhaps the most famous measure of vertex centrality used to rank websites in search engine results. %In light of our model, we discuss the challenges driven by relations between result accuracy and potential performance gains. Our experiments, even when set up for favoring \texttt{Flink} for comparability, show that \name can improve performance up to 3X speedups, while achieving result quality above 95\% when compared to results of the traditional version of PageRank without any summarization or approximation techniques.

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arXiv2019

On dynamic succinct graph representations

We address the problem of representing dynamic graphs using $k^2$-trees. The $k^2$-tree data structure is one of the succinct data structures proposed for representing static graphs, and binary relations in general. It relies on compact representations of bit vectors. Hence, by relying on compact representations of dynamic bit vectors, we can also represent dynamic graphs. In this paper we follow instead the ideas by Munro {\em et al.}, and we present an alternative implementation for representing dynamic graphs using $k^2$-trees. Our experimental results show that this new implementation is competitive in practice.

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arXiv2019

Order-Preserving Pattern Matching Indeterminate Strings

Given an indeterminate string pattern $p$ and an indeterminate string text $t$, the problem of order-preserving pattern matching with character uncertainties ($μ$OPPM) is to find all substrings of $t$ that satisfy one of the possible orderings defined by $p$. When the text and pattern are determinate strings, we are in the presence of the well-studied exact order-preserving pattern matching (OPPM) problem with diverse applications on time series analysis. Despite its relevance, the exact OPPM problem suffers from two major drawbacks: 1) the inability to deal with indetermination in the text, thus preventing the analysis of noisy time series; and 2) the inability to deal with indetermination in the pattern, thus imposing the strict satisfaction of the orders among all pattern positions. This paper provides the first polynomial algorithm to answer the $μ$OPPM problem when indetermination is observed on the pattern or text. Given two strings with length $m$ and $O(r)$ uncertain characters per string position, we show that the $μ$OPPM problem can be solved in $O(mr\lg r)$ time when one string is indeterminate and $r\in\mathbb{N}^+$. Mappings into satisfiability problems are provided when indetermination is observed on both the pattern and the text, and results concerning the general problem complexity are presented as well, with $μ$OPPM problem proved to be NP-hard in general.

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arXiv2018

Exploiting Computation-Friendly Graph Compression Methods

Computing the product of the (binary) adjacency matrix of a large graph with a real-valued vector is an important operation that lies at the heart of various graph analysis tasks, such as computing PageRank. In this paper we show that some well-known Web and social graph compression formats are computation-friendly, in the sense that they allow boosting the computation. In particular, we show that the format of Boldi and Vigna allows computing the product in time proportional to the compressed graph size. Our experimental results show speedups of at least 2 on graphs that were compressed at least 5 times with respect to the original. We show that other successful graph compression formats enjoy this property as well.

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arXiv2018

Gelly-Scheduling: Distributed Graph Processing for Network Service Placement in Community Networks

Community networks (CNs) have seen an increase in the last fifteen years. Their members contact nodes which operate Internet proxies, web servers, user file storage and video streaming services, to name a few. Detecting communities of nodes with properties (such as co-location) and assessing node eligibility for service placement is thus a key-factor in optimizing the experience of users. We present a novel solution for the problem of service placement as a two-phase approach, based on: 1) community finding using a scalable graph label propagation technique and 2) a decentralized election procedure to address the multi-objective challenge of optimizing service placement in CNs. Herein we: i) highlight the applicability of leader election heuristics which are important for service placement in community networks and scheduler-dependent scenarios; ii) present a parallel and distributed solution designed as a scalable alternative for the problem of service placement, which has mostly seen computational approaches based on centralization and sequential execution.

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arXiv2017

Study on Resource Efficiency of Distributed Graph Processing

Graphs may be used to represent many different problem domains -- a concrete example is that of detecting communities in social networks, which are represented as graphs. With big data and more sophisticated applications becoming widespread in recent years, graph processing has seen an emergence of requirements pertaining data volume and volatility. This multidisciplinary study presents a review of relevant distributed graph processing systems. Herein they are presented in groups defined by common traits (distributed processing paradigm, type of graph operations, among others), with an overview of each system's strengths and weaknesses. The set of systems is then narrowed down to a set of two, upon which quantitative analysis was performed. For this quantitative comparison of systems, focus was cast on evaluating the performance of algorithms for the problem of detecting communities. To help further understand the evaluations performed, a background is provided on graph clustering.

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arXiv2016

Beyond NGS data sharing and towards open science

Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the following is true for many areas of science: published results are usually hard to reproduce either because data is not available or tools are not readily available, which delays the adoption of new methodologies and hinders innovation. Our focus is on tool readiness and pipelines availability. Even though most tools are freely available, pipelines for data analysis are in general barely described and their configuration is far from trivial, with many parameters to be tuned. In this paper we discuss how to effectively build and use pipelines, relying on state of the art computing technologies to execute them without users need to configure, install and manage tools, servers and complex workflow management systems. We perform an in depth comparative analysis of state of the art frameworks and systems. The NGSPipes framework is proposed showing that we can have public pipelines ready to process and analyse experimental data, produced for instance by high-throughput technologies, but without relying on centralized servers or Web services. The NGSPipes framework and underlying architecture provides a major step towards open science and true collaboration in what concerns tools and pipelines among computational biology researchers and practitioners. We show that it is possible to execute data analysis pipelines in a decentralized and platform independent way. Approaches like the one proposed are crucial for archiving and reusing data analysis pipelines at medium/long-term. NGSPipes framework is freely available at http://ngspipes.github.io/.

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arXiv2012

Quick HyperVolume

We present a new algorithm to calculate exact hypervolumes. Given a set of $d$-dimensional points, it computes the hypervolume of the dominated space. Determining this value is an important subroutine of Multiobjective Evolutionary Algorithms (MOEAs). We analyze the "Quick Hypervolume" (QHV) algorithm theoretically and experimentally. The theoretical results are a significant contribution to the current state of the art. Moreover the experimental performance is also very competitive, compared with existing exact hypervolume algorithms. A full description of the algorithm is currently submitted to IEEE Transactions on Evolutionary Computation.

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