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Publications

Publications by Carlos Baquero

2023

Using survey data to estimate the impact of the omicron variant on vaccine efficacy against COVID-19 infection

Authors
Rufino, J; Baquero, C; Frey, D; Glorioso, CA; Ortega, A; Rescic, N; Roberts, JC; Lillo, RE; Menezes, R; Champati, JP; Anta, AF;

Publication
SCIENTIFIC REPORTS

Abstract
Symptoms-based detection of SARS-CoV-2 infection is not a substitute for precise diagnostic tests but can provide insight into the likely level of infection in a given population. This study uses symptoms data collected in the Global COVID-19 Trends and Impact Surveys (UMD Global CTIS), and data on variants sequencing from GISAID. This work, conducted in January of 2022 during the emergence of the Omicron variant (subvariant BA.1), aims to improve the quality of infection detection from the available symptoms and to use the resulting estimates of infection levels to assess the changes in vaccine efficacy during a change of dominant variant; from the Delta dominant to the Omicron dominant period. Our approach produced a new symptoms-based classifier, Random Forest, that was compared to a ground-truth subset of cases with known diagnostic test status. This classifier was compared with other competing classifiers and shown to exhibit an increased performance with respect to the ground-truth data. Using the Random Forest classifier, and knowing the vaccination status of the subjects, we then proceeded to analyse the evolution of vaccine efficacy towards infection during different periods, geographies and dominant variants. In South Africa, where the first significant wave of Omicron occurred, a significant reduction of vaccine efficacy is observed from August-September 2021 to December 2021. For instance, the efficacy drops from 0.81 to 0.30 for those vaccinated with 2 doses (of Pfizer/BioNTech), and from 0.51 to 0.09 for those vaccinated with one dose (of Pfizer/BioNTech or Johnson & Johnson). We also extended the study to other countries in which Omicron has been detected, comparing the situation in October 2021 (before Omicron) with that of December 2021. While the reduction measured is smaller than in South Africa, we still found, for instance, an average drop in vaccine efficacy from 0.53 to 0.45 among those vaccinated with two doses. Moreover, we found a significant negative (Pearson) correlation of around - 0.6 between the measured prevalence of Omicron in several countries and the vaccine efficacy in those same countries. This prediction, in January of 2022, of the decreased vaccine efficacy towards Omicron is in line with the subsequent increase of Omicron infections in the first half of 2022.

2022

What Ever Happened to Peer-to-Peer Systems?

Authors
Baquero, C;

Publication
COMMUNICATIONS OF THE ACM

Abstract

2023

Time-limited Bloom Filter

Authors
Rodrigues, A; Shtul, A; Baquero, C; Almeida, PS;

Publication
38TH ANNUAL ACM SYMPOSIUM ON APPLIED COMPUTING, SAC 2023

Abstract
A Bloom Filter is a probabilistic data structure designed to check, rapidly and memory-efficiently, whether an element is present in a set. It has been vastly used in various computing areas and several variants, allowing deletions, dynamic sets and working with sliding windows, have surfaced over the years. When summarizing data streams, it becomes relevant to identify the more recent elements in the stream. However, most of the sliding window schemes consider the most recent items of a data stream without considering time as a factor. While this allows, e.g., storing the most recent 10000 elements, it does not easily translate into storing elements received in the last 60 seconds, unless the insertion rate is stable and known in advance. In this paper, we present the Time-limited Bloom Filter, a new BF-based approach that can save information of a given time period and correctly identify it as present when queried, while also being able to retire data when it becomes stale. The approach supports variable insertion rates while striving to keep a target false positive rate. We also make available a reference implementation of the data structure as a Redis module.

2023

Probabilistic Causal Contexts for Scalable CRDTs

Authors
Fernandes, PH; Baquero, C;

Publication
PROCEEDINGS OF THE 10TH WORKSHOP ON PRINCIPLES AND PRACTICE OF CONSISTENCY FOR DISTRIBUTED DATA, PAPOC 2023

Abstract
Conflict-free Replicated Data Types (CRDTs) are useful to allow a distributed system to operate on data even when partitions occur, and thus preserve operational availability. Most CRDTs need to track whether data evolved concurrently at different nodes and needs to be reconciled; this requires storing causality metadata that is proportional to the number of nodes. In this paper, we try to overcome this limitation by introducing a stochastic mechanism that is no longer linear on the number of nodes, but whose accuracy is now tied to how much divergence occurs between synchronizations. This provides a new tool that can be useful in deployments with many anonymous nodes and frequent synchronizations. However, there is an underlying trade-off with classic deterministic solutions, since the approach is now probabilistic and the accuracy depends on the configurable metadata space size.

2012

Stopping ongoing broadcasts in large MANETs

Authors
Lima, R; Baquero, C; Miranda, H;

Publication
Proceedings of the 1st European Workshop on AppRoaches to MObiquitous Resilience, ARMOR '12, Sibiu, Romania, May 8-11, 2012

Abstract
Broadcast is a communication primitive building block widely used in mobile ad-hoc networks (MANETs) for the exchange of control packets and resource location for upper level services such as routing and management protocols. Flooding is the most simple broadcast algorithm, but it wastes a lot of energy and bandwidth, as flooding leads to many redundant radio transmissions. An optimization to flooding is to contain it, once the resource has been found. In this paper, we compare the impact on the latency and power consumption of four competing approaches for flooding containment. The results show that stopping ongoing broadcasts can achieve promising performance increases over other flooding base techniques, when applied in large scale MANETs with scarce power resources. In addition, results show that both network topology and the number of copies of the resource influence differently the performance of each searching approach. © 2012 ACM.

2010

Genetic Algorithm with Local Search for Community Mining in Complex Networks

Authors
Jin, D; He, DX; Liu, DY; Baquero, C;

Publication
22ND INTERNATIONAL CONFERENCE ON TOOLS WITH ARTIFICIAL INTELLIGENCE (ICTAI 2010), PROCEEDINGS, VOL 1

Abstract
Detecting communities from complex networks has triggered considerable attention in several application domains. Targeting this problem, a local search based genetic algorithm (GALS) which employs a graph-based representation (LAR) has been proposed in this work. The core of the GALS is a local search based mutation technique. Aiming to overcome the drawbacks of the existing mutation methods, a concept called marginal gene has been proposed, and then an effective and efficient mutation method, combined with a local search strategy which is based on the concept of marginal gene, has also been proposed by analyzing the modularity function. Moreover, in this paper the percolation theory on ER random graphs is employed to further clarify the effectiveness of LAR presentation; A Markov random walk based method is adopted to produce an accurate and diverse initial population; the solution space of GALS will be significantly reduced by using a graph based mechanism. The proposed GALS has been tested on both computer-generated and real-world networks, and compared with some competitive community mining algorithms. Experimental result has shown that GALS is highly effective and efficient for discovering community structure.

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