2023
Authors
Frade, MJ; Pinto, JS;
Publication
JOURNAL OF LOGICAL AND ALGEBRAIC METHODS IN PROGRAMMING
Abstract
With the incresasing importance of program verification, an issue that has been receiving more attention is the certification of verification tools, addressing the vernacular question: Who verifies the verifier?. In this paper we approach this meta-verification problem by focusing on a fundamental component of program verifiers: the Verification Conditions Generator (VCGen), responsible for producing a set of proof obligations from a program and a specification. The semantic foundations of VCGens lie in program logics, such as Hoare logic, Dynamic logic, or Separation logic, and related predicate transformers. Dynamic logic is the basis of the KeY system, one of the foremost deductive verifiers, whose logic makes use of the notion of update, which is quite intricate to formalize. In this paper we derive systematically, based on a KeY-style dynamic logic, a correct-by-construction VCGen for a toy programming language. Our workflow covers the entire process, from the logic to the VCGen. It is implemented in the Why3 tool, which is itself a program verifier. We prove the soundness and (an appropriate notion of) completeness of the logic, then define a VCGen for our language and establish its soundness. Dynamic logic is one of a variety of research topics that our dear friend and colleague Luis Soares Barbosa has, over the years, initiated and promoted at the University of Minho. It is a pleasure for us to dedicate this work to him on the occasion of his 60th birthday.
2023
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.
2023
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
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.
2023
Authors
Baquero, C;
Publication
COMMUNICATIONS OF THE ACM
Abstract
2023
Authors
Rufino, J; Ramirez, JM; Aguilar, J; Baquero, C; Champati, J; Frey, D; Lillo, RE; Fernandez Anta, A;
Publication
INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS
Abstract
Background: During the global pandemic crisis, various detection methods of COVID-19-positive cases based on self-reported information were introduced to provide quick diagnosis tools for effectively planning and managing healthcare resources. These methods typically identify positive cases based on a particular combination of symptoms, and they have been evaluated using different datasets.Purpose: This paper presents a comprehensive comparison of various COVID-19 detection methods based on self-reported information using the University of Maryland Global COVID-19 Trends and Impact Survey (UMD-CTIS), a large health surveillance platform, which was launched in partnership with Facebook.Methods: Detection methods were implemented to identify COVID-19-positive cases among UMD-CTIS participants reporting at least one symptom and a recent antigen test result (positive or negative) for six countries and two periods. Multiple detection methods were implemented for three different categories: rule-based approaches, logistic regression techniques, and tree-based machine-learning models. These methods were evaluated using different metrics including F1-score, sensitivity, specificity, and precision. An explainability analysis has also been conducted to compare methods.Results: Fifteen methods were evaluated for six countries and two periods. We identify the best method for each category: rule-based methods (F1-score: 51.48% -71.11%), logistic regression techniques (F1-score: 39.91% -71.13%), and tree-based machine learning models (F1-score: 45.07% -73.72%). According to the explainability analysis, the relevance of the reported symptoms in COVID-19 detection varies between countries and years. However, there are two variables consistently relevant across approaches: stuffy or runny nose, and aches or muscle pain.Conclusions: Regarding the categories of detection methods, evaluating detection methods using homogeneous data across countries and years provides a solid and consistent comparison. An explainability analysis of a tree-based machine-learning model can assist in identifying infected individuals specifically based on their relevant symptoms. This study is limited by the self-report nature of data, which cannot replace clinical diagnosis.
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