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Publicações

Publicações por HASLab

2023

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

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

Publicação
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

Time-limited Bloom Filter

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

Publicação
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

Autores
Fernandes, PH; Baquero, C;

Publicação
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

A Year Embedded in the Crypto-NFT Space

Autores
Baquero, C;

Publicação
COMMUNICATIONS OF THE ACM

Abstract

2023

Consistent comparison of symptom-based methods for COVID-19 infection detection

Autores
Rufino, J; Ramirez, JM; Aguilar, J; Baquero, C; Champati, J; Frey, D; Lillo, RE; Fernandez Anta, A;

Publicação
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.

2023

Efficient Embedding of Strategic Attribute Grammars via Memoization

Autores
Macedo, JN; Rodrigues, E; Viera, M; Saraiva, J;

Publicação
Proceedings of the 2023 ACM SIGPLAN International Workshop on Partial Evaluation and Program Manipulation, PEPM 2023, Boston, MA, USA, January 16-17, 2023

Abstract
Strategic term re-writing and attribute grammars are two powerful programming techniques widely used in language engineering. The former relies on strategies to apply term re-write rules in defining large-scale language transformations, while the latter is suitable to express context-dependent language processing algorithms. These two techniques can be expressed and combined via a powerful navigation abstraction: generic zippers. This results in a concise zipper-based embedding offering the expressiveness of both techniques. Such elegant embedding has a severe limitation since it recomputes attribute values. This paper presents a proper and efficient embedding of both techniques. First, attribute values are memoized in the zipper data structure, thus avoiding their re-computation. Moreover, strategic zipper based functions are adapted to access such memoized values. We have implemented our memoized embedding as the Ztrategic library and we benchmarked it against the state-of-the-art Strafunski and Kiama libraries. Our first results show that we are competitive against those two well established libraries. © 2023 ACM.

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