MOnitoring Outbreak events for Disease surveillance in a data science context

Rezultaty

Blueprints for epidemiological data collection and management

This deliverable will provide the reference on how to collect, structure, and prepare the data to inputs the models and maps developed in WP4

Risk register

Register with all the risks noted by each WP, at project submission and updated during implementation of the project. It will also consist of a detailed description of the risks, their impact, and suitable preventive and response measures. This document will be updated at M24, M36 and M48.

Project management plan

Report with procedures for providing day-to-day administrative guidance, coordination & troubleshooting for the MOOD consortium partners

Preliminary report on impact and innovation pathway

This report will describe the innovation process and set up the methodology to monitor the impact of the MOOD project through the outcome assessment and the theory of change that is at work Some preliminary results about the KeyPerformance Indicators concerning the first outputs will be given

Scientific report on prototype pathogens and disease profiles

For each selected pathogen and disease, a detailed profile based on the state-of-the-art of the scientific knowledge and knowledge gaps will be produced.

Report on outreach of outcomes

The analysis of the outreach of the outcomes will be based on two crossed sources : a multicriteria evaluation method (OASIS-like survey) to compare end-user practices in the case countries at start and end of the project and a participatory assessment based on narratives of the change and participatory indicators.

Guidelines for consideration of local stakeholders' engagement

The guidelines will be built during and following the workshops with the local stakeholders of the study case in Corsica and Occitanie.

Report on users’ needs

The synthesis of operational needs will be based on the results of the crossed socio-technical analysis of individual interviews, and also the conclusions of the 2 first workshops about the operational problems to solve.

Report on learning loops fostering the utility of social and technical innovations

The lessons learnt from the collective learning of co-conception of tools and services (3 loops) will be summarised.

Standardized datasets (covariate, disease data sets, and pattern linking)

The dataset used within the project and processed according to DL3.1. These data will be stored in a traditional structured database system and made available through this database.

Integration chain (processing algorithms and protocols) for disease datasets

This deliverable will describe the data integration toolchain, including the data processing algorithms and the data exchange protocols that are focused on disease data, associated with Task 3.3 of WP3 and also with implications regarding other tasks (e.g., Tasks 3.1 and 3.4 of WP3). The envisioned toolchain will focus on data standardization and linking between disease and covariate data, according to spatial and temporal dimensions, and combining text-mining, spatial analysis, and semantic approaches. Specifically, the toolchain will ingest and standardize the different types of data, geo-reference the disease data in order for it to be linked to particular covariates, and make the results available for subsequent tasks. Deliverable 3.2 will specifically focus on the tools regarding data integration (e.g., the geo-referencing component), tailored for the processing of disease data.

Linking chain (processing algorithms and protocols) for disease and covariate datasets

The linking task is based on algorithms and processing that will be proposed, implemented and evaluated. These linking algorithms/process need specific features (and set of features) to extract in the disease and covariate data.

MOOD project website and social media

Project website (implemented via a Content Management System) and social media pages and channels including Twitter, , Linkedin, TIB (https://av.tib.eu/), Zenodo.org, and similar. Publication steps, house-style-sheet, and roles and responsibilities will be described in the project manual.

Online materials released in the open-source

Data processing tutorials, good practice documents and technical reports will be released via github (source code) with a copy on zenodo.org using the Github-zenodo webhooks (see e.g. https://doi.org/10.25815/3YZR-1564).

Data management plan

The DMP will detail what data MOOD will generate and how, how it will be curated and preserved, what datasets will be open, whether and how datasets will be exploited or made accessible for verification and re-use. First version delivered at month 6 and updated version at month 18 and 36.

Publikacje

Systematic Review on Crimean–Congo Hemorrhagic Fever Enzootic Cycle and Factors Favoring Virus Transmission: Special Focus on France, an Apparently Free-Disease Area in Europe

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Evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside Hubei province, China: a descriptive and modelling study

Autorzy: Juanjuan Zhang, Maria Litvinova, Wei Wang, Yan Wang, Xiaowei Deng, Xinghui Chen, Mei Li, Wen Zheng, Lan Yi, Xinhua Chen, Qianhui Wu, Yuxia Liang, Xiling Wang, Juan Yang, Kaiyuan Sun, Ira M Longini, M Elizabeth Halloran, Peng Wu, Benjamin J Cowling, Stefano Merler, Cecile Viboud, Alessandro Vespignani, Marco Ajelli, Hongjie Yu
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Relax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST

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Opublikowane w: Molecular Biology and Evolution, Numer Volume 38, Numer 8, August 2021, 2021, Strona(/y) 3486–3493, ISSN 1537-1719
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Epidemic intelligence in Europe: a user needs perspective to foster innovation in digital health surveillance

Autorzy: Fanny Bouyer, Oumy Thiongane, Alexandre Hobeika, Elena Arsevska, Aurélie Binot, Déborah Corrèges, Timothée Dub, Henna Mäkelä, Esther van Kleef, Ferran Jori, Renaud Lancelot, Alize Mercier, Francesca Fagandini, Sarah Valentin, Wim Van Bortel & Claire Ruault
Opublikowane w: BMC Public Health, Numer 24, 973, 2024, ISSN 1471-2458
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Ecological and environmental factors affecting the risk of tick-borne encephalitis in Europe, 2017 to 2021

Autorzy: Francesca Dagostin, Valentina Tagliapietra, Giovanni Marini, Claudia Cataldo, Maria Bellenghi, Scilla Pizzarelli, Rosaria Rosanna Cammarano, William Wint, Neil S Alexander, Markus Neteler, Julia Haas, Timothée Dub, Luca Busani, Annapaola Rizzoli
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Combined Phylogeographic Analyses and Epidemiologic Contact Tracing to Characterize Atypically Pathogenic Avian Influenza (H3N1) Epidemic, Belgium, 2019

Autorzy: Van Borm S, Boseret G, Dellicour S, Steensels M, Roupie V, Vandenbussche F, Mathijs E, Vilain A, Driesen M, Dispas M, Delcloo AW, Lemey P, Mertens I, Gilbert M, Lambrecht B, van den Berg T
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An Evaluation Framework for Comparing Epidemic Intelligence Systems

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icumonitoring.ch: a platform for short-term forecasting of intensive care unit occupancy during the COVID-19 epidemic in Switzerland

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Spatial and temporal dynamics of West Nile virus between Africa and Europe

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Autorzy: Giovanni Marini, Andrea Pugliese, William Wint, Neil S. Alexander, Annapaola Rizzoli, Roberto Rosà
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Projecting the COVID-19 epidemic risk in France for the summer 2021

Autorzy: Mattia Mazzoli, PhD, Eugenio Valdano, PhD, Vittoria Colizza
Opublikowane w: Journal of Travel Medicine, Numer Volume 28, Numer 7, 2021, Strona(/y) aab129, ISSN 1708-8305
Wydawca: International Society of Travel Medicine
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Risk factors for tick attachment in companion animals in Great Britain: a spatiotemporal analysis covering 2014–2021

Autorzy: Elena Arsevska, Tomislav Hengl, David A. Singleton, Peter-John M. Noble, Cyril Caminade, Obiora Eneanya, Philip H. Jones, Kayleigh Hansford, Jolyon Medlock, Carmelo Bonannella, Alan D. Radford
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Planning and adjusting the COVID-19 booster vaccination campaign to reduce disease burden

Autorzy: Laura Di Domenico, Yair Goldberg, Vittoria Colizza
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Evaluating the effect of demographic factors, socioeconomic factors, and risk aversion on mobility during the COVID-19 epidemic in France under lockdown: a population-based study

Autorzy: Giulia Pullano, Eugenio Valdano, Nicola Scarpa, Stefania Rubrichi, Vittoria Colizza
Opublikowane w: The Lancet Digital Health, Numer 2/12, 2020, Strona(/y) e638-e649, ISSN 2589-7500
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Investigating COVID-19 Vaccine Impact on the Risk of Hospitalisation through the Analysis of National Surveillance Data Collected in Belgium

Autorzy: Diana Erazo, Maria F. Vincenti-Gonzalez, Joris A. F. van Loenhout, Pierre Hubin, Mathil Vandromme, Piet Maes, Maxime Taquet, Johan Van Weyenbergh, Lucy Catteau and Simon Dellicour
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Predictive Mapping of Antimicrobial Resistance for Escherichia coli, Salmonella, and Campylobacter in Food-Producing Animals, Europe, 2000–2021

Autorzy: Ranya Mulchandani, Cheng Zhao, Katie Tiseo, João Pires, Thomas Van Boeckel
Opublikowane w: Emerging Infectious Diseases, Numer Volume 30, Number 1, 2024, ISSN 1080-6059
Wydawca: Center for Disease Control and Prevention
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Global patterns and drivers of influenza decline during the COVID-19 pandemic

Autorzy: Francesco Bonacina, Pierre-Yves Boëlle, Vittoria Colizza, Olivier Lopez, Maud Thomas, Chiara Poletto
Opublikowane w: International Journal of Infectious Diseases, Numer January 03, 2023, 2023, ISSN 1878-3511
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PADI-web 3.0: A new framework for extracting and disseminating fine-grained information from the news for animal disease surveillance

Autorzy: Sarah Valentina, Elena Arsevska, Julien Rabatel, Sylvain Falala, Alizé Mercier, Renaud Lancelot, Mathieu Roche
Opublikowane w: One Health, Numer Vol 13, Dec 2021, 2021, Strona(/y) 100357, ISSN 2352-7714
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Autorzy: Mark Zeller, Karthik Gangavarapu, Catelyn Anderson, Allison R. Smither, John A. Vanchiere, Rebecca Rose, Daniel J. Snyder, Gytis Dudas, Alexander Watts, Nathaniel L. Matteson, Refugio Robles-Sikisaka, Maximilian Marshall, Amy K. Feehan, Gilberto Sabino-Santos, Antoinette R. Bell-Kareem, Laura D. Hughes, Manar Alkuzweny, Patricia Snarski, Julia Garcia-Diaz, Rona S. Scott, Lilia I. Melnik, Raphaëll
Opublikowane w: Cell, Numer Volume 184, Numer 19, 2021, 2021, Strona(/y) 4939-4952.e15, ISSN 0092-8674
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GeospatRE: extraction and geocoding of spatial relation entities in textual documents

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Modelling safe protocols for reopening schools during the COVID-19 pandemic in France

Autorzy: Laura Di Domenico, Giulia Pullano, Chiara E. Sabbatini, Pierre-Yves Boëlle, Vittoria Colizza
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A review of models applied to the geographic spread of Zika virus

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Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France

Autorzy: Laura Di Domenico, Chiara E Sabbatini, Giulia Pullano, Daniel Lévy-Bruhl, Vittoria Colizza
Opublikowane w: Eurosurveillance, Numer 26/15, 2021, ISSN 1560-7917
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Contribution of climate change to the spatial expansion of West Nile virus in Europe

Autorzy: Diana Erazo, Luke Grant, Guillaume Ghisbain, Giovanni Marini, Felipe J Colón-González, William Wint, Annapaola Rizzoli, Wim Van Bortel, Chantal B.F. Vogels, Nathan D. Grubaugh, Matthias Mengel, Katja Frieler, Wim Thiery, Simon Dellicour
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Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Among Air Passengers in China

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Opublikowane w: Clinical Infectious Diseases, Numer Volume 75, Numer 1, 1 July 2022, 2022, Strona(/y) Pages e234–e240, ISSN 1058-4838
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Autorzy: Claudia Cataldo, Maria Bellenghi, Roberta Masella, Luca Busani
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SNEToolkit: Spatial named entities disambiguation toolkit

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Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy

Autorzy: Mattia Manica, Giorgio Guzzetta, Flavia Riccardo, Antonio Valenti, Piero Poletti, Valentina Marziano, Filippo Trentini, Xanthi Andrianou, Alberto Mateo-Urdiales, Martina del Manso, Massimo Fabiani, Maria Fenicia Vescio, Matteo Spuri, Daniele Petrone, Antonino Bella, Sergio Iavicoli, Marco Ajelli, Silvio Brusaferro, Patrizio Pezzotti, Stefano Merler
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Screening and vaccination against COVID-19 to minimise school closure: a modelling study

Autorzy: Elisabetta Colosi, Giulia Bassignana, Diego Andrés Contreras, Canelle Poirier, Pierre-Yves Boëlle, Simon Cauchemez, Yazdan Yazdanpanah, Bruno Lina, Arnaud Fontanet, Alain Barrat, Vittoria Colizza
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Epidemic intelligence activities among national public and animal health agencies: a European cross-sectional study

Autorzy: Timothee Dub, Henna Mäkelä, Esther Van Kleef, Agnes Leblond, Alizé Mercier, Viviane Hénaux, Fanny Bouyer, Aurelie Binot, Oumy Thiongane, Renaud Lancelot, Valentina Delconte, Lea Zamuner, Wim Van Bortel & Elena Arsevska
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Model-based evaluation of alternative reactive class closure strategies against COVID-19.

Autorzy: Quan-Hui Liu, Juanjuan Zhang, Cheng Peng, Maria Litvinova, Shudong Huang, Piero Poletti, Filippo Trentini, Giorgio Guzzetta, Valentina Marziano, Tao Zhou, Cecile Viboud, Ana I. Bento, Jiancheng Lv, Alessandro Vespignani, Stefano Merler, Hongjie Yu & Marco Ajelli
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DOI: 10.1038/s41467-021-27939-5

Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy

Autorzy: Giulia Mencattelli, Andrea Silverj, Federica Iapaolo, Carla Ippoliti, Liana Teodori, Annapia Di Gennaro, Valentina Curini, Luca Candeloro, Annamaria Conte, Andrea Polci, Daniela Morelli, Maria Gabriella Perrotta, Giovanni Marini, Roberto Rosà, Federica Monaco, Nicola Segata, Annapaola Rizzoli, Omar Rota-Stabelli, Giovanni Savini and West Nile Working Group
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Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15010035

Epidemiology of West Nile virus in Africa: An underestimated threat

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Autorzy: Manica, Mattia; Litvinova, Maria; De Bellis, Alfredo; Guzzetta, Giorgio; Mancuso, Pamela; Vicentini, Massimo; Venturelli, Francesco; Bisaccia, Eufemia; Bento, Ana I.; Poletti, Piero; Marziano, Valentina; Zardini, Agnese; d'Andrea, Valeria; Trentini, Filippo; Bella, Antonino; Riccardo, Flavia; Pezzotti, Patrizio; Ajelli, Marco; Rossi, Paolo Giorgi; Merler, Stefano; Group, the Reggio Emilia COVID-19
Opublikowane w: arXiv, Numer 2203.07063, 2022, ISSN 2331-8422
Wydawca: Cornell University
DOI: 10.48550/arxiv.2203.07063

Expected impact of school closure and telework to mitigate COVID-19 epidemic in France

Autorzy: Di Domenico L., Pullano G., Sabbatini C.E., Boëlle P-Y., Colizza V.
Opublikowane w: Epicx-lab, report 8, Numer 8, 2020
Wydawca: INSERM

Early assessment of the Omicron variant’s presence and growth rate in regions of France

Autorzy: Mattia Mazzoli, Laura Di Domenico, EMERGEN Consortium, Vittoria Colizza
Opublikowane w: Epicx-lab, report 35, Numer 35, 2021
Wydawca: Inserm

The spatial distribution of Crimean-Congo haemorrhagic fever in Europe and neighbouring areas

Autorzy: Jane Messina, William Wint
Opublikowane w: ECDC technical report, 2023, ISBN 978-92-9498-676-4
Wydawca: European Centre for Disease Prevention and Control
DOI: 10.2900/222576

Epidemic scenarios of Delta variant in France in the summer 2021

Autorzy: Laura Di Domenico, Vittoria Colizza
Opublikowane w: Epicx-lab, report 31, Numer 31, 2021
Wydawca: INSERM

Telework and other measures reducing the presence at work to slow downCOVID-19pdmin France (Sept 2020)

Autorzy: Giulia Pullano, Laura Di Domenico, Vittoria Colizza
Opublikowane w: Epicx-lab, report 16, Numer 16, 2020
Wydawca: INSERM

Mobility during the first week of the second lockdown in France.

Autorzy: Eugenio Valdano, Jonggul Lee, Stefania Rubrichi, Vittoria Colizza
Opublikowane w: Epicx-lab, report 22, Numer 22, 2020
Wydawca: INSERM

Impact of contact data resolution on the evaluation of interventions in mathematical models of infectious diseases

Autorzy: Diego Andrés Contreras; Elisabetta Colosi; Giulia Bassignana; Vittoria Colizza; Alain Barrat
Opublikowane w: Journal of the Royal Society Interface, Numer 20545703, 2022, ISSN 2054-5703
Wydawca: Royal Society open science
DOI: 10.1098/rsif.2022.0164

Spatial modes for transmission of chikungunya virus during a large chikungunya outbreak in Italy: a modeling analysis

Autorzy: Giorgio Guzzetta, Francesco Vairo, Alessia Mammone, Simone Lanini, Piero Poletti, Mattia Manica, Roberto Rosa, Beniamino Caputo, Angelo Solimini, Alessandra Della Torre, Paola Scognamiglio, Alimuddin Zumla, Giuseppe Ippolito, Stefano Merler
Opublikowane w: BMC Medicine, Numer 18/1, 2020, ISSN 1741-7015
Wydawca: BioMed Central
DOI: 10.1186/s12916-020-01674-y

Estimating rodent population abundance using early climatic predictors

Autorzy: Giovanni Marini, Daniele Arnoldi, Annapaola Rizzoli, Valentina Tagliepietra
Opublikowane w: European Journal of Wildlife Research, Numer 69, 36, 2023, ISSN 1612-4642
Wydawca: Springer Verlag
DOI: 10.1007/s10344-023-01666-2

GeoXTag: Relative Spatial Information Extraction and Tagging

Autorzy: Mehtab Alam SYED, Elena ARSEVSKA, Mathieu ROCHE, Maguelonne TEISSEIRE
Opublikowane w: AGILE: GIScience Series, Numer 27008150, 2022, ISSN 2700-8150
Wydawca: AGILE: GIScience Series
DOI: 10.5194/agile-giss-3-16-2022

Feature Selection for Sentiment Classification of COVID-19 Tweets: H-TFIDF Featuring BERT

Autorzy: Syed, M.; Arsevska, E.; Roche, M. and Teisseire, M.
Opublikowane w: Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies - HEALTHINF, 2022, Strona(/y) 648-656, ISSN 2184-4305
Wydawca: Setúbal: SCITEPRESS - Science and Technology Publications
DOI: 10.5220/0010887800003123

How Textual Datasets Enhance the PADI-Web Tool?

Autorzy: Mathieu Roche, Elena Arsevska, Sarah Valentin, Sylvain Falala, Julien Rabatel and Renaud Lancelot
Opublikowane w: Proceedings of the 18th International Conference on Web Information Systems and Technologies, Numer Volume 1, 2022, Strona(/y) 327-331, ISBN 978-989-758-613-2
Wydawca: Science and Technology Publications
DOI: 10.5220/0011590400003318

Quantifying Valence and Arousal in Text with Multilingual Pre-trained Transformers

Autorzy: Mendes, Gonçalo Azevedo; Martins, Bruno
Opublikowane w: arXIV, Numer 2302.14021, 2023, ISSN 2331-8422
Wydawca: Cornell University
DOI: 10.48550/arxiv.2302.14021

Enriching Epidemiological Thematic Features For Disease Surveillance Corpora Classification

Autorzy: Edmond Menya, Mathieu Roche, Roberto Interdonato, Dickson Owuor
Opublikowane w: Proceedings of the Thirteenth Language Resources and Evaluation Conference, Marseille, France, Numer 2022.lrec-1.399, 2022, Strona(/y) 3741–3750, ISBN 979-10-95546-72-6
Wydawca: European Language Resources Association

Automated Processing of Multilingual Online News for the Monitoring of Animal Infectious Diseases

Autorzy: Sarah Valentin, Renaud Lancelot, Mathieu Roche
Opublikowane w: Proceedings of the LREC 2020 Workshop on Multilingual Biomedical Text Processing, 2020, Strona(/y) 33-36, ISBN 2-9517408-6-7
Wydawca: European Language Resources Association

A Data-Driven Score Model to Assess Online News Articles in Event-Based Surveillance System

Autorzy: Alam, S.M., Arsevska, E., Roche, M., Teisseire, M.
Opublikowane w: Computer and Information Science, Numer CCIS,volume 1577, 2022, Strona(/y) 264–280, ISBN 978-3-031-04446-5
Wydawca: Springer
DOI: 10.1007/978-3-031-04447-2_18

A metadata approach to classify domain-specific documents for Event-based Surveillance Systems

Autorzy: M. A. Syed, E. Arsevska, M. Roche and M. Teissere
Opublikowane w: 2023 International Conference on Communication, Computing and Digital Systems (C-CODE), 2023, Strona(/y) 2023, pp. 1-5, ISBN 979-8-3503-3239-1
Wydawca: IEEE
DOI: 10.1109/c-code58145.2023.10139883

PADI-web: an event-based surveillance system for detecting, classifying and processing online news.

Autorzy: Sarah Valentin, Elena Arsevska, Alize Mercier, Sylvain Falala, Julien Rabatel, Renaud Lancelot, Mathieu Roche.
Opublikowane w: Human language technology. Challenges for computer science and linguistics., Numer Language and Technology Conference. 8, Poznan, Pologne, 17 Novembre 2017/19 Novembre 2017, 2020, Strona(/y) 87-101, ISBN 978-3-030-66527-2
Wydawca: Springer
DOI: 10.1007/978-3-030-66527-2_7

Unsupervised Key-Phrase Extraction from Long Texts with Multilingual Sentence Transformers

Autorzy: Dias, H., Guimarães, A., Martins, B., Roche, M
Opublikowane w: Discovery Science 26th International Conference, DS 2023, Porto, Portugal, October 9–11, 2023, Numer vol 14276, 2023, Strona(/y) 141-145, ISBN 978-3-031-45275-8
Wydawca: Springer, Cham
DOI: 10.1007/978-3-031-45275-8_10

A co-training approach for spatial data disaggregation

Autorzy: João Monteiro, Bruno Martins, Miguel Costa, João M. Pires
Opublikowane w: SIGSPATIAL '22: Proceedings of the 30th International Conference on Advances in Geographic Information SystemsNovember 2022 Article No.: 91Pages 1–10https://doi.org/10.1145/3557915.3561475, Numer November 2022 Article No.: 91, 2022, Strona(/y) 1-10, ISSN 1552-5996
Wydawca: Proceedings of the ACM/IEEE Joint Conference on Digital Libraries
DOI: 10.1145/3557915.3561475

Explainable epidemiological thematic features for event based disease surveillance

Autorzy: Edmond Menya, Roberto Interdonato, Dickson Owuor, Mathieu Roche
Opublikowane w: Expert Systems with Applications, Numer Vol 250, 2024, Strona(/y) 123894, ISSN 0957-4174
Wydawca: Elsevier
DOI: 10.1016/j.eswa.2024.123894

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