Data surveillance for infectious diseases: models, complex networks and machine learning

In this thesis, we investigate the role of applied physics in epidemiological surveillance through the application of mathematical models, network science and machine learning. The spread of a communicable disease depends on many biological, social, and health factors. The large masses of data available make it possible, on the one hand, to monitor the evolution and spread of pathogenic organisms; on the other hand, to study the behavior of people, their opinions and habits. Presented here are three lines of research in which an attempt was made to solve real epidemiological problems through data analysis and the use of statistical and mathematical models. In Chapter 1, we applied language-inspired Deep Learning models to transform influenza protein sequences into vectors encoding their information content. We then attempted to reconstruct the antigenic properties of different viral strains using regression models and to identify the mutations responsible for vaccine escape. In Chapter 2, we constructed a compartmental model to describe the spread of a bacterium within a hospital ward. The model was informed and validated on time series of clinical measurements, and a sensitivity analysis was used to assess the impact of different control measures. Finally (Chapter 3) we reconstructed the network of retweets among COVID-19 themed Twitter users in the early months of the SARS-CoV-2 pandemic. By means of community detection algorithms and centrality measures, we characterized users’ attention shifts in the network, showing that scientific communities, initially the most retweeted, lost influence over time to national political communities. In the Conclusion, we highlighted the importance of the work done in light of the main contemporary challenges for epidemiological surveillance. In particular, we present reflections on the importance of nowcasting and forecasting, the relationship between data and scientific research, and the need to unite the different scales of epidemiological surveillance.

Advancing digital healthcare research and machine learning-aided knowledge extraction amidst the COVID-19 pandemic

The rapid progression of biomedical research coupled with the explosion of scientific literature has generated an exigent need for efficient and reliable systems of knowledge extraction. This dissertation contends with this challenge through a concentrated investigation of digital health, Artificial Intelligence, and specifically Machine Learning and Natural Language Processing's (NLP) potential to expedite systematic literature reviews and refine the knowledge extraction process. The surge of COVID-19 complicated the efforts of scientists, policymakers, and medical professionals in identifying pertinent articles and assessing their scientific validity. This thesis presents a substantial solution in the form of the COKE Project, an initiative that interlaces machine reading with the rigorous protocols of Evidence-Based Medicine to streamline knowledge extraction. In the framework of the COKE (“COVID-19 Knowledge Extraction framework for next-generation discovery science”) Project, this thesis aims to underscore the capacity of machine reading to create knowledge graphs from scientific texts. The project is remarkable for its innovative use of NLP techniques such as a BERT + bi-LSTM language model. This combination is employed to detect and categorize elements within medical abstracts, thereby enhancing the systematic literature review process. The COKE project's outcomes show that NLP, when used in a judiciously structured manner, can significantly reduce the time and effort required to produce medical guidelines. These findings are particularly salient during times of medical emergency, like the COVID-19 pandemic, when quick and accurate research results are critical.

Predire la borsa valori con language model neurali

Nonostante lo scetticismo di molti studiosi circa la possibilità di prevedere l'andamento della borsa valori, esistono svariate teorie ipotizzanti la possibilità di utilizzare le informazioni conosciute per predirne i movimenti futuri. L’avvento dell’intelligenza artificiale nella seconda parte dello scorso secolo ha permesso di ottenere risultati rivoluzionari in svariati ambiti, tanto che oggi tale disciplina trova ampio impiego nella nostra vita quotidiana in molteplici forme. In particolare, grazie al machine learning, è stato possibile sviluppare sistemi intelligenti che apprendono grazie ai dati, riuscendo a modellare problemi complessi. Visto il successo di questi sistemi, essi sono stati applicati anche all’arduo compito di predire la borsa valori, dapprima utilizzando i dati storici finanziari della borsa come fonte di conoscenza, e poi, con la messa a punto di tecniche di elaborazione del linguaggio naturale umano (NLP), anche utilizzando dati in linguaggio naturale, come il testo di notizie finanziarie o l’opinione degli investitori. Questo elaborato ha l’obiettivo di fornire una panoramica sull’utilizzo delle tecniche di machine learning nel campo della predizione del mercato azionario, partendo dalle tecniche più elementari per arrivare ai complessi modelli neurali che oggi rappresentano lo stato dell’arte. Vengono inoltre formalizzati il funzionamento e le tecniche che si utilizzano per addestrare e valutare i modelli di machine learning, per poi effettuare un esperimento in cui a partire da dati finanziari e soprattutto testuali si tenterà di predire correttamente la variazione del valore dell’indice di borsa S&P 500 utilizzando un language model basato su una rete neurale.

Graph-based Vision-Language Model for Multi-Modal Retrieval of Fashion Products

Artificial Intelligence is reshaping the field of fashion industry in different ways. E-commerce retailers exploit their data through AI to enhance their search engines, make outfit suggestions and forecast the success of a specific fashion product. However, it is a challenging endeavour as the data they possess is huge, complex and multi-modal. The most common way to search for fashion products online is by matching keywords with phrases in the product's description which are often cluttered, inadequate and differ across collections and sellers. A customer may also browse an online store's taxonomy, although this is time-consuming and doesn't guarantee relevant items. With the advent of Deep Learning architectures, particularly Vision-Language models, ad-hoc solutions have been proposed to model both the product image and description to solve this problems. However, the suggested solutions do not exploit effectively the semantic or syntactic information of these modalities, and the unique qualities and relations of clothing items. In this work of thesis, a novel approach is proposed to address this issues, which aims to model and process images and text descriptions as graphs in order to exploit the relations inside and between each modality and employs specific techniques to extract syntactic and semantic information. The results obtained show promising performances on different tasks when compared to the present state-of-the-art deep learning architectures.

NLG-Metricverse: An End-to-End Library for Evaluating Natural Language Generation

Driven by recent deep learning breakthroughs, natural language generation (NLG) models have been at the center of steady progress in the last few years. However, since our ability to generate human-indistinguishable artificial text lags behind our capacity to assess it, it is paramount to develop and apply even better automatic evaluation metrics. To facilitate researchers to judge the effectiveness of their models broadly, we suggest NLG-Metricverse—an end-to-end open-source library for NLG evaluation based on Python. This framework provides a living collection of NLG metrics in a unified and easy- to-use environment, supplying tools to efficiently apply, analyze, compare, and visualize them. This includes (i) the extensive support of heterogeneous automatic metrics with n-arity management, (ii) the meta-evaluation upon individual performance, metric-metric and metric-human correlations, (iii) graphical interpretations for helping humans better gain score intuitions, (iv) formal categorization and convenient documentation to accelerate metrics understanding. NLG-Metricverse aims to increase the comparability and replicability of NLG research, hopefully stimulating new contributions in the area.

Ecological Literacy And Beyond: Problem-based Learning For Future Professionals.

Ecological science contributes to solving a broad range of environmental problems. However, lack of ecological literacy in practice often limits application of this knowledge. In this paper, we highlight a critical but often overlooked demand on ecological literacy: to enable professionals of various careers to apply scientific knowledge when faced with environmental problems. Current university courses on ecology often fail to persuade students that ecological science provides important tools for environmental problem solving. We propose problem-based learning to improve the understanding of ecological science and its usefulness for real-world environmental issues that professionals in careers as diverse as engineering, public health, architecture, social sciences, or management will address. Courses should set clear learning objectives for cognitive skills they expect students to acquire. Thus, professionals in different fields will be enabled to improve environmental decision-making processes and to participate effectively in multidisciplinary work groups charged with tackling environmental issues.

FORMAÇÕES DISCURSIVAS E PROCESSOS IDENTIFICATÓRIOS NA AQUISIÇÃO DE LÍNGUAS

This paper discusses theoretical results of the research project Linguistic Identity and Identification: A Study of Functions of Second Language in Enunciating Subject Constitution. Non-cognitive factors that have a crucial incidence in the degree of success and ways of accomplishment of second language acquisition process are focused. A transdisciplinary perspective is adopted, mobilising categories from Discourse Analysis and Psychoanalysis. The most relevant ones are: discursive formation, intradiscourse, interdiscourse, forgetting n° 1, forgetting n° 2 (Pêcheux, 1982), identity, identification (Freud, 1966; Lacan, 1977; Nasio, 1995). Revuz s views (1991) are discussed. Her main claim is that during the process of learning a foreign language, the foundations of psychical structure, and consequently first language, are required. After examining how nomination and predication processes work in first and second languages, components of identity and identification processes are focused on, in an attempt to show how second language acquisition strategies depend on them. It is stated that methodological affairs of language teaching, learner s explicit motivation and the like are subordinated to the comprehension of deeper non-cognitive factors that determine the accomplishment of the second language acquisition process. It is also pointed out that those factors are to be approached, questioning the bipolar biological-social conception of subjectivity in the study of language acquisition and use and including in the analysis symbolic and significant dimensions of the discourse constitution process.

A COMPETÊNCIA LEXICAL DE ALUNOS UNIVERSITÁRIOS APRENDENDO A LER EM INGLÊS COMO LÍNGUA ESTRANGEIRA

This article presents a characterization of the lexical competence (vocabulary knowledge and use) of students learning to read in EFL in a public university in São Paulo state. Although vocabulary has been consistently cited as one of the EFL reader´s main source of difficulty, there is no data in the literature which shows the extent of the difficulties. The data for this study is part of a previous research, which investigates, from the perspective of an interactive model of reading, the relationship between lexical competence and EFL reading comprehension. Quantitative as well as qualitative data was considered. For this study, the quantitative data is the product of vocabulary tests of 49 subjects while the qualitative data comprises pause protocols of three subjects, with levels of reading ability ranging from good to poor, selected upon their performance in the quantitative study. A rich concept of vocabulary knowledge was adapted and used for the development of vocabulary tests and analysis of protocols. The results on both studies show, with a few exceptions, the lexical competence of the group to be vague and imprecise in two dimensions: quantitative (number of known words or vocabulary size) and qualitative (depth or width of this knowledge). Implications for the teaching of reading in a foreign context are discussed.

Resonancias discursivas y cortesía en prácticas de lecto-escritura

In this paper we present a study of reading comprehension based on a contrastive argumentative-discursive approach. We examine the relationship between linguistic materiality and discursive processes, observing the connection between reading in a foreign language, writing production and textual memories in the mother tongue. In addition to an interest in practical language teaching and learning processes (in this case of Spanish and Portuguese), we investigate the question of politeness and the theoretical relationship between subjectivity, language, and textuality. The latter, being understood as the result of discourse regularities, is unique for each and every production, yet is also conditioned by plural discursive memories resulting from contradictory social relationships in a specific historical context (Foucault, 1986; Pêcheux, 1990). In the experiment presented here, we follow some of the procedures of the methodology applied in the European Galatea Project developed for the study of reading strategies in the inter-comprehension between Romance languages (Dabène, 1996). We use the procedure of simulation and the subjective projection of participants as well as the notion of discursive resonance in the analysis. The results, having to do with directness and indirectness in speech and the question of politeness in two typologically close languages, lead to the conclusion that the concept of politeness goes beyond a pragmatic strategy used to avoid conflicts to be approached as a marker of cultural identity constitution. The relevance of discursive awareness and its theoretical and practical consequences are then emphasized.

As relações entre saber e poder em testes psicodiagnósticos a partir de M. Foucault

In this article my main objective is to approach some questions related to the tests used in psychodiagnostics processes of children who are considered as having learning difficulties. Having the book Discipline and Punish (1975/1986) by Foucault as theoretical basis, I intend to investigate the hypothesis that the child is considered ill or abnormal due to the factors related to imposed norms and not to organic aspects and/or neurological pathology. My interest is to analyse the signs that allow us to point out the written language conception of tests. This language is expected and privileged, however it may not be the language that the child uses and experiences every day.

O papel da interação no processo de ensino-aprendizagem de português para alunos surdos em uma escola inclusiva

In this article, it is discussed the role of interaction in the process of teaching and learning Portuguese of deaf students at an inclusive school. In the context where the research took place, the hearing teacher does not understand sign language, and there are, in her classroom, hearing students and four deaf students, being three of them sign language users. As the communication between the hearing teacher and the deaf students occurred in different codes - Portuguese and Brazilian sign language - and having a social-interactional approach of language (MOITA LOPES, 1986; FREIRE, 1999), we observed if the interaction among the subjects enabled the deaf students to understand what was being taught. The results showed that the fact of having four deaf students in the same classroom allowed them to work in a cooperative way. Besides, the sign language became more visible in this institution. On the other hand, the interaction between the teacher and her deaf students revealed to be of little significance to the learning process of this small group.

A língua inglesa no ensino fundamentl I público: diálogos com Bakhtin por uma formação plurilíngue

This article aims at discussing the contributions of the Bakhtinian Circle theories to foreign language teaching and learning (HALL et al., 2005), as far as the first years of formal education in Brazil are concerned. Up to the present moment, foreign languages, including English, are not officially part of the National Curriculum of the first five schooling years. Due to the importance of English in a globalized world and despite all the controversial socio-educational impacts of such an influence, there has been an increase in the interest in this discipline at the beginning years of Brazilian public education (ROCHA, 2006), which has been happening at an irregular pace and without official parameters. Therefore, the relevance of this work lies on the possible guidelines it may offer to support a more effective, situated and meaningful teaching-learning process in that context. Standing for a pluralistic approach to language education, we take the bakhtinian speech genres as organizers of the educational process. We strongly believe that through a dialogic, pluralistic and trans/intercultural teaching (MAHER, 2007), whose main objective is the development of multi (COPE e KALANTZIS, 2000) and critical (COMBER, 2006) literacies, the hybridization of genres and cultures, as well as the creation of third spaces (KOSTOGRIZ, 2005; KUMARAVADIVELU, 2008) can happen. From this perspective, foreign language teaching and learning play a transformative role in society and English is seen as a boundary object (STAR e GRIESEMER, 1989), in and by which diversity, pluralism and polyphony can naturally find their way.

As dimensões da linguagem em livros didáticos de inglês para o Ensino Fundamental I

This article aims at discussing and articulating views of language under sociocultural, dialogic and discourse perspectives, in order to present a theoretical framework as far as the analysis of textbooks of English as a foreign language for the Brazilian Ensino Fundamental I is concerned. Due to the limited number of studies in this field, to the still considerably structural approach of the English language teaching and learning in our country nowadays and to the important mediation role textbooks play in language education, we believe our work can contribute positively to the construction of critical and multiple literacies, which, in turn, can support an active and transformative educacional process in the present times.

Flicker perimetry in healthy subjects: influence of age and gender, learning effect and short-term fluctuation

PURPOSE: To determine the mean critical fusion frequency and the short-term fluctuation, to analyze the influence of age, gender, and the learning effect in healthy subjects undergoing flicker perimetry. METHODS: Study 1 - 95 healthy subjects underwent flicker perimetry once in one eye. Mean critical fusion frequency values were compared between genders, and the influence of age was evaluated using linear regression analysis. Study 2 - 20 healthy subjects underwent flicker perimetry 5 times in one eye. The first 3 sessions were separated by an interval of 1 to 30 days, whereas the last 3 sessions were performed within the same day. The first 3 sessions were used to investigate the presence of a learning effect, whereas the last 3 tests were used to calculate short-term fluctuation. RESULTS: Study 1 - Linear regression analysis demonstrated that mean global, foveal, central, and critical fusion frequency per quadrant significantly decreased with age (p<0.05).There were no statistically significant differences in mean critical fusion frequency values between males and females (p>0.05), with the exception of the central area and inferonasal quadrant (p=0.049 and p=0.011, respectively), where the values were lower in females. Study 2 - Mean global (p=0.014), central (p=0.008), and peripheral (p=0.03) critical fusion frequency were significantly lower in the first session compared to the second and third sessions. The mean global short-term fluctuation was 5.06±1.13 Hz, the mean interindividual and intraindividual variabilities were 11.2±2.8% and 6.4±1.5%, respectively. CONCLUSION: This study suggests that, in healthy subjects, critical fusion frequency decreases with age, that flicker perimetry is associated with a learning effect, and that a moderately high short-term fluctuation is expected.