Analysis of COVID-related symptoms from a database of Italian tweets

Twitter is a highly popular social media which on one hand allows information transmission in real time and on the other hand represents a source of open access homogeneous text data. We propose an analysis of the most common self-reported COVID symptoms from a dataset of Italian tweets to investigate the evolution of the pandemic in Italy from the end of September 2020 to the end of January 2021. After manually filtering tweets actually describing COVID symptoms from the database - which contains words related to fever, cough and sore throat - we discuss usefulness of such filtering. We then compare our time series with the daily data of new hospitalisations in Italy, with the aim of building a simple linear regression model that accounts for the delay which is observed from the tweets mentioning individual symptoms to new hospitalisations. We discuss both the results and limitations of linear regression given that our data suggests that the relationship between time series of symptoms tweets and of new hospitalisations changes towards the end of the acquisition.

Structured Approaches for Exploring Interpersonal Relationships in Natural Language Text

Human relationships have long been studied by scientists from domains like sociology, psychology, literature, etc. for understanding people's desires, goals, actions and expected behaviors. In this dissertation we study inter-personal relationships as expressed in natural language text. Modeling inter-personal relationships from text finds application in general natural language understanding, as well as real-world domains such as social networks, discussion forums, intelligent virtual agents, etc. We propose that the study of relationships should incorporate not only linguistic cues in text, but also the contexts in which these cues appear. Our investigations, backed by empirical evaluation, support this thesis, and demonstrate that the task benefits from using structured models that incorporate both types of information. We present such structured models to address the task of modeling the nature of relationships between any two given characters from a narrative. To begin with, we assume that relationships are of two types: cooperative and non-cooperative. We first describe an approach to jointly infer relationships between all characters in the narrative, and demonstrate how the task of characterizing the relationship between two characters can benefit from including information about their relationships with other characters in the narrative. We next formulate the relationship-modeling problem as a sequence prediction task to acknowledge the evolving nature of human relationships, and demonstrate the need to model the history of a relationship in predicting its evolution. Thereafter, we present a data-driven method to automatically discover various types of relationships such as familial, romantic, hostile, etc. Like before, we address the task of modeling evolving relationships but don't restrict ourselves to two types of relationships. We also demonstrate the need to incorporate not only local historical but also global context while solving this problem. Lastly, we demonstrate a practical application of modeling inter-personal relationships in the domain of online educational discussion forums. Such forums offer opportunities for its users to interact and form deeper relationships. With this view, we address the task of identifying initiation of such deeper relationships between a student and the instructor. Specifically, we analyze contents of the forums to automatically suggest threads to the instructors that require their intervention. By highlighting scenarios that need direct instructor-student interactions, we alleviate the need for the instructor to manually peruse all threads of the forum and also assist students who have limited avenues for communicating with instructors. We do this by incorporating the discourse structure of the thread through latent variables that abstractly represent contents of individual posts and model the flow of information in the thread. Such latent structured models that incorporate the linguistic cues without losing their context can be helpful in other related natural language understanding tasks as well. We demonstrate this by using the model for a very different task: identifying if a stated desire has been fulfilled by the end of a story.

Traduction statistique vers une langue à morphologie riche : combinaison d’algorithmes de segmentation morphologique et de modèles statistiques de traduction automatique

Les systèmes statistiques de traduction automatique ont pour tâche la traduction d’une langue source vers une langue cible. Dans la plupart des systèmes de traduction de référence, l'unité de base considérée dans l'analyse textuelle est la forme telle qu’observée dans un texte. Une telle conception permet d’obtenir une bonne performance quand il s'agit de traduire entre deux langues morphologiquement pauvres. Toutefois, ceci n'est plus vrai lorsqu’il s’agit de traduire vers une langue morphologiquement riche (ou complexe). Le but de notre travail est de développer un système statistique de traduction automatique comme solution pour relever les défis soulevés par la complexité morphologique. Dans ce mémoire, nous examinons, dans un premier temps, un certain nombre de méthodes considérées comme des extensions aux systèmes de traduction traditionnels et nous évaluons leurs performances. Cette évaluation est faite par rapport aux systèmes à l’état de l’art (système de référence) et ceci dans des tâches de traduction anglais-inuktitut et anglais-finnois. Nous développons ensuite un nouvel algorithme de segmentation qui prend en compte les informations provenant de la paire de langues objet de la traduction. Cet algorithme de segmentation est ensuite intégré dans le modèle de traduction à base d’unités lexicales « Phrase-Based Models » pour former notre système de traduction à base de séquences de segments. Enfin, nous combinons le système obtenu avec des algorithmes de post-traitement pour obtenir un système de traduction complet. Les résultats des expériences réalisées dans ce mémoire montrent que le système de traduction à base de séquences de segments proposé permet d’obtenir des améliorations significatives au niveau de la qualité de la traduction en terme de le métrique d’évaluation BLEU (Papineni et al., 2002) et qui sert à évaluer. Plus particulièrement, notre approche de segmentation réussie à améliorer légèrement la qualité de la traduction par rapport au système de référence et une amélioration significative de la qualité de la traduction est observée par rapport aux techniques de prétraitement de base (baseline).

Descriptive Text Mining in ambito medico: applicazione della metodologia POIROT

Poiché la nostra conoscenza collettiva continua ad essere digitalizzata e memorizzata, diventa più difficile trovare e scoprire ciò che stiamo cercando. Abbiamo bisogno di nuovi strumenti computazionali per aiutare a organizzare, rintracciare e comprendere queste vaste quantità di informazioni. I modelli di linguaggio sono potenti strumenti che possono essere impiegati per estrarre conoscenza statisticamente significativa ed interpretabile tramite apprendimento non supervisionato, testuali o nel codice sorgente. L’obiettivo di questa tesi è impiegare una metodologia di descriptive text mining, denominata POIROT, per analizzare i rapporti medici del dataset Adverse Drug Reaction (ADE). Si vogliono stabilire delle correlazioni significative che permettano di comprendere le ragioni per cui un determinato rapporto medico fornisca o meno informazioni relative a effetti collaterali dovuti all’assunzione di determinati farmaci.

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.

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.

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

Using Machine Learning Classifiers to Assist Healthcare-Related Decisions: Classification of Electronic Patient Records

Surveillance Levels (SLs) are categories for medical patients (used in Brazil) that represent different types of medical recommendations. SLs are defined according to risk factors and the medical and developmental history of patients. Each SL is associated with specific educational and clinical measures. The objective of the present paper was to verify computer-aided, automatic assignment of SLs. The present paper proposes a computer-aided approach for automatic recommendation of SLs. The approach is based on the classification of information from patient electronic records. For this purpose, a software architecture composed of three layers was developed. The architecture is formed by a classification layer that includes a linguistic module and machine learning classification modules. The classification layer allows for the use of different classification methods, including the use of preprocessed, normalized language data drawn from the linguistic module. We report the verification and validation of the software architecture in a Brazilian pediatric healthcare institution. The results indicate that selection of attributes can have a great effect on the performance of the system. Nonetheless, our automatic recommendation of surveillance level can still benefit from improvements in processing procedures when the linguistic module is applied prior to classification. Results from our efforts can be applied to different types of medical systems. The results of systems supported by the framework presented in this paper may be used by healthcare and governmental institutions to improve healthcare services in terms of establishing preventive measures and alerting authorities about the possibility of an epidemic.

Shallow Dialogue Processing Using Machine Learning Algorithms (or not)

This paper presents a shallow dialogue analysis model, aimed at human-human dialogues in the context of staff or business meetings. Four components of the model are defined, and several machine learning techniques are used to extract features from dialogue transcripts: maximum entropy classifiers for dialogue acts, latent semantic analysis for topic segmentation, or decision tree classifiers for discourse markers. A rule-based approach is proposed for solving cross-modal references to meeting documents. The methods are trained and evaluated thanks to a common data set and annotation format. The integration of the components into an automated shallow dialogue parser opens the way to multimodal meeting processing and retrieval applications.

Técnicas de machine learning para la detección de la negación en textos clínicos en español

En los últimos años han surgido nuevos campos de las tecnologías de la información que exploran el tratamiento de la gran cantidad de datos digitales existentes y cómo transformarlos en conocimiento explícito. Las técnicas de Procesamiento del Lenguaje Natural (NLP) son capaces de extraer información de los textos digitales presentados en forma narrativa. Además, las técnicas de machine learning clasifican instancias o ejemplos en función de sus atributos, en distintas categorías, aprendiendo de otros previamente clasificados. Los textos clínicos son una gran fuente de información no estructurada; en consecuencia, información no explotada en su totalidad. Algunos términos usados en textos clínicos se encuentran en una situación de afirmación, negación, hipótesis o histórica. La detección de esta situación es necesaria para la estructuración de información, pero a su vez tiene una gran complejidad. Extrayendo características lingüísticas de los elementos, o tokens, de los textos mediante NLP; transformando estos tokens en instancias y las características en atributos, podemos mediante técnicas de machine learning clasificarlos con el objetivo de detectar si se encuentran afirmados, negados, hipotéticos o históricos. La selección de los atributos que cada token debe tener para su clasificación, así como la selección del algoritmo de machine learning utilizado son elementos cruciales para la clasificación. Son, de hecho, los elementos que componen el modelo de clasificación. Consecuentemente, este trabajo aborda el proceso de extracción de características, selección de atributos y selección del algoritmo de machine learning para la detección de la negación en textos clínicos en español. Se expone un modelo para la clasificación que, mediante el algoritmo J48 y 35 atributos obtenidos de características lingüísticas (morfológicas y sintácticas) y disparadores de negación, detecta si un token está negado en 465 frases provenientes de textos clínicos con un F-Score del 73%, una exhaustividad del 66% y una precisión del 81% con una validación cruzada de 10 iteraciones. ---ABSTRACT--- New information technologies have emerged in the recent years which explore the processing of the huge amount of existing digital data and its transformation into knowledge. Natural Language Processing (NLP) techniques are able to extract certain features from digital texts. Additionally, through machine learning techniques it is feasible to classify instances according to different categories, learning from others previously classified. Clinical texts contain great amount of unstructured data, therefore information not fully exploited. Some terms (tokens) in clinical texts appear in different situations such as affirmed, negated, hypothetic or historic. Detecting this situation is necessary for the structuring of this data, however not simple. It is possible to detect whether if a token is negated, affirmed, hypothetic or historic by extracting its linguistic features by NLP; transforming these tokens into instances, the features into attributes, and classifying these instances through machine learning techniques. Selecting the attributes each instance must have, and choosing the machine learning algorithm are crucial issues for the classification. In fact, these elements set the classification model. Consequently, this work approaches the features retrieval as well as the attributes and algorithm selection process used by machine learning techniques for the detection of negation in clinical texts in Spanish. We present a classification model which, through J48 algorithm and 35 attributes from linguistic features (morphologic and syntactic) and negation triggers, detects whether if a token is negated in 465 sentences from historical records, with a result of 73% FScore, 66% recall and 81% precision using a 10-fold cross-validation.

The aid of machine learning to overcome the classification of real health discharge reports written in Spanish

Hospitals attached to the Spanish Ministry of Health are currently using the International Classification of Diseases 9 Clinical Modification (ICD9-CM) to classify health discharge records. Nowadays, this work is manually done by experts. This paper tackles the automatic classification of real Discharge Records in Spanish following the ICD9-CM standard. The challenge is that the Discharge Records are written in spontaneous language. We explore several machine learning techniques to deal with the classification problem. Random Forest resulted in the most competitive one, achieving an F-measure of 0.876.

Automatically Extracting Procedural Knowledge from Instructional Texts using Natural Language Processing

Procedural knowledge is the knowledge required to perform certain tasks, and forms an important part of expertise. A major source of procedural knowledge is natural language instructions. While these readable instructions have been useful learning resources for human, they are not interpretable by machines. Automatically acquiring procedural knowledge in machine interpretable formats from instructions has become an increasingly popular research topic due to their potential applications in process automation. However, it has been insufficiently addressed. This paper presents an approach and an implemented system to assist users to automatically acquire procedural knowledge in structured forms from instructions. We introduce a generic semantic representation of procedures for analysing instructions, using which natural language techniques are applied to automatically extract structured procedures from instructions. The method is evaluated in three domains to justify the generality of the proposed semantic representation as well as the effectiveness of the implemented automatic system.

Machine learning classification of surgical pathology reports and chunk recognition for information extraction noise reduction

Background and aims: Machine learning techniques for the text mining of cancer-related clinical documents have not been sufficiently explored. Here some techniques are presented for the pre-processing of free-text breast cancer pathology reports, with the aim of facilitating the extraction of information relevant to cancer staging.

Materials and methods: The first technique was implemented using the freely available software RapidMiner to classify the reports according to their general layout: ‘semi-structured’ and ‘unstructured’. The second technique was developed using the open source language engineering framework GATE and aimed at the prediction of chunks of the report text containing information pertaining to the cancer morphology, the tumour size, its hormone receptor status and the number of positive nodes. The classifiers were trained and tested respectively on sets of 635 and 163 manually classified or annotated reports, from the Northern Ireland Cancer Registry.

Results: The best result of 99.4% accuracy – which included only one semi-structured report predicted as unstructured – was produced by the layout classifier with the k nearest algorithm, using the binary term occurrence word vector type with stopword filter and pruning. For chunk recognition, the best results were found using the PAUM algorithm with the same parameters for all cases, except for the prediction of chunks containing cancer morphology. For semi-structured reports the performance ranged from 0.97 to 0.94 and from 0.92 to 0.83 in precision and recall, while for unstructured reports performance ranged from 0.91 to 0.64 and from 0.68 to 0.41 in precision and recall. Poor results were found when the classifier was trained on semi-structured reports but tested on unstructured.

Conclusions: These results show that it is possible and beneficial to predict the layout of reports and that the accuracy of prediction of which segments of a report may contain certain information is sensitive to the report layout and the type of information sought.

A Machine Learning Analysis of Twitter Sentiment to the Sandy Hook Shootings

Gun related violence is a complex issue and accounts for a large proportion of violent incidents. In the research reported in this paper, we set out to investigate the pro-gun and anti-gun sentiments expressed on a social media platform, namely Twitter, in response to the 2012 Sandy Hook Elementary School shooting in Connecticut, USA. Machine learning techniques are applied to classify a data corpus of over 700,000 tweets. The sentiments are captured using a public sentiment score that considers the volume of tweets as well as population. A web-based interactive tool is developed to visualise the sentiments and is available at this http://www.gunsontwitter.com. The key findings from this research are: (i) There are elevated rates of both pro-gun and anti-gun sentiments on the day of the shooting. Surprisingly, the pro-gun sentiment remains high for a number of days following the event but the anti-gun sentiment quickly falls to pre-event levels. (ii) There is a different public response from each state, with the highest pro-gun sentiment not coming from those with highest gun ownership levels but rather from California, Texas and New York.