Using Natural Language Processing to Detect Breast Cancer Recurrence in Clinical Notes: A Hierarchical Machine Learning Approach

The vast amount of data amassed in the electronic health records (EHRs) creates needs and opportunities for automated extraction of information from EHRs using machine learning techniques. Natural language processing (NLP) has the potential to substantially reduce the burden of manual chart reviewing to extract risk factors, adverse events, or outcomes, that are documented in unstructured clinical reports and progress notes. In this thesis, an NLP pipeline was built using open-source software to process a corpus of electronic clinical notes extracted from an integrated health care system in Cancer Care Manitoba (CCMB) which contains a cohort of women with early-stage incident breast cancers. The goal is to identify whether and when recurrences were diagnosed. We developed and evaluated the system using 117,365 clinical notes from 892 patients receiving EHR-documented care at CCMB between 2004 to 2007. We used a hierarchical architecture, where a model is built to provide the patient-level recurrence status, then the NLP pipeline is used to detect notes which contains information about recurrence and the date of recurrence. Class imbalance was a significant issue as the proportion of positive to negative notes was at approximately 1:22 ratio. Various techniques including undersampling and cost-based classification were used to mitigate this issue. The XGBoost classifier was the best performing model which achieved a balanced accuracy of 0.924, with sensitivity of 0.867, specificity of 0.981, precision of 0.886 and ROC of 0.924. In addition, more data was collected from the years 2008 to 2012 in a similar cohort. This dataset was used to validate the performance of the models, which include 615 patients with 78,460 notes. The model performed well with a balanced accuracy of 0.909, sensitivity of 0.843, specificity of 0.974, precision of 0.575 and Area Under the ROC Curve (AUC) value of 0.909. The study has demonstrated the ability to use natural language processing and machine learning techniques to assist in chart review by 1) excluding a large amount of notes which contain no relevant information, 2) identifying notes that most likely contain relevant recurrence information, in order to accurately identify the timing of recurrence

Recent Trends in Computational Intelligence

Traditional models struggle to cope with complexity, noise, and the existence of a changing environment, while Computational Intelligence (CI) offers solutions to complicated problems as well as reverse problems. The main feature of CI is adaptability, spanning the fields of machine learning and computational neuroscience. CI also comprises biologically-inspired technologies such as the intellect of swarm as part of evolutionary computation and encompassing wider areas such as image processing, data collection, and natural language processing. This book aims to discuss the usage of CI for optimal solving of various applications proving its wide reach and relevance. Bounding of optimization methods and data mining strategies make a strong and reliable prediction tool for handling real-life applications

Structuring the Unstructured: Unlocking pharmacokinetic data from journals with Natural Language Processing

The development of a new drug is an increasingly expensive and inefficient process. Many drug candidates are discarded due to pharmacokinetic (PK) complications detected at clinical phases. It is critical to accurately estimate the PK parameters of new drugs before being tested in humans since they will determine their efficacy and safety outcomes. Preclinical predictions of PK parameters are largely based on prior knowledge from other compounds, but much of this potentially valuable data is currently locked in the format of scientific papers. With an ever-increasing amount of scientific literature, automated systems are essential to exploit this resource efficiently. Developing text mining systems that can structure PK literature is critical to improving the drug development pipeline. This thesis studied the development and application of text mining resources to accelerate the curation of PK databases. Specifically, the development of novel corpora and suitable natural language processing architectures in the PK domain were addressed. The work presented focused on machine learning approaches that can model the high diversity of PK studies, parameter mentions, numerical measurements, units, and contextual information reported across the literature. Additionally, architectures and training approaches that could efficiently deal with the scarcity of annotated examples were explored. The chapters of this thesis tackle the development of suitable models and corpora to (1) retrieve PK documents, (2) recognise PK parameter mentions, (3) link PK entities to a knowledge base and (4) extract relations between parameter mentions, estimated measurements, units and other contextual information. Finally, the last chapter of this thesis studied the feasibility of the whole extraction pipeline to accelerate tasks in drug development research. The results from this thesis exhibited the potential of text mining approaches to automatically generate PK databases that can aid researchers in the field and ultimately accelerate the drug development pipeline. Additionally, the thesis presented contributions to biomedical natural language processing by developing suitable architectures and corpora for multiple tasks, tackling novel entities and relations within the PK domain

Attention-based Approaches for Text Analytics in Social Media and Automatic Summarization

[ES] Hoy en día, la sociedad tiene acceso y posibilidad de contribuir a grandes cantidades de contenidos presentes en Internet, como redes sociales, periódicos online, foros, blogs o plataformas de contenido multimedia. Todo este tipo de medios han tenido, durante los últimos años, un impacto abrumador en el día a día de individuos y organizaciones, siendo actualmente medios predominantes para compartir, debatir y analizar contenidos online. Por este motivo, resulta de interés trabajar sobre este tipo de plataformas, desde diferentes puntos de vista, bajo el paraguas del Procesamiento del Lenguaje Natural. En esta tesis nos centramos en dos áreas amplias dentro de este campo, aplicadas al análisis de contenido en línea: análisis de texto en redes sociales y resumen automático. En paralelo, las redes neuronales también son un tema central de esta tesis, donde toda la experimentación se ha realizado utilizando enfoques de aprendizaje profundo, principalmente basados en mecanismos de atención. Además, trabajamos mayoritariamente con el idioma español, por ser un idioma poco explorado y de gran interés para los proyectos de investigación en los que participamos. Por un lado, para el análisis de texto en redes sociales, nos enfocamos en tareas de análisis afectivo, incluyendo análisis de sentimientos y detección de emociones, junto con el análisis de la ironía. En este sentido, se presenta un enfoque basado en Transformer Encoders, que consiste en contextualizar \textit{word embeddings} pre-entrenados con tweets en español, para abordar tareas de análisis de sentimiento y detección de ironía. También proponemos el uso de métricas de evaluación como funciones de pérdida, con el fin de entrenar redes neuronales, para reducir el impacto del desequilibrio de clases en tareas \textit{multi-class} y \textit{multi-label} de detección de emociones. Adicionalmente, se presenta una especialización de BERT tanto para el idioma español como para el dominio de Twitter, que tiene en cuenta la coherencia entre tweets en conversaciones de Twitter. El desempeño de todos estos enfoques ha sido probado con diferentes corpus, a partir de varios \textit{benchmarks} de referencia, mostrando resultados muy competitivos en todas las tareas abordadas. Por otro lado, nos centramos en el resumen extractivo de artículos periodísticos y de programas televisivos de debate. Con respecto al resumen de artículos, se presenta un marco teórico para el resumen extractivo, basado en redes jerárquicas siamesas con mecanismos de atención. También presentamos dos instancias de este marco: \textit{Siamese Hierarchical Attention Networks} y \textit{Siamese Hierarchical Transformer Encoders}. Estos sistemas han sido evaluados en los corpora CNN/DailyMail y NewsRoom, obteniendo resultados competitivos en comparación con otros enfoques extractivos coetáneos. Con respecto a los programas de debate, se ha propuesto una tarea que consiste en resumir las intervenciones transcritas de los ponentes, sobre un tema determinado, en el programa "La Noche en 24 Horas". Además, se propone un corpus de artículos periodísticos, recogidos de varios periódicos españoles en línea, con el fin de estudiar la transferibilidad de los enfoques propuestos, entre artículos e intervenciones de los participantes en los debates. Este enfoque muestra mejores resultados que otras técnicas extractivas, junto con una transferibilidad de dominio muy prometedora.[CA] Avui en dia, la societat té accés i possibilitat de contribuir a grans quantitats de continguts presents a Internet, com xarxes socials, diaris online, fòrums, blocs o plataformes de contingut multimèdia. Tot aquest tipus de mitjans han tingut, durant els darrers anys, un impacte aclaparador en el dia a dia d'individus i organitzacions, sent actualment mitjans predominants per compartir, debatre i analitzar continguts en línia. Per aquest motiu, resulta d'interès treballar sobre aquest tipus de plataformes, des de diferents punts de vista, sota el paraigua de l'Processament de el Llenguatge Natural. En aquesta tesi ens centrem en dues àrees àmplies dins d'aquest camp, aplicades a l'anàlisi de contingut en línia: anàlisi de text en xarxes socials i resum automàtic. En paral·lel, les xarxes neuronals també són un tema central d'aquesta tesi, on tota l'experimentació s'ha realitzat utilitzant enfocaments d'aprenentatge profund, principalment basats en mecanismes d'atenció. A més, treballem majoritàriament amb l'idioma espanyol, per ser un idioma poc explorat i de gran interès per als projectes de recerca en els que participem. D'una banda, per a l'anàlisi de text en xarxes socials, ens enfoquem en tasques d'anàlisi afectiu, incloent anàlisi de sentiments i detecció d'emocions, juntament amb l'anàlisi de la ironia. En aquest sentit, es presenta una aproximació basada en Transformer Encoders, que consisteix en contextualitzar \textit{word embeddings} pre-entrenats amb tweets en espanyol, per abordar tasques d'anàlisi de sentiment i detecció d'ironia. També proposem l'ús de mètriques d'avaluació com a funcions de pèrdua, per tal d'entrenar xarxes neuronals, per reduir l'impacte de l'desequilibri de classes en tasques \textit{multi-class} i \textit{multi-label} de detecció d'emocions. Addicionalment, es presenta una especialització de BERT tant per l'idioma espanyol com per al domini de Twitter, que té en compte la coherència entre tweets en converses de Twitter. El comportament de tots aquests enfocaments s'ha provat amb diferents corpus, a partir de diversos \textit{benchmarks} de referència, mostrant resultats molt competitius en totes les tasques abordades. D'altra banda, ens centrem en el resum extractiu d'articles periodístics i de programes televisius de debat. Pel que fa a l'resum d'articles, es presenta un marc teòric per al resum extractiu, basat en xarxes jeràrquiques siameses amb mecanismes d'atenció. També presentem dues instàncies d'aquest marc: \textit{Siamese Hierarchical Attention Networks} i \textit{Siamese Hierarchical Transformer Encoders}. Aquests sistemes s'han avaluat en els corpora CNN/DailyMail i Newsroom, obtenint resultats competitius en comparació amb altres enfocaments extractius coetanis. Pel que fa als programes de debat, s'ha proposat una tasca que consisteix a resumir les intervencions transcrites dels ponents, sobre un tema determinat, al programa "La Noche en 24 Horas". A més, es proposa un corpus d'articles periodístics, recollits de diversos diaris espanyols en línia, per tal d'estudiar la transferibilitat dels enfocaments proposats, entre articles i intervencions dels participants en els debats. Aquesta aproximació mostra millors resultats que altres tècniques extractives, juntament amb una transferibilitat de domini molt prometedora.[EN] Nowadays, society has access, and the possibility to contribute, to large amounts of the content present on the internet, such as social networks, online newspapers, forums, blogs, or multimedia content platforms. These platforms have had, during the last years, an overwhelming impact on the daily life of individuals and organizations, becoming the predominant ways for sharing, discussing, and analyzing online content. Therefore, it is very interesting to work with these platforms, from different points of view, under the umbrella of Natural Language Processing. In this thesis, we focus on two broad areas inside this field, applied to analyze online content: text analytics in social media and automatic summarization. Neural networks are also a central topic in this thesis, where all the experimentation has been performed by using deep learning approaches, mainly based on attention mechanisms. Besides, we mostly work with the Spanish language, due to it is an interesting and underexplored language with a great interest in the research projects we participated in. On the one hand, for text analytics in social media, we focused on affective analysis tasks, including sentiment analysis and emotion detection, along with the analysis of the irony. In this regard, an approach based on Transformer Encoders, based on contextualizing pretrained Spanish word embeddings from Twitter, to address sentiment analysis and irony detection tasks, is presented. We also propose the use of evaluation metrics as loss functions, in order to train neural networks for reducing the impact of the class imbalance in multi-class and multi-label emotion detection tasks. Additionally, a specialization of BERT both for the Spanish language and the Twitter domain, that takes into account inter-sentence coherence in Twitter conversation flows, is presented. The performance of all these approaches has been tested with different corpora, from several reference evaluation benchmarks, showing very competitive results in all the tasks addressed. On the other hand, we focused on extractive summarization of news articles and TV talk shows. Regarding the summarization of news articles, a theoretical framework for extractive summarization, based on siamese hierarchical networks with attention mechanisms, is presented. Also, we present two instantiations of this framework: Siamese Hierarchical Attention Networks and Siamese Hierarchical Transformer Encoders. These systems were evaluated on the CNN/DailyMail and the NewsRoom corpora, obtaining competitive results in comparison to other contemporary extractive approaches. Concerning the TV talk shows, we proposed a text summarization task, for summarizing the transcribed interventions of the speakers, about a given topic, in the Spanish TV talk shows of the ``La Noche en 24 Horas" program. In addition, a corpus of news articles, collected from several Spanish online newspapers, is proposed, in order to study the domain transferability of siamese hierarchical approaches, between news articles and interventions of debate participants. This approach shows better results than other extractive techniques, along with a very promising domain transferability.González Barba, JÁ. (2021). Attention-based Approaches for Text Analytics in Social Media and Automatic Summarization [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/172245TESI