Robust input representations for low-resource information extraction

Recent advances in the field of natural language processing were achieved with deep learning models. This led to a wide range of new research questions concerning the stability of such large-scale systems and their applicability beyond well-studied tasks and datasets, such as information extraction in non-standard domains and languages, in particular, in low-resource environments. In this work, we address these challenges and make important contributions across fields such as representation learning and transfer learning by proposing novel model architectures and training strategies to overcome existing limitations, including a lack of training resources, domain mismatches and language barriers. In particular, we propose solutions to close the domain gap between representation models by, e.g., domain-adaptive pre-training or our novel meta-embedding architecture for creating a joint representations of multiple embedding methods. Our broad set of experiments demonstrates state-of-the-art performance of our methods for various sequence tagging and classification tasks and highlight their robustness in challenging low-resource settings across languages and domains.Die jüngsten Fortschritte auf dem Gebiet der Verarbeitung natürlicher Sprache wurden mit Deep-Learning-Modellen erzielt. Dies führte zu einer Vielzahl neuer Forschungsfragen bezüglich der Stabilität solcher großen Systeme und ihrer Anwendbarkeit über gut untersuchte Aufgaben und Datensätze hinaus, wie z. B. die Informationsextraktion für Nicht-Standardsprachen, aber auch Textdomänen und Aufgaben, für die selbst im Englischen nur wenige Trainingsdaten zur Verfügung stehen. In dieser Arbeit gehen wir auf diese Herausforderungen ein und leisten wichtige Beiträge in Bereichen wie Repräsentationslernen und Transferlernen, indem wir neuartige Modellarchitekturen und Trainingsstrategien vorschlagen, um bestehende Beschränkungen zu überwinden, darunter fehlende Trainingsressourcen, ungesehene Domänen und Sprachbarrieren. Insbesondere schlagen wir Lösungen vor, um die Domänenlücke zwischen Repräsentationsmodellen zu schließen, z.B. durch domänenadaptives Vortrainieren oder unsere neuartige Meta-Embedding-Architektur zur Erstellung einer gemeinsamen Repräsentation mehrerer Embeddingmethoden. Unsere umfassende Evaluierung demonstriert die Leistungsfähigkeit unserer Methoden für verschiedene Klassifizierungsaufgaben auf Word und Satzebene und unterstreicht ihre Robustheit in anspruchsvollen, ressourcenarmen Umgebungen in verschiedenen Sprachen und Domänen

Contributions to information extraction for spanish written biomedical text

285 p.Healthcare practice and clinical research produce vast amounts of digitised, unstructured data in multiple languages that are currently underexploited, despite their potential applications in improving healthcare experiences, supporting trainee education, or enabling biomedical research, for example. To automatically transform those contents into relevant, structured information, advanced Natural Language Processing (NLP) mechanisms are required. In NLP, this task is known as Information Extraction. Our work takes place within this growing field of clinical NLP for the Spanish language, as we tackle three distinct problems. First, we compare several supervised machine learning approaches to the problem of sensitive data detection and classification. Specifically, we study the different approaches and their transferability in two corpora, one synthetic and the other authentic. Second, we present and evaluate UMLSmapper, a knowledge-intensive system for biomedical term identification based on the UMLS Metathesaurus. This system recognises and codifies terms without relying on annotated data nor external Named Entity Recognition tools. Although technically naive, it performs on par with more evolved systems, and does not exhibit a considerable deviation from other approaches that rely on oracle terms. Finally, we present and exploit a new corpus of real health records manually annotated with negation and uncertainty information: NUBes. This corpus is the basis for two sets of experiments, one on cue andscope detection, and the other on assertion classification. Throughout the thesis, we apply and compare techniques of varying levels of sophistication and novelty, which reflects the rapid advancement of the field

Adversarial content manipulation for analyzing and improving model robustness

The recent rapid progress in machine learning systems has opened up many real-world applications --- from recommendation engines on web platforms to safety critical systems like autonomous vehicles. A model deployed in the real-world will often encounter inputs far from its training distribution. For example, a self-driving car might come across a black stop sign in the wild. To ensure safe operation, it is vital to quantify the robustness of machine learning models to such out-of-distribution data before releasing them into the real-world. However, the standard paradigm of benchmarking machine learning models with fixed size test sets drawn from the same distribution as the training data is insufficient to identify these corner cases efficiently. In principle, if we could generate all valid variations of an input and measure the model response, we could quantify and guarantee model robustness locally. Yet, doing this with real world data is not scalable. In this thesis, we propose an alternative, using generative models to create synthetic data variations at scale and test robustness of target models to these variations. We explore methods to generate semantic data variations in a controlled fashion across visual and text modalities. We build generative models capable of performing controlled manipulation of data like changing visual context, editing appearance of an object in images or changing writing style of text. Leveraging these generative models we propose tools to study robustness of computer vision systems to input variations and systematically identify failure modes. In the text domain, we deploy these generative models to improve diversity of image captioning systems and perform writing style manipulation to obfuscate private attributes of the user. Our studies quantifying model robustness explore two kinds of input manipulations, model-agnostic and model-targeted. The model-agnostic manipulations leverage human knowledge to choose the kinds of changes without considering the target model being tested. This includes automatically editing images to remove objects not directly relevant to the task and create variations in visual context. Alternatively, in the model-targeted approach the input variations performed are directly adversarially guided by the target model. For example, we adversarially manipulate the appearance of an object in the image to fool an object detector, guided by the gradients of the detector. Using these methods, we measure and improve the robustness of various computer vision systems -- specifically image classification, segmentation, object detection and visual question answering systems -- to semantic input variations.Der schnelle Fortschritt von Methoden des maschinellen Lernens hat viele neue Anwendungen ermöglicht – von Recommender-Systemen bis hin zu sicherheitskritischen Systemen wie autonomen Fahrzeugen. In der realen Welt werden diese Systeme oft mit Eingaben außerhalb der Verteilung der Trainingsdaten konfrontiert. Zum Beispiel könnte ein autonomes Fahrzeug einem schwarzen Stoppschild begegnen. Um sicheren Betrieb zu gewährleisten, ist es entscheidend, die Robustheit dieser Systeme zu quantifizieren, bevor sie in der Praxis eingesetzt werden. Aktuell werden diese Modelle auf festen Eingaben von derselben Verteilung wie die Trainingsdaten evaluiert. Allerdings ist diese Strategie unzureichend, um solche Ausnahmefälle zu identifizieren. Prinzipiell könnte die Robustheit “lokal” bestimmt werden, indem wir alle zulässigen Variationen einer Eingabe generieren und die Ausgabe des Systems überprüfen. Jedoch skaliert dieser Ansatz schlecht zu echten Daten. In dieser Arbeit benutzen wir generative Modelle, um synthetische Variationen von Eingaben zu erstellen und so die Robustheit eines Modells zu überprüfen. Wir erforschen Methoden, die es uns erlauben, kontrolliert semantische Änderungen an Bild- und Textdaten vorzunehmen. Wir lernen generative Modelle, die kontrollierte Manipulation von Daten ermöglichen, zum Beispiel den visuellen Kontext zu ändern, die Erscheinung eines Objekts zu bearbeiten oder den Schreibstil von Text zu ändern. Basierend auf diesen Modellen entwickeln wir neue Methoden, um die Robustheit von Bilderkennungssystemen bezüglich Variationen in den Eingaben zu untersuchen und Fehlverhalten zu identifizieren. Im Gebiet von Textdaten verwenden wir diese Modelle, um die Diversität von sogenannten Automatische Bildbeschriftung-Modellen zu verbessern und Schreibtstil-Manipulation zu erlauben, um private Attribute des Benutzers zu verschleiern. Um die Robustheit von Modellen zu quantifizieren, werden zwei Arten von Eingabemanipulationen untersucht: Modell-agnostische und Modell-spezifische Manipulationen. Modell-agnostische Manipulationen basieren auf menschlichem Wissen, um bestimmte Änderungen auszuwählen, ohne das entsprechende Modell miteinzubeziehen. Dies beinhaltet das Entfernen von für die Aufgabe irrelevanten Objekten aus Bildern oder Variationen des visuellen Kontextes. In dem alternativen Modell-spezifischen Ansatz werden Änderungen vorgenommen, die für das Modell möglichst ungünstig sind. Zum Beispiel ändern wir die Erscheinung eines Objekts um ein Modell der Objekterkennung täuschen. Dies ist durch den Gradienten des Modells möglich. Mithilfe dieser Werkzeuge können wir die Robustheit von Systemen zur Bildklassifizierung oder -segmentierung, Objekterkennung und Visuelle Fragenbeantwortung quantifizieren und verbessern

Multi-Stage Transfer Learning for Lung Segmentation Using Portable X-Ray Devices for Patients With COVID-19

[Abstract] One of the main challenges in times of sanitary emergency is to quickly develop computer aided diagnosis systems with a limited number of available samples due to the novelty, complexity of the case and the urgency of its implementation. This is the case during the current pandemic of COVID-19. This pathogen primarily infects the respiratory system of the afflicted, resulting in pneumonia and in a severe case of acute respiratory distress syndrome. This results in the formation of different pathological structures in the lungs that can be detected by the use of chest X-rays. Due to the overload of the health services, portable X-ray devices are recommended during the pandemic, preventing the spread of the disease. However, these devices entail different complications (such as capture quality) that, together with the subjectivity of the clinician, make the diagnostic process more difficult and suggest the necessity for computer-aided diagnosis methodologies despite the scarcity of samples available to do so. To solve this problem, we propose a methodology that allows to adapt the knowledge from a well-known domain with a high number of samples to a new domain with a significantly reduced number and greater complexity. We took advantage of a pre-trained segmentation model from brain magnetic resonance imaging of a unrelated pathology and performed two stages of knowledge transfer to obtain a robust system able to segment lung regions from portable X-ray devices despite the scarcity of samples and lesser quality. This way, our methodology obtained a satisfactory accuracy of 0.9761 ± 0.0100 for patients with COVID-19, 0.9801 ± 0.0104 for normal patients and 0.9769 ± 0.0111 for patients with pulmonary diseases with similar characteristics as COVID-19 (such as pneumonia) but not genuine COVID-19.Xunta de Galicia; ED431C 2020/24Xunta de Galicia; IN845D 2020/38Xunta de Galicia; ED431G 2019/01This research was funded by Instituto de Salud Carlos III, Government of Spain, DTS18/00136 research project; Ministerio de Ciencia e Innovación y Universidades, Government of Spain, RTI2018-095894-B-I00 research project, Ayudas para la formación de profesorado universitario (FPU), grant Ref. FPU18/02271; Ministerio de Ciencia e Innovación, Government of Spain through the research project with reference PID2019-108435RB-I00; Consellería de Cultura, Educación e Universidade, Xunta de Galicia, Grupos de Referencia Competitiva, grant Ref. ED431C 2020/24; Axencia Galega de Innovación (GAIN), Xunta de Galicia, grant Ref. IN845D 2020/38; CITIC, as Research Center accredited by Galician University System, is funded by “Consellería de Cultura, Educación e Universidade from Xunta de Galicia”, supported in an 80% through ERDF Funds, ERDF Operational Programme Galicia 2014-2020, and the remaining 20% by “Secretaría Xeral de Universidades” (Grant ED431G 2019/01)

Data Science and Knowledge Discovery

Data Science (DS) is gaining significant importance in the decision process due to a mix of various areas, including Computer Science, Machine Learning, Math and Statistics, domain/business knowledge, software development, and traditional research. In the business field, DS's application allows using scientific methods, processes, algorithms, and systems to extract knowledge and insights from structured and unstructured data to support the decision process. After collecting the data, it is crucial to discover the knowledge. In this step, Knowledge Discovery (KD) tasks are used to create knowledge from structured and unstructured sources (e.g., text, data, and images). The output needs to be in a readable and interpretable format. It must represent knowledge in a manner that facilitates inferencing. KD is applied in several areas, such as education, health, accounting, energy, and public administration. This book includes fourteen excellent articles which discuss this trending topic and present innovative solutions to show the importance of Data Science and Knowledge Discovery to researchers, managers, industry, society, and other communities. The chapters address several topics like Data mining, Deep Learning, Data Visualization and Analytics, Semantic data, Geospatial and Spatio-Temporal Data, Data Augmentation and Text Mining

Towards Orthographic and Grammatical Clinical Text Correction: a First Approach

Akats Gramatikalen Zuzenketa (GEC, ingelesetik, Grammatical Error Analysis) Hizkuntza Naturalaren Prozesamenduaren azpieremu bat da, ortogra a, puntuazio edo gramatika akatsak dituzten testuak automatikoki zuzentzea helburu duena. Orain arte, bigarren hizkuntzako ikasleek ekoitzitako testuetara bideratu da gehien bat, ingelesez idatzitako testuetara batez ere. Master-Tesi honetan gaztelaniaz idatzitako mediku-txostenetarako Akats Gramatikalen Zuzenketa lantzen da. Arlo espezi ko hau ez da asko esploratu orain arte, ez gaztelaniarako zentzu orokorrean, ezta domeinu klinikorako konkretuki ere. Hasteko, IMEC (gaztelaniatik, Informes Médicos en Español Corregidos) corpusa aurkezten da, eskuz zuzendutako mediku-txosten elektronikoen bilduma paralelo berria. Corpusa automatikoki etiketatu da zeregin honetarako egokitutako ERRANT tresna erabiliz. Horrez gain, hainbat esperimentu deskribatzen dira, zeintzuetan sare neuronaletan oinarritutako sistemak ataza honetarako diseinatutako baseline sistema batekin alderatzen diren.Grammatical Error Correction (GEC) is a sub field of Natural Language Processing that aims to automatically correct texts that include errors related to spelling, punctuation or grammar. So far, it has mainly focused on texts produced by second language learners, mostly in English. This Master's Thesis describes a first approach to Grammatical Error Correction for Spanish health records. This specific field has not been explored much until now, nor in Spanish in a general sense nor for the clinical domain specifically. For this purpose, the corpus IMEC (Informes Médicos en Español Corregidos) ---a manually-corrected parallel collection of Electronic Health Records--- is introduced. This corpus has been automatically annotated using the toolkit ERRANT, specialized in the automatic annotation of GEC parallel corpora, which was adapted to Spanish for this task. Furthermore, some experiments using neural networks and data augmentation are shown and compared with a baseline system also created specifically for this task

Multiparametric Magnetic Resonance Imaging Artificial Intelligence Pipeline for Oropharyngeal Cancer Radiotherapy Treatment Guidance

Oropharyngeal cancer (OPC) is a widespread disease and one of the few domestic cancers that is rising in incidence. Radiographic images are crucial for assessment of OPC and aid in radiotherapy (RT) treatment. However, RT planning with conventional imaging approaches requires operator-dependent tumor segmentation, which is the primary source of treatment error. Further, OPC expresses differential tumor/node mid-RT response (rapid response) rates, resulting in significant differences between planned and delivered RT dose. Finally, clinical outcomes for OPC patients can also be variable, which warrants the investigation of prognostic models. Multiparametric MRI (mpMRI) techniques that incorporate simultaneous anatomical and functional information coupled to artificial intelligence (AI) approaches could improve clinical decision support for OPC by providing immediately actionable clinical rationale for adaptive RT planning. If tumors could be reproducibly segmented, rapid response could be classified, and prognosis could be reliably determined, overall patient outcomes would be optimized to improve the therapeutic index as a function of more risk-adapted RT volumes. Consequently, there is an unmet need for automated and reproducible imaging which can simultaneously segment tumors and provide predictive value for actionable RT adaptation. This dissertation primarily seeks to explore and optimize image processing, tumor segmentation, and patient outcomes in OPC through a combination of advanced imaging techniques and AI algorithms. In the first specific aim of this dissertation, we develop and evaluate mpMRI pre-processing techniques for use in downstream segmentation, response prediction, and outcome prediction pipelines. Various MRI intensity standardization and registration approaches were systematically compared and benchmarked. Moreover, synthetic image algorithms were developed to decrease MRI scan time in an effort to optimize our AI pipelines. We demonstrated that proper intensity standardization and image registration can improve mpMRI quality for use in AI algorithms, and developed a novel method to decrease mpMRI acquisition time. Subsequently, in the second specific aim of this dissertation, we investigated underlying questions regarding the implementation of RT-related auto-segmentation. Firstly, we quantified interobserver variability for an unprecedented large number of observers for various radiotherapy structures in several disease sites (with a particular emphasis on OPC) using a novel crowdsourcing platform. We then trained an AI algorithm on a series of extant matched mpMRI datasets to segment OPC primary tumors. Moreover, we validated and compared our best model\u27s performance to clinical expert observers. We demonstrated that AI-based mpMRI OPC tumor auto-segmentation offers decreased variability and comparable accuracy to clinical experts, and certain mpMRI input channel combinations could further improve performance. Finally, in the third specific aim of this dissertation, we predicted OPC primary tumor mid-therapy (rapid) treatment response and prognostic outcomes. Using co-registered pre-therapy and mid-therapy primary tumor manual segmentations of OPC patients, we generated and characterized treatment sensitive and treatment resistant pre-RT sub-volumes. These sub-volumes were used to train an AI algorithm to predict individual voxel-wise treatment resistance. Additionally, we developed an AI algorithm to predict OPC patient progression free survival using pre-therapy imaging from an international data science competition (ranking 1st place), and then translated these approaches to mpMRI data. We demonstrated AI models could be used to predict rapid response and prognostic outcomes using pre-therapy imaging, which could help guide treatment adaptation, though further work is needed. In summary, the completion of these aims facilitates the development of an image-guided fully automated OPC clinical decision support tool. The resultant deliverables from this project will positively impact patients by enabling optimized therapeutic interventions in OPC. Future work should consider investigating additional imaging timepoints, imaging modalities, uncertainty quantification, perceptual and ethical considerations, and prospective studies for eventual clinical implementation. A dynamic version of this dissertation is publicly available and assigned a digital object identifier through Figshare (doi: 10.6084/m9.figshare.22141871)

Safeguarding Privacy Through Deep Learning Techniques

Over the last few years, there has been a growing need to meet minimum security and privacy requirements. Both public and private companies have had to comply with increasingly stringent standards, such as the ISO 27000 family of standards, or the various laws governing the management of personal data. The huge amount of data to be managed has required a huge effort from the employees who, in the absence of automatic techniques, have had to work tirelessly to achieve the certification objectives. Unfortunately, due to the delicate information contained in the documentation relating to these problems, it is difficult if not impossible to obtain material for research and study purposes on which to experiment new ideas and techniques aimed at automating processes, perhaps exploiting what is in ferment in the scientific community and linked to the fields of ontologies and artificial intelligence for data management. In order to bypass this problem, it was decided to examine data related to the medical world, which, especially for important reasons related to the health of individuals, have gradually become more and more freely accessible over time, without affecting the generality of the proposed methods, which can be reapplied to the most diverse fields in which there is a need to manage privacy-sensitive information

On Improving Generalization of CNN-Based Image Classification with Delineation Maps Using the CORF Push-Pull Inhibition Operator

Deployed image classification pipelines are typically dependent on the images captured in real-world environments. This means that images might be affected by different sources of perturbations (e.g. sensor noise in low-light environments). The main challenge arises by the fact that image quality directly impacts the reliability and consistency of classification tasks. This challenge has, hence, attracted wide interest within the computer vision communities. We propose a transformation step that attempts to enhance the generalization ability of CNN models in the presence of unseen noise in the test set. Concretely, the delineation maps of given images are determined using the CORF push-pull inhibition operator. Such an operation transforms an input image into a space that is more robust to noise before being processed by a CNN. We evaluated our approach on the Fashion MNIST data set with an AlexNet model. It turned out that the proposed CORF-augmented pipeline achieved comparable results on noise-free images to those of a conventional AlexNet classification model without CORF delineation maps, but it consistently achieved significantly superior performance on test images perturbed with different levels of Gaussian and uniform noise