Stress Testing BERT Anaphora Resolution Models for Reaction Extraction in Chemical Patents

The high volume of published chemical patents and the importance of a timely acquisition of their information gives rise to automating information extraction from chemical patents. Anaphora resolution is an important component of comprehensive information extraction, and is critical for extracting reactions. In chemical patents, there are five anaphoric relations of interest: co-reference, transformed, reaction associated, work up, and contained. Our goal is to investigate how the performance of anaphora resolution models for reaction texts in chemical patents differs in a noise-free and noisy environment and to what extent we can improve the robustness against noise of the model

Clinical text data in machine learning: Systematic review

Background: Clinical narratives represent the main form of communication within healthcare providing a personalized account of patient history and assessments, offering rich information for clinical decision making. Natural language processing (NLP) has repeatedly demonstrated its feasibility to unlock evidence buried in clinical narratives. Machine learning can facilitate rapid development of NLP tools by leveraging large amounts of text data. Objective: The main aim of this study is to provide systematic evidence on the properties of text data used to train machine learning approaches to clinical NLP. We also investigate the types of NLP tasks that have been supported by machine learning and how they can be applied in clinical practice. Methods: Our methodology was based on the guidelines for performing systematic reviews. In August 2018, we used PubMed, a multi-faceted interface, to perform a literature search against MEDLINE. We identified a total of 110 relevant studies and extracted information about the text data used to support machine learning, the NLP tasks supported and their clinical applications. The data properties considered included their size, provenance, collection methods, annotation and any relevant statistics. Results: The vast majority of datasets used to train machine learning models included only hundreds or thousands of documents. Only 10 studies used tens of thousands of documents with a handful of studies utilizing more. Relatively small datasets were utilized for training even when much larger datasets were available. The main reason for such poor data utilization is the annotation bottleneck faced by supervised machine learning algorithms. Active learning was explored to iteratively sample a subset of data for manual annotation as a strategy for minimizing the annotation effort while maximizing predictive performance of the model. Supervised learning was successfully used where clinical codes integrated with free text notes into electronic health records were utilized as class labels. Similarly, distant supervision was used to utilize an existing knowledge base to automatically annotate raw text. Where manual annotation was unavoidable, crowdsourcing was explored, but it remains unsuitable due to sensitive nature of data considered. Beside the small volume, training data were typically sourced from a small number of institutions, thus offering no hard evidence about the transferability of machine learning models. The vast majority of studies focused on the task of text classification. Most commonly, the classification results were used to support phenotyping, prognosis, care improvement, resource management and surveillance. Conclusions: We identified the data annotation bottleneck as one of the key obstacles to machine learning approaches in clinical NLP. Active learning and distant supervision were explored as a way of saving the annotation efforts. Future research in this field would benefit from alternatives such as data augmentation and transfer learning, or unsupervised learning, which does not require data annotation

Towards the extraction of cross-sentence relations through event extraction and entity coreference

Cross-sentence relation extraction deals with the extraction of relations beyond the sentence boundary. This thesis focuses on two of the NLP tasks which are of importance to the successful extraction of cross-sentence relation mentions: event extraction and coreference resolution. The first part of the thesis focuses on addressing data sparsity issues in event extraction. We propose a self-training approach for obtaining additional labeled examples for the task. The process starts off with a Bi-LSTM event tagger trained on a small labeled data set which is used to discover new event instances in a large collection of unstructured text. The high confidence model predictions are selected to construct a data set of automatically-labeled training examples. We present several ways in which the resulting data set can be used for re-training the event tagger in conjunction with the initial labeled data. The best configuration achieves statistically significant improvement over the baseline on the ACE 2005 test set (macro-F1), as well as in a 10-fold cross validation (micro- and macro-F1) evaluation. Our error analysis reveals that the augmentation approach is especially beneficial for the classification of the most under-represented event types in the original data set. The second part of the thesis focuses on the problem of coreference resolution. While a certain level of precision can be reached by modeling surface information about entity mentions, their successful resolution often depends on semantic or world knowledge. This thesis investigates an unsupervised source of such knowledge, namely distributed word representations. We present several ways in which word embeddings can be utilized to extract features for a supervised coreference resolver. Our evaluation results and error analysis show that each of these features helps improve over the baseline coreference system’s performance, with a statistically significant improvement (CoNLL F1) achieved when the proposed features are used jointly. Moreover, all features lead to a reduction in the amount of precision errors in resolving references between common nouns, demonstrating that they successfully incorporate semantic information into the process

Temporal Information in Data Science: An Integrated Framework and its Applications

Data science is a well-known buzzword, that is in fact composed of two distinct keywords, i.e., data and science. Data itself is of great importance: each analysis task begins from a set of examples. Based on such a consideration, the present work starts with the analysis of a real case scenario, by considering the development of a data warehouse-based decision support system for an Italian contact center company. Then, relying on the information collected in the developed system, a set of machine learning-based analysis tasks have been developed to answer specific business questions, such as employee work anomaly detection and automatic call classification. Although such initial applications rely on already available algorithms, as we shall see, some clever analysis workflows had also to be developed. Afterwards, continuously driven by real data and real world applications, we turned ourselves to the question of how to handle temporal information within classical decision tree models. Our research brought us the development of J48SS, a decision tree induction algorithm based on Quinlan's C4.5 learner, which is capable of dealing with temporal (e.g., sequential and time series) as well as atemporal (such as numerical and categorical) data during the same execution cycle. The decision tree has been applied into some real world analysis tasks, proving its worthiness. A key characteristic of J48SS is its interpretability, an aspect that we specifically addressed through the study of an evolutionary-based decision tree pruning technique. Next, since a lot of work concerning the management of temporal information has already been done in automated reasoning and formal verification fields, a natural direction in which to proceed was that of investigating how such solutions may be combined with machine learning, following two main tracks. First, we show, through the development of an enriched decision tree capable of encoding temporal information by means of interval temporal logic formulas, how a machine learning algorithm can successfully exploit temporal logic to perform data analysis. Then, we focus on the opposite direction, i.e., that of employing machine learning techniques to generate temporal logic formulas, considering a natural language processing scenario. Finally, as a conclusive development, the architecture of a system is proposed, in which formal methods and machine learning techniques are seamlessly combined to perform anomaly detection and predictive maintenance tasks. Such an integration represents an original, thrilling research direction that may open up new ways of dealing with complex, real-world problems.Data science is a well-known buzzword, that is in fact composed of two distinct keywords, i.e., data and science. Data itself is of great importance: each analysis task begins from a set of examples. Based on such a consideration, the present work starts with the analysis of a real case scenario, by considering the development of a data warehouse-based decision support system for an Italian contact center company. Then, relying on the information collected in the developed system, a set of machine learning-based analysis tasks have been developed to answer specific business questions, such as employee work anomaly detection and automatic call classification. Although such initial applications rely on already available algorithms, as we shall see, some clever analysis workflows had also to be developed. Afterwards, continuously driven by real data and real world applications, we turned ourselves to the question of how to handle temporal information within classical decision tree models. Our research brought us the development of J48SS, a decision tree induction algorithm based on Quinlan's C4.5 learner, which is capable of dealing with temporal (e.g., sequential and time series) as well as atemporal (such as numerical and categorical) data during the same execution cycle. The decision tree has been applied into some real world analysis tasks, proving its worthiness. A key characteristic of J48SS is its interpretability, an aspect that we specifically addressed through the study of an evolutionary-based decision tree pruning technique. Next, since a lot of work concerning the management of temporal information has already been done in automated reasoning and formal verification fields, a natural direction in which to proceed was that of investigating how such solutions may be combined with machine learning, following two main tracks. First, we show, through the development of an enriched decision tree capable of encoding temporal information by means of interval temporal logic formulas, how a machine learning algorithm can successfully exploit temporal logic to perform data analysis. Then, we focus on the opposite direction, i.e., that of employing machine learning techniques to generate temporal logic formulas, considering a natural language processing scenario. Finally, as a conclusive development, the architecture of a system is proposed, in which formal methods and machine learning techniques are seamlessly combined to perform anomaly detection and predictive maintenance tasks. Such an integration represents an original, thrilling research direction that may open up new ways of dealing with complex, real-world problems

An anonymizable entity finder in judicial decisions

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Control in free adjuncts: the 'dangling modifier' in English

In this dissertation, I present an account of the control of free adjuncts that relies on incremental processing. While many free adjuncts are controlled by the subject of the matrix clause (1a), this is not always the case. Some seem to be controlled by non-subject elements within the matrix clause (1b), others are apparently controlled by the discourse topic (1c), and still others involve the perceiver of the matrix clause in logophoric control (1d). These control patterns have raised the ire of many grammatical prescriptivists, who often label such constructions as ‘danglers’. (1) a. Turning the corner on his motorcycle, he saw a church. b. Turning the corner on his motorcycle, his grip began to slip. c. While under development, they put all other projects on hold. d. Turning the corner on my motorcycle, a church came into view. There have been several explanations of these patterns. Many researchers see free adjuncts as obligatorily controlled by the subject (1a) except where this is not possible, in which case logophoric control arises (1b,d). But such approaches cannot account for (1c), in which the controller is inanimate and thus incapable of perceiving anything. Other researchers regard non-subject control as the result of either an attempt to establish semantic coherence between two apparently unrelated clauses or an exhaustive search for alternative controllers based on a complex set of syntactic, semantic, and pragmatic clues. These approaches predict processing difficulty whenever a mismatch occurs, but most language users process sentences like (1b-d) fairly easily. My central claim is that the patterns found in adjunct control arise because the establishment of control continues throughout the process of understanding a given sentence. The language user, on encountering a free adjunct, guesses at a suitable controller. Disruption occurs when another potential controller arrives that is at least as adequate as the current guess. I support this claim through analysis of an extensive collection of attested examples, taking care to cover the relevant syntactic, semantic, pragmatic, and processing facts. I also emphasise how important it is for theoretical and descriptive studies to make specific predictions that could in principle be vindicated or falsified by future work in historical syntax or experimental psycholinguistics

Transfer Learning in Natural Language Processing through Interactive Feedback

Machine learning models cannot easily adapt to new domains and applications. This drawback becomes detrimental for natural language processing (NLP) because language is perpetually changing. Across disciplines and languages, there are noticeable differences in content, grammar, and vocabulary. To overcome these shifts, recent NLP breakthroughs focus on transfer learning. Through clever optimization and engineering, a model can successfully adapt to a new domain or task. However, these modifications are still computationally inefficient or resource-intensive. Compared to machines, humans are more capable at generalizing knowledge across different situations, especially in low-resource ones. Therefore, the research on transfer learning should carefully consider how the user interacts with the model. The goal of this dissertation is to investigate “human-in-the-loop” approaches for transfer learning in NLP. First, we design annotation frameworks for inductive transfer learning, which is the transfer of models across tasks. We create an interactive topic modeling system for users to find topics useful for classifying documents in multiple languages. The user-constructed topic model bridges improves classification accuracy and bridges cross-lingual gaps in knowledge. Next, we look at popular language models, like BERT, that can be applied to various tasks. While these models are useful, they still require a large amount of labeled data to learn a new task. To reduce labeling, we develop an active learning strategy which samples documents that surprise the language model. Users only need to annotate a small subset of these unexpected documents to adapt the language model for text classification. Then, we transition to user interaction in transductive transfer learning, which is the transfer of models across domains. We focus our efforts on low-resource languages to develop an interactive system for word embeddings. In this approach, the feedback from bilingual speakers refines the cross-lingual embedding space for classification tasks. Subsequently, we look at domain shift for tasks beyond text classification. Coreference resolution is fundamental for NLP applications, like question-answering and dialogue, but the models are typically trained and evaluated on one dataset. We use active learning to find spans of text in the new domain for users to label. Furthermore, we provide important insights on annotating spans for domain adaptation. Finally, we summarize the contributions of each chapter. We focus on aspects like the scope of applications and model complexity. We conclude with a discussion of future directions. Researchers may extend the ideas in our thesis to topics like user-centric active learning and proactive learning

Semantic networks

AbstractA semantic network is a graph of the structure of meaning. This article introduces semantic network systems and their importance in Artificial Intelligence, followed by I. the early background; II. a summary of the basic ideas and issues including link types, frame systems, case relations, link valence, abstraction, inheritance hierarchies and logic extensions; and III. a survey of ‘world-structuring’ systems including ontologies, causal link models, continuous models, relevance, formal dictionaries, semantic primitives and intersecting inference hierarchies. Speed and practical implementation are briefly discussed. The conclusion argues for a synthesis of relational graph theory, graph-grammar theory and order theory based on semantic primitives and multiple intersecting inference hierarchies