Biomedical Information Extraction Pipelines for Public Health in the Age of Deep Learning

abstract: Unstructured texts containing biomedical information from sources such as electronic health records, scientific literature, discussion forums, and social media offer an opportunity to extract information for a wide range of applications in biomedical informatics. Building scalable and efficient pipelines for natural language processing and extraction of biomedical information plays an important role in the implementation and adoption of applications in areas such as public health. Advancements in machine learning and deep learning techniques have enabled rapid development of such pipelines. This dissertation presents entity extraction pipelines for two public health applications: virus phylogeography and pharmacovigilance. For virus phylogeography, geographical locations are extracted from biomedical scientific texts for metadata enrichment in the GenBank database containing 2.9 million virus nucleotide sequences. For pharmacovigilance, tools are developed to extract adverse drug reactions from social media posts to open avenues for post-market drug surveillance from non-traditional sources. Across these pipelines, high variance is observed in extraction performance among the entities of interest while using state-of-the-art neural network architectures. To explain the variation, linguistic measures are proposed to serve as indicators for entity extraction performance and to provide deeper insight into the domain complexity and the challenges associated with entity extraction. For both the phylogeography and pharmacovigilance pipelines presented in this work the annotated datasets and applications are open source and freely available to the public to foster further research in public health.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

Automatic Identification of Addresses: A Systematic Literature Review

Cruz, P., Vanneschi, L., Painho, M., & Rita, P. (2022). Automatic Identification of Addresses: A Systematic Literature Review. ISPRS International Journal of Geo-Information, 11(1), 1-27. https://doi.org/10.3390/ijgi11010011 -----------------------------------------------------------------------The work by Leonardo Vanneschi, Marco Painho and Paulo Rita was supported by Fundação para a Ciência e a Tecnologia (FCT) within the Project: UIDB/04152/2020—Centro de Investigação em Gestão de Informação (MagIC). The work by Prof. Leonardo Vanneschi was also partially supported by FCT, Portugal, through funding of project AICE (DSAIPA/DS/0113/2019).Address matching continues to play a central role at various levels, through geocoding and data integration from different sources, with a view to promote activities such as urban planning, location-based services, and the construction of databases like those used in census operations. However, the task of address matching continues to face several challenges, such as non-standard or incomplete address records or addresses written in more complex languages. In order to better understand how current limitations can be overcome, this paper conducted a systematic literature review focused on automated approaches to address matching and their evolution across time. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed, resulting in a final set of 41 papers published between 2002 and 2021, the great majority of which are after 2017, with Chinese authors leading the way. The main findings revealed a consistent move from more traditional approaches to deep learning methods based on semantics, encoder-decoder architectures, and attention mechanisms, as well as the very recent adoption of hybrid approaches making an increased use of spatial constraints and entities. The adoption of evolutionary-based approaches and privacy preserving methods stand as some of the research gaps to address in future studies.publishersversionpublishe

Geospatial Analysis and Modeling of Textual Descriptions of Pre-modern Geography

Textual descriptions of pre-modern geography offer a different view of classical geography. The descriptions have been produced when none of the modern geographical concepts and tools were available. In this dissertation, we study pre-modern geography by primarily finding the existing structures of the descriptions and different cases of geographical data. We first explain four major geographical cases in pre-modern Arabic sources: gazetteer, administrative hierarchies, routes, and toponyms associated with people. Focusing on hierarchical divisions and routes, we offer approaches for manual annotation of administrative hierarchies and route sections as well as a semi-automated toponyms annotation. The latter starts with a fuzzy search of toponyms from an authority list and applies two different extrapolation models to infer true or false values, based on the context, for disambiguating the automatically annotated toponyms. Having the annotated data, we introduce mathematical models to shape and visualize regions based on the description of administrative hierarchies. Moreover, we offer models for comparing hierarchical divisions and route networks from different sources. We also suggest approaches to approximate geographical coordinates for places that do not have geographical coordinates - we call them unknown places - which is a major issue in visualization of pre-modern places on map. The final chapter of the dissertation introduces the new version of al-Ṯurayyā, a gazetteer and a spatial model of the classical Islamic world using georeferenced data of a pre-modern atlas with more than 2, 000 toponyms and routes. It offers search, path finding, and flood network functionalities as well as visualizations of regions using one of the models that we describe for regions. However the gazetteer is designed using the classical Islamic world data, the spatial model and features can be used for similarly prepared datasets.:1 Introduction 1 2 Related Work 8 2.1 GIS 8 2.2 NLP, Georeferencing, Geoparsing, Annotation 10 2.3 Gazetteer 15 2.4 Modeling 17 3 Classical Geographical Cases 20 3.1 Gazetteer 21 3.2 Routes and Travelogues 22 3.3 Administrative Hierarchy 24 3.4 Geographical Aspects of Biographical Data 25 4 Annotation and Extraction 27 4.1 Annotation 29 4.1.1 Manual Annotation of Geographical Texts 29 4.1.1.1 Administrative Hierarchy 30 4.1.1.2 Routes and Travelogues 32 4.1.2 Semi-Automatic Toponym Annotation 34 4.1.2.1 The Annotation Process 35 4.1.2.2 Extrapolation Models 37 4.1.2.2.1 Frequency of Toponymic N-grams 37 4.1.2.2.2 Co-occurrence Frequencies 38 4.1.2.2.3 A Supervised ML Approach 40 4.1.2.3 Summary 45 4.2 Data Extraction and Structures 45 4.2.1 Administrative Hierarchy 45 4.2.2 Routes and Distances 49 5 Modeling Geographical Data 51 5.1 Mathematical Models for Administrative Hierarchies 52 5.1.1 Sample Data 53 5.1.2 Quadtree 56 5.1.3 Voronoi Diagram 58 5.1.4 Voronoi Clippings 62 5.1.4.1 Convex Hull 62 5.1.4.2 Concave Hull 63 5.1.5 Convex Hulls 65 5.1.6 Concave Hulls 67 5.1.7 Route Network 69 5.1.8 Summary of Models for Administrative Hierarchy 69 5.2 Comparison Models 71 5.2.1 Hierarchical Data 71 5.2.1.1 Test Data 73 5.2.2 Route Networks 76 5.2.2.1 Post-processing 81 5.2.2.2 Applications 82 5.3 Unknown Places 84 6 Al-Ṯurayyā 89 6.1 Introducing al-Ṯurayyā 90 6.2 Gazetteer 90 6.3 Spatial Model 91 6.3.1 Provinces and Administrative Divisions 93 6.3.2 Pathfinding and Itineraries 93 6.3.3 Flood Network 96 6.3.4 Path Alignment Tool 97 6.3.5 Data Structure 99 6.3.5.1 Places 100 6.3.5.2 Routes and Distances 100 7 Conclusions and Further Work 10

Context-sensitive interpretation of natural language location descriptions : a thesis submitted in partial fulfilment of the requirements for the award of Doctor of Philosophy in Information Technology at Massey University, Auckland, New Zealand

People frequently describe the locations of objects using natural language. Location descriptions may be either structured, such as 26 Victoria Street, Auckland, or unstructured. Relative location descriptions (e.g., building near Sky Tower) are a common form of unstructured location description, and use qualitative terms to describe the location of one object relative to another (e.g., near, close to, in, next to). Understanding the meaning of these terms is easy for humans, but much more difficult for machines since the terms are inherently vague and context sensitive. In this thesis, we study the semantics (or meaning) of qualitative, geospatial relation terms, specifically geospatial prepositions. Prepositions are one of the most common forms of geospatial relation term, and they are commonly used to describe the location of objects in the geographic (geospatial) environment, such as rivers, mountains, buildings, and towns. A thorough understanding of the semantics of geospatial relation terms is important because it enables more accurate automated georeferencing of text location descriptions than use of place names only. Location descriptions that use geospatial prepositions are found in social media, web sites, blogs, and academic reports, and georeferencing can allow mapping of health, disaster and biological data that is currently inaccessible to the public. Such descriptions have unstructured format, so, their analysis is not straightforward. The specific research questions that we address are: RQ1. Which geospatial prepositions (or groups of prepositions) and senses are semantically similar? RQ2. Is the role of context important in the interpretation of location descriptions? RQ3. Is the object distance associated with geospatial prepositions across a range of geospatial scenes and scales accurately predictable using machine learning methods? RQ4. Is human annotation a reliable form of annotation for the analysis of location descriptions? To address RQ1, we determine the nature and degree of similarity among geospatial prepositions by analysing data collected with a human subjects experiment, using clustering, extensional mapping and t-stochastic neighbour embedding (t-SNE) plots to form a semantic similarity matrix. In addition to calculating similarity scores among prepositions, we identify the senses of three groups of geospatial prepositions using Venn diagrams, t-sne plots and density-based clustering, and define the relationships between the senses. Furthermore, we use two text mining approaches to identify the degree of similarity among geospatial prepositions: bag of words and GloVe embeddings. By using these methods and further analysis, we identify semantically similar groups of geospatial prepositions including: 1- beside, close to, near, next to, outside and adjacent to; 2- across, over and through and 3- beyond, past, by and off. The prepositions within these groups also share senses. Through is recognised as a specialisation of both across and over. Proximity and adjacency prepositions also have similar senses that express orientation and overlapping relations. Past, off and by share a proximal sense but beyond has a different sense from these, representing on the other side. Another finding is the more frequent use of the preposition close to for pairs of linear objects than near, which is used more frequently for non-linear ones. Also, next to is used to describe proximity more than touching (in contrast to other prepositions like adjacent to). Our application of text mining to identify semantically similar prepositions confirms that a geospatial corpus (NCGL) provides a better representation of the semantics of geospatial prepositions than a general corpus. Also, we found that GloVe embeddings provide adequate semantic similarity measures for more specialised geospatial prepositions, but less so for those that have more generalised applications and multiple senses. We explore the role of context (RQ2) by studying three sites that vary in size, nature, and context in London: Trafalgar Square, Buckingham Palace, and Hyde Park. We use the Google search engine to extract location descriptions that contain these three sites with 9 different geospatial prepositions (in, on, at, next to, close to, adjacent to, near, beside, outside) and calculate their acceptance profiles (the profile of the use of a preposition at different distances from the reference object) and acceptance thresholds (maximum distance from a reference object at which a preposition can acceptably be used). We use these to compare prepositions, and to explore the influence of different contexts. Our results show that near, in and outside are used for larger distances, while beside, adjacent to and at are used for smaller distances. Also, the acceptance threshold for close to is higher than for other proximity/adjacency prepositions such as next to, adjacent to and beside. The acceptance threshold of next to is larger than adjacent to, which confirms the findings in ‎Chapter 2 which identifies next to describing a proximity rather than touching spatial relation. We also found that relatum characteristics such as image schema affect the use of prepositions such as in, on and at. We address RQ3 by developing a machine learning regression model (using the SMOReg algorithm) to predict the distance associated with use of geospatial prepositions in specific expressions. We incorporate a wide range of input variables including the similarity matrix of geospatial prepositions (RQ1); preposition senses; semantic information in the form of embeddings; characteristics of the located and reference objects in the expression including their liquidity/solidity, scale and geometry type and contextual factors such as the density of features of different types in the surrounding area. We evaluate the model on two different datasets with 25% improvement against the best baseline respectively. Finally, we consider the importance of annotation of geospatial location descriptions (RQ4). As annotated data is essential for the successful study of automated interpretation of natural language descriptions, we study the impact and accuracy of human annotation on different geospatial elements. Agreement scores show that human annotators can annotate geospatial relation terms (e.g., geospatial prepositions) with higher agreement than other geospatial elements. This thesis advances understanding of the semantics of geospatial prepositions, particularly considering their semantic similarity and the impact of context on their interpretation. We quantify the semantic similarity of a set of 24 geospatial prepositions; identify senses and the relationships among them for 13 geospatial prepositions; compare the acceptance thresholds of 9 geospatial prepositions and describe the influence of context on them; and demonstrate that richer semantic and contextual information can be incorporated in predictive models to interpret relative geospatial location descriptions more accurately

Introduction to the second international symposium of platial information science

People ‘live’ and constitute places every day through recurrent practices and experience. Our everyday lives, however, are complex, and so are places. In contrast to abstract space, the way people experience places includes a range of aspects like physical setting, meaning, and emotional attachment. This inherent complexity requires researchers to investigate the concept of place from a variety of viewpoints. The formal representation of place – a major goal in GIScience related to place – is no exception and can only be successfully addressed if we consider geographical, psychological, anthropological, sociological, cognitive, and other perspectives. This year’s symposium brings together place-based researchers from different disciplines to discuss the current state of platial research. Therefore, this volume contains contributions from a range of fields including geography, psychology, cognitive science, linguistics, and cartography

Things and Strings and More: Improving Place Name Disambiguation from Short Texts by Combining Entity Co-Occurrence, Topic Modeling, and Word Embedding

Place name disambiguation, i.e., toponym disambiguation or toponym resolution, is the task of correctly identifying a place from a set of places sharing a common name. It contributes to a variety of tasks such as knowledge extraction, query answering, geographic information retrieval, and automatic tagging. Disambiguation quality relies on the ability to correctly identify and interpret contextual clues, complicating the task for short texts. Here I propose a novel approach to the disambiguation of place names from short texts that integrates three models: entity co-occurrence, topic modeling, and word embedding. The first model uses Linked Data to identify related entities to improve disambiguation quality. The second model uses topic modeling to differentiate places based on the terms used to describe them. The third model uses word embeddings to uncover the semantic relatedness between places and contexts. I evaluate this approach using a corpus of short texts collected through web scraping, determine the suitable weights for the models, and demonstrate that the combined model, i.e., Things and Strings Model, outperforms benchmark systems such as DBpedia Spotlight, TextRazor, and Open Calais by up to 85% in F-score and 46% in Precision at 1. A web service is built to demonstrate the proposed method and it can be a building block for those applications that need place name recognition and disambiguation