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

Robot Navigation in Unseen Spaces using an Abstract Map

Human navigation in built environments depends on symbolic spatial information which has unrealised potential to enhance robot navigation capabilities. Information sources such as labels, signs, maps, planners, spoken directions, and navigational gestures communicate a wealth of spatial information to the navigators of built environments; a wealth of information that robots typically ignore. We present a robot navigation system that uses the same symbolic spatial information employed by humans to purposefully navigate in unseen built environments with a level of performance comparable to humans. The navigation system uses a novel data structure called the abstract map to imagine malleable spatial models for unseen spaces from spatial symbols. Sensorimotor perceptions from a robot are then employed to provide purposeful navigation to symbolic goal locations in the unseen environment. We show how a dynamic system can be used to create malleable spatial models for the abstract map, and provide an open source implementation to encourage future work in the area of symbolic navigation. Symbolic navigation performance of humans and a robot is evaluated in a real-world built environment. The paper concludes with a qualitative analysis of human navigation strategies, providing further insights into how the symbolic navigation capabilities of robots in unseen built environments can be improved in the future.Comment: 15 pages, published in IEEE Transactions on Cognitive and Developmental Systems (http://doi.org/10.1109/TCDS.2020.2993855), see https://btalb.github.io/abstract_map/ for access to softwar

Suomenkielisen geojäsentimen kehittäminen: kuinka hankkia sijaintitietoa jäsentelemättömistä tekstiaineistoista

Alati enemmän aineistoa tuotetaan ja jaetaan internetin kautta. Aineistot ovat vaihtelevia muodoiltaan, kuten verkkoartikkelien ja sosiaalisen media julkaisujen kaltaiset digitaaliset tekstit, ja niillä on usein spatiaalinen ulottuvuus. Teksteissä geospatiaalisuutta ilmaistaan paikannimien kautta, mutta tavanomaisilla paikkatietomenetelmillä ei kyetä käsittelemään tietoa epätäsmällisessä kielellisessä asussaan. Tämä on luonut tarpeen muuntaa tekstimuotoisen sijaintitiedon näkyvään muotoon, koordinaateiksi. Ongelmaa ratkaisemaan on kehitetty geojäsentimiä, jotka tunnistavat ja paikantavat paikannimet vapaista teksteistä, ja jotka oikein toimiessaan voisivat toimia paikkatiedon lähteenä maantieteellisessä tutkimuksessa. Geojäsentämistä onkin sovellettu katastrofihallinnasta kirjallisuudentutkimukseen. Merkittävässä osassa geojäsentämisen tutkimusta tutkimusaineiston kielenä on ollut englanti ja geojäsentimetkin ovat kielikohtaisia – tämä jättää pimentoon paitsi geojäsentimien kehitykseen vaikuttavat havainnot pienemmistä kielistä myös kyseisten kielten puhujien näkemykset. Maisterintutkielmassani pyrin vastaamaan kolmeen tutkimuskysymykseen: Mitkä ovat edistyneimmät geojäsentämismenetelmät? Mitkä kielelliset ja maantieteelliset monitulkintaisuudet vaikeuttavat tämän monitahoisen ongelman ratkaisua? Ja miten arvioida geojäsentimien luotettavuutta ja käytettävyyttä? Tutkielman soveltavassa osuudessa esittelen Fingerin, geojäsentimen suomen kielelle, ja kuvaan sen kehitystä sekä suorituskyvyn arviointia. Arviointia varten loin kaksi testiaineistoa, joista toinen koostuu Twitter-julkaisuista ja toinen uutisartikkeleista. Finger-geojäsennin, testiaineistot ja relevantit ohjelmakoodit jaetaan avoimesti. Geojäsentäminen voidaan jakaa kahteen alitehtävään: paikannimien tunnistamiseen tekstivirrasta ja paikannimien ratkaisemiseen oikeaan koordinaattipisteeseen mahdollisesti useasta kandidaatista. Molemmissa vaiheissa uusimmat metodit nojaavat syväoppimismalleihin ja -menetelmiin, joiden syötteinä ovat sanaupotusten kaltaiset vektorit. Geojäsentimien suoriutumista testataan aineistoilla, joissa paikannimet ja niiden koordinaatit tiedetään. Mittatikkuna tunnistamisessa on vastaavuus ja ratkaisemisessa etäisyys oikeasta sijainnista. Finger käyttää paikannimitunnistinta, joka hyödyntää suomenkielistä BERT-kielimallia, ja suoraviivaista tietokantahakua paikannimien ratkaisemiseen. Ohjelmisto tuottaa taulukkomuotoiseksi jäsenneltyä paikkatietoa, joka sisältää syötetekstit ja niistä mahdollisesti tunnistetut paikannimet koordinaattisijainteineen. Testiaineistot eroavat aihepiireiltään, mutta Finger suoriutuu niillä likipitäen samoin, ja suoriutuu englanninkielisillä aineistoilla tehtyihin arviointeihin suhteutettuna kelvollisesti. Virheanalyysi paljastaa useita virhelähteitä, jotka johtuvat kielten tai maantieteellisen todellisuuden luontaisesta epäselvyydestä tai ovat prosessoinnin aiheuttamia, kuten perusmuotoistamisvirheet. Kaikkia osia Fingerissä voidaan parantaa, muun muassa kehittämällä kielellistä käsittelyä pidemmälle ja luomalla kattavampia testiaineistoja. Samoin tulevaisuuden geojäsentimien tulee kyetä käsittelemään monimutkaisempia kielellisiä ja maantieteellisiä kuvaustapoja kuin pelkät paikannimet ja koordinaattipisteet. Finger ei nykymuodossaan tuota valmista paikkatietoa, jota kannattaisi kritiikittä käyttää. Se on kuitenkin lupaava ensiaskel suomen kielen geojäsentimille ja astinlauta vastaisuuden soveltavalle tutkimukselle.Ever more data is available and shared through the internet. The big data masses often have a spatial dimension and can take many forms, one of which are digital texts, such as articles or social media posts. The geospatial links in these texts are made through place names, also called toponyms, but traditional GIS methods are unable to deal with the fuzzy linguistic information. This creates the need to transform the linguistic location information to an explicit coordinate form. Several geoparsers have been developed to recognize and locate toponyms in free-form texts: the task of these systems is to be a reliable source of location information. Geoparsers have been applied to topics ranging from disaster management to literary studies. Major language of study in geoparser research has been English and geoparsers tend to be language-specific, which threatens to leave the experiences provided by studying and expressed in smaller languages unexplored. This thesis seeks to answer three research questions related to geoparsing: What are the most advanced geoparsing methods? What linguistic and geographical features complicate this multi-faceted problem? And how to evaluate the reliability and usability of geoparsers? The major contributions of this work are an open-source geoparser for Finnish texts, Finger, and two test datasets, or corpora, for testing Finnish geoparsers. One of the datasets consists of tweets and the other of news articles. All of these resources, including the relevant code for acquiring the test data and evaluating the geoparser, are shared openly. Geoparsing can be divided into two sub-tasks: recognizing toponyms amid text flows and resolving them to the correct coordinate location. Both tasks have seen a recent turn to deep learning methods and models, where the input texts are encoded as, for example, word embeddings. Geoparsers are evaluated against gold standard datasets where toponyms and their coordinates are marked. Performance is measured on equivalence and distance-based metrics for toponym recognition and resolution respectively. Finger uses a toponym recognition classifier built on a Finnish BERT model and a simple gazetteer query to resolve the toponyms to coordinate points. The program outputs structured geodata, with input texts and the recognized toponyms and coordinate locations. While the datasets represent different text types in terms of formality and topics, there is little difference in performance when evaluating Finger against them. The overall performance is comparable to the performance of geoparsers of English texts. Error analysis reveals multiple error sources, caused either by the inherent ambiguousness of the studied language and the geographical world or are caused by the processing itself, for example by the lemmatizer. Finger can be improved in multiple ways, such as refining how it analyzes texts and creating more comprehensive evaluation datasets. Similarly, the geoparsing task should move towards more complex linguistic and geographical descriptions than just toponyms and coordinate points. Finger is not, in its current state, a ready source of geodata. However, the system has potential to be the first step for geoparsers for Finnish and it can be a steppingstone for future applied research

Location Reference Recognition from Texts: A Survey and Comparison

A vast amount of location information exists in unstructured texts, such as social media posts, news stories, scientific articles, web pages, travel blogs, and historical archives. Geoparsing refers to recognizing location references from texts and identifying their geospatial representations. While geoparsing can benefit many domains, a summary of its specific applications is still missing. Further, there is a lack of a comprehensive review and comparison of existing approaches for location reference recognition, which is the first and core step of geoparsing. To fill these research gaps, this review first summarizes seven typical application domains of geoparsing: geographic information retrieval, disaster management, disease surveillance, traffic management, spatial humanities, tourism management, and crime management. We then review existing approaches for location reference recognition by categorizing these approaches into four groups based on their underlying functional principle: rule-based, gazetteer matching–based, statistical learning-–based, and hybrid approaches. Next, we thoroughly evaluate the correctness and computational efficiency of the 27 most widely used approaches for location reference recognition based on 26 public datasets with different types of texts (e.g., social media posts and news stories) containing 39,736 location references worldwide. Results from this thorough evaluation can help inform future methodological developments and can help guide the selection of proper approaches based on application needs

Geospatial data analysis in Russia’s geoweb

The chapter examines the role of geospatial data in Russia’s online ecosystem. Facilitated by the rise of geographic information systems and user-generated content, the distribution of geospatial data has blurred the line between physical spaces and their virtual representations. The chapter discusses different sources of these data available for Digital Russian Studies (e.g., social data and crowdsourced databases) together with the novel techniques for extracting geolocation from various data formats (e.g., textual documents and images). It also scrutinizes different ways of using these data, varying from mapping the spatial distribution of social and political phenomena to investigating the use of geotag data for cultural practices’ digitization to exploring the use of geoweb for narrating individual and collective identities online

Automatic tagging and geotagging in video collections and communities

Automatically generated tags and geotags hold great promise to improve access to video collections and online communi- ties. We overview three tasks offered in the MediaEval 2010 benchmarking initiative, for each, describing its use scenario, definition and the data set released. For each task, a reference algorithm is presented that was used within MediaEval 2010 and comments are included on lessons learned. The Tagging Task, Professional involves automatically matching episodes in a collection of Dutch television with subject labels drawn from the keyword thesaurus used by the archive staff. The Tagging Task, Wild Wild Web involves automatically predicting the tags that are assigned by users to their online videos. Finally, the Placing Task requires automatically assigning geo-coordinates to videos. The specification of each task admits the use of the full range of available information including user-generated metadata, speech recognition transcripts, audio, and visual features

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

Spatial and Temporal Sentiment Analysis of Twitter data

The public have used Twitter world wide for expressing opinions. This study focuses on spatio-temporal variation of georeferenced Tweets’ sentiment polarity, with a view to understanding how opinions evolve on Twitter over space and time and across communities of users. More specifically, the question this study tested is whether sentiment polarity on Twitter exhibits specific time-location patterns. The aim of the study is to investigate the spatial and temporal distribution of georeferenced Twitter sentiment polarity within the area of 1 km buffer around the Curtin Bentley campus boundary in Perth, Western Australia. Tweets posted in campus were assigned into six spatial zones and four time zones. A sentiment analysis was then conducted for each zone using the sentiment analyser tool in the Starlight Visual Information System software. The Feature Manipulation Engine was employed to convert non-spatial files into spatial and temporal feature class. The spatial and temporal distribution of Twitter sentiment polarity patterns over space and time was mapped using Geographic Information Systems (GIS). Some interesting results were identified. For example, the highest percentage of positive Tweets occurred in the social science area, while science and engineering and dormitory areas had the highest percentage of negative postings. The number of negative Tweets increases in the library and science and engineering areas as the end of the semester approaches, reaching a peak around an exam period, while the percentage of negative Tweets drops at the end of the semester in the entertainment and sport and dormitory area. This study will provide some insights into understanding students and staff ’s sentiment variation on Twitter, which could be useful for university teaching and learning management