Ontology Enrichment from Free-text Clinical Documents: A Comparison of Alternative Approaches

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships, as well as difficulty in updating the ontology as domain knowledge changes. Methodologies developed in the fields of Natural Language Processing (NLP), Information Extraction (IE), Information Retrieval (IR), and Machine Learning (ML) provide techniques for automating the enrichment of ontology from free-text documents. In this dissertation, I extended these methodologies into biomedical ontology development. First, I reviewed existing methodologies and systems developed in the fields of NLP, IR, and IE, and discussed how existing methods can benefit the development of biomedical ontologies. This previously unconducted review was published in the Journal of Biomedical Informatics. Second, I compared the effectiveness of three methods from two different approaches, the symbolic (the Hearst method) and the statistical (the Church and Lin methods), using clinical free-text documents. Third, I developed a methodological framework for Ontology Learning (OL) evaluation and comparison. This framework permits evaluation of the two types of OL approaches that include three OL methods. The significance of this work is as follows: 1) The results from the comparative study showed the potential of these methods for biomedical ontology enrichment. For the two targeted domains (NCIT and RadLex), the Hearst method revealed an average of 21% and 11% new concept acceptance rates, respectively. The Lin method produced a 74% acceptance rate for NCIT; the Church method, 53%. As a result of this study (published in the Journal of Methods of Information in Medicine), many suggested candidates have been incorporated into the NCIT; 2) The evaluation framework is flexible and general enough that it can analyze the performance of ontology enrichment methods for many domains, thus expediting the process of automation and minimizing the likelihood that key concepts and relationships would be missed as domain knowledge evolves

Mrežni sintaksno-semantički okvir za izvlačenje leksičkih relacija deterministričkim modelom prirodnog jezika

Given the extraordinary growth in online documents, methods for automated extraction of semantic relations became popular, and shortly after, became necessary. This thesis proposes a new deterministic language model, with the associated artifact, which acts as an online Syntactic and Semantic Framework (SSF) for the extraction of morphosyntactic and semantic relations. The model covers all fundamental linguistic fields: Morphology (formation, composition, and word paradigms), Lexicography (storing words and their features in network lexicons), Syntax (the composition of words in meaningful parts: phrases, sentences, and pragmatics), and Semantics (determining the meaning of phrases). To achieve this, a new tagging system with more complex structures was developed. Instead of the commonly used vectored systems, this new tagging system uses tree-likeT-structures with hierarchical, grammatical Word of Speech (WOS), and Semantic of Word (SOW) tags. For relations extraction, it was necessary to develop a syntactic (sub)model of language, which ultimately is the foundation for performing semantic analysis. This was achieved by introducing a new ‘O-structure’, which represents the union of WOS/SOW features from T-structures of words and enables the creation of syntagmatic patterns. Such patterns are a powerful mechanism for the extraction of conceptual structures (e.g., metonymies, similes, or metaphors), breaking sentences into main and subordinate clauses, or detection of a sentence’s main construction parts (subject, predicate, and object). Since all program modules are developed as general and generative entities, SSF can be used for any of the Indo-European languages, although validation and network lexicons have been developed for the Croatian language only. The SSF has three types of lexicons (morphs/syllables, words, and multi-word expressions), and the main words lexicon is included in the Global Linguistic Linked Open Data (LLOD) Cloud, allowing interoperability with all other world languages. The SSF model and its artifact represent a complete natural language model which can be used to extract the lexical relations from single sentences, paragraphs, and also from large collections of documents.Pojavom velikoga broja digitalnih dokumenata u okružju virtualnih mreža (interneta i dr.), postali su zanimljivi, a nedugo zatim i nužni, načini identifikacije i strojnoga izvlačenja semantičkih relacija iz (digitalnih) dokumenata (tekstova). U ovome radu predlaže se novi, deterministički jezični model s pripadnim artefaktom (Syntactic and Semantic Framework - SSF), koji će služiti kao mrežni okvir za izvlačenje morfosintaktičkih i semantičkih relacija iz digitalnog teksta, ali i pružati mnoge druge jezikoslovne funkcije. Model pokriva sva temeljna područja jezikoslovlja: morfologiju (tvorbu, sastav i paradigme riječi) s leksikografijom (spremanjem riječi i njihovih značenja u mrežne leksikone), sintaksu (tj. skladnju riječi u cjeline: sintagme, rečenice i pragmatiku) i semantiku (određivanje značenja sintagmi). Da bi se to ostvarilo, bilo je nužno označiti riječ složenijom strukturom, umjesto do sada korištenih vektoriziranih gramatičkih obilježja predložene su nove T-strukture s hijerarhijskim, gramatičkim (Word of Speech - WOS) i semantičkim (Semantic of Word - SOW) tagovima. Da bi se relacije mogle pronalaziti bilo je potrebno osmisliti sintaktički (pod)model jezika, na kojem će se u konačnici graditi i semantička analiza. To je postignuto uvođenjem nove, tzv. O-strukture, koja predstavlja uniju WOS/SOW obilježja iz T-struktura pojedinih riječi i omogućuje stvaranje sintagmatskih uzoraka. Takvi uzorci predstavljaju snažan mehanizam za izvlačenje konceptualnih struktura (npr. metonimija, simila ili metafora), razbijanje zavisnih rečenica ili prepoznavanje rečeničnih dijelova (subjekta, predikata i objekta). S obzirom da su svi programski moduli mrežnog okvira razvijeni kao opći i generativni entiteti, ne postoji nikakav problem korištenje SSF-a za bilo koji od indoeuropskih jezika, premda su provjera njegovog rada i mrežni leksikoni izvedeni za sada samo za hrvatski jezik. Mrežni okvir ima tri vrste leksikona (morphovi/slogovi, riječi i višeriječnice), a glavni leksikon riječi već je uključen u globalni lingvistički oblak povezanih podataka, što znači da je interoperabilnost s drugim jezicima već postignuta. S ovako osmišljenim i realiziranim načinom, SSF model i njegov realizirani artefakt, predstavljaju potpuni model prirodnoga jezika s kojim se mogu izvlačiti leksičke relacije iz pojedinačne rečenice, odlomka, ali i velikog korpusa (eng. big data) podataka

Social analytics for health integration, intelligence, and monitoring

Nowadays, patient-generated social health data are abundant and Healthcare is changing from the authoritative provider-centric model to collaborative and patient-oriented care. The aim of this dissertation is to provide a Social Health Analytics framework to utilize social data to solve the interdisciplinary research challenges of Big Data Science and Health Informatics. Specific research issues and objectives are described below. The first objective is semantic integration of heterogeneous health data sources, which can vary from structured to unstructured and include patient-generated social data as well as authoritative data. An information seeker has to spend time selecting information from many websites and integrating it into a coherent mental model. An integrated health data model is designed to allow accommodating data features from different sources. The model utilizes semantic linked data for lightweight integration and allows a set of analytics and inferences over data sources. A prototype analytical and reasoning tool called “Social InfoButtons” that can be linked from existing EHR systems is developed to allow doctors to understand and take into consideration the behaviors, patterns or trends of patients’ healthcare practices during a patient’s care. The tool can also shed insights for public health officials to make better-informed policy decisions. The second objective is near-real time monitoring of disease outbreaks using social media. The research for epidemics detection based on search query terms entered by millions of users is limited by the fact that query terms are not easily accessible by non-affiliated researchers. Publically available Twitter data is exploited to develop the Epidemics Outbreak and Spread Detection System (EOSDS). EOSDS provides four visual analytics tools for monitoring epidemics, i.e., Instance Map, Distribution Map, Filter Map, and Sentiment Trend to investigate public health threats in space and time. The third objective is to capture, analyze and quantify public health concerns through sentiment classifications on Twitter data. For traditional public health surveillance systems, it is hard to detect and monitor health related concerns and changes in public attitudes to health-related issues, due to their expenses and significant time delays. A two-step sentiment classification model is built to measure the concern. In the first step, Personal tweets are distinguished from Non-Personal tweets. In the second step, Personal Negative tweets are further separated from Personal Non-Negative tweets. In the proposed classification, training data is labeled by an emotion-oriented, clue-based method, and three Machine Learning models are trained and tested. Measure of Concern (MOC) is computed based on the number of Personal Negative sentiment tweets. A timeline trend of the MOC is also generated to monitor public concern levels, which is important for health emergency resource allocations and policy making. The fourth objective is predicting medical condition incidence and progression trajectories by using patients’ self-reported data on PatientsLikeMe. Some medical conditions are correlated with each other to a measureable degree (“comorbidities”). A prediction model is provided to predict the comorbidities and rank future conditions by their likelihood and to predict the possible progression trajectories given an observed medical condition. The novel models for trajectory prediction of medical conditions are validated to cover the comorbidities reported in the medical literature

The Object of Platform Studies: Relational Materialities and the Social Platform (the case of the Nintendo Wii)

Racing the Beam: The Atari Video Computer System,by Ian Bogost and Nick Montfort, inaugurated thePlatform Studies series at MIT Press in 2009.We’ve coauthored a new book in the series, Codename: Revolution: the Nintendo Wii Video Game Console. Platform studies is a quintessentially Digital Humanities approach, since it’s explicitly focused on the interrelationship of computing and cultural expression. According to the series preface, the goal of platform studies is “to consider the lowest level of computing systems and to understand how these systems relate to culture and creativity.”In practice, this involves paying close attentionto specific hardware and software interactions--to the vertical relationships between a platform’s multilayered materialities (Hayles; Kirschenbaum),from transistors to code to cultural reception. Any given act of platform-studies analysis may focus for example on the relationship between the chipset and the OS, or between the graphics processor and display parameters or game developers’ designs.In computing terms, platform is an abstraction(Bogost and Montfort), a pragmatic frame placed around whatever hardware-and-software configuration is required in order to build or run certain specificapplications (including creative works). The object of platform studies is thus a shifting series of possibility spaces, any number of dynamic thresholds between discrete levels of a system