Distributional Semantic Models for Clinical Text Applied to Health Record Summarization

As information systems in the health sector are becoming increasingly computerized, large amounts of care-related information are being stored electronically. In hospitals clinicians continuously document treatment and care given to patients in electronic health record (EHR) systems. Much of the information being documented is in the form of clinical notes, or narratives, containing primarily unstructured free-text information. For each care episode, clinical notes are written on a regular basis, ending with a discharge summary that basically summarizes the care episode. Although EHR systems are helpful for storing and managing such information, there is an unrealized potential in utilizing this information for smarter care assistance, as well as for secondary purposes such as research and education. Advances in clinical language processing are enabling computers to assist clinicians in their interaction with the free-text information documented in EHR systems. This includes assisting in tasks like query-based search, terminology development, knowledge extraction, translation, and summarization. This thesis explores various computerized approaches and methods aimed at enabling automated semantic textual similarity assessment and information extraction based on the free-text information in EHR systems. The focus is placed on the task of (semi-)automated summarization of the clinical notes written during individual care episodes. The overall theme of the presented work is to utilize resource-light approaches and methods, circumventing the need to manually develop knowledge resources or training data. Thus, to enable computational semantic textual similarity assessment, word distribution statistics are derived from large training corpora of clinical free text and stored as vector-based representations referred to as distributional semantic models. Also resource-light methods are explored in the task of performing automatic summarization of clinical freetext information, relying on semantic textual similarity assessment. Novel and experimental methods are presented and evaluated that focus on: a) distributional semantic models trained in an unsupervised manner from statistical information derived from large unannotated clinical free-text corpora; b) representing and computing semantic similarities between linguistic items of different granularity, primarily words, sentences and clinical notes; and c) summarizing clinical free-text information from individual care episodes. Results are evaluated against gold standards that reflect human judgements. The results indicate that the use of distributional semantics is promising as a resource-light approach to automated capturing of semantic textual similarity relations from unannotated clinical text corpora. Here it is important that the semantics correlate with the clinical terminology, and with various semantic similarity assessment tasks. Improvements over classical approaches are achieved when the underlying vector-based representations allow for a broader range of semantic features to be captured and represented. These are either distributed over multiple semantic models trained with different features and training corpora, or use models that store multiple sense-vectors per word. Further, the use of structured meta-level information accompanying care episodes is explored as training features for distributional semantic models, with the aim of capturing semantic relations suitable for care episode-level information retrieval. Results indicate that such models performs well in clinical information retrieval. It is shown that a method called Random Indexing can be modified to construct distributional semantic models that capture multiple sense-vectors for each word in the training corpus. This is done in a way that retains the original training properties of the Random Indexing method, by being incremental, scalable and distributional. Distributional semantic models trained with a framework called Word2vec, which relies on the use of neural networks, outperform those trained using the classic Random Indexing method in several semantic similarity assessment tasks, when training is done using comparable parameters and the same training corpora. Finally, several statistical features in clinical text are explored in terms of their ability to indicate sentence significance in a text summary generated from the clinical notes. This includes the use of distributional semantics to enable case-based similarity assessment, where cases are other care episodes and their “solutions”, i.e., discharge summaries. A type of manual evaluation is performed, where human experts rates the different aspects of the summaries using a evaluation scheme/tool. In addition, the original clinician-written discharge summaries are explored as gold standard for the purpose of automated evaluation. Evaluation shows a high correlation between manual and automated evaluation, suggesting that such a gold standard can function as a proxy for human evaluations. --- This thesis has been published jointly with Norwegian University of Science and Technology, Norway and University of Turku, Finland.This thesis has beenpublished jointly with Norwegian University of Science and Technology, Norway.Siirretty Doriast

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

How LinkedIn Economic Graph Bonds Information and Product: Applications in LinkedIn Salary

The LinkedIn Salary product was launched in late 2016 with the goal of providing insights on compensation distribution to job seekers, so that they can make more informed decisions when discovering and assessing career opportunities. The compensation insights are provided based on data collected from LinkedIn members and aggregated in a privacy-preserving manner. Given the simultaneous desire for computing robust, reliable insights and for having insights to satisfy as many job seekers as possible, a key challenge is to reliably infer the insights at the company level when there is limited or no data at all. We propose a two-step framework that utilizes a novel, semantic representation of companies (Company2vec) and a Bayesian statistical model to address this problem. Our approach makes use of the rich information present in the LinkedIn Economic Graph, and in particular, uses the intuition that two companies are likely to be similar if employees are very likely to transition from one company to the other and vice versa. We compute embeddings for companies by analyzing the LinkedIn members' company transition data using machine learning algorithms, then compute pairwise similarities between companies based on these embeddings, and finally incorporate company similarities in the form of peer company groups as part of the proposed Bayesian statistical model to predict insights at the company level. We perform extensive validation using several different evaluation techniques, and show that we can significantly increase the coverage of insights while, in fact, even improving the quality of the obtained insights. For example, we were able to compute salary insights for 35 times as many title-region-company combinations in the U.S. as compared to previous work, corresponding to 4.9 times as many monthly active users. Finally, we highlight the lessons learned from deployment of our system.Comment: 10 pages, 5 figure

Six papers on computational methods for the analysis of structured and unstructured data in the economic domain

This work investigates the application of computational methods for structured and unstructured data. The domains of application are two closely connected fields with the common goal of promoting the stability of the financial system: systemic risk and bank supervision. The work explores different families of models and applies them to different tasks: graphical Gaussian network models to address bank interconnectivity, topic models to monitor bank news and deep learning for text classification. New applications and variants of these models are investigated posing a particular attention on the combined use of textual and structured data. In the penultimate chapter is introduced a sentiment polarity classification tool in Italian, based on deep learning, to simplify future researches relying on sentiment analysis. The different models have proven useful for leveraging numerical (structured) and textual (unstructured) data. Graphical Gaussian Models and Topic models have been adopted for inspection and descriptive tasks while deep learning has been applied more for predictive (classification) problems. Overall, the integration of textual (unstructured) and numerical (structured) information has proven useful for systemic risk and bank supervision related analysis. The integration of textual data with numerical data in fact, has brought either to higher predictive performances or enhanced capability of explaining phenomena and correlating them to other events.This work investigates the application of computational methods for structured and unstructured data. The domains of application are two closely connected fields with the common goal of promoting the stability of the financial system: systemic risk and bank supervision. The work explores different families of models and applies them to different tasks: graphical Gaussian network models to address bank interconnectivity, topic models to monitor bank news and deep learning for text classification. New applications and variants of these models are investigated posing a particular attention on the combined use of textual and structured data. In the penultimate chapter is introduced a sentiment polarity classification tool in Italian, based on deep learning, to simplify future researches relying on sentiment analysis. The different models have proven useful for leveraging numerical (structured) and textual (unstructured) data. Graphical Gaussian Models and Topic models have been adopted for inspection and descriptive tasks while deep learning has been applied more for predictive (classification) problems. Overall, the integration of textual (unstructured) and numerical (structured) information has proven useful for systemic risk and bank supervision related analysis. The integration of textual data with numerical data in fact, has brought either to higher predictive performances or enhanced capability of explaining phenomena and correlating them to other events

Luonnollisen kielen käsittelyn menetelmät sanojen samankaltaisuuden mittaamisessa

An artificial intelligence application considered in this thesis was harnessed to extract competencies from job descriptions and higher education curricula written in natural language. Using these extracted competencies, the application is able to visualize the skills supply of the schools and the skills demand of the labor market. However, to understand natural language, computer must learn to evaluate the relatedness between words. The aim of the thesis is to propose the best methods for open text data mining and measuring the semantic similarity and relatedness between words. Different words can have similar meanings in natural language. The computer can learn the relatedness between words mainly by two different methods. We can construct an ontology from the studied domain, which models the concepts of the domain as well as the relations between them. The ontology can be considered as a directed graph. The nodes are the concepts of the domain and the edges between the nodes describe their relations. The semantic similarity between the concepts can be computed based on the distance and the strength of the relations between them. The other way to measure the word relatedness is based on statistical language models. The model learns the similarity between words relying on their probability distribution in large corpora. The words appearing in similar contexts, i.e., surrounded by similar words, tend to have similar meanings. The words are often represented as continuous distributed word vectors, each dimension representing some feature of the word. The feature can be either semantic, syntactic or morphological. However, the feature is latent, and usually not under understandable to a human. If the angle between the word vectors in the feature space is small, the words share same features and hence are similar. The study was conducted by reviewing available literature and implementing a web scraper for retrieving open text data from the web. The scraped data was fed into the AI application, which extracted the skills from the data and visualized the result in semantic maps