Wikipedia-Based Automatic Diagnosis Prediction in Clinical Decision Support Systems

When making clinical decisions, physicians often consult biomedical literatures for reference. In this case, an effective clinical decision support system, provided with a patient’s health information, should be able to generate accurate queries and return to the physicians with useful articles. Related works in the Clinical Decision Support (CDS) track of TREC 2015 demonstrated the usefulness of knowing patients’ diagnosis information for supporting more effective retrieval, but the diagnosis information is often missing in most cases. Furthermore, it is still a great challenge to perform large-scale automatic diagnosis prediction. This motivates us to propose an automatic diagnosis prediction method to enhance the retrieval in a clinical decision support system, where the evidence for the prediction is extracted from Wikipedia. Through the evaluation conducted on 2014 CDS tasks, our method reaches the best performance among all submitted runs. In the next step, graph structured evidence will be integrated to make the prediction more accurate

BigEAR: Inferring the Ambient and Emotional Correlates from Smartphone-based Acoustic Big Data

This paper presents a novel BigEAR big data framework that employs psychological audio processing chain (PAPC) to process smartphone-based acoustic big data collected when the user performs social conversations in naturalistic scenarios. The overarching goal of BigEAR is to identify moods of the wearer from various activities such as laughing, singing, crying, arguing, and sighing. These annotations are based on ground truth relevant for psychologists who intend to monitor/infer the social context of individuals coping with breast cancer. We pursued a case study on couples coping with breast cancer to know how the conversations affect emotional and social well being. In the state-of-the-art methods, psychologists and their team have to hear the audio recordings for making these inferences by subjective evaluations that not only are time-consuming and costly, but also demand manual data coding for thousands of audio files. The BigEAR framework automates the audio analysis. We computed the accuracy of BigEAR with respect to the ground truth obtained from a human rater. Our approach yielded overall average accuracy of 88.76% on real-world data from couples coping with breast cancer.Comment: 6 pages, 10 equations, 1 Table, 5 Figures, IEEE International Workshop on Big Data Analytics for Smart and Connected Health 2016, June 27, 2016, Washington DC, US

Sense-based biomedical indexing and retrieval

International audienceThis paper tackles the problem of term ambiguity, especially for biomedical literature. We propose and evaluate two methods of Word Sense Disambiguation (WSD) for biomedical terms and integrate them to a sense-based document indexing and retrieval framework. Ambiguous biomedical terms in documents and queries are disambiguated using the Medical Subject Headings (MeSH) thesaurus and semantically indexed with their associated correct sense. Experimental evaluation carried out on the TREC9-FT 2000 collection shows that our approach of WSD and sense-based indexing and retrieval is promising

A New Term Frequency with Gaussian Technique for Text Classification and Sentiment Analysis

This paper proposes a new term frequency with a Gaussian technique (TF-G) to classify the risk of suicide from Thai clinical notes and to perform sentiment analysis based on Thai customer reviews and English tweets of travelers that use US airline services. This research compared TF-G with term weighting techniques based on Thai text classification methods from previous researches, including the bag-of-words (BoW), term frequency (TF), term frequency-inverse document frequency (TF-IDF), and term frequency-inverse corpus document frequency (TF-ICF) techniques. Suicide risk classification and sentiment analysis were performed with the decision tree (DT), naïve Bayes (NB), support vector machine (SVM), random forest (RF), and multilayer perceptron (MLP) techniques. The experimental results showed that TF-G is appropriate for feature extraction to classify the risk of suicide and to analyze the sentiments of customer reviews and tweets of travelers. The TF-G technique was more accurate than BoW, TF, TF-IDF and TF-ICF for term weighting in Thai suicide risk classification, for term weighting in sentiment analysis of Thai customer reviews for Burger King, Pizza Hut, and Sizzler restaurants, and for the sentiment analysis of English tweets of travelers using US airline services

A comparative study of machine learning methods for verbal autopsy text classification

A Verbal Autopsy is the record of an interview about the circumstances of an uncertified death. In developing countries, if a death occurs away from health facilities, a field-worker interviews a relative of the deceased about the circumstances of the death; this Verbal Autopsy can be reviewed offsite. We report on a comparative study of the processes involved in Text Classification applied to classifying Cause of Death: feature value representation; machine learning classification algorithms; and feature reduction strategies in order to identify the suitable approaches applicable to the classification of Verbal Autopsy text. We demonstrate that normalised term frequency and the standard TFiDF achieve comparable performance across a number of classifiers. The results also show Support Vector Machine is superior to other classification algorithms employed in this research. Finally, we demonstrate the effectiveness of employing a ’locally-semisupervised’ feature reduction strategy in order to increase performance accuracy

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

Feedforward and feedback control in apraxia of speech: effects of noise masking on vowel production

PURPOSE: This study was designed to test two hypotheses about apraxia of speech (AOS) derived from the Directions Into Velocities of Articulators (DIVA) model (Guenther et al., 2006): the feedforward system deficit hypothesis and the feedback system deficit hypothesis. METHOD: The authors used noise masking to minimize auditory feedback during speech. Six speakers with AOS and aphasia, 4 with aphasia without AOS, and 2 groups of speakers without impairment (younger and older adults) participated. Acoustic measures of vowel contrast, variability, and duration were analyzed. RESULTS: Younger, but not older, speakers without impairment showed significantly reduced vowel contrast with noise masking. Relative to older controls, the AOS group showed longer vowel durations overall (regardless of masking condition) and a greater reduction in vowel contrast under masking conditions. There were no significant differences in variability. Three of the 6 speakers with AOS demonstrated the group pattern. Speakers with aphasia without AOS did not differ from controls in contrast, duration, or variability. CONCLUSION: The greater reduction in vowel contrast with masking noise for the AOS group is consistent with the feedforward system deficit hypothesis but not with the feedback system deficit hypothesis; however, effects were small and not present in all individual speakers with AOS. Theoretical implications and alternative interpretations of these findings are discussed.R01 DC002852 - NIDCD NIH HHS; R01 DC007683 - NIDCD NIH HH