Natural Language Processing to Quantify Microbial Keratitis Measurements.
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ABSTRACT:
SUBMITTER: Maganti N
PROVIDER: S-EPMC6875613 | biostudies-literature | 2019 Dec
REPOSITORIES: biostudies-literature
Publications
Natural Language Processing to Quantify Microbial Keratitis Measurements.
Maganti Nenita N Tan Huan H Niziol Leslie M LM Amin Sejal S Hou Andrew A Singh Karandeep K Ballouz Dena D Woodward Maria A MA
Ophthalmology 20190611 12
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Project description:BackgroundAccumulating quantitative outcome parameters may contribute to constructing a healthcare organization in which outcomes of clinical procedures are reproducible and predictable. In imaging studies, measurements are the principal category of quantitative para meters.ObjectivesThe purpose of this work is to develop and evaluate two natural language processing engines that extract finding and organ measurements from narrative radiology reports and to categorize extracted measurements by their "temporality".MethodsThe measurement extraction engine is developed as a set of regular expressions. The engine was evaluated against a manually created ground truth. Automated categorization of measurement temporality is defined as a machine learning problem. A ground truth was manually developed based on a corpus of radiology reports. A maximum entropy model was created using features that characterize the measurement itself and its narrative context. The model was evaluated in a ten-fold cross validation protocol.ResultsThe measurement extraction engine has precision 0.994 and recall 0.991. Accuracy of the measurement classification engine is 0.960.ConclusionsThe work contributes to machine understanding of radiology reports and may find application in software applications that process medical data.
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Project description:BackgroundLanguage impairment is an important marker of neurodegenerative disorders. Despite this, there is no universal system of terminology used to describe these impairments and large inter-rater variability can exist between clinicians assessing language. The use of natural language processing (NLP) and automated speech analysis (ASA) is emerging as a novel and potentially more objective method to assess language in individuals with mild cognitive impairment (MCI) and Alzheimer's dementia (AD). No studies have analyzed how variables extracted through NLP and ASA might also be correlated to language impairments identified by a clinician.MethodsAudio recordings (n=30) from participants with AD, MCI, and controls were rated by clinicians for word-finding difficulty, incoherence, perseveration, and errors in speech. Speech recordings were also transcribed, and linguistic and acoustic variables were extracted through NLP and ASA. Correlations between clinician-rated speech characteristics and the variables were compared using Spearman's correlation. Exploratory factor analysis was applied to find common factors between variables for each speech characteristic.ResultsClinician agreement was high in three of the four speech characteristics: word-finding difficulty (ICC = 0.92, p<0.001), incoherence (ICC = 0.91, p<0.001), and perseveration (ICC = 0.88, p<0.001). Word-finding difficulty and incoherence were useful constructs at distinguishing MCI and AD from controls, while perseveration and speech errors were less relevant. Word-finding difficulty as a construct was explained by three factors, including number and duration of pauses, word duration, and syntactic complexity. Incoherence was explained by two factors, including increased average word duration, use of past tense, and changes in age of acquisition, and more negative valence.ConclusionsVariables extracted through automated acoustic and linguistic analysis of MCI and AD speech were significantly correlated with clinician ratings of speech and language characteristics. Our results suggest that correlating NLP and ASA with clinician observations is an objective and novel approach to measuring speech and language changes in neurodegenerative disorders.
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Project description:In this paper we present a new method for automatic transliteration and segmentation of Unicode cuneiform glyphs using Natural Language Processing (NLP) techniques. Cuneiform is one of the earliest known writing system in the world, which documents millennia of human civilizations in the ancient Near East. Hundreds of thousands of cuneiform texts were found in the nineteenth and twentieth centuries CE, most of which are written in Akkadian. However, there are still tens of thousands of texts to be published. We use models based on machine learning algorithms such as recurrent neural networks (RNN) with an accuracy reaching up to 97% for automatically transliterating and segmenting standard Unicode cuneiform glyphs into words. Therefore, our method and results form a major step towards creating a human-machine interface for creating digitized editions. Our code, Akkademia, is made publicly available for use via a web application, a python package, and a github repository.
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Project description:We address the problem of calibrating prediction confidence for output entities of interest in natural language processing (NLP) applications. It is important that NLP applications such as named entity recognition and question answering produce calibrated confidence scores for their predictions, especially if the applications are to be deployed in a safety-critical domain such as healthcare. However, the output space of such structured prediction models is often too large to adapt binary or multi-class calibration methods directly. In this study, we propose a general calibration scheme for output entities of interest in neural network based structured prediction models. Our proposed method can be used with any binary class calibration scheme and a neural network model. Additionally, we show that our calibration method can also be used as an uncertainty-aware, entity-specific decoding step to improve the performance of the underlying model at no additional training cost or data requirements. We show that our method outperforms current calibration techniques for named-entity-recognition, part-of-speech and question answering. We also improve our model's performance from our decoding step across several tasks and benchmark datasets. Our method improves the calibration and model performance on out-ofdomain test scenarios as well.
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Project description:BackgroundDespite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear.ResultsPaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article.ConclusionWe show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully.
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Project description:IntroductionThis study investigates whether it is possible to predict a final diagnosis based on a written nephropathological description-as a surrogate for image analysis-using various NLP methods.MethodsFor this work, 1107 unlabelled nephropathological reports were included. (i) First, after separating each report into its microscopic description and diagnosis section, the diagnosis sections were clustered unsupervised to less than 20 diagnostic groups using different clustering techniques. (ii) Second, different text classification methods were used to predict the diagnostic group based on the microscopic description section.ResultsThe best clustering results (i) could be achieved with HDBSCAN, using BoW-based feature extraction methods. Based on keywords, these clusters can be mapped to certain diagnostic groups. A transformer encoder-based approach as well as an SVM worked best regarding diagnosis prediction based on the histomorphological description (ii). Certain diagnosis groups reached F1-scores of up to 0.892 while others achieved weak classification metrics.ConclusionWhile textual morphological description alone enables retrieving the correct diagnosis for some entities, it does not work sufficiently for other entities. This is in accordance with a previous image analysis study on glomerular change patterns, where some diagnoses are associated with one pattern, but for others, there exists a complex pattern combination.
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Project description:ObjectiveStructured data on mammographic findings are difficult to obtain without manual review. We developed and evaluated a rule-based natural language processing (NLP) system to extract mammographic findings from free-text mammography reports.Materials and methodsThe NLP system extracted four mammographic findings: mass, calcification, asymmetry, and architectural distortion, using a dictionary look-up method on 93,705 mammography reports from Group Health. Status annotations and anatomical location annotation were associated to each NLP detected finding through association rules. After excluding negated, uncertain, and historical findings, affirmative mentions of detected findings were summarized. Confidence flags were developed to denote reports with highly confident NLP results and reports with possible NLP errors. A random sample of 100 reports was manually abstracted to evaluate the accuracy of the system.ResultsThe NLP system correctly coded 96-99 out of our sample of 100 reports depending on findings. Measures of sensitivity, specificity and negative predictive values exceeded 0.92 for all findings. Positive predictive values were relatively low for some findings due to their low prevalence.DiscussionOur NLP system was implemented entirely in SAS Base, which makes it portable and easy to implement. It performed reasonably well with multiple applications, such as using confidence flags as a filter to improve the efficiency of manual review. Refinements of library and association rules, and testing on more diverse samples may further improve its performance.ConclusionOur NLP system successfully extracts clinically useful information from mammography reports. Moreover, SAS is a feasible platform for implementing NLP algorithms.
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Project description:ObjectiveTo provide a scoping review of papers on clinical natural language processing (NLP) shared tasks that use publicly available electronic health record data from a cohort of patients.Materials and methodsWe searched 6 databases, including biomedical research and computer science literature databases. A round of title/abstract screening and full-text screening were conducted by 2 reviewers. Our method followed the PRISMA-ScR guidelines.ResultsA total of 35 papers with 48 clinical NLP tasks met inclusion criteria between 2007 and 2021. We categorized the tasks by the type of NLP problems, including named entity recognition, summarization, and other NLP tasks. Some tasks were introduced as potential clinical decision support applications, such as substance abuse detection, and phenotyping. We summarized the tasks by publication venue and dataset type.DiscussionThe breadth of clinical NLP tasks continues to grow as the field of NLP evolves with advancements in language systems. However, gaps exist with divergent interests between the general domain NLP community and the clinical informatics community for task motivation and design, and in generalizability of the data sources. We also identified issues in data preparation.ConclusionThe existing clinical NLP tasks cover a wide range of topics and the field is expected to grow and attract more attention from both general domain NLP and clinical informatics community. We encourage future work to incorporate multidisciplinary collaboration, reporting transparency, and standardization in data preparation. We provide a listing of all the shared task papers and datasets from this review in a GitLab repository.
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