51,345 research outputs found
Building a semantically annotated corpus of clinical texts
In this paper, we describe the construction of a semantically annotated corpus of clinical texts for use in the development and evaluation of systems for automatically extracting clinically significant information from the textual component of patient records. The paper details the sampling of textual material from a collection of 20,000 cancer patient records, the development of a semantic annotation scheme, the annotation methodology, the distribution of annotations in the final corpus, and the use of the corpus for development of an adaptive information extraction system. The resulting corpus is the most richly semantically annotated resource for clinical text processing built to date, whose value has been demonstrated through its use in developing an effective information extraction system. The detailed presentation of our corpus construction and annotation methodology will be of value to others seeking to build high-quality semantically annotated corpora in biomedical domains
A Robust Interpretable Deep Learning Classifier for Heart Anomaly Detection Without Segmentation
Traditionally, abnormal heart sound classification is framed as a three-stage
process. The first stage involves segmenting the phonocardiogram to detect
fundamental heart sounds; after which features are extracted and classification
is performed. Some researchers in the field argue the segmentation step is an
unwanted computational burden, whereas others embrace it as a prior step to
feature extraction. When comparing accuracies achieved by studies that have
segmented heart sounds before analysis with those who have overlooked that
step, the question of whether to segment heart sounds before feature extraction
is still open. In this study, we explicitly examine the importance of heart
sound segmentation as a prior step for heart sound classification, and then
seek to apply the obtained insights to propose a robust classifier for abnormal
heart sound detection. Furthermore, recognizing the pressing need for
explainable Artificial Intelligence (AI) models in the medical domain, we also
unveil hidden representations learned by the classifier using model
interpretation techniques. Experimental results demonstrate that the
segmentation plays an essential role in abnormal heart sound classification.
Our new classifier is also shown to be robust, stable and most importantly,
explainable, with an accuracy of almost 100% on the widely used PhysioNet
dataset
Recommended from our members
An improved hidden vector state model approach and its adaptation in extracting protein interaction information from biomedical literature
Large quantity of knowledge, which is important for biological researchers to unveil the mechanism of life, often hides in the literature, such as journal articles, reports, books and so on. Many approaches focusing on extracting information from unstructured text, such as pattern matching, shallow and full parsing, have been proposed especially for biomedical applications. In this paper, we present an information extraction system employing a semantic parser using the Hidden Vector State (HVS) model for protein-protein interactions. We found that it performed better than other established statistical methods and achieved 58.3% and 76.8% in recall and precision respectively. Moreover, the pure data-driven HVS model can be easily adapted to other domains, which is rarely mentioned and possessed by other approaches. Experimental results prove that the model trained on one domain can still generate satisfactory results when shifting to another domain with a small amount of adaptation training data
Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text
We advance the state of the art in biomolecular interaction extraction with
three contributions: (i) We show that deep, Abstract Meaning Representations
(AMR) significantly improve the accuracy of a biomolecular interaction
extraction system when compared to a baseline that relies solely on surface-
and syntax-based features; (ii) In contrast with previous approaches that infer
relations on a sentence-by-sentence basis, we expand our framework to enable
consistent predictions over sets of sentences (documents); (iii) We further
modify and expand a graph kernel learning framework to enable concurrent
exploitation of automatically induced AMR (semantic) and dependency structure
(syntactic) representations. Our experiments show that our approach yields
interaction extraction systems that are more robust in environments where there
is a significant mismatch between training and test conditions.Comment: Appearing in Proceedings of the Thirtieth AAAI Conference on
Artificial Intelligence (AAAI-16
A comparison of parsing technologies for the biomedical domain
This paper reports on a number of experiments which are designed to investigate the extent to which current nlp resources are able to syntactically and semantically analyse biomedical text. We address two tasks: parsing a real corpus with a hand-built widecoverage grammar, producing both syntactic analyses and logical forms; and automatically computing the interpretation of compound nouns where the head is a nominalisation (e.g., hospital arrival means an arrival at hospital, while patient arrival means an arrival of a patient). For the former task we demonstrate that exible and yet constrained `preprocessing ' techniques are crucial to success: these enable us to use part-of-speech tags to overcome inadequate lexical coverage, and to `package up' complex technical expressions prior to parsing so that they are blocked from creating misleading amounts of syntactic complexity. We argue that the xml-processing paradigm is ideally suited for automatically preparing the corpus for parsing. For the latter task, we compute interpretations of the compounds by exploiting surface cues and meaning paraphrases, which in turn are extracted from the parsed corpus. This provides an empirical setting in which we can compare the utility of a comparatively deep parser vs. a shallow one, exploring the trade-o between resolving attachment ambiguities on the one hand and generating errors in the parses on the other. We demonstrate that a model of the meaning of compound nominalisations is achievable with the aid of current broad-coverage parsers
- ā¦