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Register a new userIntelligent Word Embeddings of Free-Text Radiology Reports
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Added by
Imon Banerjee
Publication date
2017
fields
Informatics Engineering
and research's language is
English
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Radiology reports are a rich resource for advancing deep learning applications in medicine by leveraging the large volume of data continuously being updated, integrated, and shared. However, there are significant challenges as well, largely due to the ambiguity and subtlety of natural language. We propose a hybrid strategy that combines semantic-dictionary mapping and word2vec modeling for creating dense vector embeddings of free-text radiology reports. Our method leverages the benefits of both semantic-dictionary mapping as well as unsupervised learning. Using the vector representation, we automatically classify the radiology reports into three classes denoting confidence in the diagnosis of intracranial hemorrhage by the interpreting radiologist. We performed experiments with varying hyperparameter settings of the word embeddings and a range of different classifiers. Best performance achieved was a weighted precision of 88% and weighted recall of 90%. Our work offers the potential to leverage unstructured electronic health record data by allowing direct analysis of narrative clinical notes.
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Despite the rapid development of natural language processing (NLP) implementation in electronic medical records (EMRs), Chinese EMRs processing remains challenging due to the limited corpus and specific grammatical characteristics, especially for radiology reports. In this study, we designed an NLP pipeline for the direct extraction of clinically relevant features from Chinese radiology reports, which is the first key step in computer-aided radiologic diagnosis. The pipeline was comprised of named entity recognition, synonyms normalization, and relationship extraction to finally derive the radiological features composed of one or more terms. In named entity recognition, we incorporated lexicon into deep learning model bidirectional long short-term memory-conditional random field (BiLSTM-CRF), and the model finally achieved an F1 score of 93.00%. With the extracted radiological features, least absolute shrinkage and selection operator and machine learning methods (support vector machine, random forest, decision tree, and logistic regression) were used to build the classifiers for liver cancer prediction. For liver cancer diagnosis, random forest had the highest predictive performance in liver cancer diagnosis (F1 score 86.97%, precision 87.71%, and recall 86.25%). This work was a comprehensive NLP study focusing on Chinese radiology reports and the application of NLP in cancer risk prediction. The proposed NLP pipeline for the radiological feature extraction could be easily implemented in other kinds of Chinese clinical texts and other disease predictive tasks.
Learning knowledge graph embedding from an existing knowledge graph is very important to knowledge graph completion. For a fact $(h,r,t)$ with the head entity $h$ having a relation $r$ with the tail entity $t$, the current approaches aim to learn low dimensional representations $(mathbf{h},mathbf{r},mathbf{t})$, each of which corresponds to the elements in $(h, r, t)$, respectively. As $(mathbf{h},mathbf{r},mathbf{t})$ is learned from the existing facts within a knowledge graph, these representations can not be used to detect unknown facts (if the entities or relations never occur in the knowledge graph). This paper proposes a new approach called TransW, aiming to go beyond the current work by composing knowledge graph embeddings using word embeddings. Given the fact that an entity or a relation contains one or more words (quite often), it is sensible to learn a mapping function from word embedding spaces to knowledge embedding spaces, which shows how entities are constructed using human words. More importantly, composing knowledge embeddings using word embeddings makes it possible to deal with the emerging new facts (either new entities or relations). Experimental results using three public datasets show the consistency and outperformance of the proposed TransW.
We present Query2Prod2Vec, a model that grounds lexical representations for product search in product embeddings: in our model, meaning is a mapping between words and a latent space of products in a digital shop. We leverage shopping sessions to learn the underlying space and use merchandising annotations to build lexical analogies for evaluation: our experiments show that our model is more accurate than known techniques from the NLP and IR literature. Finally, we stress the importance of data efficiency for product search outside of retail giants, and highlight how Query2Prod2Vec fits with practical constraints faced by most practitioners.
Inspired by Curriculum Learning, we propose a consecutive (i.e., image-to-text-to-text) generation framework where we divide the problem of radiology report generation into two steps. Contrary to generating the full radiology report from the image at once, the model generates global concepts from the image in the first step and then reforms them into finer and coherent texts using a transformer architecture. We follow the transformer-based sequence-to-sequence paradigm at each step. We improve upon the state-of-the-art on two benchmark datasets.
Segmental models are sequence prediction models in which scores of hypotheses are based on entire variable-length segments of frames. We consider segmental models for whole-word (acoustic-to-word) speech recognition, with the feature vectors defined using vector embeddings of segments. Such models are computationally challenging as the number of paths is proportional to the vocabulary size, which can be orders of magnitude larger than when using subword units like phones. We describe an efficient approach for end-to-end whole-word segmental models, with forward-backward and Viterbi decoding performed on a GPU and a simple segment scoring function that reduces space complexity. In addition, we investigate the use of pre-training via jointly trained acoustic word embeddings (AWEs) and acoustically grounded word embeddings (AGWEs) of written word labels. We find that word error rate can be reduced by a large margin by pre-training the acoustic segment representation with AWEs, and additional (smaller) gains can be obtained by pre-training the word prediction layer with AGWEs. Our final models improve over prior A2W models.
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