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Multi-Label Annotation of Chest Abdomen Pelvis Computed Tomography Text Reports Using Deep Learning

arXiv.org Artificial Intelligence

To develop a high throughput multi-label annotator for body Computed Tomography (CT) reports that can be applied to a variety of diseases, organs, and cases. First, we used a dictionary approach to develop a rule-based algorithm (RBA) for extraction of disease labels from radiology text reports. We targeted three organ systems (lungs/pleura, liver/gallbladder, kidneys/ureters) with four diseases per system based on their prevalence in our dataset. To expand the algorithm beyond pre-defined keywords, an attention-guided recurrent neural network (RNN) was trained using the RBA-extracted labels to classify the reports as being positive for one or more diseases or normal for each organ system. Confounding effects on model performance were evaluated using random or pre-trained embedding as well as different sizes of training datasets. Performance was evaluated using the receiver operating characteristic (ROC) area under the curve (AUC) against 2,158 manually obtained labels. Our model extracted disease labels from 261,229 radiology reports of 112,501 unique subjects. Pre-trained models outperformed random embedding across all diseases. As the training dataset size was reduced, performance was robust except for a few diseases with relatively small number of cases. Pre-trained Classification AUCs achieved > 0.95 for all five disease outcomes across all three organ systems. Our label-extracting pipeline was able to encompass a variety of cases and diseases by generalizing beyond strict rules with exceptional accuracy. As a framework, this model can be easily adapted to enable automated labeling of hospital-scale medical data sets for training image-based disease classifiers.


Deep Learning to Quantify Pulmonary Edema in Chest Radiographs

#artificialintelligence

"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This article will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. To develop a machine learning model to classify the severity grades of pulmonary edema on chest radiographs. In this retrospective study, 369,071 chest radiographs and associated radiology reports from 64,581 (mean age, 51.71; 54.51% women) patients from the MIMIC-CXR chest radiograph dataset were included.


A Scalable Machine Learning Approach for Inferring Probabilistic US-LI-RADS Categorization

arXiv.org Artificial Intelligence

We propose a scalable computerized approach for large-scale inference of Liver Imaging Reporting and Data System (LI-RADS) final assessment categories in narrative ultrasound (US) reports. Although our model was trained on reports created using a LI-RADS template, it was also able to infer LI-RADS scoring for unstructured reports that were created before the LI-RADS guidelines were established. No human-labelled data was required in any step of this study; for training, LI-RADS scores were automatically extracted from those reports that contained structured LI-RADS scores, and it translated the derived knowledge to reasoning on unstructured radiology reports. By providing automated LI-RADS categorization, our approach may enable standardizing screening recommendations and treatment planning of patients at risk for hepatocellular carcinoma, and it may facilitate AI-based healthcare research with US images by offering large scale text mining and data gathering opportunities from standard hospital clinical data repositories.


CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison

arXiv.org Artificial Intelligence

Large, labeled datasets have driven deep learning methods to achieve expert-level performance on a variety of medical imaging tasks. We present CheXpert, a large dataset that contains 224,316 chest radiographs of 65,240 patients. We design a labeler to automatically detect the presence of 14 observations in radiology reports, capturing uncertainties inherent in radiograph interpretation. We investigate different approaches to using the uncertainty labels for training convolutional neural networks that output the probability of these observations given the available frontal and lateral radiographs. On a validation set of 200 chest radiographic studies which were manually annotated by 3 board-certified radiologists, we find that different uncertainty approaches are useful for different pathologies. We then evaluate our best model on a test set composed of 500 chest radiographic studies annotated by a consensus of 5 board-certified radiologists, and compare the performance of our model to that of 3 additional radiologists in the detection of 5 selected pathologies. On Cardiomegaly, Edema, and Pleural Effusion, the model ROC and PR curves lie above all 3 radiologist operating points. We release the dataset to the public as a standard benchmark to evaluate performance of chest radiograph interpretation models. The dataset is freely available at https://stanfordmlgroup.github.io/competitions/chexpert .


Query-Focused EHR Summarization to Aid Imaging Diagnosis

arXiv.org Machine Learning

Electronic Health Records (EHRs) provide vital contextual information to radiologists and other physicians when making a diagnosis. Unfortunately, because a given patient's record may contain hundreds of notes and reports, identifying relevant information within these in the short time typically allotted to a case is very difficult. We propose and evaluate models that extract relevant text snippets from patient records to provide a rough case summary intended to aid physicians considering one or more diagnoses. This is hard because direct supervision (i.e., physician annotations of snippets relevant to specific diagnoses in medical records) is prohibitively expensive to collect at scale. We propose a distantly supervised strategy in which we use groups of International Classification of Diseases (ICD) codes observed in 'future' records as noisy proxies for 'downstream' diagnoses. Using this we train a transformer-based neural model to perform extractive summarization conditioned on potential diagnoses. This model defines an attention mechanism that is conditioned on potential diagnoses (queries) provided by the diagnosing physician. We train (via distant supervision) and evaluate variants of this model on EHR data from a local hospital and MIMIC-III (the latter to facilitate reproducibility). Evaluations performed by radiologists demonstrate that these distantly supervised models yield better extractive summaries than do unsupervised approaches. Such models may aid diagnosis by identifying sentences in past patient reports that are clinically relevant to a potential diagnoses.