Towards a New Science of a Clinical Data Intelligence

In this paper we define Clinical Data Intelligence as the analysis of data generated in the clinical routine with the goal of improving patient care. We define a science of a Clinical Data Intelligence as a data analysis that permits the derivation of scientific, i.e., generalizable and reliable results. We argue that a science of a Clinical Data Intelligence is sensible in the context of a Big Data analysis, i.e., with data from many patients and with complete patient information. We discuss that Clinical Data Intelligence requires the joint efforts of knowledge engineering, information extraction (from textual and other unstructured data), and statistics and statistical machine learning. We describe some of our main results as conjectures and relate them to a recently funded research project involving two major German university hospitals.Comment: NIPS 2013 Workshop: Machine Learning for Clinical Data Analysis and Healthcare, 201

Highly accurate model for prediction of lung nodule malignancy with CT scans

Computed tomography (CT) examinations are commonly used to predict lung nodule malignancy in patients, which are shown to improve noninvasive early diagnosis of lung cancer. It remains challenging for computational approaches to achieve performance comparable to experienced radiologists. Here we present NoduleX, a systematic approach to predict lung nodule malignancy from CT data, based on deep learning convolutional neural networks (CNN). For training and validation, we analyze >1000 lung nodules in images from the LIDC/IDRI cohort. All nodules were identified and classified by four experienced thoracic radiologists who participated in the LIDC project. NoduleX achieves high accuracy for nodule malignancy classification, with an AUC of ~0.99. This is commensurate with the analysis of the dataset by experienced radiologists. Our approach, NoduleX, provides an effective framework for highly accurate nodule malignancy prediction with the model trained on a large patient population. Our results are replicable with software available at http://bioinformatics.astate.edu/NoduleX

High-Throughput Classification of Radiographs Using Deep Convolutional Neural Networks.

The study aimed to determine if computer vision techniques rooted in deep learning can use a small set of radiographs to perform clinically relevant image classification with high fidelity. One thousand eight hundred eighty-five chest radiographs on 909 patients obtained between January 2013 and July 2015 at our institution were retrieved and anonymized. The source images were manually annotated as frontal or lateral and randomly divided into training, validation, and test sets. Training and validation sets were augmented to over 150,000 images using standard image manipulations. We then pre-trained a series of deep convolutional networks based on the open-source GoogLeNet with various transformations of the open-source ImageNet (non-radiology) images. These trained networks were then fine-tuned using the original and augmented radiology images. The model with highest validation accuracy was applied to our institutional test set and a publicly available set. Accuracy was assessed by using the Youden Index to set a binary cutoff for frontal or lateral classification. This retrospective study was IRB approved prior to initiation. A network pre-trained on 1.2 million greyscale ImageNet images and fine-tuned on augmented radiographs was chosen. The binary classification method correctly classified 100 % (95 % CI 99.73-100 %) of both our test set and the publicly available images. Classification was rapid, at 38 images per second. A deep convolutional neural network created using non-radiological images, and an augmented set of radiographs is effective in highly accurate classification of chest radiograph view type and is a feasible, rapid method for high-throughput annotation