Pulmonary/Respiratory Diseases

Integrating genomic features for non-invasive early lung cancer detection


Radiologic screening of high-risk adults reduces lung-cancer-related mortality1,2; however, a small minority of eligible individuals undergo such screening in the United States3,4. The availability of blood-based tests could increase screening uptake. Here we introduce improvements to cancer personalized profiling by deep sequencing (CAPP-Seq)5, a method for the analysis of circulating tumour DNA (ctDNA), to better facilitate screening applications. We show that, although levels are very low in early-stage lung cancers, ctDNA is present prior to treatment in most patients and its presence is strongly prognostic. We also find that the majority of somatic mutations in the cell-free DNA (cfDNA) of patients with lung cancer and of risk-matched controls reflect clonal haematopoiesis and are non-recurrent.

AI system can predict air pollution before it happens


Air pollution kills an estimated seven million people every year and cities around the world are being forced to take action to do what they can to lower the risk to inhabitants. A team of Loughborough University computer scientists believe their AI system has the potential to provide new insight into the environmental factors that have significant impacts on air pollution levels. In particular it focuses on the amount of'PM2.5' In 2013, a study involving 312,944 people in nine European countries revealed that there was no safe level of particulates. PM2.5 particulates were found to be particularly deadly, blamed for a 36 per cent increase in lung cancer per 10 μg/m3 as they can penetrate deep into the lungs.

Researchers create AI that listens for coughs and sneezes to identify respiratory illnesses

Daily Mail - Science & tech

Researchers from the University of Massachusetts Amherst have created an AI that listens for coughing and sneezing sounds to estimate what percentage of people in a public space have a respiratory illness. The device, called FluSense, was initially tested over an eight month period in four clinic waiting rooms on the university's campus. In addition to recording'non-speech' audio samples, FluSense is also equipped with a thermal camera to scan for people with elevated temperatures. According to its co-creator, Tauhidur Rahman, the device isn't meant to single out individual cases of illness but capture trends at the population level to see if something is developing that may not yet have been picked up in medical testing. 'I thought if we could capture coughing or sneezing sounds from public spaces where a lot of people naturally congregate, we could utilize this information as a new source of data for predicting epidemiologic trends,' he told UMass Amherst's news blog.

£2.5m trial of AI system to help patients at risk of lung failure


Doctors are turning to artificial intelligence in a bid to boost survival rates for the sickest NHS patients. Researchers at Imperial College London are to trial a device at the Royal Brompton hospital, in Chelsea, that will aim to reduce the risk to patients on ventilators in intensive care units. Four in five ICU patients require ventilation to help them breathe but there is a danger of over-inflating the lungs, causing their condition to deteriorate and leading to fatal lung failure. About a quarter of ventilated patients already have acute respiratory distress syndrome (ARDS) -- placing them at higher risk of effectively drowning. The £2.5 million study, funded by the EU's Horizon 2020 programme, will use software that controls the amount of air on a breath-by-breath basis -- and which can sound an alert if the patient's lungs start deteriorating.

Weak Supervision in Convolutional Neural Network for Semantic Segmentation of Diffuse Lung Diseases Using Partially Annotated Dataset

arXiv.org Machine Learning

Computer-aided diagnosis system for diffuse lung diseases (DLDs) is necessary for the objective assessment of the lung diseases. In this paper, we develop semantic segmentation model for 5 kinds of DLDs. DLDs considered in this work are consolidation, ground glass opacity, honeycombing, emphysema, and normal. Convolutional neural network (CNN) is one of the most promising technique for semantic segmentation among machine learning algorithms. While creating annotated dataset for semantic segmentation is laborious and time consuming, creating partially annotated dataset, in which only one chosen class is annotated for each image, is easier since annotators only need to focus on one class at a time during the annotation task. In this paper, we propose a new weak supervision technique that effectively utilizes partially annotated dataset. The experiments using partially annotated dataset composed 372 CT images demonstrated that our proposed technique significantly improved segmentation accuracy.

Estimating the number and effect sizes of non-null hypotheses

arXiv.org Machine Learning

We study the problem of estimating the distribution of effect sizes (the mean of the test statistic under the alternate hypothesis) in a multiple testing setting. Knowing this distribution allows us to calculate the power (type II error) of any experimental design. We show that it is possible to estimate this distribution using an inexpensive pilot experiment, which takes significantly fewer samples than would be required by an experiment that identified the discoveries. Our estimator can be used to guarantee the number of discoveries that will be made using a given experimental design in a future experiment. We prove that this simple and computationally efficient estimator enjoys a number of favorable theoretical properties, and demonstrate its effectiveness on data from a gene knockout experiment on influenza inhibition in Drosophila.

Generative-based Airway and Vessel Morphology Quantification on Chest CT Images

arXiv.org Machine Learning

Accurately and precisely characterizing the morphology of small pulmonary structures from Computed Tomography (CT) images, such as airways and vessels, is becoming of great importance for diagnosis of pulmonary diseases. The smaller conducting airways are the major site of increased airflow resistance in chronic obstructive pulmonary disease (COPD), while accurately sizing vessels can help identify arterial and venous changes in lung regions that may determine future disorders. However, traditional methods are often limited due to image resolution and artifacts. We propose a Convolutional Neural Regressor (CNR) that provides cross-sectional measurement of airway lumen, airway wall thickness, and vessel radius. CNR is trained with data created by a generative model of synthetic structures which is used in combination with Simulated and Unsupervised Generative Adversarial Network (SimGAN) to create simulated and refined airways and vessels with known ground-truth. For validation, we first use synthetically generated airways and vessels produced by the proposed generative model to compute the relative error and directly evaluate the accuracy of CNR in comparison with traditional methods. Then, in-vivo validation is performed by analyzing the association between the percentage of the predicted forced expiratory volume in one second (FEV1\%) and the value of the Pi10 parameter, two well-known measures of lung function and airway disease, for airways. For vessels, we assess the correlation between our estimate of the small-vessel blood volume and the lungs' diffusing capacity for carbon monoxide (DLCO). The results demonstrate that Convolutional Neural Networks (CNNs) provide a promising direction for accurately measuring vessels and airways on chest CT images with physiological correlates.

Quantifying the Value of Lateral Views in Deep Learning for Chest X-rays

arXiv.org Machine Learning

Most deep learning models in chest X-ray prediction utilize the posteroanterior (PA) view due to the lack of other views available. PadChest is a large-scale chest X-ray dataset that has almost 200 labels and multiple views available. In this work, we use PadChest to explore multiple approaches to merging the PA and lateral views for predicting the radiological labels associated with the X-ray image. We find that different methods of merging the model utilize the lateral view differently. We also find that including the lateral view increases performance for 32 labels in the dataset, while being neutral for the others. The increase in overall performance is comparable to the one obtained by using only the PA view with twice the amount of patients in the training set.

Separation of target anatomical structure and occlusions in chest radiographs

arXiv.org Machine Learning

Chest radiographs are commonly performed low-cost exams for screening and diagnosis. However, radiographs are 2D representations of 3D structures causing considerable clutter impeding visual inspection and automated image analysis. Here, we propose a Fully Convolutional Network to suppress, for a specific task, undesired visual structure from radiographs while retaining the relevant image information such as lung-parenchyma. The proposed algorithm creates reconstructed radiographs and ground-truth data from high resolution CT-scans. Results show that removing visual variation that is irrelevant for a classification task improves the performance of a classifier when only limited training data are available. This is particularly relevant because a low number of ground-truth cases is common in medical imaging.