482 research outputs found
Self-paced Convolutional Neural Network for Computer Aided Detection in Medical Imaging Analysis
Tissue characterization has long been an important component of Computer
Aided Diagnosis (CAD) systems for automatic lesion detection and further
clinical planning. Motivated by the superior performance of deep learning
methods on various computer vision problems, there has been increasing work
applying deep learning to medical image analysis. However, the development of a
robust and reliable deep learning model for computer-aided diagnosis is still
highly challenging due to the combination of the high heterogeneity in the
medical images and the relative lack of training samples. Specifically,
annotation and labeling of the medical images is much more expensive and
time-consuming than other applications and often involves manual labor from
multiple domain experts. In this work, we propose a multi-stage, self-paced
learning framework utilizing a convolutional neural network (CNN) to classify
Computed Tomography (CT) image patches. The key contribution of this approach
is that we augment the size of training samples by refining the unlabeled
instances with a self-paced learning CNN. By implementing the framework on high
performance computing servers including the NVIDIA DGX1 machine, we obtained
the experimental result, showing that the self-pace boosted network
consistently outperformed the original network even with very scarce manual
labels. The performance gain indicates that applications with limited training
samples such as medical image analysis can benefit from using the proposed
framework.Comment: accepted by 8th International Workshop on Machine Learning in Medical
Imaging (MLMI 2017
Transfer learning for multicenter classification of chronic obstructive pulmonary disease
Chronic obstructive pulmonary disease (COPD) is a lung disease which can be
quantified using chest computed tomography (CT) scans. Recent studies have
shown that COPD can be automatically diagnosed using weakly supervised learning
of intensity and texture distributions. However, up till now such classifiers
have only been evaluated on scans from a single domain, and it is unclear
whether they would generalize across domains, such as different scanners or
scanning protocols. To address this problem, we investigate classification of
COPD in a multi-center dataset with a total of 803 scans from three different
centers, four different scanners, with heterogenous subject distributions. Our
method is based on Gaussian texture features, and a weighted logistic
classifier, which increases the weights of samples similar to the test data. We
show that Gaussian texture features outperform intensity features previously
used in multi-center classification tasks. We also show that a weighting
strategy based on a classifier that is trained to discriminate between scans
from different domains, can further improve the results. To encourage further
research into transfer learning methods for classification of COPD, upon
acceptance of the paper we will release two feature datasets used in this study
on http://bigr.nl/research/projects/copdComment: Accepted at Journal of Biomedical and Health Informatic
Tree-space statistics and approximations for large-scale analysis of anatomical trees
Statistical analysis of anatomical trees is hard to perform due to differences in the topological structure of the trees. In this paper we define statistical properties of leaf-labeled anatomical trees with geometric edge attributes by considering the anatomical trees as points in the geometric space of leaf-labeled trees. This tree-space is a geodesic metric space where any two trees are connected by a unique shortest path, which corresponds to a tree deformation. However, tree-space is not a manifold, and the usual strategy of performing statistical analysis in a tangent space and projecting onto tree-space is not available. Using tree-space and its shortest paths, a variety of statistical properties, such as mean, principal component, hypothesis testing and linear discriminant analysis can be defined. For some of these properties it is still an open problem how to compute them; others (like the mean) can be computed, but efficient alternatives are helpful in speeding up algorithms that use means iteratively, like hypothesis testing. In this paper, we take advantage of a very large dataset (N = 8016) to obtain computable approximations, under the assumption that the data trees parametrize the relevant parts of tree-space well. Using the developed approximate statistics, we illustrate how the structure and geometry of airway trees vary across a population and show that airway trees with Chronic Obstructive Pulmonary Disease come from a different distribution in tree-space than healthy ones. Software is available from http://image.diku.dk/aasa/software.php
Metabolomic profiles predict individual multidisease outcomes
Publisher Copyright: © 2022, The Author(s).Risk stratification is critical for the early identification of high-risk individuals and disease prevention. Here we explored the potential of nuclear magnetic resonance (NMR) spectroscopy-derived metabolomic profiles to inform on multidisease risk beyond conventional clinical predictors for the onset of 24 common conditions, including metabolic, vascular, respiratory, musculoskeletal and neurological diseases and cancers. Specifically, we trained a neural network to learn disease-specific metabolomic states from 168 circulating metabolic markers measured in 117,981 participants with ~1.4 million person-years of follow-up from the UK Biobank and validated the model in four independent cohorts. We found metabolomic states to be associated with incident event rates in all the investigated conditions, except breast cancer. For 10-year outcome prediction for 15 endpoints, with and without established metabolic contribution, a combination of age and sex and the metabolomic state equaled or outperformed established predictors. Moreover, metabolomic state added predictive information over comprehensive clinical variables for eight common diseases, including type 2 diabetes, dementia and heart failure. Decision curve analyses showed that predictive improvements translated into clinical utility for a wide range of potential decision thresholds. Taken together, our study demonstrates both the potential and limitations of NMR-derived metabolomic profiles as a multidisease assay to inform on the risk of many common diseases simultaneously.Peer reviewe
Context Matters: Graph-based Self-supervised Representation Learning for Medical Images
Supervised learning method requires a large volume of annotated datasets.
Collecting such datasets is time-consuming and expensive. Until now, very few
annotated COVID-19 imaging datasets are available. Although self-supervised
learning enables us to bootstrap the training by exploiting unlabeled data, the
generic self-supervised methods for natural images do not sufficiently
incorporate the context. For medical images, a desirable method should be
sensitive enough to detect deviation from normal-appearing tissue of each
anatomical region; here, anatomy is the context. We introduce a novel approach
with two levels of self-supervised representation learning objectives: one on
the regional anatomical level and another on the patient-level. We use graph
neural networks to incorporate the relationship between different anatomical
regions. The structure of the graph is informed by anatomical correspondences
between each patient and an anatomical atlas. In addition, the graph
representation has the advantage of handling any arbitrarily sized image in
full resolution. Experiments on large-scale Computer Tomography (CT) datasets
of lung images show that our approach compares favorably to baseline methods
that do not account for the context. We use the learnt embedding to quantify
the clinical progression of COVID-19 and show that our method generalizes well
to COVID-19 patients from different hospitals. Qualitative results suggest that
our model can identify clinically relevant regions in the images.Comment: Accepted to AAAI 202
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