Deep segmentation of the liver and the hepatic tumors from abdomen tomography images

A pipelined framework is proposed for accurate, automated, simultaneous segmentation of the liver as well as the hepatic tumors from computed tomography (CT) images. The introduced framework composed of three pipelined levels. First, two different transfers deep convolutional neural networks (CNN) are applied to get high-level compact features of CT images. Second, a pixel-wise classifier is used to obtain two output-classified maps for each CNN model. Finally, a fusion neural network (FNN) is used to integrate the two maps. Experimentations performed on the MICCAI’2017 database of the liver tumor segmentation (LITS) challenge, result in a dice similarity coefficient (DSC) of 93.5% for the segmentation of the liver and of 74.40% for the segmentation of the lesion, using a 5-fold cross-validation scheme. Comparative results with the state-of-the-art techniques on the same data show the competing performance of the proposed framework for simultaneous liver and tumor segmentation.

Myocardial Infarction Quantification from Late Gadolinium Enhancement MRI Using Top-Hat Transforms and Neural Networks

Late gadolinium enhancement (LGE) MRI is the gold standard technique for myocardial viability assessment. Although the technique accurately reflects the damaged tissue, there is no clinical standard to quantify myocardial infarction (MI). Moreover, commercial software used in clinical practice are mostly semi-automatic, and hence require direct intervention of experts. In this work, a new automatic method for MI quantification from LGE-MRI is proposed. Our novel segmentation approach is devised for accurately detecting not only hyper-enhanced lesions, but also microvascular obstruction areas. Moreover, it includes a myocardial disease detection step which extends the algorithm for working under healthy scans. The method is based on a cascade approach where firstly, diseased slices are identified by a convolutional neural network (CNN). Secondly, by means of morphological operations a fast coarse scar segmentation is obtained. Thirdly, the segmentation is refined by a boundary-voxel reclassification strategy using an ensemble of very light CNNs. We tested the method on a LGE-MRI database with healthy (n = 20) and diseased (n = 80) cases following a 5-fold cross-validation scheme. Our approach segmented myocardial scars with an average Dice coefficient of 77.22 ± 14.3% and with a volumetric error of 1.0 ± 6.9 cm3. In a comparison against nine reference algorithms, the proposed method achieved the highest agreement in volumetric scar quantification with the expert delineations (p< 0.001 when compared to the other approaches). Moreover, it was able to reproduce the scar segmentation intra- and inter-rater variability. Our approach was shown to be a good first attempt towards automatic and accurate myocardial scar segmentation, although validation over larger LGE-MRI databases is needed.

An Adaptive Piecewise Harmonic Analysis Method for Reconstructing Multi-Year Sea Surface Chlorophyll-A Time Series

High-quality remotely sensed satellite data series are important for many ecological and environmental applications. Unfortunately, irregular spatiotemporal samples, frequent image gaps and inevitable observational biases can greatly hinder their application. As one of the most effective gap filling and noise reduction approaches, the harmonic analysis of time series (HANTS) method has been widely used to reconstruct geographical variables; however, when applied on multi-year time series over large spatial areas, the optimal harmonic formulas are generally varied in different locations or change across different years. The question of how to choose the optimal harmonic formula is still unanswered due to the deficiency of appropriate criteria. In this study, an adaptive piecewise harmonic analysis method (AP-HA) is proposed to reconstruct multi-year seasonal data series. The method introduces a cross-validation scheme to adaptively determine the optimal harmonic model and employs an iterative piecewise scheme to better track the local traits. Whenapplied to the satellite-derived sea surface chlorophyll-a time series over the Bohai and Yellow Seas of China, the AP-HA obtains reliable reconstruction results and outperforms the conventional HANTS methods, achieving improved accuracy. Due to its generic approach to filling missing observations and tracking detailed traits, the AP-HA method has a wide range of applications for other seasonal geographical variables.

Application of augmented topic model to predicting biomarkers and therapeutic targets using multiple human disease-omics datasets

Human diseases are multifactorial - hence it is important to characterize diseases on the basis of multiple disease-omics. However, the capability of the existing methods is largely limited to classifying diseases based on a single type or a few closely related omics data. Herein, we report a topic model framework that allows for characterizing diseases according to their multiple omics data. We also show that this method can be utilized to predict potential biomarkers and/or therapeutic targets. In this study, we illustrate a computational concept of this augmented topic model and demonstrate its prediction performance by a leave one-disease features out cross-validation scheme. Furthermore, we exploit this method together with human disease tissue/organ-transcriptome data and identify putative biomarkers and/or therapeutic targets across 79 diseases. In conclusion, this method and the prediction framework shown reported herein provide important tools for understanding complex human diseases and also facilitate diagnostic and/or therapeutic development.

Steganography in Color Animated Image Sequence for Secret Data Sharing Using Secure Hash Algorithm

This paper presents a high capacity steganographic approach with secret message validation scheme at the receiver end. The proposed idea develops specifically for animated GIF, the cover media, to conceal secret text messages where Least Significant Digit (LSD) method is employed to embed secret information in the form of ASCII value. To validate the secret information at the receiver end, the secret text is encoded with Secure Hash Algorithm-1(SHA1) which is subsequently embedded in certain pre-defined portion of the cover media. The proposed algorithm is experimented on a large set of colored animated image sequences by varying text messages which produces satisfactory results. The proposed method also maintains good visual perceptibility while securing high embedding capacity

Loss of Smell and Taste Can Accurately Predict COVID-19 Infection: A Machine-Learning Approach

The COVID-19 outbreak has spread extensively around the world. Loss of smell and taste have emerged as main predictors for COVID-19. The objective of our study is to develop a comprehensive machine learning (ML) modelling framework to assess the predictive value of smell and taste disorders, along with other symptoms, in COVID-19 infection. A multicenter case-control study was performed, in which suspected cases for COVID-19, who were tested by real-time reverse-transcription polymerase chain reaction (RT-PCR), informed about the presence and severity of their symptoms using visual analog scales (VAS). ML algorithms were applied to the collected data to predict a COVID-19 diagnosis using a 50-fold cross-validation scheme by randomly splitting the patients in training (75%) and testing datasets (25%). A total of 777 patients were included. Loss of smell and taste were found to be the symptoms with higher odds ratios of 6.21 and 2.42 for COVID-19 positivity. The ML algorithms applied reached an average accuracy of 80%, a sensitivity of 82%, and a specificity of 78% when using VAS to predict a COVID-19 diagnosis. This study concludes that smell and taste disorders are accurate predictors, with ML algorithms constituting helpful tools for COVID-19 diagnostic prediction.