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Signal Processing and Machine Learning for Biomedical Data
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Signal Processing and Machine Learning for Biomedical Data

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Computing and Artificial Intelligence".

Deadline for manuscript submissions: closed (31 July 2020) | Viewed by 108396

Special Issue Editors

Prof. Dr. Giuseppe Raso

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Guest Editor
Department of Physics and Chemistry, University of Palermo, 90133 Palermo, Italy
Interests: medical imaging; artificial intelligence; applied physics; high-energy physics
Prof. Dr. Donato Cascio

E-Mail Website
Guest Editor
Dipartimento di Fisica e Chimica-“E. Segrè”, Università di Palermo, 90133 Palermo, Italy
Interests: artificial intelligence; applied physics; medical imaging; artificial vision
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue focus on advanced techniques in signal processing, analysis, modelling, and classification, applied to a variety of medical diagnostic problems. Biomedical data play a fundamental role in many fields of research and clinical practice. Very often the complexity of these data and their large volume makes it necessary to develop advanced analysis techniques and systems. Furthermore, the introduction of new techniques and methodologies for diagnostic purposes, especially in the field of medical imaging, requires new signal processing and machine learning methods.

The recent progress in machine learning techniques, and in particular deep learning, has revolutionized various fields of artificial vision, significantly pushing the state of the art of artificial vision systems into a wide range of high-level tasks. Such progress can help address problems in the analysis of biomedical data.

This Special Issue places particular emphasis on contributions dealing with practical, applications-led research on the use of methods and devices in clinical diagnosis and patient monitoring and management.

Prof. Dr. Giuseppe Raso
Prof. Dr. Donato Cascio
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Applied Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Computer-aided diagnosis
  • Artificial neural networks
  • Machine learning
  • Deep learning
  • Big data
  • Pattern recognition
  • Image reconstruction
  • Multi-modality fusion
  • Medical image analysis
  • Statistical pattern recognition
  • Segmentation
  • Image fusion
  • Image retrieval. biological imaging Molecular/pathologic image analysis gene data analysis multiple modalities X-ray CT MRI PET ultrasound

Published Papers (22 papers)

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Editorial

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5 pages, 196 KiB  
Editorial
Special Issue on Signal Processing and Machine Learning for Biomedical Data
by Giuseppe Raso and Donato Cascio
Appl. Sci. 2021, 11(8), 3399; https://0-doi-org.brum.beds.ac.uk/10.3390/app11083399 - 10 Apr 2021
Cited by 1 | Viewed by 1329
Abstract
This Special Issue is focused on advanced techniques in signal processing, analysis, modelling, and classification, applied to a variety of medical diagnostic problems [...] Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)

Research

Jump to: Editorial, Other

11 pages, 1399 KiB  
Article
Breast Cancer Mass Detection in DCE–MRI Using Deep-Learning Features Followed by Discrimination of Infiltrative vs. In Situ Carcinoma through a Machine-Learning Approach
by Luana Conte, Benedetta Tafuri, Maurizio Portaluri, Alessandro Galiano, Eleonora Maggiulli and Giorgio De Nunzio
Appl. Sci. 2020, 10(17), 6109; https://0-doi-org.brum.beds.ac.uk/10.3390/app10176109 - 03 Sep 2020
Cited by 12 | Viewed by 2469
Abstract
Breast cancer is the leading cause of cancer deaths worldwide in women. This aggressive tumor can be categorized into two main groups—in situ and infiltrative, with the latter being the most common malignant lesions. The current use of magnetic resonance imaging (MRI) was [...] Read more.
Breast cancer is the leading cause of cancer deaths worldwide in women. This aggressive tumor can be categorized into two main groups—in situ and infiltrative, with the latter being the most common malignant lesions. The current use of magnetic resonance imaging (MRI) was shown to provide the highest sensitivity in the detection and discrimination between benign vs. malignant lesions, when interpreted by expert radiologists. In this article, we present the prototype of a computer-aided detection/diagnosis (CAD) system that could provide valuable assistance to radiologists for discrimination between in situ and infiltrating tumors. The system consists of two main processing levels—(1) localization of possibly tumoral regions of interest (ROIs) through an iterative procedure based on intensity values (ROI Hunter), followed by a deep-feature extraction and classification method for false-positive rejection; and (2) characterization of the selected ROIs and discrimination between in situ and invasive tumor, consisting of Radiomics feature extraction and classification through a machine-learning algorithm. The CAD system was developed and evaluated using a DCE–MRI image database, containing at least one confirmed mass per image, as diagnosed by an expert radiologist. When evaluating the accuracy of the ROI Hunter procedure with respect to the radiologist-drawn boundaries, sensitivity to mass detection was found to be 75%. The AUC of the ROC curve for discrimination between in situ and infiltrative tumors was 0.70. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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21 pages, 2114 KiB  
Article
Automatic Segmentation and Classification of Heart Sounds Using Modified Empirical Wavelet Transform and Power Features
by Pedro Narváez, Steven Gutierrez and Winston S. Percybrooks
Appl. Sci. 2020, 10(14), 4791; https://0-doi-org.brum.beds.ac.uk/10.3390/app10144791 - 13 Jul 2020
Cited by 27 | Viewed by 4302
Abstract
A system for the automatic classification of cardiac sounds can be of great help for doctors in the diagnosis of cardiac diseases. Generally speaking, the main stages of such systems are (i) the pre-processing of the heart sound signal, (ii) the segmentation of [...] Read more.
A system for the automatic classification of cardiac sounds can be of great help for doctors in the diagnosis of cardiac diseases. Generally speaking, the main stages of such systems are (i) the pre-processing of the heart sound signal, (ii) the segmentation of the cardiac cycles, (iii) feature extraction and (iv) classification. In this paper, we propose methods for each of these stages. The modified empirical wavelet transform (EWT) and the normalized Shannon average energy are used in pre-processing and automatic segmentation to identify the systolic and diastolic intervals in a heart sound recording; then, six power characteristics are extracted (three for the systole and three for the diastole)—the motivation behind using power features is to achieve a low computational cost to facilitate eventual real-time implementations. Finally, different models of machine learning (support vector machine (SVM), k-nearest neighbor (KNN), random forest and multilayer perceptron) are used to determine the classifier with the best performance. The automatic segmentation method was tested with the heart sounds from the Pascal Challenge database. The results indicated an error (computed as the sum of the differences between manual segmentation labels from the database and the segmentation labels obtained by the proposed algorithm) of 843,440.8 for dataset A and 17,074.1 for dataset B, which are better values than those reported with the state-of-the-art methods. For automatic classification, 805 sample recordings from different databases were used. The best accuracy result was 99.26% using the KNN classifier, with a specificity of 100% and a sensitivity of 98.57%. These results compare favorably with similar works using the state-of-the-art methods. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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18 pages, 545 KiB  
Article
Combined Generative Adversarial Network and Fuzzy C-Means Clustering for Multi-Class Voice Disorder Detection with an Imbalanced Dataset
by Kwok Tai Chui, Miltiadis D. Lytras and Pandian Vasant
Appl. Sci. 2020, 10(13), 4571; https://0-doi-org.brum.beds.ac.uk/10.3390/app10134571 - 01 Jul 2020
Cited by 38 | Viewed by 3199
Abstract
The world has witnessed the success of artificial intelligence deployment for smart healthcare applications. Various studies have suggested that the prevalence of voice disorders in the general population is greater than 10%. An automatic diagnosis for voice disorders via machine learning algorithms is [...] Read more.
The world has witnessed the success of artificial intelligence deployment for smart healthcare applications. Various studies have suggested that the prevalence of voice disorders in the general population is greater than 10%. An automatic diagnosis for voice disorders via machine learning algorithms is desired to reduce the cost and time needed for examination by doctors and speech-language pathologists. In this paper, a conditional generative adversarial network (CGAN) and improved fuzzy c-means clustering (IFCM) algorithm called CGAN-IFCM is proposed for the multi-class voice disorder detection of three common types of voice disorders. Existing benchmark datasets for voice disorders, the Saarbruecken Voice Database (SVD) and the Voice ICar fEDerico II Database (VOICED), use imbalanced classes. A generative adversarial network offers synthetic data to reduce bias in the detection model. Improved fuzzy c-means clustering considers the relationship between adjacent data points in the fuzzy membership function. To explain the necessity of CGAN and IFCM, a comparison is made between the algorithm with CGAN and that without CGAN. Moreover, the performance is compared between IFCM and traditional fuzzy c-means clustering. Lastly, the proposed CGAN-IFCM outperforms existing models in its true negative rate and true positive rate by 9.9–12.9% and 9.1–44.8%, respectively. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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14 pages, 7017 KiB  
Article
A Fast Self-Learning Subspace Reconstruction Method for Non-Uniformly Sampled Nuclear Magnetic Resonance Spectroscopy
by Zhangren Tu, Huiting Liu, Jiaying Zhan and Di Guo
Appl. Sci. 2020, 10(11), 3939; https://0-doi-org.brum.beds.ac.uk/10.3390/app10113939 - 05 Jun 2020
Cited by 4 | Viewed by 2891
Abstract
Multidimensional nuclear magnetic resonance (NMR) spectroscopy is one of the most crucial detection tools for molecular structure analysis and has been widely used in biomedicine and chemistry. However, the development of NMR spectroscopy is hampered by long data collection time. Non-uniform sampling empowers [...] Read more.
Multidimensional nuclear magnetic resonance (NMR) spectroscopy is one of the most crucial detection tools for molecular structure analysis and has been widely used in biomedicine and chemistry. However, the development of NMR spectroscopy is hampered by long data collection time. Non-uniform sampling empowers rapid signal acquisition by collecting a small subset of data. Since the sampling rate is lower than that of the Nyquist sampling ratio, undersampling artifacts arise in reconstructed spectra. To obtain a high-quality spectrum, it is necessary to apply reasonable prior constraints in spectrum reconstruction models. The self-learning subspace method has been shown to possess superior advantages than that of the state-of-the-art low-rank Hankel matrix method when adopting high acceleration in data sampling. However, the self-learning subspace method is time-consuming due to the singular value decomposition in iterations. In this paper, we propose a fast self-learning subspace method to enable fast and high-quality reconstructions. Aided by parallel computing, the experiment results show that the proposed method can reconstruct high-fidelity spectra but spend less than 10% of the time required by the non-parallel self-learning subspace method. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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16 pages, 1597 KiB  
Article
Individual Topological Analysis of Synchronization-Based Brain Connectivity
by Angela Lombardi, Nicola Amoroso, Domenico Diacono, Alfonso Monaco, Sabina Tangaro and Roberto Bellotti
Appl. Sci. 2020, 10(9), 3275; https://0-doi-org.brum.beds.ac.uk/10.3390/app10093275 - 08 May 2020
Cited by 1 | Viewed by 2523
Abstract
Functional connectivity analysis aims at assessing the strength of functional coupling between the signal responses in distinct brain areas. Usually, functional magnetic resonance imaging (fMRI) time series connections are estimated through zero-lag correlation metrics that quantify the statistical similarity between pairs of regions [...] Read more.
Functional connectivity analysis aims at assessing the strength of functional coupling between the signal responses in distinct brain areas. Usually, functional magnetic resonance imaging (fMRI) time series connections are estimated through zero-lag correlation metrics that quantify the statistical similarity between pairs of regions or spectral measures that assess synchronization at a frequency band of interest. Here, we explored the application of a new metric to assess the functional synchronization in phase space between fMRI time series in a resting state. We applied a complete topological analysis to the resulting connectivity matrix to uncover both the macro-scale organization of the brain and detect the most important nodes. The synchronization metric is also compared with Pearson’s correlation coefficient and spectral coherence to highlight similarities and differences between the topologies of the three functional networks. We found that the individual topological organization of the resulting synchronization-based connectivity networks shows a finer modular organization than that identified with the other two metrics and a low overlap with the modular partitions of the other two networks suggesting that the derived topological information is not redundant and could be potentially integrated to provide a multi-scale description of functional connectivity. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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16 pages, 3298 KiB  
Article
Complex Network Characterization Using Graph Theory and Fractal Geometry: The Case Study of Lung Cancer DNA Sequences
by Matej Babič, Jurij Mihelič and Michele Calì
Appl. Sci. 2020, 10(9), 3037; https://0-doi-org.brum.beds.ac.uk/10.3390/app10093037 - 27 Apr 2020
Cited by 19 | Viewed by 3617
Abstract
This paper discusses an approach developed for exploiting the local elementary movements of evolution to study complex networks in terms of shared common embedding and, consequently, shared fractal properties. This approach can be useful for the analysis of lung cancer DNA sequences and [...] Read more.
This paper discusses an approach developed for exploiting the local elementary movements of evolution to study complex networks in terms of shared common embedding and, consequently, shared fractal properties. This approach can be useful for the analysis of lung cancer DNA sequences and their properties by using the concepts of graph theory and fractal geometry. The proposed method advances a renewed consideration of network complexity both on local and global scales. Several researchers have illustrated the advantages of fractal mathematics, as well as its applicability to lung cancer research. Nevertheless, many researchers and clinicians continue to be unaware of its potential. Therefore, this paper aims to examine the underlying assumptions of fractals and analyze the fractal dimension and related measurements for possible application to complex networks and, especially, to the lung cancer network. The strict relationship between the lung cancer network properties and the fractal dimension is proved. Results show that the fractal dimension decreases in the lung cancer network while the topological properties of the network increase in the lung cancer network. Finally, statistical and topological significance between the complexity of the network and lung cancer network is shown. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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15 pages, 3341 KiB  
Article
Development of Computer-Aided Semi-Automatic Diagnosis System for Chronic Post-Stroke Aphasia Classification with Temporal and Parietal Lesions: A Pilot Study
by Bhagya Nathali Silva, Murad Khan, Ruchire Eranga Wijesinghe, Samantha Thelijjagoda and Kijun Han
Appl. Sci. 2020, 10(8), 2984; https://0-doi-org.brum.beds.ac.uk/10.3390/app10082984 - 24 Apr 2020
Cited by 5 | Viewed by 3376
Abstract
Survivors of either a hemorrhagic or ischemic stroke tend to acquire aphasia and experience spontaneous recovery during the first six months. Nevertheless, a considerable number of patients sustain aphasia and require speech and language therapy to overcome the difficulties. As a preliminary study, [...] Read more.
Survivors of either a hemorrhagic or ischemic stroke tend to acquire aphasia and experience spontaneous recovery during the first six months. Nevertheless, a considerable number of patients sustain aphasia and require speech and language therapy to overcome the difficulties. As a preliminary study, this article aims to distinguish aphasia caused from a temporoparietal lesion. Typically, temporal and parietal lesions cause Wernicke’s aphasia and Anomic aphasia. Differential diagnosis between Anomic and Wernicke’s has become controversial and subjective due to the close resemblance of Wernicke’s to Anomic aphasia when recovering. Hence, this article proposes a clinical diagnosis system that incorporates normal coupling between the acoustic frequencies of speech signals and the language ability of temporoparietal aphasias to delineate classification boundary lines. The proposed inspection system is a hybrid scheme consisting of automated components, such as confrontation naming, repetition, and a manual component, such as comprehension. The study was conducted involving 30 participants clinically diagnosed with temporoparietal aphasias after a stroke and 30 participants who had experienced a stroke without aphasia. The plausibility of accurate classification of Wernicke’s and Anomic aphasia was confirmed using the distinctive acoustic frequency profiles of selected controls. Accuracy of the proposed system and algorithm was confirmed by comparing the obtained diagnosis with the conventional manual diagnosis. Though this preliminary work distinguishes between Anomic and Wernicke’s aphasia, we can claim that the developed algorithm-based inspection model could be a worthwhile solution towards objective classification of other aphasia types. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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14 pages, 1120 KiB  
Article
A Novel Simplified Convolutional Neural Network Classification Algorithm of Motor Imagery EEG Signals Based on Deep Learning
by Feng Li, Fan He, Fei Wang, Dengyong Zhang, Yi Xia and Xiaoyu Li
Appl. Sci. 2020, 10(5), 1605; https://0-doi-org.brum.beds.ac.uk/10.3390/app10051605 - 28 Feb 2020
Cited by 69 | Viewed by 5820
Abstract
Left and right hand motor imagery electroencephalogram (MI-EEG) signals are widely used in brain-computer interface (BCI) systems to identify a participant intent in controlling external devices. However, due to a series of reasons, including low signal-to-noise ratios, there are great challenges for efficient [...] Read more.
Left and right hand motor imagery electroencephalogram (MI-EEG) signals are widely used in brain-computer interface (BCI) systems to identify a participant intent in controlling external devices. However, due to a series of reasons, including low signal-to-noise ratios, there are great challenges for efficient motor imagery classification. The recognition of left and right hand MI-EEG signals is vital for the application of BCI systems. Recently, the method of deep learning has been successfully applied in pattern recognition and other fields. However, there are few effective deep learning algorithms applied to BCI systems, particularly for MI based BCI. In this paper, we propose an algorithm that combines continuous wavelet transform (CWT) and a simplified convolutional neural network (SCNN) to improve the recognition rate of MI-EEG signals. Using the CWT, the MI-EEG signals are mapped to time-frequency image signals. Then the image signals are input into the SCNN to extract the features and classify them. Tested by the BCI Competition IV Dataset 2b, the experimental results show that the average classification accuracy of the nine subjects is 83.2%, and the mean kappa value is 0.651, which is 11.9% higher than that of the champion in the BCI Competition IV. Compared with other algorithms, the proposed CWT-SCNN algorithm has a better classification performance and a shorter training time. Therefore, this algorithm could enhance the classification performance of MI based BCI and be applied in real-time BCI systems for use by disabled people. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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23 pages, 66205 KiB  
Article
Phase Space Reconstruction from a Biological Time Series: A Photoplethysmographic Signal Case Study
by Javier de Pedro-Carracedo, David Fuentes-Jimenez, Ana María Ugena and Ana Pilar Gonzalez-Marcos
Appl. Sci. 2020, 10(4), 1430; https://0-doi-org.brum.beds.ac.uk/10.3390/app10041430 - 20 Feb 2020
Cited by 20 | Viewed by 7448
Abstract
In the analysis of biological time series, the state space is comprised of a framework for the study of systems with presumably deterministic and stationary properties. However, a physiological experiment typically captures an observable that characterizes the temporal response of the physiological system [...] Read more.
In the analysis of biological time series, the state space is comprised of a framework for the study of systems with presumably deterministic and stationary properties. However, a physiological experiment typically captures an observable that characterizes the temporal response of the physiological system under study; the dynamic variables that make up the state of the system at any time are not available. Only from the acquired observations should state vectors be reconstructed to emulate the different states of the underlying system. This is what is known as the reconstruction of the state space, called the phase space in real-world signals, in many cases satisfactorily resolved using the method of delays. Each state vector consists of m components, extracted from successive observations delayed a time τ . The morphology of the geometric structure described by the state vectors, as well as their properties depends on the chosen parameters τ and m. The real dynamics of the system under study is subject to the correct determination of the parameters τ and m. Only in this way can be deduced features have true physical meaning, revealing aspects that reliably identify the dynamic complexity of the physiological system. The biological signal presented in this work, as a case study, is the photoplethysmographic (PPG) signal. We find that m is five for all the subjects analyzed and that τ depends on the time interval in which it is evaluated. The Hénon map and the Lorenz flow are used to facilitate a more intuitive understanding of the applied techniques. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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13 pages, 1580 KiB  
Article
Net-Net AutoML Selection of Artificial Neural Network Topology for Brain Connectome Prediction
by Enrique Barreiro, Cristian R. Munteanu, Marcos Gestal, Juan Ramón Rabuñal, Alejandro Pazos, Humberto González-Díaz and Julián Dorado
Appl. Sci. 2020, 10(4), 1308; https://0-doi-org.brum.beds.ac.uk/10.3390/app10041308 - 14 Feb 2020
Cited by 2 | Viewed by 2548
Abstract
Brain Connectome Networks (BCNs) are defined by brain cortex regions (nodes) interacting with others by electrophysiological co-activation (edges). The experimental prediction of new interactions in BCNs represents a difficult task due to the large number of edges and the complex connectivity patterns. Fortunately, [...] Read more.
Brain Connectome Networks (BCNs) are defined by brain cortex regions (nodes) interacting with others by electrophysiological co-activation (edges). The experimental prediction of new interactions in BCNs represents a difficult task due to the large number of edges and the complex connectivity patterns. Fortunately, we can use another special type of networks to achieve this goal—Artificial Neural Networks (ANNs). Thus, ANNs could use node descriptors such as Shannon Entropies (Sh) to predict node connectivity for large datasets including complex systems such as BCN. However, the training of a high number of ANNs for BCNs is a time-consuming task. In this work, we propose the use of a method to automatically determine which ANN topology is more efficient for the BCN prediction. Since a network (ANN) is used to predict the connectivity in another network (BCN), this method was entitled Net-Net AutoML. The algorithm uses Sh descriptors for pairs of nodes in BCNs and for ANN predictors of BCNs. Therefore, it is able to predict the efficiency of new ANN topologies to predict BCNs. The current study used a set of 500,470 examples from 10 different ANNs to predict node connectivity in BCNs and 20 features. After testing five Machine Learning classifiers, the best classification model to predict the ability of an ANN to evaluate node interactions in BCNs was provided by Random Forest (mean test AUROC of 0.9991 ± 0.0001, 10-fold cross-validation). Net-Net AutoML algorithms based on entropy descriptors may become a useful tool in the design of automatic expert systems to select ANN topologies for complex biological systems. The scripts and dataset for this project are available in an open GitHub repository. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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14 pages, 3363 KiB  
Article
A Noniterative Simultaneous Rigid Registration Method for Serial Sections of Biological Tissues
by Chang Shu, Lin-Lin Li, Guoqing Li, Xi Chen and Hua Han
Appl. Sci. 2020, 10(3), 1156; https://0-doi-org.brum.beds.ac.uk/10.3390/app10031156 - 08 Feb 2020
Cited by 1 | Viewed by 1840
Abstract
In this paper, we propose a novel noniterative algorithm to simultaneously estimate optimal rigid transformations for serial section images, which is a key component in performing volume reconstructions of serial sections of biological tissue. To avoid the error accumulation and propagation caused by [...] Read more.
In this paper, we propose a novel noniterative algorithm to simultaneously estimate optimal rigid transformations for serial section images, which is a key component in performing volume reconstructions of serial sections of biological tissue. To avoid the error accumulation and propagation caused by current algorithms, we add an extra condition: that the positions of the first and last section images should remain unchanged. This constrained simultaneous registration problem has not previously been solved. Our solution is noniterative; thus, it can simultaneously compute rigid transformations for a large number of serial section images in a short time. We demonstrate that our algorithm obtains optimal solutions under ideal conditions and shows great robustness under nonideal circumstances. Further, we experimentally show that our algorithm outperforms state-of-the-art methods in terms of speed and accuracy. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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17 pages, 4597 KiB  
Article
A Novel Transfer Learning Based Approach for Pneumonia Detection in Chest X-ray Images
by Vikash Chouhan, Sanjay Kumar Singh, Aditya Khamparia, Deepak Gupta, Prayag Tiwari, Catarina Moreira, Robertas Damaševičius and Victor Hugo C. de Albuquerque
Appl. Sci. 2020, 10(2), 559; https://0-doi-org.brum.beds.ac.uk/10.3390/app10020559 - 12 Jan 2020
Cited by 467 | Viewed by 31618
Abstract
Pneumonia is among the top diseases which cause most of the deaths all over the world. Virus, bacteria and fungi can all cause pneumonia. However, it is difficult to judge the pneumonia just by looking at chest X-rays. The aim of this study [...] Read more.
Pneumonia is among the top diseases which cause most of the deaths all over the world. Virus, bacteria and fungi can all cause pneumonia. However, it is difficult to judge the pneumonia just by looking at chest X-rays. The aim of this study is to simplify the pneumonia detection process for experts as well as for novices. We suggest a novel deep learning framework for the detection of pneumonia using the concept of transfer learning. In this approach, features from images are extracted using different neural network models pretrained on ImageNet, which then are fed into a classifier for prediction. We prepared five different models and analyzed their performance. Thereafter, we proposed an ensemble model that combines outputs from all pretrained models, which outperformed individual models, reaching the state-of-the-art performance in pneumonia recognition. Our ensemble model reached an accuracy of 96.4% with a recall of 99.62% on unseen data from the Guangzhou Women and Children’s Medical Center dataset. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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22 pages, 7383 KiB  
Article
AISAC: An Artificial Immune System for Associative Classification Applied to Breast Cancer Detection
by David González-Patiño, Yenny Villuendas-Rey, Amadeo José Argüelles-Cruz, Oscar Camacho-Nieto and Cornelio Yáñez-Márquez
Appl. Sci. 2020, 10(2), 515; https://0-doi-org.brum.beds.ac.uk/10.3390/app10020515 - 10 Jan 2020
Cited by 11 | Viewed by 3272
Abstract
Early breast cancer diagnosis is crucial, as it can prevent further complications and save the life of the patient by treating the disease at its most curable stage. In this paper, we propose a new artificial immune system model for associative classification with [...] Read more.
Early breast cancer diagnosis is crucial, as it can prevent further complications and save the life of the patient by treating the disease at its most curable stage. In this paper, we propose a new artificial immune system model for associative classification with competitive performance for breast cancer detection. The proposed model has its foundations in the biological immune system; it mimics the detection skills of the immune system to provide correct identification of antigens. The Wilcoxon test was used to identify the statistically significant differences between our proposal and other classification algorithms based on the same bio-inspired model. These statistical tests evidenced the enhanced performance shown by the proposed model by outperforming other immune-based algorithms. The proposed model proved to be competitive with respect to other well-known classification models. In addition, the model benefits from a low computational cost. The success of this model for classification tasks shows that swarm intelligence is useful for this kind of problem, and that it is not limited to optimization tasks. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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11 pages, 2393 KiB  
Article
A Non-Contact Photoplethysmography Technique for the Estimation of Heart Rate via Smartphone
by J. Rodolfo Maestre-Rendon, Tomas A. Rivera-Roman, Arturo A. Fernandez-Jaramillo, Nancy E. Guerrón Paredes and José Javier Serrano Olmedo
Appl. Sci. 2020, 10(1), 154; https://0-doi-org.brum.beds.ac.uk/10.3390/app10010154 - 23 Dec 2019
Cited by 11 | Viewed by 3407
Abstract
This paper describes the development of an application for mobile devices under the iOS platform which has the objective of monitoring patients with alterations or affections from cardiac pathologies. The software tool developed for mobile devices provides a patient and a specialist doctor [...] Read more.
This paper describes the development of an application for mobile devices under the iOS platform which has the objective of monitoring patients with alterations or affections from cardiac pathologies. The software tool developed for mobile devices provides a patient and a specialist doctor the ability to handle and treat disease remotely while monitoring through the technique of non-contact photoplethysmography (PPG). The mobile application works by processing red, green, and blue (RGB) color video images on a specific region of the face, thus obtaining the intensity of the pixels in the green channel. The results are then processed using mathematical algorithms and Fourier transform, moving from the time domain to the frequency domain to ensure proper interpretation and to obtain the pulses per minute (PPM). The results are favorable because a comparison of the results was made with respect to the application of a medical-grade pulse-oximeter, where an error rate of 3% was obtained, indicating the acceptable performance of our application. The present technological development provides an application tool with significant potential in the area of health. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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27 pages, 4071 KiB  
Article
Automatic Segmentation of Coronary Arteries in X-ray Angiograms using Multiscale Analysis and Artificial Neural Networks
by Fernando Cervantes-Sanchez, Ivan Cruz-Aceves, Arturo Hernandez-Aguirre, Martha Alicia Hernandez-Gonzalez and Sergio Eduardo Solorio-Meza
Appl. Sci. 2019, 9(24), 5507; https://0-doi-org.brum.beds.ac.uk/10.3390/app9245507 - 14 Dec 2019
Cited by 44 | Viewed by 5326
Abstract
This paper presents a novel method for the automatic segmentation of coronary arteries in X-ray angiograms, based on multiscale analysis and neural networks. The multiscale analysis is performed by using Gaussian filters in the spatial domain and Gabor filters in the frequency domain, [...] Read more.
This paper presents a novel method for the automatic segmentation of coronary arteries in X-ray angiograms, based on multiscale analysis and neural networks. The multiscale analysis is performed by using Gaussian filters in the spatial domain and Gabor filters in the frequency domain, which are used as inputs by a multilayer perceptron (MLP) for the enhancement of vessel-like structures. The optimal design of the MLP is selected following a statistical comparative analysis, using a training set of 100 angiograms, and the area under the ROC curve ( A z ) for assessment of the detection performance. The detection results of the proposed method are compared with eleven state-of-the-art blood vessel enhancement methods, obtaining the highest performance of A z = 0.9775 , with a test set of 30 angiograms. The database of 130 X-ray coronary angiograms has been outlined by a specialist and approved by a medical ethics committee. On the other hand, the vessel extraction technique was selected from fourteen binary classification algorithms applied to the multiscale filter response. Finally, the proposed segmentation method is compared with twelve state-of-the-art vessel segmentation methods in terms of six binary evaluation metrics, where the proposed method provided the most accurate coronary arteries segmentation with a classification rate of 0.9698 and Dice coefficient of 0.6857 , using the test set of angiograms. In addition to the experimental results, the performance in the detection and segmentation steps of the proposed method have also shown that it can be highly suitable for systems that perform computer-aided diagnosis in X-ray imaging. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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14 pages, 731 KiB  
Article
Ensemble Discrete Wavelet Transform and Gray-Level Co-Occurrence Matrix for Microcalcification Cluster Classification in Digital Mammography
by Annarita Fanizzi, Teresa Maria Basile, Liliana Losurdo, Roberto Bellotti, Ubaldo Bottigli, Francesco Campobasso, Vittorio Didonna, Alfonso Fausto, Raffaella Massafra, Alberto Tagliafico, Pasquale Tamborra, Sabina Tangaro, Vito Lorusso and Daniele La Forgia
Appl. Sci. 2019, 9(24), 5388; https://0-doi-org.brum.beds.ac.uk/10.3390/app9245388 - 09 Dec 2019
Cited by 38 | Viewed by 3488
Abstract
The presence of clusters of microcalcifications is a primary sign of breast cancer. Their identification is still difficult today for radiologists, and the wrong evaluations involve unnecessary biopsies. In this paper, an automatic tool for characterizing and discriminating clusters of microcalcifications into benign/malignant [...] Read more.
The presence of clusters of microcalcifications is a primary sign of breast cancer. Their identification is still difficult today for radiologists, and the wrong evaluations involve unnecessary biopsies. In this paper, an automatic tool for characterizing and discriminating clusters of microcalcifications into benign/malignant in digital mammograms is proposed. A set of 104 digital mammograms including microcalcification clusters was randomly extracted from a public available database and manually labeled by our radiologists, obtaining 96 abnormal ROIs. For each so-identified ROI, a multi-scale image decomposition based on the Haar wavelet transform was performed. On the decomposition, a textural features extraction step was carried out both on each sub-image and on the corresponding gray-level co-occurrence matrix. Then, a random forest classifier was employed for classifying microcalcification clusters into benign and malignant. The study found that the most discriminant features extracted from the ROIs decomposition by Haar transform were variance and relative smoothness, whereas as regards the textural features calculated on the GLCMs corresponding to the Haar-decomposed ROI, it emerged that the relationship between the pixels of the sub-image in the diagonal direction had high discriminating power for the classification of microcalcification clusters into benign and malignant. The proposed method was evaluated in cross-validation and performed highly in the prediction of the benign/malignant ROIs, with a mean AUC value of 97.39 ± 0.01 % . Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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13 pages, 838 KiB  
Article
Gradient-Guided Convolutional Neural Network for MRI Image Super-Resolution
by Xiaofeng Du and Yifan He
Appl. Sci. 2019, 9(22), 4874; https://0-doi-org.brum.beds.ac.uk/10.3390/app9224874 - 14 Nov 2019
Cited by 14 | Viewed by 3607
Abstract
Super-resolution (SR) technology is essential for improving image quality in magnetic resonance imaging (MRI). The main challenge of MRI SR is to reconstruct high-frequency (HR) details from a low-resolution (LR) image. To address this challenge, we develop a gradient-guided convolutional neural network for [...] Read more.
Super-resolution (SR) technology is essential for improving image quality in magnetic resonance imaging (MRI). The main challenge of MRI SR is to reconstruct high-frequency (HR) details from a low-resolution (LR) image. To address this challenge, we develop a gradient-guided convolutional neural network for improving the reconstruction accuracy of high-frequency image details from the LR image. A gradient prior is fully explored to supply the information of high-frequency details during the super-resolution process, thereby leading to a more accurate reconstructed image. Experimental results of image super-resolution on public MRI databases demonstrate that the gradient-guided convolutional neural network achieves better performance over the published state-of-art approaches. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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11 pages, 1020 KiB  
Article
Multiscale Entropy Analysis with Low-Dimensional Exhaustive Search for Detecting Heart Failure
by Hsuan-Hao Chao, Chih-Wei Yeh, Chang Francis Hsu, Long Hsu and Sien Chi
Appl. Sci. 2019, 9(17), 3496; https://0-doi-org.brum.beds.ac.uk/10.3390/app9173496 - 24 Aug 2019
Cited by 6 | Viewed by 2545
Abstract
Multiscale entropy (MSE) is widely used to analyze heartbeat signals. Even though cardiologists do not use MSE to diagnose heart failure at present, these studies are of importance and have potential clinical applications. In previous studies, MSE discrimination between old congestive heart failure [...] Read more.
Multiscale entropy (MSE) is widely used to analyze heartbeat signals. Even though cardiologists do not use MSE to diagnose heart failure at present, these studies are of importance and have potential clinical applications. In previous studies, MSE discrimination between old congestive heart failure (CHF) and healthy individuals has remained controversial. Few studies have been published on the discrimination between them, using only MSE with machine learning for automatic multidimensional analysis, with reported testing accuracies of less than 86%. In this study, we determined the optimal MSE scales for discrimination by using a low-dimensional exhaustive search along with three classifiers—linear discriminant analysis (LDA), support vector machine (SVM), and k-nearest neighbor (KNN). In younger people (<55 years), the results showed an accuracy of up to 95.5% with two optimal MSE scales (2D) and up to 97.7% with four optimal MSE scales (4D) in discriminating between young CHF and healthy participants. In older people (≥55 years), the discrimination accuracy reached 90.1% using LDA in 2D, SVM in 3D (three optimal MSE scales), and KNN in 5D (five optimal MSE scales). LDA with a 3D exhaustive search also achieved 94.4% accuracy in older people. Therefore, the results indicate that MSE analysis can differentiate between CHF and healthy individuals of any age. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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14 pages, 3344 KiB  
Article
Application of Heartbeat-Attention Mechanism for Detection of Myocardial Infarction Using 12-Lead ECG Records
by Yue Zhang and Jie Li
Appl. Sci. 2019, 9(16), 3328; https://0-doi-org.brum.beds.ac.uk/10.3390/app9163328 - 13 Aug 2019
Cited by 15 | Viewed by 4091
Abstract
Early detection and effective treatment of myocardial infarction can prevent the deterioration of ischemic heart disease and greatly reduce the possibility of sudden death. On the basis of standard 12-lead electrocardiogram (ECG) records, this paper proposes a bidirectional, long short-term memory (Bi-LSTM) network [...] Read more.
Early detection and effective treatment of myocardial infarction can prevent the deterioration of ischemic heart disease and greatly reduce the possibility of sudden death. On the basis of standard 12-lead electrocardiogram (ECG) records, this paper proposes a bidirectional, long short-term memory (Bi-LSTM) network with a heartbeat-attention mechanism to effectively and automatically detect myocardial infarction (MI). First, we divide the standard 12-lead ECG records into sliding windows with the same number of heartbeats. Subsequently, we do not use any labels of heartbeats to train the Bi-LSTM network and the heartbeat-attention mechanism is applied to automatically weight the difference between unlabeled heartbeats. Finally, our method is validated by patients’ complete ECG records and real labels in the Physikalisch-Technische Bundesanstalt (PTB) diagnostic ECG database. When compared with the same network without the heartbeat-attention mechanism or other existing methods, our method achieves comparable or better performance. The accuracy, sensitivity, and specificity reach 94.77%, 95.58%, and 90.48%, respectively. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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20 pages, 2002 KiB  
Technical Note
Performance of Fine-Tuning Convolutional Neural Networks for HEp-2 Image Classification
by Vincenzo Taormina, Donato Cascio, Leonardo Abbene and Giuseppe Raso
Appl. Sci. 2020, 10(19), 6940; https://0-doi-org.brum.beds.ac.uk/10.3390/app10196940 - 03 Oct 2020
Cited by 17 | Viewed by 1928
Abstract
The search for anti-nucleus antibodies (ANA) represents a fundamental step in the diagnosis of autoimmune diseases. The test considered the gold standard for ANA research is indirect immunofluorescence (IIF). The best substrate for ANA detection is provided by Human Epithelial type 2 (HEp-2) [...] Read more.
The search for anti-nucleus antibodies (ANA) represents a fundamental step in the diagnosis of autoimmune diseases. The test considered the gold standard for ANA research is indirect immunofluorescence (IIF). The best substrate for ANA detection is provided by Human Epithelial type 2 (HEp-2) cells. The first phase of HEp-2 type image analysis involves the classification of fluorescence intensity in the positive/negative classes. However, the analysis of IIF images is difficult to perform and particularly dependent on the experience of the immunologist. For this reason, the interest of the scientific community in finding relevant technological solutions to the problem has been high. Deep learning, and in particular the Convolutional Neural Networks (CNNs), have demonstrated their effectiveness in the classification of biomedical images. In this work the efficacy of the CNN fine-tuning method applied to the problem of classification of fluorescence intensity in HEp-2 images was investigated. For this purpose, four of the best known pre-trained networks were analyzed (AlexNet, SqueezeNet, ResNet18, GoogLeNet). The classifying power of CNN was investigated with different training modalities; three levels of freezing weights and scratch. Performance analysis was conducted, in terms of area under the ROC (Receiver Operating Characteristic) curve (AUC) and accuracy, using a public database. The best result achieved an AUC equal to 98.6% and an accuracy of 93.9%, demonstrating an excellent ability to discriminate between the positive/negative fluorescence classes. For an effective performance comparison, the fine-tuning mode was compared to those in which CNNs are used as feature extractors, and the best configuration found was compared with other state-of-the-art works. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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15 pages, 2736 KiB  
Benchmark
Benchmarking MRI Reconstruction Neural Networks on Large Public Datasets
by Zaccharie Ramzi, Philippe Ciuciu and Jean-Luc Starck
Appl. Sci. 2020, 10(5), 1816; https://0-doi-org.brum.beds.ac.uk/10.3390/app10051816 - 06 Mar 2020
Cited by 29 | Viewed by 5633
Abstract
Deep learning is starting to offer promising results for reconstruction in Magnetic Resonance Imaging (MRI). A lot of networks are being developed, but the comparisons remain hard because the frameworks used are not the same among studies, the networks are not properly re-trained, [...] Read more.
Deep learning is starting to offer promising results for reconstruction in Magnetic Resonance Imaging (MRI). A lot of networks are being developed, but the comparisons remain hard because the frameworks used are not the same among studies, the networks are not properly re-trained, and the datasets used are not the same among comparisons. The recent release of a public dataset, fastMRI, consisting of raw k-space data, encouraged us to write a consistent benchmark of several deep neural networks for MR image reconstruction. This paper shows the results obtained for this benchmark, allowing to compare the networks, and links the open source implementation of all these networks in Keras. The main finding of this benchmark is that it is beneficial to perform more iterations between the image and the measurement spaces compared to having a deeper per-space network. Full article
(This article belongs to the Special Issue Signal Processing and Machine Learning for Biomedical Data)
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