Filter and Wrapper Stacking Ensemble (FWSE): a robust approach for reliable biomarker discovery in high-dimensional omics data.

Selecting informative features, such as accurate biomarkers for disease diagnosis, prognosis and response to treatment, is an essential task in the field of bioinformatics. Medical data often contain thousands of features and identifying potential biomarkers is challenging due to small number of samples in the data, method dependence and non-reproducibility. This paper proposes a novel ensemble feature selection method, named Filter and Wrapper Stacking Ensemble (FWSE), to identify reproducible biomarkers from high-dimensional omics data. In FWSE, filter feature selection methods are run on numerous subsets of the data to eliminate irrelevant features, and then wrapper feature selection methods are applied to rank the top features. The method was validated on four high-dimensional medical datasets related to mental illnesses and cancer. The results indicate that the features selected by FWSE are stable and statistically more significant than the ones obtained by existing methods while also demonstrating biological relevance. Furthermore, FWSE is a generic method, applicable to various high-dimensional datasets in the fields of machine intelligence and bioinformatics.

Integrating Spatial and Temporal Information for Violent Activity Detection from Video Using Deep Spiking Neural Networks.

Increasing violence in workplaces such as hospitals seriously challenges public safety. However, it is time- and labor-consuming to visually monitor masses of video data in real time. Therefore, automatic and timely violent activity detection from videos is vital, especially for small monitoring systems. This paper proposes a two-stream deep learning architecture for video violent activity detection named SpikeConvFlowNet. First, RGB frames and their optical flow data are used as inputs for each stream to extract the spatiotemporal features of videos. After that, the spatiotemporal features from the two streams are concatenated and fed to the classifier for the final decision. Each stream utilizes a supervised neural network consisting of multiple convolutional spiking and pooling layers. Convolutional layers are used to extract high-quality spatial features within frames, and spiking neurons can efficiently extract temporal features across frames by remembering historical information. The spiking neuron-based optical flow can strengthen the capability of extracting critical motion information. This method combines their advantages to enhance the performance and efficiency for recognizing violent actions. The experimental results on public datasets demonstrate that, compared with the latest methods, this approach greatly reduces parameters and achieves higher inference efficiency with limited accuracy loss. It is a potential solution for applications in embedded devices that provide low computing power but require fast processing speeds.

Denoising of Fluorescence Image on the Surface of Quantum Dot/Nanoporous Silicon Biosensors.

In the process of biological detection of porous silicon photonic crystals based on quantum dots, the concentration of target organisms can be indirectly measured via the change in the gray value of the fluorescence emitted from the quantum dots in the porous silicon pores before and after the biological reaction on the surface of the device. However, due to the disordered nanostructures in porous silicon and the roughness of the surface, the fluorescence images on the surface contain noise. This paper analyzes the type of noise and its influence on the gray value of fluorescent images. The change in the gray value caused by noise greatly reduces the detection sensitivity. To reduce the influence of noise on the gray value of quantum dot fluorescence images, this paper proposes a denoising method based on gray compression and nonlocal anisotropic diffusion filtering. We used the proposed method to denoise the quantum dot fluorescence image after DNA hybridization in a Bragg structure porous silicon device. The experimental results show that the sensitivity of digital image detection improved significantly after denoising.

Video Desnowing and Deraining via Saliency and Dual Adaptive Spatiotemporal Filtering.

Outdoor vision sensing systems often struggle with poor weather conditions, such as snow and rain, which poses a great challenge to existing video desnowing and deraining methods. In this paper, we propose a novel video desnowing and deraining model that utilizes the salience information of moving objects to address this problem. First, we remove the snow and rain from the video by low-rank tensor decomposition, which makes full use of the spatial location information and the correlation between the three channels of the color video. Second, because existing algorithms often regard sparse snowflakes and rain streaks as moving objects, this paper injects salience information into moving object detection, which reduces the false alarms and missed alarms of moving objects. At the same time, feature point matching is used to mine the redundant information of moving objects in continuous frames, and a dual adaptive minimum filtering algorithm in the spatiotemporal domain is proposed by us to remove snow and rain in front of moving objects. Both qualitative and quantitative experimental results show that the proposed algorithm is more competitive than other state-of-the-art snow and rain removal methods.

Detail Preserving Low Illumination Image and Video Enhancement Algorithm Based on Dark Channel Prior.

In low illumination situations, insufficient light in the monitoring device results in poor visibility of effective information, which cannot meet practical applications. To overcome the above problems, a detail preserving low illumination video image enhancement algorithm based on dark channel prior is proposed in this paper. First, a dark channel refinement method is proposed, which is defined by imposing a structure prior to the initial dark channel to improve the image brightness. Second, an anisotropic guided filter (AnisGF) is used to refine the transmission, which preserves the edges of the image. Finally, a detail enhancement algorithm is proposed to avoid the problem of insufficient detail in the initial enhancement image. To avoid video flicker, the next video frames are enhanced based on the brightness of the first enhanced frame. Qualitative and quantitative analysis shows that the proposed algorithm is superior to the contrast algorithm, in which the proposed algorithm ranks first in average gradient, edge intensity, contrast, and patch-based contrast quality index. It can be effectively applied to the enhancement of surveillance video images and for wider computer vision applications.

Deep Learning of Explainable EEG Patterns as Dynamic Spatiotemporal Clusters and Rules in a Brain-Inspired Spiking Neural Network.

The paper proposes a new method for deep learning and knowledge discovery in a brain-inspired Spiking Neural Networks (SNN) architecture that enhances the model's explainability while learning from streaming spatiotemporal brain data (STBD) in an incremental and on-line mode of operation. This led to the extraction of spatiotemporal rules from SNN models that explain why a certain decision (output prediction) was made by the model. During the learning process, the SNN created dynamic neural clusters, captured as polygons, which evolved in time and continuously changed their size and shape. The dynamic patterns of the clusters were quantitatively analyzed to identify the important STBD features that correspond to the most activated brain regions. We studied the trend of dynamically created clusters and their spike-driven events that occur together in specific space and time. The research contributes to: (1) enhanced interpretability of SNN learning behavior through dynamic neural clustering; (2) feature selection and enhanced accuracy of classification; (3) spatiotemporal rules to support model explainability; and (4) a better understanding of the dynamics in STBD in terms of feature interaction. The clustering method was applied to a case study of Electroencephalogram (EEG) data, recorded from a healthy control group (n = 21) and opiate use (n = 18) subjects while they were performing a cognitive task. The SNN models of EEG demonstrated different trends of dynamic clusters across the groups. This suggested to select a group of marker EEG features and resulted in an improved accuracy of EEG classification to 92%, when compared with all-feature classification. During learning of EEG data, the areas of neurons in the SNN model that form adjacent clusters (corresponding to neighboring EEG channels) were detected as fuzzy boundaries that explain overlapping activity of brain regions for each group of subjects.

FusionSense: Emotion Classification Using Feature Fusion of Multimodal Data and Deep Learning in a Brain-Inspired Spiking Neural Network.

Using multimodal signals to solve the problem of emotion recognition is one of the emerging trends in affective computing. Several studies have utilized state of the art deep learning methods and combined physiological signals, such as the electrocardiogram (EEG), electroencephalogram (ECG), skin temperature, along with facial expressions, voice, posture to name a few, in order to classify emotions. Spiking neural networks (SNNs) represent the third generation of neural networks and employ biologically plausible models of neurons. SNNs have been shown to handle Spatio-temporal data, which is essentially the nature of the data encountered in emotion recognition problem, in an efficient manner. In this work, for the first time, we propose the application of SNNs in order to solve the emotion recognition problem with the multimodal dataset. Specifically, we use the NeuCube framework, which employs an evolving SNN architecture to classify emotional valence and evaluate the performance of our approach on the MAHNOB-HCI dataset. The multimodal data used in our work consists of facial expressions along with physiological signals such as ECG, skin temperature, skin conductance, respiration signal, mouth length, and pupil size. We perform classification under the Leave-One-Subject-Out (LOSO) cross-validation mode. Our results show that the proposed approach achieves an accuracy of 73.15% for classifying binary valence when applying feature-level fusion, which is comparable to other deep learning methods. We achieve this accuracy even without using EEG, which other deep learning methods have relied on to achieve this level of accuracy. In conclusion, we have demonstrated that the SNN can be successfully used for solving the emotion recognition problem with multimodal data and also provide directions for future research utilizing SNN for Affective computing. In addition to the good accuracy, the SNN recognition system is requires incrementally trainable on new data in an adaptive way. It only one pass training, which makes it suitable for practical and on-line applications. These features are not manifested in other methods for this problem.

Application of a Brain-Inspired Spiking Neural Network Architecture to Odor Data Classification.

Existing methods in neuromorphic olfaction mainly focus on implementing the data transformation based on the neurobiological architecture of the olfactory pathway. While the transformation is pivotal for the sparse spike-based representation of odor data, classification techniques based on the bio-computations of the higher brain areas, which process the spiking data for identification of odor, remain largely unexplored. This paper argues that brain-inspired spiking neural networks constitute a promising approach for the next generation of machine intelligence for odor data processing. Inspired by principles of brain information processing, here we propose the first spiking neural network method and associated deep machine learning system for classification of odor data. The paper demonstrates that the proposed approach has several advantages when compared to the current state-of-the-art methods. Based on results obtained using a benchmark dataset, the model achieved a high classification accuracy for a large number of odors and has the capacity for incremental learning on new data. The paper explores different spike encoding algorithms and finds that the most suitable for the task is the step-wise encoding function. Further directions in the brain-inspired study of odor machine classification include investigation of more biologically plausible algorithms for mapping, learning, and interpretation of odor data along with the realization of these algorithms on some highly parallel and low power consuming neuromorphic hardware devices for real-world applications.

Interpretability of Spatiotemporal Dynamics of the Brain Processes Followed by Mindfulness Intervention in a Brain-Inspired Spiking Neural Network Architecture.

Mindfulness training is associated with improvements in psychological wellbeing and cognition, yet the specific underlying neurophysiological mechanisms underpinning these changes are uncertain. This study uses a novel brain-inspired artificial neural network to investigate the effect of mindfulness training on electroencephalographic function. Participants completed a 4-tone auditory oddball task (that included targets and physically similar distractors) at three assessment time points. In Group A (n = 10), these tasks were given immediately prior to 6-week mindfulness training, immediately after training and at a 3-week follow-up; in Group B (n = 10), these were during an intervention waitlist period (3 weeks prior to training), pre-mindfulness training and post-mindfulness training. Using a spiking neural network (SNN) model, we evaluated concurrent neural patterns generated across space and time from features of electroencephalographic data capturing the neural dynamics associated with the event-related potential (ERP). This technique capitalises on the temporal dynamics of the shifts in polarity throughout the ERP and spatially across electrodes. Findings support anteriorisation of connection weights in response to distractors relative to target stimuli. Right frontal connection weights to distractors were associated with trait mindfulness (positively) and depression (inversely). Moreover, mindfulness training was associated with an increase in connection weights to targets (bilateral frontal, left frontocentral, and temporal regions only) and distractors. SNN models were superior to other machine learning methods in the classification of brain states as a function of mindfulness training. Findings suggest SNN models can provide useful information that differentiates brain states based on distinct task demands and stimuli, as well as changes in brain states as a function of psychological intervention.

A Dynamic DNA Color Image Encryption Method Based on SHA-512.

This paper presents a dynamic deoxyribonucleic acid (DNA) image encryption based on Secure Hash Algorithm-512 (SHA-512), having the structure of two rounds of permutation-diffusion, by employing two chaotic systems, dynamic DNA coding, DNA sequencing operations, and conditional shifting. We employed the SHA-512 algorithm to generate a 512-bit hash value and later utilized this value with the natural DNA sequence to calculate the initial values for the chaotic systems and the eight intermittent parameters. We implemented a two-dimensional rectangular transform (2D-RT) on the permutation. We used four-wing chaotic systems and Lorentz systems to generate chaotic sequences and recombined three channel matrices and chaotic matrices with intermittent parameters. We calculated hamming distances of DNA matrices, updated the initial values of two chaotic systems, and generated the corresponding chaotic matrices to complete the diffusion operation. After diffusion, we decoded and decomposed the DNA matrices, and then scrambled and merged these matrices into an encrypted image. According to experiments, the encryption method in this paper not only was able to withstand statistical attacks, plaintext attacks, brute-force attacks, and a host of other attacks, but also could reduce the complexity of the algorithm because it adopted DNA sequencing operations that were different from traditional DNA sequencing operations.

Erratum: Lou, X.; Jia, Z.; Yang, J.; Kasabov, N. Change Detection in SAR Images Based on the ROF Model Semi-Implicit Denoising Method. Sensors 2019, 19, 1179.

The authors wish to make the following erratum to this paper [...].

Applying Speckle Noise Suppression to Refractive Indices Change Detection in Porous Silicon Microarrays.

The gray value method can be used to detect gray value changes of each unit almost parallel to the surface image of PSi (porous silicon) microarrays and indirectly measure the refractive index changes of each unit. However, the speckles of different noise intensities produced by lasers on a porous silicon surface have different effects on the gray value of the measured image. This results in inaccurate results of refractive index changes obtained from the change in gray value. Therefore, it is very important to reduce the influence of speckle noise on measurement results. In this paper, a new algorithm based on the concepts of probability-based nonlocal-means filtering (PNLM), gradient operator, and median filtering is proposed for gray value restoration of porous silicon microarray images. A good linear relationship between gray value change and refractive index change is obtained, which can reduce the influence of speckle noise on the gray value of the PSi microarray image, improving detection accuracy. This means the method based on gray value change detection can be applied to the biological detection of PSi microarray arrays.

Change Detection of Optical Remote Sensing Image Disturbed by Thin Cloud Using Wavelet Coefficient Substitution Algorithm.

The detection of changes in optical remote sensing images under the interference of thin clouds is studied for the first time in this paper. First, the optical remote sensing image is subjected to thin cloud removal processing, and then the processed remote sensing image is subjected to image change detection. Based on the analysis of the characteristics of thin cloud images, a method for removing thin clouds based on wavelet coefficient substitution is proposed in this paper. Based on the change in the wavelet coefficient, the high- and low-frequency parts of the remote sensing image are replaced separately, and the low-frequency clouds are suppressed while maintaining the high-frequency detail of the image, which achieves good results. Then, an unsupervised change detection algorithm based on a combined difference graph and fuzzy c-means clustering algorithm (FCM) clustering is applied. First, the image is transformed into a logarithmic domain, and the image is denoised using Frost filtering. Then, the mean ratio method and the difference method are used to obtain two graph difference maps, and the combined difference graph method is used to obtain the final difference image. The experimental results show that the algorithm can effectively solve the problem of image change detection under thin cloud interference.

Change Detection in SAR Images Based on the ROF Model Semi-Implicit Denoising Method.

The explicit solution of the traditional ROF model in image denoising has the disadvantages of unstable results and requiring many iterations. To solve the problem, a new method, ROF model semi-implicit denoising, is proposed in this paper and applied to change detections of synthetic aperture radar (SAR) images. All remote sensing images used in this article have been calibrated by ENVI software. First, the ROF model semi-implicit denoising method is used to denoise the remote sensing images. Second, for the denoised images, difference images are obtained by the logarithmic ratio and mean ratio methods. The final difference image is obtained by principal component analysis fusion (PCA fusion) of the two difference images. Finally, the final difference image is clustered by fuzzy local information C-means clustering (FLICM) to obtain the change regions. The research results show that the proposed method has high detection accuracy and time operation efficiency.

Image Processing of Porous Silicon Microarray in Refractive Index Change Detection.

A new method for extracting the dots is proposed by the reflected light image of porous silicon (PSi) microarray utilization in this paper. The method consists of three parts: pretreatment, tilt correction and spot segmentation. First, based on the characteristics of different components in HSV (Hue, Saturation, Value) space, a special pretreatment is proposed for the reflected light image to obtain the contour edges of the array cells in the image. Second, through the geometric relationship of the target object between the initial external rectangle and the minimum bounding rectangle (MBR), a new tilt correction algorithm based on the MBR is proposed to adjust the image. Third, based on the specific requirements of the reflected light image segmentation, the array cells are segmented into dots as large as possible and the distance between the dots is equal in the corrected image. Experimental results show that the pretreatment part of this method can effectively avoid the influence of complex background and complete the binarization processing of the image. The tilt correction algorithm has a shorter computation time, which makes it highly suitable for tilt correction of reflected light images. The segmentation algorithm makes the dots in a regular arrangement, excludes the edges and the bright spots. This method could be utilized in the fast, accurate and automatic dots extraction of the PSi microarray reflected light image.

Remote Sensing Image Change Detection Based on NSCT-HMT Model and Its Application.

Traditional image change detection based on a non-subsampled contourlet transform always ignores the neighborhood information's relationship to the non-subsampled contourlet coefficients, and the detection results are susceptible to noise interference. To address these disadvantages, we propose a denoising method based on the non-subsampled contourlet transform domain that uses the Hidden Markov Tree model (NSCT-HMT) for change detection of remote sensing images. First, the ENVI software is used to calibrate the original remote sensing images. After that, the mean-ratio operation is adopted to obtain the difference image that will be denoised by the NSCT-HMT model. Then, using the Fuzzy Local Information C-means (FLICM) algorithm, the difference image is divided into the change area and unchanged area. The proposed algorithm is applied to a real remote sensing data set. The application results show that the proposed algorithm can effectively suppress clutter noise, and retain more detailed information from the original images. The proposed algorithm has higher detection accuracy than the Markov Random Field-Fuzzy C-means (MRF-FCM), the non-subsampled contourlet transform-Fuzzy C-means clustering (NSCT-FCM), the pointwise approach and graph theory (PA-GT), and the Principal Component Analysis-Nonlocal Means (PCA-NLM) denosing algorithm. Finally, the five algorithms are used to detect the southern boundary of the Gurbantunggut Desert in Xinjiang Uygur Autonomous Region of China, and the results show that the proposed algorithm has the best effect on real remote sensing image change detection.

Identifying overlapping mutated driver pathways by constructing gene networks in cancer.

BACKGROUND: Large-scale cancer genomic projects are providing lots of data on genomic, epigenomic and gene expression aberrations in many cancer types. One key challenge is to detect functional driver pathways and to filter out nonfunctional passenger genes in cancer genomics. Vandin et al. introduced the Maximum Weight Sub-matrix Problem to find driver pathways and showed that it is an NP-hard problem. METHODS: To find a better solution and solve the problem more efficiently, we present a network-based method (NBM) to detect overlapping driver pathways automatically. This algorithm can directly find driver pathways or gene sets de novo from somatic mutation data utilizing two combinatorial properties, high coverage and high exclusivity, without any prior information. We firstly construct gene networks based on the approximate exclusivity between each pair of genes using somatic mutation data from many cancer patients. Secondly, we present a new greedy strategy to add or remove genes for obtaining overlapping gene sets with driver mutations according to the properties of high exclusivity and high coverage. RESULTS: To assess the efficiency of the proposed NBM, we apply the method on simulated data and compare results obtained from the NBM, RME, Dendrix and Multi-Dendrix. NBM obtains optimal results in less than nine seconds on a conventional computer and the time complexity is much less than the three other methods. To further verify the performance of NBM, we apply the method to analyze somatic mutation data from five real biological data sets such as the mutation profiles of 90 glioblastoma tumor samples and 163 lung carcinoma samples. NBM detects groups of genes which overlap with known pathways, including P53, RB and RTK/RAS/PI(3)K signaling pathways. New gene sets with p-value less than 1e-3 are found from the somatic mutation data. CONCLUSIONS: NBM can detect more biologically relevant gene sets. Results show that NBM outperforms other algorithms for detecting driver pathways or gene sets. Further research will be conducted with the use of novel machine learning techniques.

A holistic comparative analysis of diagnostic tests for urothelial carcinoma: a study of Cxbladder Detect, UroVysion® FISH, NMP22® and cytology based on imputation of multiple datasets.

BACKGROUND: Comparing the relative utility of diagnostic tests is challenging when available datasets are small, partial or incomplete. The analytical leverage associated with a large sample size can be gained by integrating several small datasets to enable effective and accurate across-dataset comparisons. Accordingly, we propose a methodology for a holistic comparative analysis and ranking of cancer diagnostic tests through dataset integration and imputation of missing values, using urothelial carcinoma (UC) as a case study. METHODS: Five datasets comprising samples from 939 subjects, including 89 with UC, where up to four diagnostic tests (cytology, NMP22®, UroVysion® Fluorescence In-Situ Hybridization (FISH) and Cxbladder Detect) were integrated into a single dataset containing all measured records and missing values. The tests were firstly ranked using three criteria: sensitivity, specificity and a standard variable (feature) ranking method popularly known as signal-to-noise ratio (SNR) index derived from the mean values for all subjects clinically known to have UC versus healthy subjects. Secondly, step-wise unsupervised and supervised imputation (the latter accounting for the 'clinical truth' as determined by cystoscopy) was performed using personalized modelling, k-nearest-neighbour methods, multiple logistic regression and multilayer perceptron neural networks. All imputation models were cross-validated by comparing their post-imputation predictive accuracy for UC with their pre-imputation accuracy. Finally, the post-imputation tests were re-ranked using the same three criteria. RESULTS: In both measured and imputed data sets, Cxbladder Detect ranked higher for sensitivity, and urine cytology a higher specificity, when compared with other UC tests. Cxbladder Detect consistently ranked higher than FISH and all other tests when SNR analyses were performed on measured, unsupervised and supervised imputed datasets. Supervised imputation resulted in a smaller cross-validation error. Cxbladder Detect was robust to imputation showing a 2% difference in its predictive versus clinical accuracy, outperforming FISH, NMP22 and cytology. CONCLUSION: All data analysed, pre- and post-imputation showed that Cxbladder Detect had higher SNR and outperformed all other comparator tests, including FISH. The methodology developed and validated for comparative ranking of the diagnostic tests for detecting UC, may be further applied to other cancer diagnostic datasets across population groups and multiple datasets.

Geomagnetic storms can trigger stroke: evidence from 6 large population-based studies in Europe and Australasia.

BACKGROUND AND PURPOSE: Although the research linking cardiovascular disorders to geomagnetic activity is accumulating, robust evidence for the impact of geomagnetic activity on stroke occurrence is limited and controversial. METHODS: We used a time-stratified case-crossover study design to analyze individual participant and daily geomagnetic activity (as measured by Ap Index) data from several large population-based stroke incidence studies (with information on 11 453 patients with stroke collected during 16 031 764 person-years of observation) in New Zealand, Australia, United Kingdom, France, and Sweden conducted between 1981 and 2004. Hazard ratios and corresponding 95% confidence intervals (CIs) were calculated. RESULTS: Overall, geomagnetic storms (Ap Index 60+) were associated with 19% increase in the risk of stroke occurrence (95% CI, 11%-27%). The triggering effect of geomagnetic storms was most evident across the combined group of all strokes in those aged <65 years, increasing stroke risk by >50%: moderate geomagnetic storms (60-99 Ap Index) were associated with a 27% (95% CI, 8%-48%) increased risk of stroke occurrence, strong geomagnetic storms (100-149 Ap Index) with a 52% (95% CI, 19%-92%) increased risk, and severe/extreme geomagnetic storms (Ap Index 150+) with a 52% (95% CI, 19%-94%) increased risk (test for trend, P<2×10(-16)). CONCLUSIONS: Geomagnetic storms are associated with increased risk of stroke and should be considered along with other established risk factors. Our findings provide a framework to advance stroke prevention through future investigation of the contribution of geomagnetic factors to the risk of stroke occurrence and pathogenesis.

Diagnostic biomarker discovery from brain EEG data using LSTM, reservoir-SNN, and NeuCube methods in a pilot study comparing epilepsy and migraine.

The study introduces a new online spike encoding algorithm for spiking neural networks (SNN) and suggests new methods for learning and identifying diagnostic biomarkers using three prominent deep learning neural network models: deep BiLSTM, reservoir SNN, and NeuCube. EEG data from datasets related to epilepsy, migraine, and healthy subjects are employed. Results reveal that BiLSTM hidden neurons capture biological significance, while reservoir SNN activities and NeuCube spiking dynamics identify EEG channels as diagnostic biomarkers. BiLSTM and reservoir SNN achieve 90 and 85% classification accuracy, while NeuCube achieves 97%, all methods pinpointing potential biomarkers like T6, F7, C4, and F8. The research bears implications for refining online EEG classification, analysis, and early brain state diagnosis, enhancing AI models with interpretability and discovery. The proposed techniques hold promise for streamlined brain-computer interfaces and clinical applications, representing a significant advancement in pattern discovery across the three most popular neural network methods for addressing a crucial problem. Further research is planned to study how early can these diagnostic biomarkers predict an onset of brain states.