Multiresolution directed transfer function approach for segment-wise seizure classification of epileptic EEG signal

Currently, with the bloom in artificial intelligence (AI) algorithms, various human-centered smart systems can be utilized, especially in cognitive computing, for the detection of various chronic brain diseases such as epileptic seizure. The primary goal of this research article is to propose a novel human-centered cognitive computing (HCCC) method for segment-wise seizure classification by employing multiresolution extracted data with directed transfer function (DTF) features, termed as the multiresolution directed transfer function (MDTF) approach. Initially, the multiresolution information of the epileptic seizure signal is extracted using a multiresolution adaptive filtering (MRAF) method. These seizure details are passed to the DTF where the information flow of high frequency bands is computed. Thereafter, different measures of complexity such as approximate entropy (AEN) and sample entropy (SAEN) are computed from the extracted high frequency bands. Lastly, a k-nearest neighbor (k-NN) and support vector machine (SVM) are used for classifying the EEG signal into non-seizure and seizure data depending on the multiresolution based information flow characteristics. The MDTF approach is tested on a standard dataset and validated using a dataset from a local hospital. The proposed technique has obtained an average sensitivity of 98.31%, specificity of 96.13% and accuracy of 98.89% using SVM classifier. The average detection rate of the MDTF approach is 97.72% which is greater than the existing approaches. The proposed MDTF method will help neuro-specialists to locate seizure information drift which occurs within the consecutive segments and between two channels. The main advantage of the MDTF approach is its capability to locate the seizure activity contained by the EEG signal with accuracy. This will assist the neurologists with the precise localization of the epileptic seizure automatically and hence will reduce the burden of time-consuming epileptic seizure analysis.

Predicting long-term time to cardiovascular incidents using myocardial perfusion imaging and deep convolutional neural networks

Myocardial perfusion imaging (MPI) is a clinical tool which can assess the heart's perfusion status, thereby revealing impairments in patients' cardiac function. Within the MPI modality, the acquired three-dimensional signals are typically represented as a sequence of two-dimensional grayscale tomographic images. Here, we proposed an end-to-end survival training approach for processing gray-scale MPI tomograms to generate a risk score which reflects subsequent time to cardiovascular incidents, including cardiovascular death, non-fatal myocardial infarction, and non-fatal ischemic stroke (collectively known as Major Adverse Cardiovascular Events; MACE) as well as Congestive Heart Failure (CHF). We recruited a total of 1928 patients who had undergone MPI followed by coronary interventions. Among them, 80% (n = 1540) were randomly reserved for the training and 5- fold cross-validation stage, while 20% (n = 388) were set aside for the testing stage. The end-to-end survival training can converge well in generating effective AI models via the fivefold cross-validation approach with 1540 patients. When a candidate model is evaluated using independent images, the model can stratify patients into below-median-risk (n = 194) and above-median-risk (n = 194) groups, the corresponding survival curves of the two groups have significant difference (P < 0.0001). We further stratify the above-median-risk group to the quartile 3 and 4 group (n = 97 each), and the three patient strata, referred to as the high, intermediate and low risk groups respectively, manifest statistically significant difference. Notably, the 5-year cardiovascular incident rate is less than 5% in the low-risk group (accounting for 50% of all patients), while the rate is nearly 40% in the high-risk group (accounting for 25% of all patients). Evaluation of patient subgroups revealed stronger effect size in patients with three blocked arteries (Hazard ratio [HR]: 18.377, 95% CI 3.719-90.801, p < 0.001), followed by those with two blocked vessels at HR 7.484 (95% CI 1.858-30.150; p = 0.005). Regarding stent placement, patients with a single stent displayed a HR of 4.410 (95% CI 1.399-13.904; p = 0.011). Patients with two stents show a HR of 10.699 (95% CI 2.262-50.601; p = 0.003), escalating notably to a HR of 57.446 (95% CI 1.922-1717.207; p = 0.019) for patients with three or more stents, indicating a substantial relationship between the disease severity and the predictive capability of the AI for subsequent cardiovascular inciidents. The success of the MPI AI model in stratifying patients into subgroups with distinct time-to-cardiovascular incidents demonstrated the feasibility of proposed end-to-end survival training approach.

Multiscale analysis of count data through topic alignment

Topic modeling is a popular method used to describe biological count data. With topic models, the user must specify the number of topics $K$. Since there is no definitive way to choose $K$ and since a true value might not exist, we develop a method, which we call topic alignment, to study the relationships across models with different $K$. In addition, we present three diagnostics based on the alignment. These techniques can show how many topics are consistently present across different models, if a topic is only transiently present, or if a topic splits into more topics when $K$ increases. This strategy gives more insight into the process of generating the data than choosing a single value of $K$ would. We design a visual representation of these cross-model relationships, show the effectiveness of these tools for interpreting the topics on simulated and real data, and release an accompanying R package, alto.

Comparison of different algorithms based on TKEO for EMG change point detection

OBJECTIVE

A significant challenge in surface electromyography (EMG) is the accurate identification of onset and offset of muscle activation while maintaining high real-time performance. Teager-Kaiser energy operator (TKEO) is widely used in muscle activity monitoring systems because of its computational simplicity and strong real-time performance. However, in contrast to TKEO ontology, few studies have examined how well the energy operator variants from multiple fields perform in conditioning EMG signals. This paper aims to investigate the role of the energy operator and its variants in EMG change point detection by a threshold detector.

APPROACH

To compare the stability and accuracy of TKEO and its variants for EMG change point detection, the EMG data of extensor carpi radialis longus and flexor carpi radialis were acquired from twenty participants operating a controller under normal and disturbed conditions, and EMG change point detection was performed by four energy operators and their rectified versions.

MAIN RESULTS

Based on the "standard" change points collected by the controller, the detection results were evaluated by three evaluation indexes: detection rate, F1 Score, and accuracy. The experimental results show that the multiresolution energy operator (MTEO) and the TKEO with rectified (abs-TKEO) are more suitable for EMG change point detection.

SIGNIFICANCE

This paper compared the effect of the energy operator and its variants on a threshold-based EMG change point detector. The experimental results in this paper can provide a reference for the selection of EMG signal conditioning methods to improve the detection performance of the EMG change point detector.

Combining dual-tree complex wavelets and multiresolution in iterative CT reconstruction with application to metal artifact reduction

Background

This paper investigates the benefits of data filtering via complex dual wavelet transform for metal artifact reduction (MAR). The advantage of using complex dual wavelet basis for MAR was studied on simulated dental computed tomography (CT) data for its efficiency in terms of noise suppression and removal of secondary artifacts. Dual-tree complex wavelet transform (DT-CWT) was selected due to its enhanced directional analysis of image details compared to the ordinary wavelet transform. DT-CWT was used for multiresolution decomposition within a modified total variation (TV) regularized inversion algorithm.

Methods

In this study, we have tested the multiresolution TV (MRTV) approach with DT-CWT on a 2D polychromatic jaw phantom model with Gaussian and Poisson noise. High noise and sparse measurement settings were used to assess the performance of DT-CWT. The results were compared to the outcome of the single-resolution reconstruction and filtered back-projection (FBP) techniques as well as reconstructions with Haar wavelet basis.

Results

The results indicate that filtering of wavelet coefficients with DT-CWT effectively removes the noise without introducing new artifacts after inpainting. Furthermore, adoption of multiple resolution levels yield to a more robust algorithm compared to varying the regularization strength.

Conclusions

The multiresolution reconstruction with DT-CWT is also more robust when reconstructing the data with sparse projections compared to the single-resolution approach and Haar wavelets.

Multiresolution vessel detection in magnetic particle imaging using wavelets and a Gaussian mixture model

PURPOSE

Magnetic particle imaging is a tomographic imaging technique that allows one to measure the spatial distribution of superparamagnetic nanoparticles, which are used as tracer. The magnetic particle imaging scanner measures the voltage induced due to the nonlinear magnetization behavior of the nanoparticles. The tracer distribution can be reconstructed from the voltage signal by solving an inverse problem. A possible application is the imaging of vessel structures. In this and many other cases, the tracer is only located inside the structures and a large part of the image is related to background. A detection of the tracer support in early stages of the reconstruction process could improve reconstruction results.

METHODS

In this work, a multiresolution wavelet-based reconstruction combined with a segmentation of the foreground structures is performed. For this, different wavelets are compared with respect to their reconstruction quality. For the detection of the foreground, a segmentation with a Gaussian mixture model is performed, which leads to a threshold-based binary segmentation. This segmentation is done on a coarse level of the reconstruction and then transferred to the next finer level, where it is used as prior knowledge for the reconstruction. This is repeated until the finest resolution is reached.

RESULTS

The approach is evaluated on simulated vessel phantoms and on two real measurements. The results show that this method improves the structural similarity index of the reconstructed images significantly. Among the compared wavelets, the 9/7 wavelets led to the best reconstruction results.

CONCLUSIONS

The early detection of the vessel structures at low resolution helps to improve the image quality. For the wavelet decomposition, the use of 9/7 wavelets is recommended.

Zebrafish larvae heartbeat detection from body deformation in low resolution and low frequency video

Zebrafish (Danio rerio) is a powerful animal model used in many areas of genetics and disease research. Despite its advantages for cardiac research, the heartbeat pattern of zebrafish larvae under different stress conditions is not well documented quantitatively. Several effective automated heartbeat detection methods have been developed to reduce the workload for larva heartbeat analysis. However, most require complex experimental setups and necessitate direct observation of the larva heart. In this paper, we propose the Zebrafish Heart Rate Automatic Method (Z-HRAM), which detects and tracks the heartbeats of immobilized, ventrally positioned zebrafish larvae without direct larva heart observation. Z-HRAM tracks localized larva body deformation that is highly correlated with heart movement. Multiresolution dense optical flow-based motion tracking and principal component analysis are used to identify heartbeats. Here, we present results of Z-HRAM on estimating heart rate from video recordings of seizure-induced larvae, which were of low resolution (1024 × 760) and low frame rate (3 to 4 fps). Heartbeats detected from Z-HRAM were shown to correlate reliably with those determined through corresponding electrocardiogram and manual video inspection. We conclude that Z-HRAM is a robust, computationally efficient, and easily applicable tool for studying larva cardiac function in general laboratory conditions. Graphical abstract Flowchart of the automatic zebrafish heartbeat detection.

Multiresolution image registration for multimodal brain images and fusion for better neurosurgical planning

Background

Imaging modalities in medicine gives complementary information. Inadequacy in clinical information made single imaging modality insufficient. There is a need for computer-based system that permits rapid acquisition of digital medical images and performs multi-modality registration, segmentation and three-dimensional planning of minimally invasive neurosurgical procedures. In this regard proposed article presents multimodal brain image registration and fusion for better neurosurgical planning.

Methods

In proposed work brain data is acquired from Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) modalities. CT and MRI images are pre-processed and given for image registration. BSpline deformable registration and multiresolution image registration is performed on the CT and MRI sequence. CT is fixed image and MRI is moving image for registration. Later end result is fusion of CT and registered MRI sequences.

Results

BSpline deformable registration is performed on the slices gave promising results but on the sequences noise have been introduced in the resultant image because of multimodal and multiresolution input images. Then multiresolution registration technique is performed on the CT and MRI sequence of the brain which gave promising results.

Conclusion

The end resultant fused images are validated by the radiologists and mutual information measure is used to validate registration results. It is found that CT and MRI sequence with more number of slices gave promising results. Few cases with deformation during misregistrations recorded with low mutual information of about 0.3 and which is not acceptable and few recorded with 0.6 and above mutual information during registration gives promising results.

Five multiresolution-based calcium volume measurement techniques from coronary IVUS videos: A comparative approach

BACKGROUND AND OBJECTIVE

Fast intravascular ultrasound (IVUS) video processing is required for calcium volume computation during the planning phase of percutaneous coronary interventional (PCI) procedures. Nonlinear multiresolution techniques are generally applied to improve the processing time by down-sampling the video frames.

METHODS

This paper presents four different segmentation methods for calcium volume measurement, namely Threshold-based, Fuzzy c-Means (FCM), K-means, and Hidden Markov Random Field (HMRF) embedded with five different kinds of multiresolution techniques (bilinear, bicubic, wavelet, Lanczos, and Gaussian pyramid). This leads to 20 different kinds of combinations. IVUS image data sets consisting of 38,760 IVUS frames taken from 19 patients were collected using 40 MHz IVUS catheter (Atlantis® SR Pro, Boston Scientific®, pullback speed of 0.5 mm/sec.). The performance of these 20 systems is compared with and without multiresolution using the following metrics: (a) computational time; (b) calcium volume; (c) image quality degradation ratio; and (d) quality assessment ratio.

RESULTS

Among the four segmentation methods embedded with five kinds of multiresolution techniques, FCM segmentation combined with wavelet-based multiresolution gave the best performance. FCM and wavelet experienced the highest percentage mean improvement in computational time of 77.15% and 74.07%, respectively. Wavelet interpolation experiences the highest mean precision-of-merit (PoM) of 94.06 ± 3.64% and 81.34 ± 16.29% as compared to other multiresolution techniques for volume level and frame level respectively. Wavelet multiresolution technique also experiences the highest Jaccard Index and Dice Similarity of 0.7 and 0.8, respectively. Multiresolution is a nonlinear operation which introduces bias and thus degrades the image. The proposed system also provides a bias correction approach to enrich the system, giving a better mean calcium volume similarity for all the multiresolution-based segmentation methods. After including the bias correction, bicubic interpolation gives the largest increase in mean calcium volume similarity of 4.13% compared to the rest of the multiresolution techniques. The system is automated and can be adapted in clinical settings.

CONCLUSIONS

We demonstrated the time improvement in calcium volume computation without compromising the quality of IVUS image. Among the 20 different combinations of multiresolution with calcium volume segmentation methods, the FCM embedded with wavelet-based multiresolution gave the best performance.

Clustering analysis of proteins from microbial genomes at multiple levels of resolution

Background

Microbial genomes at the National Center for Biotechnology Information (NCBI) represent a large collection of more than 35,000 assemblies. There are several complexities associated with the data: a great variation in sampling density since human pathogens are densely sampled while other bacteria are less represented; different protein families occur in annotations with different frequencies; and the quality of genome annotation varies greatly. In order to extract useful information from these sophisticated data, the analysis needs to be performed at multiple levels of phylogenomic resolution and protein similarity, with an adequate sampling strategy.

Results

Protein clustering is used to construct meaningful and stable groups of similar proteins to be used for analysis and functional annotation. Our approach is to create protein clusters at three levels. First, tight clusters in groups of closely-related genomes (species-level clades) are constructed using a combined approach that takes into account both sequence similarity and genome context. Second, clustroids of conservative in-clade clusters are organized into seed global clusters. Finally, global protein clusters are built around the the seed clusters. We propose filtering strategies that allow limiting the protein set included in global clustering.

The in-clade clustering procedure, subsequent selection of clustroids and organization into seed global clusters provides a robust representation and high rate of compression. Seed protein clusters are further extended by adding related proteins. Extended seed clusters include a significant part of the data and represent all major known cell machinery. The remaining part, coming from either non-conservative (unique) or rapidly evolving proteins, from rare genomes, or resulting from low-quality annotation, does not group together well. Processing these proteins requires significant computational resources and results in a large number of questionable clusters.

Conclusion

The developed filtering strategies allow to identify and exclude such peripheral proteins limiting the protein dataset in global clustering. Overall, the proposed methodology allows the relevant data at different levels of details to be obtained and data redundancy eliminated while keeping biologically interesting variations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-1112-8) contains supplementary material, which is available to authorized users.

Multimodal fusion framework: a multiresolution approach for emotion classification and recognition from physiological signals

The purpose of this paper is twofold: (i) to investigate the emotion representation models and find out the possibility of a model with minimum number of continuous dimensions and (ii) to recognize and predict emotion from the measured physiological signals using multiresolution approach. The multimodal physiological signals are: Electroencephalogram (EEG) (32 channels) and peripheral (8 channels: Galvanic skin response (GSR), blood volume pressure, respiration pattern, skin temperature, electromyogram (EMG) and electrooculogram (EOG)) as given in the DEAP database. We have discussed the theories of emotion modeling based on i) basic emotions, ii) cognitive appraisal and physiological response approach and iii) the dimensional approach and proposed a three continuous dimensional representation model for emotions. The clustering experiment on the given valence, arousal and dominance values of various emotions has been done to validate the proposed model. A novel approach for multimodal fusion of information from a large number of channels to classify and predict emotions has also been proposed. Discrete Wavelet Transform, a classical transform for multiresolution analysis of signal has been used in this study. The experiments are performed to classify different emotions from four classifiers. The average accuracies are 81.45%, 74.37%, 57.74% and 75.94% for SVM, MLP, KNN and MMC classifiers respectively. The best accuracy is for 'Depressing' with 85.46% using SVM. The 32 EEG channels are considered as independent modes and features from each channel are considered with equal importance. May be some of the channel data are correlated but they may contain supplementary information. In comparison with the results given by others, the high accuracy of 85% with 13 emotions and 32 subjects from our proposed method clearly proves the potential of our multimodal fusion approach.

Multimodal fusion framework: a multiresolution approach for emotion classification and recognition from physiological signals

The purpose of this paper is twofold: (i) to investigate the emotion representation models and find out the possibility of a model with minimum number of continuous dimensions and (ii) to recognize and predict emotion from the measured physiological signals using multiresolution approach. The multimodal physiological signals are: Electroencephalogram (EEG) (32 channels) and peripheral (8 channels: Galvanic skin response (GSR), blood volume pressure, respiration pattern, skin temperature, electromyogram (EMG) and electrooculogram (EOG)) as given in the DEAP database. We have discussed the theories of emotion modeling based on i) basic emotions, ii) cognitive appraisal and physiological response approach and iii) the dimensional approach and proposed a three continuous dimensional representation model for emotions. The clustering experiment on the given valence, arousal and dominance values of various emotions has been done to validate the proposed model. A novel approach for multimodal fusion of information from a large number of channels to classify and predict emotions has also been proposed. Discrete Wavelet Transform, a classical transform for multiresolution analysis of signal has been used in this study. The experiments are performed to classify different emotions from four classifiers. The average accuracies are 81.45%, 74.37%, 57.74% and 75.94% for SVM, MLP, KNN and MMC classifiers respectively. The best accuracy is for 'Depressing' with 85.46% using SVM. The 32 EEG channels are considered as independent modes and features from each channel are considered with equal importance. May be some of the channel data are correlated but they may contain supplementary information. In comparison with the results given by others, the high accuracy of 85% with 13 emotions and 32 subjects from our proposed method clearly proves the potential of our multimodal fusion approach.