Fusion of multi-view ultrasonic data for increased detection performance in non-destructive evaluation.
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ABSTRACT:
SUBMITTER: Wilcox PD
PROVIDER: S-EPMC7735296 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Photoacoustic (PA) imaging of arbitrarily-shaped or oriented objects may miss important features because PA waves propagate normal to structure boundaries and may miss the acoustic detectors when the detection view has a limited angular range. To overcome this long-standing problem, we present an ultrasonic thermal encoding approach that is universally applicable. We exploit the temperature dependence of the Grueneisen parameter and encode a confined [[What does confined mean here?]] voxel using heat generated by a focused ultrasonic transducer. The PA amplitude from the encoded voxel is increased while those from the neighboring voxels are unchanged. Consequently, the amplitude-increased PA waves propagate in all directions due to the round cross-section of the encoded region and thus can be received at any viewing angle on the cross-sectional plane [[Please check throughout the manuscript for similar places.]]. We built a mathematical model for the thermally encoded PA tomography, performed a numerical simulation, and experimentally validated the ultrasonic thermal encoding efficiency. As a proof of concept, we demonstrate full-view in vivo vascular imaging and compare it to the original linear-array PA tomography system, showing dramatically enhanced imaging of arbitrarily oriented blood vessels. Since ultrasonic heating can be focused deeply, this method can be applied to deep tissue imaging and is promising for full-view imaging of other features of biomedical interest, such as tumor margins.
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Project description:This paper presents a novel approach to recover true fine surface detail of deforming meshes reconstructed from multi-view video. Template-based methods for performance capture usually produce a coarse-to-medium scale detail 4D surface reconstruction which does not contain the real high-frequency geometric detail present in the original video footage. Fine scale deformation is often incorporated in a second pass by using stereo constraints, features, or shading-based refinement. In this paper, we propose an alternative solution to this second stage by formulating dense dynamic surface reconstruction as a global optimization problem of the densely deforming surface. Our main contribution is an implicit representation of a deformable mesh that uses a set of Gaussian functions on the surface to represent the initial coarse mesh, and a set of Gaussians for the images to represent the original captured multi-view images. We effectively find the fine scale deformations for all mesh vertices, which maximize photo-temporal-consistency, by densely optimizing our model-to-image consistency energy on all vertex positions. Our formulation yields a smooth closed form energy with implicit occlusion handling and analytic derivatives. Furthermore, it does not require error-prone correspondence finding or discrete sampling of surface displacement values. We demonstrate our approach on a variety of datasets of human subjects wearing loose clothing and performing different motions. We qualitatively and quantitatively demonstrate that our technique successfully reproduces finer detail than the input baseline geometry.
| S-EPMC6979538 | biostudies-literature
Project description:BackgroundDNA methylation plays an important role in multiple biological processes that are closely related to human health. The study of DNA methylation can provide an insight into the mechanism behind human health and can also have a positive effect on the assessment of human health status. However, the available sequencing technology is limited by incomplete CpG coverage. Therefore, it is crucial to discover an efficient and convenient method capable of distinguishing between the states of CpG sites. Previous studies focused on identifying methylation states of the CpG sites in single cell, which only evaluated sequence information or structural information.ResultsIn this paper, we propose a novel model, LightCpG, which combines the positional features with the sequence and structural features to provide information on the CpG sites at two stages. Next, we used the LightGBM model for training of the CpG site identification, and further utilized sample extraction and merged features to reduce the training time. Our results indicate that our method achieves outstanding performance in recognition of DNA methylation. The average AUC values of our method using the 25 human hepatocellular carcinoma cells (HCC) cell datasets and six human heptoplastoma-derived (HepG2) cell datasets were 0.9616 and 0.9213, respectively. Moreover, the average training times for our method on the HCC and HepG2 datasets were 8.3 and 5.06 s, respectively. Furthermore, the computational complexity of our model was much lower compared with other available methods that detect methylation states of the CpG sites.ConclusionsIn summary, LightCpG is an accurate model for identifying the DNA methylation status of CpG sites in single cells. Furthermore, three types of feature extraction methods and two strategies used in LightCpG are helpful for other prediction problems.
| S-EPMC6480911 | biostudies-literature
Project description:In many biomedical research, multiple views of data (e.g. genomics, proteomics) are available, and a particular interest might be the detection of sample subgroups characterized by specific groups of variables. Biclustering methods are well-suited for this problem as they assume that specific groups of variables might be relevant only to specific groups of samples. Many biclustering methods exist for detecting row-column clusters in a view but few methods exist for data from multiple views. The few existing algorithms are heavily dependent on regularization parameters for getting row-column clusters, and they impose unnecessary burden on users thus limiting their use in practice. We extend an existing biclustering method based on sparse singular value decomposition for single-view data to data from multiple views. Our method, integrative sparse singular value decomposition (iSSVD), incorporates stability selection to control Type I error rates, estimates the probability of samples and variables to belong to a bicluster, finds stable biclusters, and results in interpretable row-column associations. Simulations and real data analyses show that integrative sparse singular value decomposition outperforms several other single- and multi-view biclustering methods and is able to detect meaningful biclusters. iSSVD is a user-friendly, computationally efficient algorithm that will be useful in many disease subtyping applications.
| S-EPMC10153449 | biostudies-literature
Project description:In real world applications, data sets are often comprised of multiple views, which provide consensus and complementary information to each other. Embedding learning is an effective strategy for nearest neighbour search and dimensionality reduction in large data sets. This paper attempts to learn a unified probability distribution of the points across different views and generates a unified embedding in a low-dimensional space to optimally preserve neighbourhood identity. Probability distributions generated for each point for each view are combined by conflation method to create a single unified distribution. The goal is to approximate this unified distribution as much as possible when a similar operation is performed on the embedded space. As a cost function, the sum of Kullback-Leibler divergence over the samples is used, which leads to a simple gradient adjusting the position of the samples in the embedded space. The proposed methodology can generate embedding from both complete and incomplete multi-view data sets. Finally, a multi-objective clustering technique (AMOSA) is applied to group the samples in the embedded space. The proposed methodology, Multi-view Neighbourhood Embedding (MvNE), shows an improvement of approximately 2-3% over state-of-the-art models when evaluated on 10 omics data sets.
| S-EPMC7423957 | biostudies-literature
Project description:It is a vital task to design an integrated machine learning model to discover cancer subtypes and understand the heterogeneity of cancer based on multiple omics data. In recent years, some multi-view clustering algorithms have been proposed and applied to the prediction of cancer subtypes. Among them, the multi-view clustering methods based on graph learning are widely concerned. These multi-view approaches usually have one or more of the following problems. Many multi-view algorithms use the original omics data matrix to construct the similarity matrix and ignore the learning of the similarity matrix. They separate the data clustering process from the graph learning process, resulting in a highly dependent clustering performance on the predefined graph. In the process of graph fusion, these methods simply take the average value of the affinity graph of multiple views to represent the result of the fusion graph, and the rich heterogeneous information is not fully utilized. To solve the above problems, in this paper, a Multi-view Spectral Clustering Based on Multi-smooth Representation Fusion (MRF-MSC) method was proposed. Firstly, MRF-MSC constructs a smooth representation for each data type, which can be viewed as a sample (patient) similarity matrix. The smooth representation can explicitly enhance the grouping effect. Secondly, MRF-MSC integrates the smooth representation of multiple omics data to form a similarity matrix containing all biological data information through graph fusion. In addition, MRF-MSC adaptively gives weight factors to the smooth regularization representation of each omics data by using the self-weighting method. Finally, MRF-MSC imposes constrained Laplacian rank on the fusion similarity matrix to get a better cluster structure. The above problems can be transformed into spectral clustering for solving, and the clustering results can be obtained. MRF-MSC unifies the above process of graph construction, graph fusion and spectral clustering under one framework, which can learn better data representation and high-quality graphs, so as to achieve better clustering effect. In the experiment, MRF-MSC obtained good experimental results on the TCGA cancer data sets.
| S-EPMC8450448 | biostudies-literature
Project description:BackgroundMultiple high-throughput molecular profiling by omics technologies can be collected for the same individuals. Combining these data, rather than exploiting them separately, can significantly increase the power of clinically relevant patients subclassifications.ResultsWe propose a multi-view approach in which the information from different data layers (views) is integrated at the levels of the results of each single view clustering iterations. It works by factorizing the membership matrices in a late integration manner. We evaluated the effectiveness and the performance of our method on six multi-view cancer datasets. In all the cases, we found patient sub-classes with statistical significance, identifying novel sub-groups previously not emphasized in literature. Our method performed better as compared to other multi-view clustering algorithms and, unlike other existing methods, it is able to quantify the contribution of single views on the final results.ConclusionOur observations suggest that integration of prior information with genomic features in the subtyping analysis is an effective strategy in identifying disease subgroups. The methodology is implemented in R and the source code is available online at http://neuronelab.unisa.it/a-multi-view-genomic-data-integration-methodology/ .
| S-EPMC4539887 | biostudies-literature
Project description:After decades of independent morphological and functional brain research, a key point in neuroscience nowadays is to understand the combined relationships between the structure of the brain and its components and their dynamics on multiple scales, ranging from circuits of neurons at micro or mesoscale to brain regions at macroscale. With such a goal in mind, there is a vast amount of research focusing on modeling and simulating activity within neuronal structures, and these simulations generate large and complex datasets which have to be analyzed in order to gain the desired insight. In such context, this paper presents ViSimpl, which integrates a set of visualization and interaction tools that provide a semantic view of brain data with the aim of improving its analysis procedures. ViSimpl provides 3D particle-based rendering that allows visualizing simulation data with their associated spatial and temporal information, enhancing the knowledge extraction process. It also provides abstract representations of the time-varying magnitudes supporting different data aggregation and disaggregation operations and giving also focus and context clues. In addition, ViSimpl tools provide synchronized playback control of the simulation being analyzed. Finally, ViSimpl allows performing selection and filtering operations relying on an application called NeuroScheme. All these views are loosely coupled and can be used independently, but they can also work together as linked views, both in centralized and distributed computing environments, enhancing the data exploration and analysis procedures.
| S-EPMC5054003 | biostudies-literature
Project description:Physicians use sonographic characteristics as a reference for the possible diagnosis of thyroid cancers. The purpose of this study was to investigate whether physicians were more effective in their tentative diagnosis based on the information provided by a computer-aided detection (CAD) system. A computer compared software-defined and physician-adjusted tumor loci. A multicenter, multireader, and multicase (MRMC) study was designed to compare clinician performance without and with the use of CAD. Interobserver variability was also analyzed. Excellent, satisfactory, and poor segmentations were observed in 25.3%, 58.9%, and 15.8% of nodules, respectively. There were 200 patients with 265 nodules in the study set. Nineteen physicians scored the malignancy potential of the nodules. The average area under the curve (AUC) of all readers was 0.728 without CAD and significantly increased to 0.792 with CAD. The average standard deviation of the malignant potential score significantly decreased from 18.97 to 16.29. The mean malignant potential score significantly decreased from 35.01 to 31.24 for benign cases. With the CAD system, an additional 7.6% of malignant nodules would be suggested for further evaluation, and biopsy would not be recommended for an additional 10.8% of benign nodules. The results demonstrated that applying a CAD system would improve clinicians' interpretations and lessen the variability in diagnosis. However, more studies are needed to explore the use of the CAD system in an actual ultrasound diagnostic situation where much more benign thyroid nodules would be seen.
| S-EPMC7072687 | biostudies-literature
Project description:BackgroundAccurate identification of Transcriptional Regulator binding locations is essential for analysis of genomic regions, including Cis Regulatory Elements. The customary NGS approaches, predominantly ChIP-Seq, can be obscured by data anomalies and biases which are difficult to detect without supervision.ResultsHere, we develop a method to leverage the usual combinations between many experimental series to mark such atypical peaks. We use deep learning to perform a lossy compression of the genomic regions' representations with multiview convolutions. Using artificial data, we show that our method correctly identifies groups of correlating series and evaluates CRE according to group completeness. It is then applied to the ReMap database's large volume of curated ChIP-seq data. We show that peaks lacking known biological correlators are singled out and less confirmed in real data. We propose normalization approaches useful in interpreting black-box models.ConclusionOur approach detects peaks that are less corroborated than average. It can be extended to other similar problems, and can be interpreted to identify correlation groups. It is implemented in an open-source tool called atyPeak.
| S-EPMC8467021 | biostudies-literature