Bayesian meta-analysis for identifying periodically expressed genes in fission yeast cell cycle

The effort to identify genes with periodic expression during the cell cycle from genome-wide microarray time series data has been ongoing for a decade. However, the lack of rigorous modeling of periodic expression as well as the lack of a comprehensive model for integrating information across genes and experiments has impaired the effort for the accurate identification of periodically expressed genes. To address the problem, we introduce a Bayesian model to integrate multiple independent microarray data sets from three recent genome-wide cell cycle studies on fission yeast. A hierarchical model was used for data integration. In order to facilitate an efficient Monte Carlo sampling from the joint posterior distribution, we develop a novel Metropolis--Hastings group move. A surprising finding from our integrated analysis is that more than 40% of the genes in fission yeast are significantly periodically expressed, greatly enhancing the reported 10--15% of the genes in the current literature. It calls for a reconsideration of the periodically expressed gene detection problem.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS300 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs

In this work we address the task of semantic image segmentation with Deep Learning and make three main contributions that are experimentally shown to have substantial practical merit. First, we highlight convolution with upsampled filters, or 'atrous convolution', as a powerful tool in dense prediction tasks. Atrous convolution allows us to explicitly control the resolution at which feature responses are computed within Deep Convolutional Neural Networks. It also allows us to effectively enlarge the field of view of filters to incorporate larger context without increasing the number of parameters or the amount of computation. Second, we propose atrous spatial pyramid pooling (ASPP) to robustly segment objects at multiple scales. ASPP probes an incoming convolutional feature layer with filters at multiple sampling rates and effective fields-of-views, thus capturing objects as well as image context at multiple scales. Third, we improve the localization of object boundaries by combining methods from DCNNs and probabilistic graphical models. The commonly deployed combination of max-pooling and downsampling in DCNNs achieves invariance but has a toll on localization accuracy. We overcome this by combining the responses at the final DCNN layer with a fully connected Conditional Random Field (CRF), which is shown both qualitatively and quantitatively to improve localization performance. Our proposed "DeepLab" system sets the new state-of-art at the PASCAL VOC-2012 semantic image segmentation task, reaching 79.7% mIOU in the test set, and advances the results on three other datasets: PASCAL-Context, PASCAL-Person-Part, and Cityscapes. All of our code is made publicly available online.Comment: Accepted by TPAM

Decision fusion in healthcare and medicine : a narrative review

Objective: To provide an overview of the decision fusion (DF) technique and describe the applications of the technique in healthcare and medicine at prevention, diagnosis, treatment and administrative levels. Background: The rapid development of technology over the past 20 years has led to an explosion in data growth in various industries, like healthcare. Big data analysis within the healthcare systems is essential for arriving to a value-based decision over a period of time. Diversity and uncertainty in big data analytics have made it impossible to analyze data by using conventional data mining techniques and thus alternative solutions are required. DF is a form of data fusion techniques that could increase the accuracy of diagnosis and facilitate interpretation, summarization and sharing of information. Methods: We conducted a review of articles published between January 1980 and December 2020 from various databases such as Google Scholar, IEEE, PubMed, Science Direct, Scopus and web of science using the keywords decision fusion (DF), information fusion, healthcare, medicine and big data. A total of 141 articles were included in this narrative review. Conclusions: Given the importance of big data analysis in reducing costs and improving the quality of healthcare; along with the potential role of DF in big data analysis, it is recommended to know the full potential of this technique including the advantages, challenges and applications of the technique before its use. Future studies should focus on describing the methodology and types of data used for its applications within the healthcare sector

A review of technical factors to consider when designing neural networks for semantic segmentation of Earth Observation imagery

Semantic segmentation (classification) of Earth Observation imagery is a crucial task in remote sensing. This paper presents a comprehensive review of technical factors to consider when designing neural networks for this purpose. The review focuses on Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Generative Adversarial Networks (GANs), and transformer models, discussing prominent design patterns for these ANN families and their implications for semantic segmentation. Common pre-processing techniques for ensuring optimal data preparation are also covered. These include methods for image normalization and chipping, as well as strategies for addressing data imbalance in training samples, and techniques for overcoming limited data, including augmentation techniques, transfer learning, and domain adaptation. By encompassing both the technical aspects of neural network design and the data-related considerations, this review provides researchers and practitioners with a comprehensive and up-to-date understanding of the factors involved in designing effective neural networks for semantic segmentation of Earth Observation imagery.Comment: 145 pages with 32 figure

Evaluation and analysis of hybrid intelligent pattern recognition techniques for speaker identification

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The rapid momentum of the technology progress in the recent years has led to a tremendous rise in the use of biometric authentication systems. The objective of this research is to investigate the problem of identifying a speaker from its voice regardless of the content (i.e. text-independent), and to design efficient methods of combining face and voice in producing a robust authentication system. A novel approach towards speaker identification is developed using wavelet analysis, and multiple neural networks including Probabilistic Neural Network (PNN), General Regressive Neural Network (GRNN)and Radial Basis Function-Neural Network (RBF NN) with the AND voting scheme. This approach is tested on GRID and VidTIMIT cor-pora and comprehensive test results have been validated with state- of-the-art approaches. The system was found to be competitive and it improved the recognition rate by 15% as compared to the classical Mel-frequency Cepstral Coe±cients (MFCC), and reduced the recognition time by 40% compared to Back Propagation Neural Network (BPNN), Gaussian Mixture Models (GMM) and Principal Component Analysis (PCA). Another novel approach using vowel formant analysis is implemented using Linear Discriminant Analysis (LDA). Vowel formant based speaker identification is best suitable for real-time implementation and requires only a few bytes of information to be stored for each speaker, making it both storage and time efficient. Tested on GRID and Vid-TIMIT, the proposed scheme was found to be 85.05% accurate when Linear Predictive Coding (LPC) is used to extract the vowel formants, which is much higher than the accuracy of BPNN and GMM. Since the proposed scheme does not require any training time other than creating a small database of vowel formants, it is faster as well. Furthermore, an increasing number of speakers makes it di±cult for BPNN and GMM to sustain their accuracy, but the proposed score-based methodology stays almost linear. Finally, a novel audio-visual fusion based identification system is implemented using GMM and MFCC for speaker identi¯cation and PCA for face recognition. The results of speaker identification and face recognition are fused at different levels, namely the feature, score and decision levels. Both the score-level and decision-level (with OR voting) fusions were shown to outperform the feature-level fusion in terms of accuracy and error resilience. The result is in line with the distinct nature of the two modalities which lose themselves when combined at the feature-level. The GRID and VidTIMIT test results validate that the proposed scheme is one of the best candidates for the fusion of face and voice due to its low computational time and high recognition accuracy

SkipcrossNets: Adaptive Skip-cross Fusion for Road Detection

Multi-modal fusion is increasingly being used for autonomous driving tasks, as images from different modalities provide unique information for feature extraction. However, the existing two-stream networks are only fused at a specific network layer, which requires a lot of manual attempts to set up. As the CNN goes deeper, the two modal features become more and more advanced and abstract, and the fusion occurs at the feature level with a large gap, which can easily hurt the performance. In this study, we propose a novel fusion architecture called skip-cross networks (SkipcrossNets), which combines adaptively LiDAR point clouds and camera images without being bound to a certain fusion epoch. Specifically, skip-cross connects each layer to each layer in a feed-forward manner, and for each layer, the feature maps of all previous layers are used as input and its own feature maps are used as input to all subsequent layers for the other modality, enhancing feature propagation and multi-modal features fusion. This strategy facilitates selection of the most similar feature layers from two data pipelines, providing a complementary effect for sparse point cloud features during fusion processes. The network is also divided into several blocks to reduce the complexity of feature fusion and the number of model parameters. The advantages of skip-cross fusion were demonstrated through application to the KITTI and A2D2 datasets, achieving a MaxF score of 96.85% on KITTI and an F1 score of 84.84% on A2D2. The model parameters required only 2.33 MB of memory at a speed of 68.24 FPS, which could be viable for mobile terminals and embedded devices

Time warping of evolutionary distant temporal gene expression data based on noise suppression

<p>Abstract</p> <p>Background</p> <p>Comparative analysis of genome wide temporal gene expression data has a broad potential area of application, including evolutionary biology, developmental biology, and medicine. However, at large evolutionary distances, the construction of global alignments and the consequent comparison of the time-series data are difficult. The main reason is the accumulation of variability in expression profiles of orthologous genes, in the course of evolution.</p> <p>Results</p> <p>We applied Pearson distance matrices, in combination with other noise-suppression techniques and data filtering to improve alignments. This novel framework enhanced the capacity to capture the similarities between the temporal gene expression datasets separated by large evolutionary distances. We aligned and compared the temporal gene expression data in budding (<it>Saccharomyces cerevisiae</it>) and fission (<it>Schizosaccharomyces pombe</it>) yeast, which are separated by more then ~400 myr of evolution. We found that the global alignment (time warping) properly matched the duration of cell cycle phases in these distant organisms, which was measured in prior studies. At the same time, when applied to individual ortholog pairs, this alignment procedure revealed groups of genes with distinct alignments, different from the global alignment.</p> <p>Conclusion</p> <p>Our alignment-based predictions of differences in the cell cycle phases between the two yeast species were in a good agreement with the existing data, thus supporting the computational strategy adopted in this study. We propose that the existence of the alternative alignments, specific to distinct groups of genes, suggests presence of different synchronization modes between the two organisms and possible functional decoupling of particular physiological gene networks in the course of evolution.</p