Brain Evoked Response Qualification Using Multi-Set Consensus Clustering: Toward Single-Trial EEG Analysis.

In event-related potential (ERP) analysis, it is commonly assumed that individual trials from a subject share similar properties and originate from comparable neural sources, allowing reliable interpretation of group-averages. Nevertheless, traditional group-level ERP analysis methods, including cluster analysis, often overlook critical information about individual subjects' neural processes due to using fixed measurement intervals derived from averaging. We developed a multi-set consensus clustering pipeline to examine cognitive processes at the individual subject level. Initially, consensus clustering from diverse methods was applied to single-trial EEG epochs of individual subjects. Subsequently, a second level of consensus clustering was performed across the trials of each subject. A newly modified time window determination method was then employed to identify individual subjects' ERP(s) of interest. We validated our method with simulated data for ERP components N2 and P3, and real data from a visual oddball task to confirm the P3 component. Our findings revealed that estimated time windows for individual subjects provide precise ERP identification compared to fixed time windows across all subjects. Additionally, Monte Carlo simulations with synthetic single-trial data demonstrated stable scores for the N2 and P3 components, confirming the reliability of our method. The proposed method enhances the examination of brain-evoked responses at the individual subject level by considering single-trial EEG data, thereby extracting mutual information relevant to the neural process. This approach offers a significant improvement over conventional ERP analysis, which relies on the averaging mechanism and fixed measurement interval.

Optimal Number of Clusters by Measuring Similarity Among Topographies for Spatio-Temporal ERP Analysis.

Averaging amplitudes over consecutive time samples (i.e., time window) is widely used to calculate the peak amplitude of event-related potentials (ERPs). Cluster analysis of the spatio-temporal ERP data is a promising tool to determine the time window of an ERP of interest. However, determining an appropriate number of clusters to optimally represent ERPs is still challenging. Here, we develop a new method to estimate the optimal number of clusters utilizing consensus clustering. Various polarity dependent clustering methods, namely, k-means, hierarchical clustering, fuzzy c-means, self-organizing map, spectral clustering, and Gaussian mixture model, are used to configure consensus clustering after assessing them individually. When a range of clusters is applied many times, the optimal number of clusters should correspond to the expectation, which is the average of the obtained mean inner-similarities of estimated time windows across all conditions and groups converge in the satisfactory thresholds. In order to assess our method, the proposed method has been applied to simulated data and prospective memory experiment ERP data aimed to qualify N2 and P3, and N300 and prospective positivity components, respectively. The results of determining the optimal number of clusters meet at six cluster maps for both ERP data. In addition, our results revealed that the proposed method could be reliably applied to ERP data to determine the appropriate time window for the ERP of interest when the measurement interval is not accurately defined.

Intelligent Fault Diagnosis Framework for Modular Multilevel Converters in HVDC Transmission.

Open circuit failure mode in insulated-gate bipolar transistors (IGBT) is one of the most common faults in modular multilevel converters (MMCs). Several techniques for MMC fault diagnosis based on threshold parameters have been proposed, but very few studies have considered artificial intelligence (AI) techniques. Using thresholds has the difficulty of selecting suitable threshold values for different operating conditions. In addition, very little attention has been paid to the importance of developing fast and accurate techniques for the real-life application of open-circuit failures of IGBT fault diagnosis. To achieve high classification accuracy and reduced computation time, a fault diagnosis framework with a combination of the AC-side three-phase current, and the upper and lower bridges' currents of the MMCs to automatically classify health conditions of MMCs is proposed. In this framework, the principal component analysis (PCA) is used for feature extraction. Then, two classification algorithms-multiclass support vector machine (SVM) based on error-correcting output codes (ECOC) and multinomial logistic regression (MLR)-are used for classification. The effectiveness of the proposed framework is validated by a two-terminal simulation model of the MMC-high-voltage direct current (HVDC) transmission power system using PSCAD/EMTDC software. The simulation results demonstrate that the proposed framework is highly effective in diagnosing the health conditions of MMCs compared to recently published results.

Intrinsic Dimension Estimation-Based Feature Selection and Multinomial Logistic Regression for Classification of Bearing Faults Using Compressively Sampled Vibration Signals.

As failures of rolling bearings lead to major failures in rotating machines, recent vibration-based rolling bearing fault diagnosis techniques are focused on obtaining useful fault features from the huge collection of raw data. However, too many features reduce the classification accuracy and increase the computation time. This paper proposes an effective feature selection technique based on intrinsic dimension estimation of compressively sampled vibration signals. First, compressive sampling (CS) is used to get compressed measurements from the collected raw vibration signals. Then, a global dimension estimator, the geodesic minimal spanning tree (GMST), is employed to compute the minimal number of features needed to represent efficiently the compressively sampled signals. Finally, a feature selection process, combining the stochastic proximity embedding (SPE) and the neighbourhood component analysis (NCA), is used to select fewer features for bearing fault diagnosis. With regression analysis-based predictive modelling technique and the multinomial logistic regression (MLR) classifier, the selected features are assessed in two case studies of rolling bearings vibration signals under different working loads. The experimental results demonstrate that the proposed method can successfully select fewer features, with which the MLR-based trained model achieves high classification accuracy and significantly reduced computation times compared to published research.

Utilizing SVD and VMD for Denoising Non-Stationary Signals of Roller Bearings.

In view of the fact that vibration signals of rolling bearings are much contaminated by noise in the early failure period, this paper presents a new denoising SVD-VMD method by combining singular value decomposition (SVD) and variational mode decomposition (VMD). SVD is used to determine the structure of the underlying model, which is referred to as signal and noise subspaces, and VMD is used to decompose the original signal into several band-limited modes. Then the effective components are selected from these modes to reconstruct the denoised signal according to the difference spectrum (DS) of singular values and kurtosis values. Simulated signals and experimental signals of roller bearing faults have been analyzed using this proposed method and compared with SVD-DS. The results demonstrate that the proposed method can effectively retain the useful signals and denoise the bearing signals in extremely noisy backgrounds.

Open-Circuit Fault Detection and Classification of Modular Multilevel Converters in High Voltage Direct Current Systems (MMC-HVDC) with Long Short-Term Memory (LSTM) Method.

Fault detection and classification are two of the challenging tasks in Modular Multilevel Converters in High Voltage Direct Current (MMC-HVDC) systems. To directly classify the raw sensor data without certain feature extraction and classifier design, a long short-term memory (LSTM) neural network is proposed and used for seven states of the MMC-HVDC transmission power system simulated by Power Systems Computer Aided Design/Electromagnetic Transients including DC (PSCAD/EMTDC). It is observed that the LSTM method can detect faults with 100% accuracy and classify different faults as well as provide promising fault classification performance. Compared with a bidirectional LSTM (BiLSTM), the LSTM can get similar classification accuracy, requiring less training time and testing time. Compared with Convolutional Neural Networks (CNN) and AutoEncoder-based deep neural networks (AE-based DNN), the LSTM method can get better classification accuracy around the middle of the testing data proportion, but it needs more training time.

Prediction paradigm involving time series applied to total blood issues data from England.

BACKGROUND: Blood products are essential for modern medicine, but managing their collection and supply in the face of fluctuating demands represents a major challenge. As deterministic models based on predicted changes in population have been problematic, there remains a need for more precise and reliable prediction of demands. Here, we propose a paradigm incorporating four different time-series methods to predict red blood cell (RBC) issues 4 to 24 weeks ahead. STUDY DESIGN AND METHODS: We used daily aggregates of RBC units issued from 2005 to 2011 from the National Health Service Blood and Transplant. We generated a new set of nonoverlapping weekly data by summing the daily data over 7 days and derived the average blood issues per week over 4-week periods. We used four methods for linear prediction of blood demand by computing the coefficients with the minimum mean squared error and weighted least squares error algorithms. RESULTS: We optimized the time-window size, order of the prediction, and order of the polynomial fit for our data set. The four time-series methods, essentially using different weightings to data points, gave very similar results and predicted mean RBC issues with a standard deviation of the percentage error of 3.0% for 4 weeks ahead and 4.0% for 24 weeks ahead. CONCLUSION: This paradigm allows prediction of demand for RBCs and could be developed to provide reliable and precise prediction up to 24 weeks ahead to improve the efficiency of blood services and sufficiency of blood supply with reduced costs.

Improved long-term time-series predictions of total blood use data from England.

BACKGROUND: Red blood cells are essential for modern medicine but managing their collection and supply to cope with fluctuating demands represents a major challenge. As deterministic models based on predicted population changes have been problematic, there remains a need for more precise and reliable prediction of use. Here, we develop three new time-series methods to predict red cell use 4 to 52 weeks ahead. STUDY DESIGN AND METHODS: From daily aggregates of red blood cell (RBC) units issued from 2005 to 2011 from the NHS Blood and Transplant, we generated a new set of non-overlapping weekly data by summing the daily data over 7 days and derived the average blood use per week over 4-week and 52-week periods. We used three new methods for linear prediction of blood use by computing the coefficients using Minimum Mean Squared Error (MMSE) algorithm. RESULTS: We optimized the time-window size, order of the prediction, and order of the polynomial fit for our data set. By exploiting the annual periodicity of the data, we achieved significant improvements in long-term predictions, as well as modest improvements in short-term predictions. The new methods predicted mean RBC use with a standard deviation of the percentage error of 2.5% for 4 weeks ahead and 3.4% for 52 weeks ahead. CONCLUSION: This paradigm allows short- and long-term prediction of RBC use and could provide reliable and precise prediction up to 52 weeks ahead to improve the efficiency of blood services and sufficiency of blood supply with reduced costs.

Fault Detection and Classification in MMC-HVDC Systems Using Learning Methods.

In this paper, we explore learning methods to improve the performance of the open-circuit fault diagnosis of modular multilevel converters (MMCs). Two deep learning methods, namely, convolutional neural networks (CNN) and auto encoder based deep neural networks (AE-based DNN), as well as stand-alone SoftMax classifier are explored for the detection and classification of faults of MMC-based high voltage direct current converter (MMC-HVDC). Only AC-side three-phase current and the upper and lower bridges' currents of the MMCs are used directly in our proposed approaches without any explicit feature extraction or feature subset selection. The two-terminal MMC-HVDC system is implemented in Power Systems Computer-Aided Design/Electromagnetic Transients including DC (PSCAD/EMTDC) to verify and compare our methods. The simulation results indicate CNN, AE-based DNN, and SoftMax classifier can detect and classify faults with high detection accuracy and classification accuracy. Compared with CNN and AE-based DNN, the SoftMax classifier performed better in detection and classification accuracy as well as testing speed. The detection accuracy of AE-based DNN is a little better than CNN, while CNN needs less training time than the AE-based DNN and SoftMax classifier.

In vitro downregulated hypoxia transcriptome is associated with poor prognosis in breast cancer.

BACKGROUND: Hypoxia is a characteristic of breast tumours indicating poor prognosis. Based on the assumption that those genes which are up-regulated under hypoxia in cell-lines are expected to be predictors of poor prognosis in clinical data, many signatures of poor prognosis were identified. However, it was observed that cell line data do not always concur with clinical data, and therefore conclusions from cell line analysis should be considered with caution. As many transcriptomic cell-line datasets from hypoxia related contexts are available, integrative approaches which investigate these datasets collectively, while not ignoring clinical data, are required. RESULTS: We analyse sixteen heterogeneous breast cancer cell-line transcriptomic datasets in hypoxia-related conditions collectively by employing the unique capabilities of the method, UNCLES, which integrates clustering results from multiple datasets and can address questions that cannot be answered by existing methods. This has been demonstrated by comparison with the state-of-the-art iCluster method. From this collection of genome-wide datasets include 15,588 genes, UNCLES identified a relatively high number of genes (>1000 overall) which are consistently co-regulated over all of the datasets, and some of which are still poorly understood and represent new potential HIF targets, such as RSBN1 and KIAA0195. Two main, anti-correlated, clusters were identified; the first is enriched with MYC targets participating in growth and proliferation, while the other is enriched with HIF targets directly participating in the hypoxia response. Surprisingly, in six clinical datasets, some sub-clusters of growth genes are found consistently positively correlated with hypoxia response genes, unlike the observation in cell lines. Moreover, the ability to predict bad prognosis by a combined signature of one sub-cluster of growth genes and one sub-cluster of hypoxia-induced genes appears to be comparable and perhaps greater than that of known hypoxia signatures. CONCLUSIONS: We present a clustering approach suitable to integrate data from diverse experimental set-ups. Its application to breast cancer cell line datasets reveals new hypoxia-regulated signatures of genes which behave differently when in vitro (cell-line) data is compared with in vivo (clinical) data, and are of a prognostic value comparable or exceeding the state-of-the-art hypoxia signatures.

Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors.

BACKGROUND: Human-induced pluripotent stem cells (hiPSCs) are a potentially invaluable resource for regenerative medicine, including the in vitro manufacture of blood products. HiPSC-derived red blood cells are an attractive therapeutic option in hematology, yet exhibit unexplained proliferation and enucleation defects that presently preclude such applications. We hypothesised that substantial differential regulation of gene expression during erythroid development accounts for these important differences between hiPSC-derived cells and those from adult or cord-blood progenitors. We thus cultured erythroblasts from each source for transcriptomic analysis to investigate differential gene expression underlying these functional defects. RESULTS: Our high resolution transcriptional view of definitive erythropoiesis captures the regulation of genes relevant to cell-cycle control and confers statistical power to deploy novel bioinformatics methods. Whilst the dynamics of erythroid program elaboration from adult and cord blood progenitors were very similar, the emerging erythroid transcriptome in hiPSCs revealed radically different program elaboration compared to adult and cord blood cells. We explored the function of differentially expressed genes in hiPSC-specific clusters defined by our novel tunable clustering algorithms (SMART and Bi-CoPaM). HiPSCs show reduced expression of c-KIT and key erythroid transcription factors SOX6, MYB and BCL11A, strong HBZ-induction, and aberrant expression of genes involved in protein degradation, lysosomal clearance and cell-cycle regulation. CONCLUSIONS: Together, these data suggest that hiPSC-derived cells may be specified to a primitive erythroid fate, and implies that definitive specification may more accurately reflect adult development. We have therefore identified, for the first time, distinct gene expression dynamics during erythroblast differentiation from hiPSCs which may cause reduced proliferation and enucleation of hiPSC-derived erythroid cells. The data suggest several mechanistic defects which may partially explain the observed aberrant erythroid differentiation from hiPSCs.

UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets.

BACKGROUND: Collective analysis of the increasingly emerging gene expression datasets are required. The recently proposed binarisation of consensus partition matrices (Bi-CoPaM) method can combine clustering results from multiple datasets to identify the subsets of genes which are consistently co-expressed in all of the provided datasets in a tuneable manner. However, results validation and parameter setting are issues that complicate the design of such methods. Moreover, although it is a common practice to test methods by application to synthetic datasets, the mathematical models used to synthesise such datasets are usually based on approximations which may not always be sufficiently representative of real datasets. RESULTS: Here, we propose an unsupervised method for the unification of clustering results from multiple datasets using external specifications (UNCLES). This method has the ability to identify the subsets of genes consistently co-expressed in a subset of datasets while being poorly co-expressed in another subset of datasets, and to identify the subsets of genes consistently co-expressed in all given datasets. We also propose the M-N scatter plots validation technique and adopt it to set the parameters of UNCLES, such as the number of clusters, automatically. Additionally, we propose an approach for the synthesis of gene expression datasets using real data profiles in a way which combines the ground-truth-knowledge of synthetic data and the realistic expression values of real data, and therefore overcomes the problem of faithfulness of synthetic expression data modelling. By application to those datasets, we validate UNCLES while comparing it with other conventional clustering methods, and of particular relevance, biclustering methods. We further validate UNCLES by application to a set of 14 real genome-wide yeast datasets as it produces focused clusters that conform well to known biological facts. Furthermore, in-silico-based hypotheses regarding the function of a few previously unknown genes in those focused clusters are drawn. CONCLUSIONS: The UNCLES method, the M-N scatter plots technique, and the expression data synthesis approach will have wide application for the comprehensive analysis of genomic and other sources of multiple complex biological datasets. Moreover, the derived in-silico-based biological hypotheses represent subjects for future functional studies.

Comprehensive analysis of forty yeast microarray datasets reveals a novel subset of genes (APha-RiB) consistently negatively associated with ribosome biogenesis.

BACKGROUND: The scale and complexity of genomic data lend themselves to analysis using sophisticated mathematical techniques to yield information that can generate new hypotheses and so guide further experimental investigations. An ensemble clustering method has the ability to perform consensus clustering over the same set of genes from different microarray datasets by combining results from different clustering methods into a single consensus result. RESULTS: In this paper we have performed comprehensive analysis of forty yeast microarray datasets. One recently described Bi-CoPaM method can analyse expressions of the same set of genes from various microarray datasets while using different clustering methods, and then combine these results into a single consensus result whose clusters' tightness is tunable from tight, specific clusters to wide, overlapping clusters. This has been adopted in a novel way over genome-wide data from forty yeast microarray datasets to discover two clusters of genes that are consistently co-expressed over all of these datasets from different biological contexts and various experimental conditions. Most strikingly, average expression profiles of those clusters are consistently negatively correlated in all of the forty datasets while neither profile leads or lags the other. CONCLUSIONS: The first cluster is enriched with ribosomal biogenesis genes. The biological processes of most of the genes in the second cluster are either unknown or apparently unrelated although they show high connectivity in protein-protein and genetic interaction networks. Therefore, it is possible that this mostly uncharacterised cluster and the ribosomal biogenesis cluster are transcriptionally oppositely regulated by some common machinery. Moreover, we anticipate that the genes included in this previously unknown cluster participate in generic, in contrast to specific, stress response processes. These novel findings illuminate coordinated gene expression in yeast and suggest several hypotheses for future experimental functional work. Additionally, we have demonstrated the usefulness of the Bi-CoPaM-based approach, which may be helpful for the analysis of other groups of (microarray) datasets from other species and systems for the exploration of global genetic co-expression.

DPFNet: Fast Reconstruction of Multi-coil MRI Based on Dual Domain Parallel Fusion Network.

There are relatively few studies on the multicoil reconstruction task of existing Magnetic resonance imaging (MRI) methods, as there are problems with insufficient reconstruction details, high memory occupation during training, etc. Therefore, a new Dual domain Parallel Fusion Reconstruction Network (DPFNet) is proposed in this paper. The whole network consists of coil sensitivity graph estimation module, dual domain feature extraction module, dual domain dynamic error correction module, and dual domain dynamic fusion module. A U-Net has been used as the backbone network. The network reconstructs undersampled MRI images and K-space data simultaneously in two branches of the image domain and K-space domain, and the fusion module realizes the reconstruction information interaction between the two branches. In addition, a new dual domain consistency loss is also proposed, which reduces the error between the same MRI slice image and K-space data with dual domain output, and achieves high quality reconstruction. In this paper, a series of comparative experiments and ablation experiments are conducted in the open Calgary-Campinas-359 brain MRI data set. The results of the experiments show that the proposed DPFNet achieves the most advanced level at present and is superior to other traditional algorithms and reconstruction methods based on deep learning. In particular, the reconstruction results from Cartesian sampling are very good.

From Vivaldi to Beatles and back: predicting lateralized brain responses to music.

We aimed at predicting the temporal evolution of brain activity in naturalistic music listening conditions using a combination of neuroimaging and acoustic feature extraction. Participants were scanned using functional Magnetic Resonance Imaging (fMRI) while listening to two musical medleys, including pieces from various genres with and without lyrics. Regression models were built to predict voxel-wise brain activations which were then tested in a cross-validation setting in order to evaluate the robustness of the hence created models across stimuli. To further assess the generalizability of the models we extended the cross-validation procedure by including another dataset, which comprised continuous fMRI responses of musically trained participants to an Argentinean tango. Individual models for the two musical medleys revealed that activations in several areas in the brain belonging to the auditory, limbic, and motor regions could be predicted. Notably, activations in the medial orbitofrontal region and the anterior cingulate cortex, relevant for self-referential appraisal and aesthetic judgments, could be predicted successfully. Cross-validation across musical stimuli and participant pools helped identify a region of the right superior temporal gyrus, encompassing the planum polare and the Heschl's gyrus, as the core structure that processed complex acoustic features of musical pieces from various genres, with or without lyrics. Models based on purely instrumental music were able to predict activation in the bilateral auditory cortices, parietal, somatosensory, and left hemispheric primary and supplementary motor areas. The presence of lyrics on the other hand weakened the prediction of activations in the left superior temporal gyrus. Our results suggest spontaneous emotion-related processing during naturalistic listening to music and provide supportive evidence for the hemispheric specialization for categorical sounds with realistic stimuli. We herewith introduce a powerful means to predict brain responses to music, speech, or soundscapes across a large variety of contexts.

Global gene expression analysis of human erythroid progenitors.

Understanding the pattern of gene expression during erythropoiesis is crucial for a synthesis of erythroid developmental biology. Here, we isolated 4 distinct populations at successive erythropoietin-dependent stages of erythropoiesis, including the terminal, pyknotic stage. The transcriptome was determined using Affymetrix arrays. First, we demonstrated the importance of using defined cell populations to identify lineage and temporally specific patterns of gene expression. Cells sorted by surface expression profile not only express significantly fewer genes than unsorted cells but also demonstrate significantly greater differences in the expression levels of particular genes between stages than unsorted cells. Second, using standard software, we identified more than 1000 transcripts not previously observed to be differentially expressed during erythroid maturation, 13 of which are highly significantly terminally regulated, including RFXAP and SMARCA4. Third, using matched filtering, we identified 12 transcripts not previously reported to be continuously up-regulated in maturing human primary erythroblasts. Finally, using transcription factor binding site analysis, we identified potential transcription factors that may regulate gene expression during terminal erythropoiesis. Our stringent lists of differentially regulated and continuously expressed transcripts containing many genes with undiscovered functions in erythroblasts are a resource for future functional studies of erythropoiesis. Our Human Erythroid Maturation database is available at https://cellline.molbiol.ox.ac.uk/eryth/index.html. [corrected].

Semi-Supervised Medical Image Segmentation Using Adversarial Consistency Learning and Dynamic Convolution Network.

Popular semi-supervised medical image segmentation networks often suffer from error supervision from unlabeled data since they usually use consistency learning under different data perturbations to regularize model training. These networks ignore the relationship between labeled and unlabeled data, and only compute single pixel-level consistency leading to uncertain prediction results. Besides, these networks often require a large number of parameters since their backbone networks are designed depending on supervised image segmentation tasks. Moreover, these networks often face a high over-fitting risk since a small number of training samples are popular for semi-supervised image segmentation. To address the above problems, in this paper, we propose a novel adversarial self-ensembling network using dynamic convolution (ASE-Net) for semi-supervised medical image segmentation. First, we use an adversarial consistency training strategy (ACTS) that employs two discriminators based on consistency learning to obtain prior relationships between labeled and unlabeled data. The ACTS can simultaneously compute pixel-level and image-level consistency of unlabeled data under different data perturbations to improve the prediction quality of labels. Second, we design a dynamic convolution-based bidirectional attention component (DyBAC) that can be embedded in any segmentation network, aiming at adaptively adjusting the weights of ASE-Net based on the structural information of input samples. This component effectively improves the feature representation ability of ASE-Net and reduces the overfitting risk of the network. The proposed ASE-Net has been extensively tested on three publicly available datasets, and experiments indicate that ASE-Net is superior to state-of-the-art networks, and reduces computational costs and memory overhead. The code is available at: https://github.com/SUST-reynole/ASE-Nethttps://github.com/SUST-reynole/ASE-Net.

SGU-Net: Shape-Guided Ultralight Network for Abdominal Image Segmentation.

Convolutional neural networks (CNNs) have achieved significant success in medical image segmentation. However, they also suffer from the requirement of a large number of parameters, leading to a difficulty of deploying CNNs to low-source hardwares, e.g., embedded systems and mobile devices. Although some compacted or small memory-hungry models have been reported, most of them may cause degradation in segmentation accuracy. To address this issue, we propose a shape-guided ultralight network (SGU-Net) with extremely low computational costs. The proposed SGU-Net includes two main contributions: it first presents an ultralight convolution that is able to implement double separable convolutions simultaneously, i.e., asymmetric convolution and depthwise separable convolution. The proposed ultralight convolution not only effectively reduces the number of parameters but also enhances the robustness of SGU-Net. Secondly, our SGUNet employs an additional adversarial shape-constraint to let the network learn shape representation of targets, which can significantly improve the segmentation accuracy for abdomen medical images using self-supervision. The SGU-Net is extensively tested on four public benchmark datasets, LiTS, CHAOS, NIH-TCIA and 3Dircbdb. Experimental results show that SGU-Net achieves higher segmentation accuracy using lower memory costs, and outperforms state-of-the-art networks. Moreover, we apply our ultralight convolution into a 3D volume segmentation network, which obtains a comparable performance with fewer parameters and memory usage. The available code of SGUNet is released at https://github.com/SUST-reynole/SGUNet.

Identifying Phage Sequences From Metagenomic Data Using Deep Neural Network With Word Embedding and Attention Mechanism.

Phages are the functional viruses that infect bacteria and they play important roles in microbial communities and ecosystems. Phage research has attracted great attention due to the wide applications of phage therapy in treating bacterial infection in recent years. Metagenomics sequencing technique can sequence microbial communities directly from an environmental sample. Identifying phage sequences from metagenomic data is a vital step in the downstream of phage analysis. However, the existing methods for phage identification suffer from some limitations in the utilization of the phage feature for prediction, and therefore their prediction performance still need to be improved further. In this article, we propose a novel deep neural network (called MetaPhaPred) for identifying phages from metagenomic data. In MetaPhaPred, we first use a word embedding technique to encode the metagenomic sequences into word vectors, extracting the latent feature vectors of DNA words. Then, we design a deep neural network with a convolutional neural network (CNN) to capture the feature maps in sequences, and with a bi-directional long short-term memory network (Bi-LSTM) to capture the long-term dependencies between features from both forward and backward directions. The feature map consists of a set of feature patterns, each of which is the weighted feature extracted by a convolution filter with convolution kernels in the CNN slide along the input feature vectors. Next, an attention mechanism is used to enhance contributions of important features. Experimental results on both simulated and real metagenomic data with different lengths demonstrate the superiority of the proposed MetaPhaPred over the state-of-the-art methods in identifying phage sequences.