Light diffraction by sarcomeres produces iridescence in transmission in the transparent ghost catfish.

Despite the elaborate varieties of iridescent colors in biological species, most of them are reflective. Here we show the rainbow-like structural colors found in the ghost catfish (Kryptopterus vitreolus), which exist only in transmission. The fish shows flickering iridescence throughout the transparent body. The iridescence originates from the collective diffraction of light after passing through the periodic band structures of the sarcomeres inside the tightly stacked myofibril sheets, and the muscle fibers thus work as transmission gratings. The length of the sarcomeres varies from ~1 µm from the body neutral plane near the skeleton to ~2 µm next to the skin, and the iridescence of a live fish mainly results from the longer sarcomeres. The length of the sarcomere changes by ~80 nm as it relaxes and contracts, and the fish shows a quickly blinking dynamic diffraction pattern as it swims. While similar diffraction colors are also observed in thin slices of muscles from non-transparent species such as the white crucian carps, a transparent skin is required indeed to have such iridescence in live species. The ghost catfish skin is of a plywood structure of collagen fibrils, which allows more than 90% of the incident light to pass directly into the muscles and the diffracted light to exit the body. Our findings could also potentially explain the iridescence in other transparent aquatic species, including the eel larvae (Leptocephalus) and the icefishes (Salangidae).

A Novel Tensor Ring Sparsity Measurement for Image Completion.

As a promising data analysis technique, sparse modeling has gained widespread traction in the field of image processing, particularly for image recovery. The matrix rank, served as a measure of data sparsity, quantifies the sparsity within the Kronecker basis representation of a given piece of data in the matrix format. Nevertheless, in practical scenarios, much of the data are intrinsically multi-dimensional, and thus, using a matrix format for data representation will inevitably yield sub-optimal outcomes. Tensor decomposition (TD), as a high-order generalization of matrix decomposition, has been widely used to analyze multi-dimensional data. In a direct generalization to the matrix rank, low-rank tensor modeling has been developed for multi-dimensional data analysis and achieved great success. Despite its efficacy, the connection between TD rank and the sparsity of the tensor data is not direct. In this work, we introduce a novel tensor ring sparsity measurement (TRSM) for measuring the sparsity of the tensor. This metric relies on the tensor ring (TR) Kronecker basis representation of the tensor, providing a unified interpretation akin to matrix sparsity measurements, wherein the Kronecker basis serves as the foundational representation component. Moreover, TRSM can be efficiently computed by the product of the ranks of the mode-2 unfolded TR-cores. To enhance the practical performance of TRSM, the folded-concave penalty of the minimax concave penalty is introduced as a nonconvex relaxation. Lastly, we extend the TRSM to the tensor completion problem and use the alternating direction method of the multipliers scheme to solve it. Experiments on image and video data completion demonstrate the effectiveness of the proposed method.

Hybrid Convolutional Neural Network for Localization of Epileptic Focus Based on iEEG.

Epileptic focus localization by analysing intracranial electroencephalogram (iEEG) plays a critical role in successful surgical therapy of resection of the epileptogenic lesion. However, manual analysis and classification of the iEEG signal by clinicians are arduous and time-consuming and excessively depend on the experience. Due to individual differences of patients, the iEEG signal from different patients usually shows very diverse features even if the features belong to the same class. Accordingly, automatic detection of epileptic focus is required to improve the accuracy and to shorten the time for treatment. In this paper, we propose a novel feature fusion-based iEEG classification method, a deep learning model termed Time-Frequency Hybrid Network (TF-HybridNet), in which short-time Fourier transform (STFT) and 1d convolution layers are performed on the input iEEG in parallel to extract features of the time-frequency domain and feature maps. And then, the time-frequency features and feature maps are fused and fed to a 2d convolutional neural network (CNN). We used the Bern-Barcelona iEEG dataset for evaluating the performance of TF-HybridNet, and the experimental results show that our approach is able to differentiate the focal from nonfocal iEEG signal with an average classification accuracy of 94.3% and demonstrates an improved accuracy rate compared to the model using only STFT or one-dimensional convolutional layers as feature extraction.

Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm.

MOTIVATION: Genome-wide identification of the transcriptomic responses of human cell lines to drug treatments is a challenging issue in medical and pharmaceutical research. However, drug-induced gene expression profiles are largely unknown and unobserved for all combinations of drugs and human cell lines, which is a serious obstacle in practical applications. RESULTS: Here, we developed a novel computational method to predict unknown parts of drug-induced gene expression profiles for various human cell lines and predict new drug therapeutic indications for a wide range of diseases. We proposed a tensor-train weighted optimization (TT-WOPT) algorithm to predict the potential values for unknown parts in tensor-structured gene expression data. Our results revealed that the proposed TT-WOPT algorithm can accurately reconstruct drug-induced gene expression data for a range of human cell lines in the Library of Integrated Network-based Cellular Signatures. The results also revealed that in comparison with the use of original gene expression profiles, the use of imputed gene expression profiles improved the accuracy of drug repositioning. We also performed a comprehensive prediction of drug indications for diseases with gene expression profiles, which suggested many potential drug indications that were not predicted by previous approaches. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Chromaticity of structural color in polymer thin film photonic crystals.

A three-dimensional goniometric study of thin-film polymer photonic crystals investigates how the chromaticity of structural color is correlated to structural ordering. Characterization of chromaticity and the angular properties of structural color are presented in terms of CIE 1931 color spaces. We examine the viewing angle dependency of the Bragg scattering cone relative to sample symmetry planes, and our results demonstrate how increased ordering influences angular scattering width and anisotropy. Understanding how the properties of structural color can be quantified and manipulated has significant implications for the manufacture of functional photonic crystals in sensors, smart fabrics, coatings, and other optical device applications.

The Dynamic EEG Microstates in Mental Rotation.

Mental rotation is generally analyzed based on event-related potential (ERP) in a time domain with several characteristic electrodes, but neglects the whole spatial-temporal brain pattern in the cognitive process which may reflect the underlying cognitive mechanism. In this paper, we mainly proposed an approach based on microstates to examine the encoding of mental rotation from the spatial-temporal changes of EEG signals. In particular, we collected EEG data from 11 healthy subjects in a mental rotation cognitive task using 12 different stimulus pictures representing left and right hands at various rotational angles. We applied the microstate method to investigate the microstates conveyed by the event-related potential extracted from EEG data during mental rotation, and obtained four microstate modes (referred to as modes A, B, C, D, respectively). Subsequently, we defined several measures, including microstate sequences, topographical map, hemispheric lateralization, and duration of microstate, to characterize the dynamics of microstates during mental rotation. We observed that (1) the microstates sequence had a specified progressing mode, i.e., A → B → A ; (2) the activation of the right parietal occipital region was stronger than that of the left parietal occipital region according to the hemispheric lateralization of the microstates mode A; and (3) the duration of the second microstates mode A showed the shorter duration in the vertical stimuli, named "angle effect".

Experimental study on the effect of quaternary ammonium salt + monoethylene glycol compound to methane hydrate agglomeration in oil-water system.

Natural gas hydrate has been a critical risk to the safety of offshore oil and gas well test and subsea transportation. Herein, the effect of three quaternary ammonium salt (QAS) surfactants with monoethylene glycol (MEG) to methane hydrate agglomeration in water-oil system was experimentally studied by a rocking cell. Based on the hydrate volume fraction and the slider trajectory, a classification method of the gas hydrate anti-agglomerants was established. All the QASs in this work show the capability of reducing hydrate agglomeration, among which N1,N3-didodecyl-N1,N1,N3,N3-tetramethylpropane-1,3-diaminium chloride (AA-2) has the best anti-agglomerating performance, and the slider moved at a large trajectory of 61-174 mm. The three QASs were compounded with 5, 10, and 15 wt% (based on water) MEG, respectively. Experimental results showed that AA-2 compounded with MEG (10 wt%) can effectively prevent hydrate agglomeration. The slider moved in the cell at the full trajectory range, showing the compound of grade A performance. The compound of QAS and MEG shows a synergistic effect. The addition of QAS can significantly reduce the required MEG dosage for the hydrate blockage prevention than the MEG only situation. Considering the economic factors of the filed hydrate management, the combination application of QAS + MEG may provide a promising option.

Nonparametric tensor ring decomposition with scalable amortized inference.

Multi-dimensional data are common in many applications, such as videos and multi-variate time series. While tensor decomposition (TD) provides promising tools for analyzing such data, there still remains several limitations. First, traditional TDs assume multi-linear structures of the latent embeddings, which greatly limits their expressive power. Second, TDs cannot be straightforwardly applied to datasets with massive samples. To address these issues, we propose a nonparametric TD with amortized inference networks. Specifically, we establish a non-linear extension of tensor ring decomposition, using neural networks, to model complex latent structures. To jointly model the cross-sample correlations and physical structures, a matrix Gaussian process (GP) prior is imposed over the core tensors. From learning perspective, we develop a VAE-like amortized inference network to infer the posterior of core tensors corresponding to new tensor data, which enables TDs to be applied to large datasets. Our model can be also viewed as a kind of decomposition of VAE, which can additionally capture hidden tensor structure and enhance the expressiveness power. Finally, we derive an evidence lower bound such that a scalable optimization algorithm is developed. The advantages of our method have been evaluated extensively by data imputation on the Healing MNIST dataset and four multi-variate time series data.

Generalized latent multi-view clustering with tensorized bipartite graph.

Tensor-based multi-view spectral clustering algorithms use tensors to model the structure of multi-dimensional data to take advantage of the complementary information and high-order correlations embedded in the graph, thus achieving impressive clustering performance. However, these algorithms use linear models to obtain consensus, which prevents the learned consensus from adequately representing the nonlinear structure of complex data. In order to address this issue, we propose a method called Generalized Latent Multi-View Clustering with Tensorized Bipartite Graph (GLMC-TBG). Specifically, in this paper we introduce neural networks to learn highly nonlinear mappings that encode nonlinear structures in graphs into latent representations. In addition, multiple views share the same latent consensus through nonlinear interactions. In this way, a more comprehensive common representation from multiple views can be achieved. An Augmented Lagrangian Multiplier with Alternating Direction Minimization (ALM-ADM) framework is designed to optimize the model. Experiments on seven real-world data sets verify that the proposed algorithm is superior to state-of-the-art algorithms.

Bayesian tensor network structure search and its application to tensor completion.

Tensor network (TN) has demonstrated remarkable efficacy in the compact representation of high-order data. In contrast to the TN methods with pre-determined structures, the recently introduced tensor network structure search (TNSS) methods automatically learn a compact TN structure from the data, gaining increasing attention. Nonetheless, TNSS requires time-consuming manual adjustments of the penalty parameters that control the model complexity to achieve better performance, especially in the presence of missing or noisy data. To provide an effective solution to this problem, in this paper, we propose a parameters tuning-free TNSS algorithm based on Bayesian modeling, aiming at conducting TNSS in a fully data-driven manner. Specifically, the uncertainty in the data corruption is well-incorporated in the prior setting of the probabilistic model. For TN structure determination, we reframe it as a rank learning problem of the fully-connected tensor network (FCTN), integrating the generalized inverse Gaussian (GIG) distribution for low-rank promotion. To eliminate the need for hyperparameter tuning, we adopt a fully Bayesian approach and propose an efficient Markov chain Monte Carlo (MCMC) algorithm for posterior distribution sampling. Compared with the previous TNSS method, experiment results demonstrate the proposed algorithm can effectively and efficiently find the latent TN structures of the data under various missing and noise conditions and achieves the best recovery results. Furthermore, our method exhibits superior performance in tensor completion with real-world data compared to other state-of-the-art tensor-decomposition-based completion methods.

Balanced Unfolding Induced Tensor Nuclear Norms for High-Order Tensor Completion.

The recently proposed tensor tubal rank has been witnessed to obtain extraordinary success in real-world tensor data completion. However, existing works usually fix the transform orientation along the third mode and may fail to turn multidimensional low-tubal-rank structure into account. To alleviate these bottlenecks, we introduce two unfolding induced tensor nuclear norms (TNNs) for the tensor completion (TC) problem, which naturally extends tensor tubal rank to high-order data. Specifically, we show how multidimensional low-tubal-rank structure can be captured by utilizing a novel balanced unfolding strategy, upon which two TNNs, namely, overlapped TNN (OTNN) and latent TNN (LTNN), are developed. We also show the immediate relationship between the tubal rank of unfolding tensor and the existing tensor network (TN) rank, e.g., CANDECOMP/PARAFAC (CP) rank, Tucker rank, and tensor ring (TR) rank, to demonstrate its efficiency and practicality. Two efficient TC models are then proposed with theoretical guarantees by analyzing a unified nonasymptotic upper bound. To solve optimization problems, we develop two alternating direction methods of multipliers (ADMM) based algorithms. The proposed models have been demonstrated to exhibit superior performance based on experimental findings involving synthetic and real-world tensors, including facial images, light field images, and video sequences.

TSFAN: tensorized spatial-frequency attention network with domain adaptation for cross-session EEG-based biometric recognition.

Objective.Electroencephalogram (EEG) signals are promising biometrics owning to their invisibility, adapting to the application scenarios with high-security requirements. However, It is challenging to explore EEG identity features without the interference of device and state differences of the subject across sessions. Existing methods treat training sessions as a single domain, affected by the different data distribution among sessions. Although most multi-source unsupervised domain adaptation (MUDA) methods bridge the domain gap between multiple source and target domains individually, relationships among the domain-invariant features of each distribution alignment are neglected.Approach.In this paper, we propose a MUDA method, Tensorized Spatial-Frequency Attention Network (TSFAN), to assist the performance of the target domain for EEG-based biometric recognition. Specifically, significant relationships of domain-invariant features are modeled via a tensorized attention mechanism. It jointly incorporates appropriate common spatial-frequency representations of pairwise source and target but also cross-source domains, without the effect of distribution discrepancy among source domains. Additionally, considering the curse of dimensionality, our TSFAN is approximately represented in Tucker format. Benefiting the low-rank Tucker Network, the TSFAN can scale linearly in the number of domains, providing us the great flexibility to extend TSFAN to the case associated with an arbitrary number of sessions.Main results.Extensive experiments on the representative benchmarks demonstrate the effectiveness of TSFAN in EEG-based biometric recognition, outperforming state-of-the-art approaches, as verified by cross-session validation.Significance.The proposed TSFAN aims to investigate the presence of consistent EEG identity features across sessions. It is achieved by utilizing a novel tensorized attention mechanism that collaborates intra-source transferable information with inter-source interactions, while remaining unaffected by domain shifts in multiple source domains. Furthermore, the electrode selection shows that EEG-based identity features across sessions are distributed across brain regions, and 20 electrodes based on 10-20 standard system are able to extract stable identity information.

Tensor Robust Kernel PCA for Multidimensional Data.

Recently, the tensor nuclear norm (TNN)-based tensor robust principle component analysis (TRPCA) has achieved impressive performance in multidimensional data processing. The underlying assumption in TNN is the low-rankness of frontal slices of the tensor in the transformed domain (e.g., Fourier domain). However, the low-rankness assumption is usually violative for real-world multidimensional data (e.g., video and image) due to their intrinsically nonlinear structure. How to effectively and efficiently exploit the intrinsic structure of multidimensional data remains a challenge. In this article, we first suggest a kernelized TNN (KTNN) by leveraging the nonlinear kernel mapping in the transform domain, which faithfully captures the intrinsic structure (i.e., implicit low-rankness) of multidimensional data and is computed at a lower cost by introducing kernel trick. Armed with KTNN, we propose a tensor robust kernel PCA (TRKPCA) model for handling multidimensional data, which decomposes the observed tensor into an implicit low-rank component and a sparse component. To tackle the nonlinear and nonconvex model, we develop an efficient alternating direction method of multipliers (ADMM)-based algorithm. Extensive experiments on real-world applications collectively verify that TRKPCA achieves superiority over the state-of-the-art RPCA methods.

Strain to shine: stretching-induced three-dimensional symmetries in nanoparticle-assembled photonic crystals.

Stretching elastic materials containing nanoparticle lattices is common in research and industrial settings, yet our knowledge of the deformation process remains limited. Understanding how such lattices reconfigure is critically important, as changes in microstructure lead to significant alterations in their performance. This understanding has been extremely difficult to achieve due to a lack of fundamental rules governing the rearrangements. Our study elucidates the physical processes and underlying mechanisms of three-dimensional lattice transformations in a polymeric photonic crystal from 0% to over 200% strain during uniaxial stretching. Corroborated by comprehensive experimental characterizations, we present analytical models that precisely predict both the three-dimensional lattice structures and the macroscale deformations throughout the stretching process. These models reveal how the nanoparticle lattice and matrix polymer jointly determine the resultant structures, which breaks the original structural symmetry and profoundly changes the dispersion of photonic bandgaps. Stretching induces shifting of the main pseudogap structure out from the 1st Brillouin zone and the merging of different symmetry points. Evolutions of multiple photonic bandgaps reveal potential optical singularities shifting with strain. This work sets a new benchmark for the reconfiguration of soft material structures and may lay the groundwork for the study of stretchable three-dimensional topological photonic crystals.

Graph-Regularized Non-Negative Tensor-Ring Decomposition for Multiway Representation Learning.

Tensor-ring (TR) decomposition is a powerful tool for exploiting the low-rank property of multiway data and has been demonstrated great potential in a variety of important applications. In this article, non-negative TR (NTR) decomposition and graph-regularized NTR (GNTR) decomposition are proposed. The former equips TR decomposition with the ability to learn the parts-based representation by imposing non-negativity on the core tensors, and the latter additionally introduces a graph regularization to the NTR model to capture manifold geometry information from tensor data. Both of the proposed models extend TR decomposition and can be served as powerful representation learning tools for non-negative multiway data. The optimization algorithms based on an accelerated proximal gradient are derived for NTR and GNTR. We also empirically justified that the proposed methods can provide more interpretable and physically meaningful representations. For example, they are able to extract parts-based components with meaningful color and line patterns from objects. Extensive experimental results demonstrated that the proposed methods have better performance than state-of-the-art tensor-based methods in clustering and classification tasks.

Construction and application of flow pressure drop model of perforated well considering pressure loss of perforation hole.

Perforating well is one of the main production wells in reservoir development. Perforating effect directly affects well production, so the optimization of perforating parameters has attracted wide attention. Because pressure difference serves as the driving force for fluid flowing from formation to wellbore, it is important to understand the composition of production pressure difference in perforating well, which can guide the optimization of perforating parameters and the evaluation of perforating effect. In order to clarify the composition of production pressure difference during the production process of perforated wells, a pressure drop model pressure drop model is established based on fluid mechanics theory, which includes a pressure drop model of formation and a pressure drop model of perforation hole. The pressure drop model of formation is firstly constructed based on the Darcy's law and the equivalent resistance method, and the pressure drop model of perforation hole is built by the fluid tube-flow theory. Secondly, the numerical calculation method is adopted to realize the coupling solution of models, and the accuracy of this model is verified by comparison of the Karakas-Tariq model. Finally, the effects of formation physical properties and perforating parameters on flow pressure drop are discussed. The results show that there is a difference of more than 2 orders of magnitude between the pressure drop generated in perforation hole and flow pressure difference, and pressure drop of perforation hole can be neglected in practical applications. Comparing with medium-high permeability reservoirs, optimizing perforation parameters in low permeability reservoirs has a more significant impact on flow pressure drop. Among perforating parameters, perforation length and perforation density have great influence on flow pressure difference, while perforation diameter and phase angle have relatively little influence. These results have certain guiding significance for optimizing perforating parameters in different permeability reservoirs.

Comprehensive Multiview Representation Learning via Deep Autoencoder-Like Nonnegative Matrix Factorization.

Learning a comprehensive representation from multiview data is crucial in many real-world applications. Multiview representation learning (MRL) based on nonnegative matrix factorization (NMF) has been widely adopted by projecting high-dimensional space into a lower order dimensional space with great interpretability. However, most prior NMF-based MRL techniques are shallow models that ignore hierarchical information. Although deep matrix factorization (DMF)-based methods have been proposed recently, most of them only focus on the consistency of multiple views and have cumbersome clustering steps. To address the above issues, in this article, we propose a novel model termed deep autoencoder-like NMF for MRL (DANMF-MRL), which obtains the representation matrix through the deep encoding stage and decodes it back to the original data. In this way, through a DANMF-based framework, we can simultaneously consider the multiview consistency and complementarity, allowing for a more comprehensive representation. We further propose a one-step DANMF-MRL, which learns the latent representation and final clustering labels matrix in a unified framework. In this approach, the two steps can negotiate with each other to fully exploit the latent clustering structure, avoid previous tedious clustering steps, and achieve optimal clustering performance. Furthermore, two efficient iterative optimization algorithms are developed to solve the proposed models both with theoretical convergence analysis. Extensive experiments on five benchmark datasets demonstrate the superiority of our approaches against other state-of-the-art MRL methods.

TT-Net: Tensorized Transformer Network for 3D medical image segmentation.

Accurate segmentation of organs, tissues and lesions is essential for computer-assisted diagnosis. Previous works have achieved success in the field of automatic segmentation. However, there exists two limitations. (1) They are remain challenged by complex conditions, such as segmentation target is variable in location, size and shape, especially for different imaging modalities. (2) Existing transformer-based networks suffer from a high parametric complexity. To solve these limitations, we propose a new Tensorized Transformer Network (TT-Net). In this paper, (1) Multi-scale transformer with layers-fusion is proposed to faithfully capture context interaction information. (2) Cross Shared Attention (CSA) module that based on pHash similarity fusion (pSF) is well-designed to extract the global multi-variate dependency features. (3) Tensorized Self-Attention (TSA) module is proposed to deal with the large number of parameters, which can also be easily embedded into other models. In addition, TT-Net gains a good explainability through visualizing the transformer layers. The proposed method is evaluated on three widely accepted public datasets and one clinical dataset, which contains different imaging modalities. Comprehensive results show that TT-Net outperforms other state-of-the-art methods for the four different segmentation tasks. Besides, the compression module which can be easily embedded into other transformer-based methods achieves lower computation with comparable segmentation performance.

Fractional Tensor Recurrent Unit (fTRU): A Stable Forecasting Model With Long Memory.

The tensor recurrent model is a family of nonlinear dynamical systems, of which the recurrence relation consists of a p -fold (called degree- p ) tensor product. Despite such models frequently appearing in advanced recurrent neural networks (RNNs), to this date, there are limited studies on their long memory properties and stability in sequence tasks. In this article, we propose a fractional tensor recurrent model, where the tensor degree p is extended from the discrete domain to the continuous domain, so it is effectively learnable from various datasets. Theoretically, we prove that a large degree p is essential to achieve the long memory effect in a tensor recurrent model, yet it could lead to unstable dynamical behaviors. Hence, our new model, named fractional tensor recurrent unit (fTRU), is expected to seek the saddle point between long memory property and model stability during the training. We experimentally show that the proposed model achieves competitive performance with a long memory and stable manners in several forecasting tasks compared to various advanced RNNs.

Classification of the Epileptic Seizure Onset Zone Based on Partial Annotation.

Epilepsy is a chronic disorder caused by excessive electrical discharges. Currently, clinical experts identify the seizure onset zone (SOZ) channel through visual judgment based on long-time intracranial electroencephalogram (iEEG), which is a very time-consuming, difficult and experience-based task. Therefore, there is a need for high-accuracy diagnostic aids to reduce the workload of clinical experts. In this article, we propose a method in which, the iEEG is split into the 20-s segment and for each patient, we ask clinical experts to label a part of the data, which is used to train a model and classify the remaining iEEG data. In recent years, machine learning methods have been successfully applied to solve some medical problems. Filtering, entropy and short-time Fourier transform (STFT) are used for extracting features. We compare them to wavelet transform (WT), empirical mode decomposition (EMD) and other traditional methods with the aim of obtaining the best possible discriminating features. Finally, we look for their medical interpretation, which is important for clinical experts. We achieve high-performance results for SOZ and non-SOZ data classification by using the labeled iEEG data and support vector machine (SVM), fully connected neural network (FCNN) and convolutional neural network (CNN) as classification models. In addition, we introduce the positive unlabeled (PU) learning to further reduce the workload of clinical experts. By using PU learning, we can learn a binary classifier with a small amount of labeled data and a large amount of unlabeled data. This can greatly reduce the amount and difficulty of annotation work by clinical experts. All together, we show that using 105 minutes of labeled data we achieve a classification result of 91.46% on average for multiple patients.