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The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and spatial omics data remains challenging. First, single-cell sequencing data are high-dimensional and sparse, often contaminated by noise and uncertainty, obscuring the underlying biological signals. Second, these data often encompass multiple modalities, including gene expression, epigenetic modifications, and spatial locations. Integrating these diverse data modalities is crucial for enhancing prediction accuracy and biological interpretability. Third, while the scale of single-cell sequencing has expanded to millions of cells, high-quality annotated datasets are still limited. Fourth, the complex correlations of biological tissues make it difficult to accurately reconstruct cellular states and spatial contexts. Traditional feature engineering-based analysis methods struggle to deal with the various challenges presented by intricate biological networks. Deep learning has emerged as a powerful tool capable of handling high-dimensional complex data and automatically identifying meaningful patterns, offering significant promise in addressing these challenges. This review systematically analyzes these challenges and discusses related deep learning approaches. Moreover, we have curated 21 datasets from 9 benchmarks, encompassing 58 computational methods, and evaluated their performance on the respective modeling tasks. Finally, we highlight three areas for future development from a technical, dataset, and application perspective. This work will serve as a valuable resource for understanding how deep learning can be effectively utilized in single-cell and spatial transcriptomics analyses, while inspiring novel approaches to address emerging challenges.

The programmable metasurface is regarded as one of the most promising transformative technologies for next-generation wireless system applications. Due to the lack of effective perception ability of the external electromagnetic environment, there are numerous challenges in the intelligent regulation of wireless channels, and it still relies on external sensors to reshape electromagnetic environment as desired. To address that problem, we propose an adaptive metasurface (AMS) which integrates the capabilities of acquiring wireless environment information and manipulating reflected electromagnetic (EM) waves in a programmable manner. The proposed design endows the metasurfaces with excellent capabilities to sense the complex electromagnetic field distributions around them and then dynamically manipulate the waves and signals in real time under the guidance of the sensed information, eliminating the need for prior knowledge or external inputs about the wireless environment. For verification, a prototype of the proposed AMS is constructed, and its dual capabilities of sensing and manipulation are experimentally validated. Additionally, different integrated sensing and communication (ISAC) scenarios with and without the aid of the AMS are established. The effectiveness of the AMS in enhancing communication quality is well demonstrated in complex electromagnetic environments, highlighting its beneficial application potential in future wireless systems.

With the versatile manipulation capability, programmable metasurfaces are rapidly advancing in their intelligence, integration, and commercialization levels. However, as the programmable metasurfaces scale up, their control configuration becomes increasingly complicated, posing significant challenges and limitations. Here, we propose a multiple-partition cross-modulation (MPCM) programmable metasurface to enhance the wireless communication coverage with low hardware complexity. We firstly propose an innovative encoding scheme to multiply the control voltage vectors of row-column crossing, achieving high beamforming precision in free space while maintaining low control hardware complexity and reducing memory requirements for coding sequences. We then design and fabricate an MPCM programmable metasurface to confirm the effectiveness of the proposed encoding scheme. The simulated and experimental results show good agreements with the theoretically calculated outcomes in beam scanning across the E and H planes and in free-space beam pointing. The MPCM programmable metasurface offers strong flexibility and low complexity by allowing various numbers and combinations of partition items in modulation methods, catering to diverse precision demands in various scenarios. We demonstrate the performance of MPCM programmable metasurface in a realistic indoor setting, where the transmissions of videos to specific receiver positions are successfully achieved, surpassing the capabilities of traditional programmable metasurfaces. We believe that the proposed programmable metasurface has great potentials in significantly empowering the wireless communications while addressing the challenges associated with the programmable metasurface's design and implementation.

Modern radar typically employs a chain architecture that consists of radio-frequency (RF) and intermediate frequency (IF) units, baseband digital signal processor, and information display. However, this architecture often results in high costs, significant hardware demands, and integration challenges. Here we propose a simplified radar architecture based on space-time-coding (STC) information metasurfaces. With their powerful capabilities to generate multiple harmonic frequencies and customize their phases, the STC metasurfaces play a key role in chirp signal generation, transmission, and echo reception. Remarkably, the receiving STC metasurface can implement dechirp processing directly on the RF level and realize the digital information outputs, which are beneficial to lower the hardware requirement at the receiving end while potentially shortening the time needed for conventional digital processing. As a proof of concept, the proposed metasurface radar is tested in a series of experiments for target detection and range/speed measurement, yielding results comparable to those obtained by conventional methods. This study provides valuable inspiration for a new radar system paradigm to combine the RF front ends and signal processors on the information metasurface platform that offers essential functionalities while significantly reducing the system complexity and cost., Comment: 25 pages, 10 figures

To satisfy the increasing demands for transmission rates of wireless communications, it is necessary to use spatial resources of electromagnetic (EM) waves. In this context, EM information theory (EIT) has become a hot topic by integrating the theoretical framework of deterministic mathematics and stochastic statistics to explore the transmission mechanisms of continuous EM waves. However, the previous studies were primarily focused on frame analysis, with limited exploration of practical applications and a comprehensive understanding of its essential physical characteristics. In this paper, we present a three-dimensional (3-D) line-of-sight channel capacity formula that captures the vector EM physics and accommodates both near- and far-field scenes. Based on the rigorous mathematical equation and the physical mechanism of fast multipole expansion, a channel model is established, and the finite angular spectral bandwidth feature of scattered waves is revealed. To adapt to the feature of the channel, an optimization problem is formulated for determining the mode currents on the transmitter, aiming to obtain the optimal design of the precoder and combiner. We make comprehensive analyses to investigate the relationship among the spatial degree of freedom, noise, and transmitted power, thereby establishing a rigorous upper bound of channel capacity. A series of simulations are conducted to validate the theoretical model and numerical method. This work offers a novel perspective and methodology for understanding and leveraging EIT, and provides a theoretical foundation for the design and optimization of future wireless communications., Comment: 31pages, 8 figures

The classification of histopathological images is crucial for the early and precise detection of breast cancer. This study investigates the efficiency of deep learning models in distinguishing between Invasive Ductal Carcinoma (IDC) and non-IDC in histopathology slides. We conducted a thorough comparison examination of eight sophisticated models: ResNet-50, DenseNet-121, ResNeXt-50, Vision Transformer (ViT), GoogLeNet (Inception v3), EfficientNet, MobileNet, and SqueezeNet. This analysis was carried out using a large dataset of 277,524 image patches. Our research makes a substantial contribution to the field by offering a comprehensive assessment of the performance of each model. We particularly highlight the exceptional efficacy of attention-based mechanisms in the ViT model, which achieved a remarkable validation accuracy of 93\%, surpassing conventional convolutional networks. This study highlights the promise of advanced machine learning approaches in clinical settings, offering improved precision as well as efficiency in breast cancer diagnosis.

The field-free and highly efficient diodes with the nonreciprocity of supercurrent are believed to be the core block of the superconducting computing devices without dissipation. In this paper, we propose a Josephson diode based upon altermagnets with the vanishing net macroscopic magnetization. The nonreciprocity of supercurrent can be realized without applying any external magnetic field or ferromagnetic exchange field, which can avoid the magnetic cross-talk between the basic elements of the devices. The high efficiency exceeding $40\%$ can be obtained and the efficiency shows the high stability when the structure parameters are changed. The diode efficiency is antisymmetric about the relative orientation angle of the superconducting leads, so that its sign can easily be inverted by adjusting the relative orientation angle. The symmetries satisfied by the current-phase difference relations and the diode efficiency are analyzed by considering the transformations of the junctions under the time-reversal, the spin-rotation and the mirror reflection operations. The high efficiency and the high stability of the Josephson diode effect in our junctions provide the possibility for the design of the field-free dissipationless diode devices., Comment: 13pages,6figures

Time series classification (TSC) on multivariate time series is a critical problem. We propose a novel multi-view approach integrating frequency-domain and time-domain features to provide complementary contexts for TSC. Our method fuses continuous wavelet transform spectral features with temporal convolutional or multilayer perceptron features. We leverage the Mamba state space model for efficient and scalable sequence modeling. We also introduce a novel tango scanning scheme to better model sequence relationships. Experiments on 10 standard benchmark datasets demonstrate our approach achieves an average 6.45% accuracy improvement over state-of-the-art TSC models.

Magnetic impurities in superconductors are of increasing interest due to emergent Yu-Shiba-Rusinov (YSR) states and Majorana zero modes for fault-tolerant quantum computation. However, a direct relationship between the YSR multiple states and magnetic anisotropy splitting of quantum impurity spins remains poorly characterized. By using scanning tunneling microscopy, we resolve systematically individual transition-metal (Fe, Cr and Ni) impurities induced YSR multiplets as well as their Zeeman effects in K$_3$C$_{60}$ superconductor. The YSR multiplets show identical $d$ orbital-like wave functions that are symmetry-mismatched to the threefold K$_3$C$_{60}$(111) host surface, breaking point-group symmetries of the spatial distribution of YSR bound states in real space. Remarkably, we identify an unprecedented fermion-parity-preserving quantum phase transition between ground states with opposite signs of the uniaxial magnetic anisotropy that can be manipulated by an external magnetic field. These findings can be readily understood in terms of anisotropy splitting of quantum impurity spins, and thus elucidate the intricate interplay between the magnetic anisotropy and YSR multiplets., Comment: 38 pages, 4 figures in the main text

Long-term time-series forecasting remains challenging due to the difficulty in capturing long-term dependencies, achieving linear scalability, and maintaining computational efficiency. We introduce TimeMachine, an innovative model that leverages Mamba, a state-space model, to capture long-term dependencies in multivariate time series data while maintaining linear scalability and small memory footprints. TimeMachine exploits the unique properties of time series data to produce salient contextual cues at multi-scales and leverage an innovative integrated quadruple-Mamba architecture to unify the handling of channel-mixing and channel-independence situations, thus enabling effective selection of contents for prediction against global and local contexts at different scales. Experimentally, TimeMachine achieves superior performance in prediction accuracy, scalability, and memory efficiency, as extensively validated using benchmark datasets. Code availability: https://github.com/Atik-Ahamed/TimeMachine, Comment: 27TH EUROPEAN CONFERENCE ON ARTIFICIAL INTELLIGENCE (ECAI-2024)

We study the Josephson effect in the spin-singlet superconductor/altermagnet/spin-triplet superconductor junctions using the Green's function method. The current-phase difference relationships in the junctions strongly depend on the orientation of altermagnet and the types of the Cooper pairs. For the orientation angle equal to odd multiples of $\pi/4$, the current-phase difference relationships are of the $\sin{2\phi}$ type, which are irrespective of the pairing wave functions in superconductors. For the other orientation angles, the emergence of the lowest order current becomes possible and its form, $\sin\phi$ or $\cos\phi$, depends on the pairing wave functions in superconductors. The $\phi_{0}$ phase and the $0$-$\pi$ transition can be realized in our junctions due to the appearance of the lowest order current. The selection rules for the lowest order current are presented. The symmetric relations satisfied by the current-phase difference relationships are analyzed through considering the transformations of the junctions under the mirror reflection, the time-reversal and the spin rotation operations. Our results not only provide a method to detect the intrinsic spin-triplet superconductivity but also possess application values in the design of the field-free quantum devices., Comment: 10pages,3figures

Despite the prevalence of images and texts in machine learning, tabular data remains widely used across various domains. Existing deep learning models, such as convolutional neural networks and transformers, perform well however demand extensive preprocessing and tuning limiting accessibility and scalability. This work introduces an innovative approach based on a structured state-space model (SSM), MambaTab, for tabular data. SSMs have strong capabilities for efficiently extracting effective representations from data with long-range dependencies. MambaTab leverages Mamba, an emerging SSM variant, for end-to-end supervised learning on tables. Compared to state-of-the-art baselines, MambaTab delivers superior performance while requiring significantly fewer parameters, as empirically validated on diverse benchmark datasets. MambaTab's efficiency, scalability, generalizability, and predictive gains signify it as a lightweight, "plug-and-play" solution for diverse tabular data with promise for enabling wider practical applications., Comment: Accepted by IEEE 7th International Conference on Multimedia Information Processing and Retrieval (MIPR), 2024

We study the crossed Andreev reflection and the nonlocal transport in the proximitized graphene/supercondcutor/proximitized graphene junctions with the pseudospin staggered potential and the intrinsic spin-orbit coupling. The crossed Andreev reflection with the local Andreev reflection and the elastic cotunneling being completely eliminated can be realized for the electrons with the specific spin-valley index when the intrinsic spin-orbit couplings in the left graphene and the right graphene possess the opposite sign. The perfect crossed Andreev reflection with its probability equal to $100\%$ can be obtained in the space consisting of the incident angle and the energy of the electrons. The crossed conductance and its oscillation with the superconductor length are also investigated. The energy ranges for the crossed Andreev reflection without the local Andreev reflection and the elastic cotunneling are clarified for the different magnitudes of the pseudospin potential and the spin-orbit coupling. The spin-valley index of the electrons responsible for the perfect crossed Andreev reflection can be switched by changing the sign of the intrinsic spin-orbit coupling or exchanging the biases applied on the left graphene and the right graphene. Our results are helpful for designing the flexible and high-efficiency Cooper pair splitter based on the spin-valley degree of freedom., Comment: 9 pages,4 figures

We study the Andreev reflections and the quantum transport in the proximitized graphene/superconductor junction. The proximitized graphene possesses the pseudospin staggered potential and the intrinsic spin-orbit coupling induced by substrate, which are responsible for the spin-valley dependent double Andreev reflections and the anomalous transport properties in the junction. The pure specular Andreev reflection can happen in the superconducting gap for the $K\uparrow$ and $K'\downarrow$ electrons while the pure retro-Andreev reflection happens for the $K\downarrow$ and $K'\uparrow$ electrons. The coexisting two types of Andreev reflections related to the fixed spin-valley indices strongly depend on the chemical potential of the proximitized graphene. The condition of the emergence of the specific type of Andreev reflection for the electrons with the fixed spin-valley index is clarified. The spin-valley dependent Andreev reflections bring about the peculiar conductance spectra of the junction, which can help determine the values of the pseudospin staggered potential and the intrinsic spin-orbit coupling induced in graphene. Hence, our research results not only provide an experimental method to detect the induced potential and coupling in graphene but also establish the foundation of the superconductor electronics based on the spin-valley indices., Comment: 7figures

Reconfigurable intelligent surface (RIS)-empowered communication, has been considered widely as one of the revolutionary technologies for next generation networks. However, due to the novel propagation characteristics of RISs, underlying RIS channel modeling and measurement research is still in its infancy and not fully investigated. In this paper, we conduct multi-scenario broadband channel measurements and modeling for RIS-assisted communications at the sub-6 GHz band. The measurements are carried out in three scenarios covering outdoor, indoor, and outdoor-to-indoor (O2I) environments, which suffer from non-line-of-sight (NLOS) propagation inherently. Three propagation modes including intelligent reflection with RIS, specular reflection with RIS and the mode without RIS, are taken into account in each scenario. In addition, considering the cascaded characteristics of RIS-assisted channel by nature, two modified empirical models including floating-intercept (FI) and close-in (CI) are proposed, which cover distance and angle domains. The measurement results rooted in 2096 channel acquisitions verify the prediction accuracy of these proposed models. Moreover, the propagation characteristics for RIS-assisted channels, including path loss (PL) gain, PL exponent, spatial consistency, time dispersion, frequency stationarity, etc., are compared and analyzed comprehensively. These channel measurement and modeling results may lay the groundwork for future applications of RIS-assisted communication systems in practice.

Motivated by the maneuvering target tracking with sensors such as radar and sonar, this paper considers the joint and recursive estimation of the dynamic state and the time-varying process noise covariance in nonlinear state space models. Due to the nonlinearity of the models and the non-conjugate prior, the state estimation problem is generally intractable as it involves integrals of general nonlinear functions and unknown process noise covariance, resulting in the posterior probability distribution functions lacking closed-form solutions. This paper presents a recursive solution for joint nonlinear state estimation and model parameters identification based on the approximate Bayesian inference principle. The stochastic search variational inference is adopted to offer a flexible, accurate, and effective approximation of the posterior distributions. We make two contributions compared to existing variational inference-based noise adaptive filtering methods. First, we introduce an auxiliary latent variable to decouple the latent variables of dynamic state and process noise covariance, thereby improving the flexibility of the posterior inference. Second, we split the variational lower bound optimization into conjugate and non-conjugate parts, whereas the conjugate terms are directly optimized that admit a closed-form solution and the non-conjugate terms are optimized by natural gradients, achieving the trade-off between inference speed and accuracy. The performance of the proposed method is verified on radar target tracking applications by both simulated and real-world data., Comment: 11 pages

We propose theoretically a Josephson diode consisting of the conventional superconductors with the plain s-wave pairing and a chiral quantum dot. When an external magnetic field is exerted on the quantum dot, the critical current of the Josephson structure is different for the opposite directions of current flow. The strong nonreciprocity can be obtained in a large area of the parameter space. The inversion and the on/off state of the nonreciprocity can be conveniently regulated by adjusting the direction of the external field. The dependences of the nonreciprocal behaviors on the the hopping amplitude, the magnitude of the magnetic field and the energy level of the quantum dot are investigated in details using the Keldysh nonequilibrium Green's function formalism under the self-consistent procedure. The symmetric and the antisymmetric properties of the nonreciprocity are analyzed from symmetries satisfied by the superconductors. The proposed diode effect also applies to other chiral conductors as interlayer. Its formation has no restriction on the type of the current-phase difference relations. The generality and flexibility of our proposed diode effect provides more possibilities for the design of the dissipationless diode devices., Comment: 4figures

Achieving integrated sensing and communication (ISAC) via uplink transmission is challenging due to the unknown waveform and the coupling of communication and sensing echoes. In this paper, a joint uplink communication and imaging system is proposed for the first time, where a reconfigurable intelligent surface (RIS) is used to manipulate the electromagnetic signals for echo decoupling at the base station (BS). Aiming to enhance the transmission gain in desired directions and generate required radiation pattern in the region of interest (RoI), a phase optimization problem for RIS is formulated, which is high dimensional and nonconvex with discrete constraints. To tackle this problem, a back propagation based phase design scheme for both continuous and discrete phase models is developed. Moreover, the echo decoupling problem is tackled using the Bayesian method with the factor graph technique, where the problem is represented by a graph model which consists of difficult local functions. Based on the graph model, a message-passing algorithm is derived, which can efficiently cooperate with the adaptive sparse Bayesian learning (SBL) to achieve joint communication and imaging. Numerical results show that the proposed method approaches the relevant lower bound asymptotically, and the communication performance can be enhanced with the utilization of imaging echoes., Comment: 13 pages, 14 figures

The reconfigurable intelligent surface (RIS) has received a lot of interest because of its capacity to reconfigure the wireless communication environment in a cost- and energy-efficient way. However, the realistic power consumption modeling and measurement validation of RIS has received far too little attention. Therefore, in this work, we model the power consumption of RIS and conduct measurement validations using various RISs to fill this vacancy. Firstly, we propose a practical power consumption model of RIS. The RIS hardware is divided into three basic parts: the FPGA control board, the drive circuits, and the RIS unit cells. The power consumption of the first two parts is modeled as $P_{\text {static}}$ and that of the last part is modeled as $P_{\text {units}}$. Expressions of $P_{\text {static}}$ and $P_{\text {units}}$ vary amongst different types of RISs. Secondly, we conduct measurements on various RISs to validate the proposed model. Five different RISs including the PIN diode, varactor diode, and RF switch types are measured, and measurement results validate the generality and applicability of the proposed power consumption model of RIS. Finally, we summarize the measurement results and discuss the approaches to achieve the low-power-consumption design of RIS-assisted wireless communication systems.