arXiv subjects
Publications and source records attributed to Jun Zhang.
We prove that if the $m$-th homotopy group for $m \geq 2$ of a closed manifold has non-trivial invariants or coinvariants under the action of the fundamental group, then there exist infinitely many geometrically distinct closed geodesics for a $C^4$-generic Riemannian metric. If moreover there are infinitely many conjugacy classes in the fundamental group, then the same holds for every Riemannian metric.
Motivation: Enhancers are important cis-regulatory elements that regulate a wide range of biological functions and enhance the transcription of target genes. Although many feature extraction methods have been proposed to improve the performance of enhancer identification, they cannot learn position-related multiscale contextual information from raw DNA sequences. Results: In this article, we propose a novel enhancer identification method (iEnhancer-ELM) based on BERT-like enhancer language models. iEnhancer-ELM tokenizes DNA sequences with multi-scale k-mers and extracts contextual information of different scale k-mers related with their positions via an multi-head attention mechanism. We first evaluate the performance of different scale k-mers, then ensemble them to improve the performance of enhancer identification. The experimental results on two popular benchmark datasets show that our model outperforms stateof-the-art methods. We further illustrate the interpretability of iEnhancer-ELM. For a case study, we discover 30 enhancer motifs via a 3-mer-based model, where 12 of motifs are verified by STREME and JASPAR, demonstrating our model has a potential ability to unveil the biological mechanism of enhancer. Availability and implementation: The models and associated code are available at https://github.com/chen-bioinfo/iEnhancer-ELM Contact: junjiechen@hit.edu.cn Supplementary information: Supplementary data are available at Bioinformatics Advances online.
Recently, observational hints for supermassive black holes have been accumulating, which has inspired ones to wonder: Can primordial black holes (PBHs) be supermassive, in particular with the mass $M\gtrsim 10^{9}M_\odot$? A supercritical bubble (with an inflating baby universe inside it) that nucleated during inflation can develop into a PBH in our observable Universe. Here, we find that when the inflaton slowly passes by a neighboring vacuum, the nucleating rate of supercritical bubbles would inevitably attain a peak, so the mass distribution of multiverse PBHs, and the mass of peak can be up to $M\gtrsim 10^{11}M_\odot$. Thus our mechanism naturally provides a primordial origin of supermassive BHs.
This study investigates the impact of molecular thermal fluctuations on compressible decaying isotropic turbulence using the unified stochastic particle (USP) method, encompassing both two-dimensional (2D) and three-dimensional (3D) scenarios. The findings reveal that the turbulent spectra of velocity and thermodynamic variables follow the wavenumber scaling law of ${k}^{(d-1)}$ for different spatial dimensions $d$ within the high wavenumber range, indicating the impact of thermal fluctuations on small-scale turbulent statistics. With the application of Helmholtz decomposition, it is found that the thermal fluctuation spectra of solenoidal and compressible velocity components (${\vec{u}}_{s}$ and ${\vec{u}}_{c}$) follow an energy ratio of 1:1 for 2D cases, while the ratio changes to 2:1 for 3D cases. Comparisons between 3D turbulent spectra obtained through USP simulations and direct numerical simulations of the Navier-Stokes equations demonstrate that thermal fluctuations dominate the spectra at length scales comparable to the Kolmogorov length scale. Additionally, the effect of thermal fluctuations on the spectrum of ${\vec{u}}_{c}$ is significantly influenced by variations in the turbulent Mach number. We further study the impact of thermal fluctuations on the predictability of turbulence. With initial differences caused by thermal fluctuations, different flow realizations display significant disparities in velocity and thermodynamic fields at larger scales after a certain period of time, which can be characterized by "inverse error cascades". Moreover, the results suggest a strong correlation between the predictabilities of thermodynamic fields and the predictability of ${\vec{u}}_{c}$.
We demonstrate photon-counting single-pixel imaging in the ultraviolet region. Toward this target, we develop a high-performance compact single-photon detector based on a 4H-SiC single-photon avalanche diode (SPAD), where a tailored readout circuit with active hold-off time is designed to restrain detector noise and operate the SPAD in free-running mode. We use structured illumination to reconstruct 192$\times$192 compressed images at a 4 fps frame rate. To show the superior capability of ultraviolet characteristics, we use our single-pixel imaging system to identify and distinguish different transparent objects under low-intensity irradiation, and image ultraviolet light sources. The results provide a practical solution for general ultraviolet imaging applications.
Millimeter-wave (MMW) imaging is emerging as a promising technique for safe security inspection. It achieves a delicate balance between imaging resolution, penetrability and human safety, resulting in higher resolution compared to low-frequency microwave, stronger penetrability compared to visible light, and stronger safety compared to X ray. Despite of recent advance in the last decades, the high cost of requisite large-scale antenna array hinders widespread adoption of MMW imaging in practice. To tackle this challenge, we report a large-scale single-shot MMW imaging framework using sparse antenna array, achieving low-cost but high-fidelity security inspection under an interpretable learning scheme. We first collected extensive full-sampled MMW echoes to study the statistical ranking of each element in the large-scale array. These elements are then sampled based on the ranking, building the experimentally optimal sparse sampling strategy that reduces the cost of antenna array by up to one order of magnitude. Additionally, we derived an untrained interpretable learning scheme, which realizes robust and accurate image reconstruction from sparsely sampled echoes. Last, we developed a neural network for automatic object detection, and experimentally demonstrated successful detection of concealed centimeter-sized targets using 10% sparse array, whereas all the other contemporary approaches failed at the same sample sampling ratio. The performance of the reported technique presents higher than 50% superiority over the existing MMW imaging schemes on various metrics including precision, recall, and mAP50. With such strong detection ability and order-of-magnitude cost reduction, we anticipate that this technique provides a practical way for large-scale single-shot MMW imaging, and could advocate its further practical applications.
Flow field segmentation and classification help researchers to understand vortex structure and thus turbulent flow. Existing deep learning methods mainly based on global information and focused on 2D circumstance. Based on flow field theory, we propose novel flow field segmentation and classification deep learning methods in three-dimensional space. We construct segmentation criterion based on local velocity information and classification criterion based on the relationship between local vorticity and vortex wake, to identify vortex structure in 3D flow field, and further classify the type of vortex wakes accurately and rapidly. Simulation experiment results showed that, compared with existing methods, our segmentation method can identify the vortex area more accurately, while the time consumption is reduced more than 50%; our classification method can reduce the time consumption by more than 90% while maintaining the same classification accuracy level.
Diamond is generally considered to have high thermal conductivity, so little attention has been paid to the laser heating effects at low excitation power. However, defects during the growth process can result in a great degradation of thermal conductivity, especially at low temperatures. Here, we observed the dynamic redshift and broadening of zero phonon line (ZPL) of silicon-vacancy (SiV) centers in diamondin the experiment. Utilizing the intrinsic temperature response of the fine structure spectra of SiV as a probe, we confirmed that the laser heating effect appears and the temperature rising results from high defect concentration. By simulating the thermal diffusion process, we have estimated the thermal conductivity of around 1 W/(mK) at the local site, which is a two order magnitude lower than that of single-crystal diamond. Our results provide a feasible scheme for characterizing the laser heating effect of diamond at low temperatures.
Code-switching speech recognition (CSSR) transcribes speech that switches between multiple languages or dialects within a single sentence. The main challenge in this task is that different languages often have similar pronunciations, making it difficult for models to distinguish between them. In this paper, we propose a method for solving the CSSR task from the perspective of language-specific acoustic boundary learning. We introduce language-specific weight estimators (LSWE) to model acoustic boundary learning in different languages separately. Additionally, a non-autoregressive (NAR) decoder and a language change detection (LCD) module are employed to assist in training. Evaluated on the SEAME corpus, our method achieves a state-of-the-art mixed error rate (MER) of 16.29% and 22.81% on the test_man and test_sge sets. We also demonstrate the effectiveness of our method on a 9000-hour in-house meeting code-switching dataset, where our method achieves a relatively 7.9% MER reduction.
Terahertz ultra-massive MIMO (THz UM-MIMO) is envisioned as one of the key enablers of 6G wireless networks, for which channel estimation is highly challenging. Traditional analytical estimation methods are no longer effective, as the enlarged array aperture and the small wavelength result in a mixture of far-field and near-field paths, constituting a hybrid-field channel. Deep learning (DL)-based methods, despite the competitive performance, generally lack theoretical guarantees and scale poorly with the size of the array. In this paper, we propose a general DL framework for THz UM-MIMO channel estimation, which leverages existing iterative channel estimators and is with provable guarantees. Each iteration is implemented by a fixed point network (FPN), consisting of a closed-form linear estimator and a DL-based non-linear estimator. The proposed method perfectly matches the THz UM-MIMO channel estimation due to several unique advantages. First, the complexity is low and adaptive. It enjoys provable linear convergence with a low per-iteration cost and monotonically increasing accuracy, which enables an adaptive accuracy-complexity tradeoff. Second, it is robust to practical distribution shifts and can directly generalize to a variety of heavily out-of-distribution scenarios with almost no performance loss, which is suitable for the complicated THz channel conditions. For practical usage, the proposed framework is further extended to wideband THz UM-MIMO systems with beam squint effect. Theoretical analysis and extensive simulation results are provided to illustrate the advantages over the state-of-the-art methods in estimation accuracy, convergence rate, complexity, and robustness.
Domain adaptation using text-only corpus is challenging in end-to-end(E2E) speech recognition. Adaptation by synthesizing audio from text through TTS is resource-consuming. We present a method to learn Unified Speech-Text Representation in Conformer Transducer(USTR-CT) to enable fast domain adaptation using the text-only corpus. Different from the previous textogram method, an extra text encoder is introduced in our work to learn text representation and is removed during inference, so there is no modification for online deployment. To improve the efficiency of adaptation, single-step and multi-step adaptations are also explored. The experiments on adapting LibriSpeech to SPGISpeech show the proposed method reduces the word error rate(WER) by relatively 44% on the target domain, which is better than those of TTS method and textogram method. Also, it is shown the proposed method can be combined with internal language model estimation(ILME) to further improve the performance.
The recent advancements of three-dimensional (3D) data acquisition devices have spurred a new breed of applications that rely on point cloud data processing. However, processing a large volume of point cloud data brings a significant workload on resource-constrained mobile devices, prohibiting from unleashing their full potentials. Built upon the emerging paradigm of device-edge co-inference, where an edge device extracts and transmits the intermediate feature to an edge server for further processing, we propose Branchy-GNN for efficient graph neural network (GNN) based point cloud processing by leveraging edge computing platforms. In order to reduce the on-device computational cost, the Branchy-GNN adds branch networks for early exiting. Besides, it employs learning-based joint source-channel coding (JSCC) for the intermediate feature compression to reduce the communication overhead. Our experimental results demonstrate that the proposed Branchy-GNN secures a significant latency reduction compared with several benchmark methods.
In frequency-division duplexing (FDD) massive multiple-input multiple-output (MIMO) systems, downlink channel state information (CSI) needs to be sent back to the base station (BS) by the users, which causes prohibitive feedback overhead. In this paper, we propose a lightweight and flexible deep learning-based CSI feedback approach by capitalizing on deep equilibrium models. Different from existing deep learning-based methods that stack multiple explicit layers, we propose an implicit equilibrium block to mimic the behavior of an infinite-depth neural network. In particular, the implicit equilibrium block is defined by a fixed-point iteration and the trainable parameters in different iterations are shared, which results in a lightweight model. Furthermore, the number of forward iterations can be adjusted according to users' computation capability, enabling a flexible accuracy-efficiency trade-off. Simulation results will show that the proposed design obtains a comparable performance as the benchmarks but with much-reduced complexity and permits an accuracy-efficiency trade-off at runtime.
Dynamical decoupling (DD) is normally ineffective when applied to DC measurement. In its straightforward implementation, DD nulls out DC signal as well while suppressing noise. This work proposes a phase relay method (PRM) that is capable of continuously interrogating the DC signal over many DD cycles. We illustrate its efficacy when applied to measurement of a weak DC magnetic field with an atomic spinor Bose-Einstein condensate. Sensitivities approaching standard quantum limit (SQL) or Heisenberg limit (HL) are potentially realizable for a coherent spin state (CSS) or a squeezed spin state (SSS) of 10,000 atoms respectively, while ambient laboratory level noise is suppressed by DD. Our work offers a practical approach to mitigate the limitations of DD to DC measurement and will like find other applications for resorting coherence in quantum sensing and quantum information processing research.
Tumor mutational burden (TMB) is a potential genomic biomarker of immunotherapy. However, TMB detected through whole exome sequencing lacks clinical penetration in low-resource settings. In this study, we proposed a multi-scale deep learning framework to address the detection of TMB status from routinely used whole slide images for a multiple cancer TMB prediction model (MC- TMB). The MC-TMB achieved a mean area under the curve (AUC) of 0.818 (0.804-0.831) in the cross-validation cohort, which showed superior performance to each single-scale model. The improvements of MC-TMB over the single-tumor models were also confirmed by the ablation tests on x10 magnification, and the highly concerned regions typically correspond to dense lymphocytic infiltration and heteromorphic tumor cells. MC-TMB algorithm also exhibited good generalization on the external validation cohort with an AUC of 0.732 (0.683-0.761), and better performance when compared to other methods. In conclusion, we proposed a deep learning-based approach to reveal tumor mutational burden status from routinely used pathological slides across multiple cancer types.
Speech or text representation generated by pre-trained models contains modal-specific information that could be combined for benefiting spoken language understanding (SLU) tasks. In this work, we propose a novel pre-training paradigm termed Continuous Integrate-and-Fire Pre-Training (CIF-PT). It relies on a simple but effective frame-to-token alignment: continuous integrate-and-fire (CIF) to bridge the representations between speech and text. It jointly performs speech-to-text training and language model distillation through CIF as the pre-training (PT). Evaluated on SLU benchmark SLURP dataset, CIF-PT outperforms the state-of-the-art model by 1.94% of accuracy and 2.71% of SLU-F1 on the tasks of intent classification and slot filling, respectively. We also observe the cross-modal representation extracted by CIF-PT obtains better performance than other neural interfaces for the tasks of SLU, including the dominant speech representation learned from self-supervised pre-training.
Learning communication strategies in cooperative multi-agent reinforcement learning (MARL) has recently attracted intensive attention. Early studies typically assumed a fully-connected communication topology among agents, which induces high communication costs and may not be feasible. Some recent works have developed adaptive communication strategies to reduce communication overhead, but these methods cannot effectively obtain valuable information from agents that are beyond the communication range. In this paper, we consider a realistic communication model where each agent has a limited communication range, and the communication topology dynamically changes. To facilitate effective agent communication, we propose a novel communication protocol called Adaptively Controlled Two-Hop Communication (AC2C). After an initial local communication round, AC2C employs an adaptive two-hop communication strategy to enable long-range information exchange among agents to boost performance, which is implemented by a communication controller. This controller determines whether each agent should ask for two-hop messages and thus helps to reduce the communication overhead during distributed execution. We evaluate AC2C on three cooperative multi-agent tasks, and the experimental results show that it outperforms relevant baselines with lower communication costs.
Most existing studies on joint activity detection and channel estimation for grant-free massive random access (RA) systems assume perfect synchronization among all active users, which is hard to achieve in practice. Therefore, this paper considers asynchronous grant-free massive RA systems and develops novel algorithms for joint user activity detection, synchronization delay detection, and channel estimation. In particular, the framework of orthogonal approximate message passing (OAMP) is first utilized to deal with the non-independent and identically distributed (i.i.d.) pilot matrix in asynchronous grant-free massive RA systems, and an OAMP-based algorithm capable of leveraging the common sparsity among the received pilot signals from multiple base station antennas is developed. To reduce the computational complexity, a memory AMP (MAMP)based algorithm is further proposed that eliminates the matrix inversions in the OAMP-based algorithm. Simulation results demonstrate the effectiveness of the two proposed algorithms over the baseline methods. Besides, the MAMP-based algorithm reduces 37% of the computations while maintaining comparable detection/estimation accuracy, compared with the OAMP-based algorithm.