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Jun Zhang

Publications and source records attributed to Jun Zhang.

At least 685 records · Page 38Linked to original sources
arXiv2023

DSDP: A Blind Docking Strategy Accelerated by GPUs

Virtual screening, including molecular docking, plays an essential role in drug discovery. Many traditional and machine-learning based methods are available to fulfil the docking task. The traditional docking methods are normally extensively time-consuming, and their performance in blind docking remains to be improved. Although the runtime of docking based on machine learning is significantly decreased, their accuracy is still limited. In this study, we take the advantage of both traditional and machine-learning based methods, and present a method Deep Site and Docking Pose (DSDP) to improve the performance of blind docking. For the traditional blind docking, the entire protein is covered by a cube, and the initial positions of ligands are randomly generated in the cube. In contract, DSDP can predict the binding site of proteins and provide an accurate searching space and initial positions for the further conformational sampling. The docking task of DSDP makes use of the score function and a similar but modified searching strategy of AutoDock Vina, accelerated by implementation in GPUs. We systematically compare its performance with the state-of-the-art methods, including Autodock Vina, GNINA, QuickVina, SMINA, and DiffDock. DSDP reaches a 29.8% top-1 success rate (RMSD < 2 Å) on an unbiased and challenging test dataset with 1.2 s wall-clock computational time per system. Its performances on DUD-E dataset and the time-split PDBBind dataset used in EquiBind, TankBind, and DiffDock are also effective, presenting a 57.2% and 41.8% top-1 success rate with 0.8 s and 1.0 s per system, respectively.

physics.chem-ph↗
arXiv2023

CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

cs.CV↗
arXiv2023

Cell-Free Massive MIMO Detection: A Distributed Expectation Propagation Approach

Cell-free massive MIMO is one of the core technologies for future wireless networks. It is expected to bring enormous benefits, including ultra-high reliability, data throughput, energy efficiency, and uniform coverage. As a radically distributed system, the performance of cell-free massive MIMO critically relies on efficient distributed processing algorithms. In this paper, we propose a distributed expectation propagation (EP) detector for cell-free massive MIMO, which consists of two modules: a nonlinear module at the central processing unit (CPU) and a linear module at each access point (AP). The turbo principle in iterative channel decoding is utilized to compute and pass the extrinsic information between the two modules. An analytical framework is provided to characterize the asymptotic performance of the proposed EP detector with a large number of antennas. Furthermore, a distributed iterative channel estimation and data detection (ICD) algorithm is developed to handle the practical setting with imperfect channel state information (CSI). Simulation results will show that the proposed method outperforms existing detectors for cell-free massive MIMO systems in terms of the bit-error rate and demonstrate that the developed theoretical analysis accurately predicts system performance. Finally, it is shown that with imperfect CSI, the proposed ICD algorithm improves the system performance significantly and enables non-orthogonal pilots to reduce the pilot overhead.

cs.IT↗
arXiv2023

Spectral stability of near-extremal spacetimes

It has been suggested that the spectrum of quasinormal modes of rotating black holes is unstable against additional potential terms in the perturbation equation, as the operator associated with the equation is non-self-adjoint. We point out that a bi-linear form has been constructed previously to allow a perturbation analysis of the spectrum, which was applied to study the quasinormal modes of weakly charged Kerr-Newman black holes [Phys. Rev. D 91, 044025 (2015)]. The proposed spectral instability should be restated as instability against potential terms that have infinitesimal ``energy" norm that is specifically defined by the type of inner products introduced by Jaramillo et al. and preserving the physical meaning of energy. We argue that it is necessary to address the stability of all previous mode analysis results to reveal their susceptibility to energetically infinitesimal perturbations. In particular, for near extremal Kerr spacetime, we show that the spectrum of zero-damping modes, which have slow decay rates, is unstable (with order unity fractional change in decay rates) with fine-tuned modification of the potential. The decay rates are, however, always positive with energetically infinitesimal perturbations. If finite potential modifications are allowed near the black hole, it is possible to find superradiantly unstable modes, i.e., a ``black hole bomb" without an explicit outer shell. For the zero-damping modes in near-extremal Reissner-Nordström-de Sitter black holes, which are relevant for the breakdown of strong cosmic censorship, we find that the corresponding spectrum is stable under energetically infinitesimal perturbations.

gr-qc↗
arXiv2023

Dark against luminous matter around isolated central galaxies: a comparative study between modern surveys and Illustris-TNG

Based on independent shear measurements using the DECaLS/DR8 imaging data, we measure the weak lensing signals around isolated central galaxies (ICGs) from SDSS/DR7 at $z\sim0.1$. The projected stellar mass density profiles of surrounding satellite galaxies are further deduced, using photometric sources from the Hyper Suprime-Cam (HSC) survey (pDR3). The signals of ICGs $+$ their extended stellar halos are taken from Wang et al.(2021). All measurements are compared with predictions by the Illustris-TNG300-1 simulation. We find, overall, a good agreement between observation and TNG300. In particular, a correction to the stellar mass of massive observed ICGs is applied based on the calibration of He et al.(2013), which brings a much better agreement with TNG300 predicted lensing signals at $\log_{10}M_\ast/M_\odot>11.1$. In real observation, red ICGs are hosted by more massive dark matter halos, have more satellites and more extended stellar halos than blue ICGs at fixed stellar mass. However, in TNG300 there are more satellites around blue ICGs at fixed stellar mass, and the outer stellar halos of red and blue ICGs are similar. The stellar halos of TNG galaxies are more extended compared with real observed galaxies, especially for blue ICGs with $\log_{10}M_\ast/M_\odot>10.8$. We find the same trend for TNG100 galaxies and for true halo central galaxies. The tensions between TNG and real galaxies might indicate that satellite disruptions are stronger in TNG. In both TNG300 and observation, satellites approximately trace the underlying dark matter distribution beyond $0.1R_{200}$, but the fraction of total stellar mass in TNG300 does not show the same radial distribution as real galaxies.

astro-ph.GA↗
arXiv2023

Hybrid Far- and Near-Field Channel Estimation for THz Ultra-Massive MIMO via Fixed Point Networks

Terahertz ultra-massive multiple-input multiple-output (THz UM-MIMO) is envisioned as one of the key enablers of 6G wireless systems. Due to the joint effect of its array aperture and small wavelength, the near-field region of THz UM-MIMO is greatly enlarged. The high-dimensional channel of such systems thus consists of a stochastic mixture of far and near fields, which renders channel estimation extremely challenging. Previous works based on uni-field assumptions cannot capture the hybrid far- and near-field features, thus suffering significant performance loss. This motivates us to consider hybrid-field channel estimation. We draw inspirations from fixed point theory to develop an efficient deep learning based channel estimator with adaptive complexity and linear convergence guarantee. Built upon classic orthogonal approximate message passing, we transform each iteration into a contractive mapping, comprising a closed-form linear estimator and a neural network based non-linear estimator. A major algorithmic innovation involves applying fixed point iteration to compute the channel estimate while modeling neural networks with arbitrary depth and adapting to the hybrid-field channel conditions. Simulation results verify our theoretical analysis and show significant performance gains over state-of-the-art approaches in the estimation accuracy and convergence rate.

eess.SP↗
arXiv2023

Interlayer donor-acceptor pair excitons in MoSe2/WSe2 moiré heterobilayer

Localized interlayer excitons (LIXs) in two-dimensional moiré superlattices exhibit sharp and dense emission peaks, making them promising as highly tunable single-photon sources. However, the fundamental nature of these LIXs is still elusive. Here, we show the donor-acceptor pair (DAP) mechanism as one of the origins of these excitonic peaks. Numerical simulation results of the DAP model agree with the experimental photoluminescence spectra of LIX in the moiré MoSe2/WSe2 heterobilayer. In particular, we find that the emission energy-lifetime correlation and the nonmonotonic power dependence of the lifetime agree well with the DAP IX model. Our results provide insight into the physical mechanism of LIX formation in moiré heterostructures and pave new directions for engineering interlayer exciton properties in moiré superlattices.

cond-mat.mes-hall↗
arXiv2023

Free-running 4H-SiC single-photon detector with ultralow afterpulse probability at 266 nm

Ultraviolet single-photon detector (UVSPD) provides a key tool for the applications requiring ultraweak light detection in the wavelength band. Here, we report a 4H-SiC single-photon avalanche diode (SPAD) based free-running UVSPD with ultralow afterpulse probability. We design and fabricate the 4H-SiC SPAD with a beveled mesa structure, which exhibits the characteristic of ultralow dark current. We further develop a readout circuit of passive quenching and active reset with tunable hold-off time setting to considerably suppress the afterpulsing effect. The nonuniformity of photon detection efficiency (PDE) across the SPAD active area with a diameter of $\sim$ 180 $μ$m is investigated for performance optimization. The compact UVSPD is then characterized, exhibiting a typical performance of 10.3% PDE, 133 kcps dark count rate and 0.3% afterpulse probability at 266 nm. Such performance indicates that the compact UVSPD could be used for practical ultraviolet photon-counting applications

physics.ins-det↗
arXiv2023

Probing higher-spin particles with gravitational waves from compact binary inspirals

Under the framework of gravitational effective field theory, we propose a theory agnostic strategy of searching for higher-spin particles with gravitational waves from compact binary inspirals. Using this strategy, we analyze gravitational wave signals from the binary black hole merger events GW151226 and GW170608, as well as the binary neutron star merger event GW170817. We find that the existence of higher-spin particles with mass ranged from $10^{-12} {\rm eV}$ to $10^{-11} {\rm eV}$ is strongly disfavored by these events unless the particles precisely combine within a supersymmetric supermultiplet. We argue that the gravitational effective field theory also provides a framework to search for signals beyond GR from other GW observations, such as extreme-mass-ratio-inspirals.

gr-qc↗
arXiv2023

Alleviating both $H_0$ and $S_8$ tensions: early dark energy lifts the CMB-lockdown on ultralight axion

The existence of ultralight axion (ULA) with mass $\mathcal{O}( 10^{-26}\text{eV})$ is not favored by the CMB observations in the standard $Λ$CDM model. We show that the inclusion of early dark energy (EDE) will lift the CMB-lockdown on such ULA, and possibly other forms of dark matter beyond cold dark matter. By performing Monte Carlo Markov Chain analysis, it is found that, as opposed to $Λ$CDM, the AdS-EDE cosmology (with an Anti-de Sitter phase around recombination) now allows the existence of axion with mass $10^{-26}$ eV and predicts $6\%$ of the matter in our Universe to be such ULA, which can also help alleviating the $S_8$ tension in EDE.

astro-ph.CO↗
arXiv2023

Hyperspectral Image Super Resolution with Real Unaligned RGB Guidance

Fusion-based hyperspectral image (HSI) super-resolution has become increasingly prevalent for its capability to integrate high-frequency spatial information from the paired high-resolution (HR) RGB reference image. However, most of the existing methods either heavily rely on the accurate alignment between low-resolution (LR) HSIs and RGB images, or can only deal with simulated unaligned RGB images generated by rigid geometric transformations, which weakens their effectiveness for real scenes. In this paper, we explore the fusion-based HSI super-resolution with real RGB reference images that have both rigid and non-rigid misalignments. To properly address the limitations of existing methods for unaligned reference images, we propose an HSI fusion network with heterogenous feature extractions, multi-stage feature alignments, and attentive feature fusion. Specifically, our network first transforms the input HSI and RGB images into two sets of multi-scale features with an HSI encoder and an RGB encoder, respectively. The features of RGB reference images are then processed by a multi-stage alignment module to explicitly align the features of RGB reference with the LR HSI. Finally, the aligned features of RGB reference are further adjusted by an adaptive attention module to focus more on discriminative regions before sending them to the fusion decoder to generate the reconstructed HR HSI. Additionally, we collect a real-world HSI fusion dataset, consisting of paired HSI and unaligned RGB reference, to support the evaluation of the proposed model for real scenes. Extensive experiments are conducted on both simulated and our real-world datasets, and it shows that our method obtains a clear improvement over existing single-image and fusion-based super-resolution methods on quantitative assessment as well as visual comparison.

cs.CV↗
arXiv2023

In-Context Learning with Many Demonstration Examples

Large pre-training language models (PLMs) have shown promising in-context learning abilities. However, due to the backbone transformer architecture, existing PLMs are bottlenecked by the memory and computational cost when scaling up to a large context size, leaving instruction tuning and in-context learning of many demonstration examples, as well as long-range language modeling under-explored. In this study, we propose a long-range language model EVALM based on an efficient transformer mechanism. EVALM is trained with 8k tokens per batch line and can test up to 256k-lengthed contexts with extrapolation, 128 times to the limit of existing PLMs (e.g. GPT3). Based on EVALM, we scale up the size of examples efficiently in both instruction tuning and in-context learning to explore the boundary of the benefits from more annotated data. Experimental results on a diverse set of tasks show that EVALM achieves 4.1% higher accuracy on average, and the average length of achieving the best accuracy score over tasks is around 12k. We find that in-context learning can achieve higher performance with more demonstrations under many-shot instruction tuning (8k), and further extending the length of instructions (16k) can further improve the upper bound of scaling in-context learning.

cs.CL↗
arXiv2023

Blind Performance Prediction for Deep Learning Based Ultra-Massive MIMO Channel Estimation

Reliability is of paramount importance for the physical layer of wireless systems due to its decisive impact on end-to-end performance. However, the uncertainty of prevailing deep learning (DL)-based physical layer algorithms is hard to quantify due to the black-box nature of neural networks. This limitation is a major obstacle that hinders their practical deployment. In this paper, we attempt to quantify the uncertainty of an important category of DL-based channel estimators. An efficient statistical method is proposed to make blind predictions for the mean squared error of the DL-estimated channel solely based on received pilots, without knowledge of the ground-truth channel, the prior distribution of the channel, or the noise statistics. The complexity of the blind performance prediction is low and scales only linearly with the number of antennas. Simulation results for ultra-massive multiple-input multiple-output (UM-MIMO) channel estimation with a mixture of far-field and near-field paths are provided to verify the accuracy and efficiency of the proposed method.

eess.SP↗
arXiv2023

A Self-adaptive Neuroevolution Approach to Constructing Deep Neural Network Architectures Across Different Types

Neuroevolution has greatly promoted Deep Neural Network (DNN) architecture design and its applications, while there is a lack of methods available across different DNN types concerning both their scale and performance. In this study, we propose a self-adaptive neuroevolution (SANE) approach to automatically construct various lightweight DNN architectures for different tasks. One of the key settings in SANE is the search space defined by cells and organs self-adapted to different DNN types. Based on this search space, a constructive evolution strategy with uniform evolution settings and operations is designed to grow DNN architectures gradually. SANE is able to self-adaptively adjust evolution exploration and exploitation to improve search efficiency. Moreover, a speciation scheme is developed to protect evolution from early convergence by restricting selection competition within species. To evaluate SANE, we carry out neuroevolution experiments to generate different DNN architectures including convolutional neural network, generative adversarial network and long short-term memory. The results illustrate that the obtained DNN architectures could have smaller scale with similar performance compared to existing DNN architectures. Our proposed SANE provides an efficient approach to self-adaptively search DNN architectures across different types.

cs.NE↗
arXiv2023

Positively curved Kähler metrics on tube domains and their applications to optimal transport

In this article, we study a class of Kähler manifolds defined on tube domains in $\mathbb{C}^n$, and in particular those which have $O(n) \times \mathbb{R}^n$ symmetry. For these, we prove a uniqueness result showing that any such manifold which is complete and has non-negative orthogonal bisectional curvature ($n \geq 3$) or non-negative bisectional curvature ($n \geq 2$) is biholomorphically isometric to $\mathbb{C}^n$. We also consider another curvature tensor called the \emph{orthogonal anti-bisectional curvature}. We find necessary and sufficient conditions for a complete $O(n)$-symmetric tube domain to have non-negative orthogonal anti-bisectional curvature and provide several examples of complete metrics which satisfy this condition. Finally, we discuss some applications of these spaces within optimal transport. In particular, we study "synthetic" curvature bounds for non-smooth geometries and how they can be applied to the rough geometry induced by the Monge cost $c(x,y)=\|x-y\|$.

math.DG↗
arXiv2023

Sparse Mixture-of-Experts are Domain Generalizable Learners

Human visual perception can easily generalize to out-of-distributed visual data, which is far beyond the capability of modern machine learning models. Domain generalization (DG) aims to close this gap, with existing DG methods mainly focusing on the loss function design. In this paper, we propose to explore an orthogonal direction, i.e., the design of the backbone architecture. It is motivated by an empirical finding that transformer-based models trained with empirical risk minimization (ERM) outperform CNN-based models employing state-of-the-art (SOTA) DG algorithms on multiple DG datasets. We develop a formal framework to characterize a network's robustness to distribution shifts by studying its architecture's alignment with the correlations in the dataset. This analysis guides us to propose a novel DG model built upon vision transformers, namely Generalizable Mixture-of-Experts (GMoE). Extensive experiments on DomainBed demonstrate that GMoE trained with ERM outperforms SOTA DG baselines by a large margin. Moreover, GMoE is complementary to existing DG methods and its performance is substantially improved when trained with DG algorithms.

cs.CV↗
arXiv2023

Learning Task-Oriented Communication for Edge Inference: An Information Bottleneck Approach

This paper investigates task-oriented communication for edge inference, where a low-end edge device transmits the extracted feature vector of a local data sample to a powerful edge server for processing. It is critical to encode the data into an informative and compact representation for low-latency inference given the limited bandwidth. We propose a learning-based communication scheme that jointly optimizes feature extraction, source coding, and channel coding in a task-oriented manner, i.e., targeting the downstream inference task rather than data reconstruction. Specifically, we leverage an information bottleneck (IB) framework to formalize a rate-distortion tradeoff between the informativeness of the encoded feature and the inference performance. As the IB optimization is computationally prohibitive for the high-dimensional data, we adopt a variational approximation, namely the variational information bottleneck (VIB), to build a tractable upper bound. To reduce the communication overhead, we leverage a sparsity-inducing distribution as the variational prior for the VIB framework to sparsify the encoded feature vector. Furthermore, considering dynamic channel conditions in practical communication systems, we propose a variable-length feature encoding scheme based on dynamic neural networks to adaptively adjust the activated dimensions of the encoded feature to different channel conditions. Extensive experiments evidence that the proposed task-oriented communication system achieves a better rate-distortion tradeoff than baseline methods and significantly reduces the feature transmission latency in dynamic channel conditions.

eess.SP↗
arXiv2023

Artificial intelligence for diagnosing and predicting survival of patients with renal cell carcinoma: Retrospective multi-center study

Background: Clear cell renal cell carcinoma (ccRCC) is the most common renal-related tumor with high heterogeneity. There is still an urgent need for novel diagnostic and prognostic biomarkers for ccRCC. Methods: We proposed a weakly-supervised deep learning strategy using conventional histology of 1752 whole slide images from multiple centers. Our study was demonstrated through internal cross-validation and external validations for the deep learning-based models. Results: Automatic diagnosis for ccRCC through intelligent subtyping of renal cell carcinoma was proved in this study. Our graderisk achieved aera the curve (AUC) of 0.840 (95% confidence interval: 0.805-0.871) in the TCGA cohort, 0.840 (0.805-0.871) in the General cohort, and 0.840 (0.805-0.871) in the CPTAC cohort for the recognition of high-grade tumor. The OSrisk for the prediction of 5-year survival status achieved AUC of 0.784 (0.746-0.819) in the TCGA cohort, which was further verified in the independent General cohort and the CPTAC cohort, with AUC of 0.774 (0.723-0.820) and 0.702 (0.632-0.765), respectively. Cox regression analysis indicated that graderisk, OSrisk, tumor grade, and tumor stage were found to be independent prognostic factors, which were further incorporated into the competing-risk nomogram (CRN). Kaplan-Meier survival analyses further illustrated that our CRN could significantly distinguish patients with high survival risk, with hazard ratio of 5.664 (3.893-8.239, p < 0.0001) in the TCGA cohort, 35.740 (5.889-216.900, p < 0.0001) in the General cohort and 6.107 (1.815 to 20.540, p < 0.0001) in the CPTAC cohort. Comparison analyses conformed that our CRN outperformed current prognosis indicators in the prediction of survival status, with higher concordance index for clinical prognosis.

eess.IV↗