arXiv subjects

Dong Xu

Publications and source records attributed to Dong Xu.

At least 163 records · Page 9Linked to original sources

arXiv2023

Photometric and Spectroscopic Observations of GRB 190106A: Emission from Reverse and Forward Shocks with Late-time Energy Injection

Early optical observations of gamma-ray bursts can significantly contribute to the study of the central engine and physical processes therein. However, of the thousands observed so far, still only a few have data at optical wavelengths in the first minutes after the onset of the prompt emission. Here we report on GRB\,190106A, whose afterglow was observed in optical bands just 36 s after the {\em Swift}/BAT trigger, i.e., during the prompt emission phase. The early optical afterglow exhibits a bimodal structure followed by a normal decay, with a faster decay after $\sim \rm T_{0}+$1 day. We present optical photometric and spectroscopic observations of GRB\,190106A. We derive the redshift via metal absorption lines from Xinglong 2.16-m/BFOSC spectroscopic observations. From the BFOSC spectrum, we measure $z= 1.861\pm0.002$. The double-peak optical light curve is a significant feature predicted by the reverse-forward external shock model. The shallow decay followed by a normal decay in both the X-ray and optical light curves is well explained with the standard forward-shock model with late-time energy injection. Therefore, GRB\,190106A offers a case study for GRBs emission from both reverse and forward shocks.

astro-ph.HE↗

arXiv2023

Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action

Denoising diffusion models have emerged as one of the most powerful generative models in recent years. They have achieved remarkable success in many fields, such as computer vision, natural language processing (NLP), and bioinformatics. Although there are a few excellent reviews on diffusion models and their applications in computer vision and NLP, there is a lack of an overview of their applications in bioinformatics. This review aims to provide a rather thorough overview of the applications of diffusion models in bioinformatics to aid their further development in bioinformatics and computational biology. We start with an introduction of the key concepts and theoretical foundations of three cornerstone diffusion modeling frameworks (denoising diffusion probabilistic models, noise-conditioned scoring networks, and stochastic differential equations), followed by a comprehensive description of diffusion models employed in the different domains of bioinformatics, including cryo-EM data enhancement, single-cell data analysis, protein design and generation, drug and small molecule design, and protein-ligand interaction. The review is concluded with a summary of the potential new development and applications of diffusion models in bioinformatics.

cs.LG↗

arXiv2023

Signatures of Chiral Superconductivity in Chiral Molecule Intercalated Tantalum Disulfide

Chiral superconductors, a unique class of unconventional superconductors in which the complex superconducting order parameter winds clockwise or counter-clockwise in the momentum space, represent a topologically non-trivial system with direct implications for topological quantum computing. Intrinsic chiral superconductors are extremely rare, with only a few arguable examples including heavy fermion metals (UTe$_2$, UPt$_3$) and perovskite superconductor Sr$_2$RuO$_4$. Chiral molecules with neither mirror nor inversion symmetry have been widely investigated, in which the spin degeneracy may be lifted by the molecular chirality. Thus, a combination of superconductivity with chiral molecules may lead to a spin-polarized ground state for realizing chiral superconductivity. Herein we report the first investigation of unconventional superconductivity in chiral molecule intercalated tantalum disulfide (TaS$_2$) and reveal key signatures of chiral superconductivity. Little-Parks measurements demonstrate a robust and reproducible half-flux quantum phase shift in both left- and right-handed chiral molecule intercalated TaS$_2$, which is absent in pristine TaS$_2$ or achiral molecule intercalated TaS$_2$, highlighting the essential role of molecular chirality in inducing unconventional superconductivity. The robust half-flux quantum phase shift demonstrates unconventional superconductivity and constitutes strong evidence supporting a chiral superconducting ordering parameter. Critical current measurements at lower temperature reveal a peculiar asymmetric phase shift under opposite supercurrent, with a relative phase difference approaching the unity of π at below 0.5 K, further supporting topologically non-trivial superconductivity. Our study signifies the potential of hybrid superlattices with intriguing coupling between the crystalline atomic layers and the self-assembled molecular layers.

cond-mat.supr-con↗

arXiv2022

SketchSampler: Sketch-based 3D Reconstruction via View-dependent Depth Sampling

Reconstructing a 3D shape based on a single sketch image is challenging due to the large domain gap between a sparse, irregular sketch and a regular, dense 3D shape. Existing works try to employ the global feature extracted from sketch to directly predict the 3D coordinates, but they usually suffer from losing fine details that are not faithful to the input sketch. Through analyzing the 3D-to-2D projection process, we notice that the density map that characterizes the distribution of 2D point clouds (i.e., the probability of points projected at each location of the projection plane) can be used as a proxy to facilitate the reconstruction process. To this end, we first translate a sketch via an image translation network to a more informative 2D representation that can be used to generate a density map. Next, a 3D point cloud is reconstructed via a two-stage probabilistic sampling process: first recovering the 2D points (i.e., the x and y coordinates) by sampling the density map; and then predicting the depth (i.e., the z coordinate) by sampling the depth values at the ray determined by each 2D point. Extensive experiments are conducted, and both quantitative and qualitative results show that our proposed approach significantly outperforms other baseline methods.

cs.CV↗

arXiv2022

Content Adaptive Latents and Decoder for Neural Image Compression

In recent years, neural image compression (NIC) algorithms have shown powerful coding performance. However, most of them are not adaptive to the image content. Although several content adaptive methods have been proposed by updating the encoder-side components, the adaptability of both latents and the decoder is not well exploited. In this work, we propose a new NIC framework that improves the content adaptability on both latents and the decoder. Specifically, to remove redundancy in the latents, our content adaptive channel dropping (CACD) method automatically selects the optimal quality levels for the latents spatially and drops the redundant channels. Additionally, we propose the content adaptive feature transformation (CAFT) method to improve decoder-side content adaptability by extracting the characteristic information of the image content, which is then used to transform the features in the decoder side. Experimental results demonstrate that our proposed methods with the encoder-side updating algorithm achieve the state-of-the-art performance.

cs.CV↗

arXiv2022

Photometric and Spectroscopic Observations of GRB 210104A: Bright Reverse shock Emission and Dense Circumburst Environment

Early afterglow observations of gamma-ray bursts (GRBs) are valuable for exploring the properties of their jets and ambient medium. We report our photometric and spectroscopic observations of GRB 210104A and discuss its jet properties with multiwavelength data. Our spectroscopic observation reveals several absorption features and a tentative redshift of 0.46 is identified. A bright optical flare that has a peak brightness of $R=13$ mag at $112\pm 7$~s was observed in the $R$ band during $67\sim 165$ seconds post the GRB trigger. The flux of the $R$-band afterglow decays with a slope of $α_{\rm O}={-0.91\pm 0.03}$ at $t>650$~s. The early X-ray afterglow lightcurve is a smooth bump, and it decays with a slope of $α_{\rm X}=-1.18\pm 0.01$ at late epoch. Our joint spectral fit to the optical-X-ray afterglows during $(1.1-1.3)\times 10^{4}$~s yields a photon index $Γ_{\rm O,X}=-1.82\pm 0.04$. The derived host galaxy extinction is $A_{R}=0.87$. Attributing the early optical flare to the reverse-shock (RS) emission and the late optical-X-ray emission to the forward shock emission; the optical and X-ray lightcurves at $t<3\times 10^4$~s can be well fit adopting an Markov Chain Monte Carlo algorithm. Comparing the properties of GRB 210104A with other GRBs that have detection of bright RS emission, we show that its jet is mildly magnetized ($R_{\rm B}=28$), with high radiation efficiency ($77\%$), is sub-energetic ($E_{\rm k, iso}=4.5\times 10^{51}$ erg), and moderately relativistic ($Γ_0\sim 35$) in a density medium ($n_{0}\sim 417\;{\rm cm}^{-3}$). It follows the tight $L_{γ,\rm iso}-E_{\rm p,z}-Γ_{0}$ relation as with typical GRBs.

astro-ph.HE↗

arXiv2022

Slow Motion Matters: A Slow Motion Enhanced Network for Weakly Supervised Temporal Action Localization

Weakly supervised temporal action localization (WTAL) aims to localize actions in untrimmed videos with only weak supervision information (e.g. video-level labels). Most existing models handle all input videos with a fixed temporal scale. However, such models are not sensitive to actions whose pace of the movements is different from the ``normal" speed, especially slow-motion action instances, which complete the movements with a much slower speed than their counterparts with a normal speed. Here arises the slow-motion blurred issue: It is hard to explore salient slow-motion information from videos at ``normal" speed. In this paper, we propose a novel framework termed Slow Motion Enhanced Network (SMEN) to improve the ability of a WTAL network by compensating its sensitivity on slow-motion action segments. The proposed SMEN comprises a Mining module and a Localization module. The mining module generates mask to mine slow-motion-related features by utilizing the relationships between the normal motion and slow motion; while the localization module leverages the mined slow-motion features as complementary information to improve the temporal action localization results. Our proposed framework can be easily adapted by existing WTAL networks and enable them be more sensitive to slow-motion actions. Extensive experiments on three benchmarks are conducted, which demonstrate the high performance of our proposed framework.

cs.CV↗

arXiv2022

Towards Explainable 3D Grounded Visual Question Answering: A New Benchmark and Strong Baseline

Recently, 3D vision-and-language tasks have attracted increasing research interest. Compared to other vision-and-language tasks, the 3D visual question answering (VQA) task is less exploited and is more susceptible to language priors and co-reference ambiguity. Meanwhile, a couple of recently proposed 3D VQA datasets do not well support 3D VQA task due to their limited scale and annotation methods. In this work, we formally define and address a 3D grounded VQA task by collecting a new 3D VQA dataset, referred to as FE-3DGQA, with diverse and relatively free-form question-answer pairs, as well as dense and completely grounded bounding box annotations. To achieve more explainable answers, we labelled the objects appeared in the complex QA pairs with different semantic types, including answer-grounded objects (both appeared and not appeared in the questions), and contextual objects for answer-grounded objects. We also propose a new 3D VQA framework to effectively predict the completely visually grounded and explainable answer. Extensive experiments verify that our newly collected benchmark datasets can be effectively used to evaluate various 3D VQA methods from different aspects and our newly proposed framework also achieves state-of-the-art performance on the new benchmark dataset. Both the newly collected dataset and our codes will be publicly available at http://github.com/zlccccc/3DGQA.

cs.CV↗

arXiv2022

Improving RGB-D Point Cloud Registration by Learning Multi-scale Local Linear Transformation

Point cloud registration aims at estimating the geometric transformation between two point cloud scans, in which point-wise correspondence estimation is the key to its success. In addition to previous methods that seek correspondences by hand-crafted or learnt geometric features, recent point cloud registration methods have tried to apply RGB-D data to achieve more accurate correspondence. However, it is not trivial to effectively fuse the geometric and visual information from these two distinctive modalities, especially for the registration problem. In this work, we propose a new Geometry-Aware Visual Feature Extractor (GAVE) that employs multi-scale local linear transformation to progressively fuse these two modalities, where the geometric features from the depth data act as the geometry-dependent convolution kernels to transform the visual features from the RGB data. The resultant visual-geometric features are in canonical feature spaces with alleviated visual dissimilarity caused by geometric changes, by which more reliable correspondence can be achieved. The proposed GAVE module can be readily plugged into recent RGB-D point cloud registration framework. Extensive experiments on 3D Match and ScanNet demonstrate that our method outperforms the state-of-the-art point cloud registration methods even without correspondence or pose supervision. The code is available at: https://github.com/514DNA/LLT.

cs.CV↗

arXiv2022

Coarse-to-fine Deep Video Coding with Hyperprior-guided Mode Prediction

The previous deep video compression approaches only use the single scale motion compensation strategy and rarely adopt the mode prediction technique from the traditional standards like H.264/H.265 for both motion and residual compression. In this work, we first propose a coarse-to-fine (C2F) deep video compression framework for better motion compensation, in which we perform motion estimation, compression and compensation twice in a coarse to fine manner. Our C2F framework can achieve better motion compensation results without significantly increasing bit costs. Observing hyperprior information (i.e., the mean and variance values) from the hyperprior networks contains discriminant statistical information of different patches, we also propose two efficient hyperprior-guided mode prediction methods. Specifically, using hyperprior information as the input, we propose two mode prediction networks to respectively predict the optimal block resolutions for better motion coding and decide whether to skip residual information from each block for better residual coding without introducing additional bit cost while bringing negligible extra computation cost. Comprehensive experimental results demonstrate our proposed C2F video compression framework equipped with the new hyperprior-guided mode prediction methods achieves the state-of-the-art performance on HEVC, UVG and MCL-JCV datasets.

cs.CV↗

arXiv2022

ET White Paper: To Find the First Earth 2.0

We propose to develop a wide-field and ultra-high-precision photometric survey mission, temporarily named "Earth 2.0 (ET)". This mission is designed to measure, for the first time, the occurrence rate and the orbital distributions of Earth-sized planets. ET consists of seven 30cm telescopes, to be launched to the Earth-Sun's L2 point. Six of these are transit telescopes with a field of view of 500 square degrees. Staring in the direction that encompasses the original Kepler field for four continuous years, this monitoring will return tens of thousands of transiting planets, including the elusive Earth twins orbiting solar-type stars. The seventh telescope is a 30cm microlensing telescope that will monitor an area of 4 square degrees toward the galactic bulge. This, combined with simultaneous ground-based KMTNet observations, will measure masses for hundreds of long-period and free-floating planets. Together, the transit and the microlensing telescopes will revolutionize our understandings of terrestrial planets across a large swath of orbital distances and free space. In addition, the survey data will also facilitate studies in the fields of asteroseismology, Galactic archeology, time-domain sciences, and black holes in binaries.

astro-ph.IM↗

arXiv2022

Salient Object Detection via Integrity Learning

Although current salient object detection (SOD) works have achieved significant progress, they are limited when it comes to the integrity of the predicted salient regions. We define the concept of integrity at both a micro and macro level. Specifically, at the micro level, the model should highlight all parts that belong to a certain salient object. Meanwhile, at the macro level, the model needs to discover all salient objects in a given image. To facilitate integrity learning for SOD, we design a novel Integrity Cognition Network (ICON), which explores three important components for learning strong integrity features. 1) Unlike existing models, which focus more on feature discriminability, we introduce a diverse feature aggregation (DFA) component to aggregate features with various receptive fields (i.e., kernel shape and context) and increase feature diversity. Such diversity is the foundation for mining the integral salient objects. 2) Based on the DFA features, we introduce an integrity channel enhancement (ICE) component with the goal of enhancing feature channels that highlight the integral salient objects, while suppressing the other distracting ones. 3) After extracting the enhanced features, the part-whole verification (PWV) method is employed to determine whether the part and whole object features have strong agreement. Such part-whole agreements can further improve the micro-level integrity for each salient object. To demonstrate the effectiveness of our ICON, comprehensive experiments are conducted on seven challenging benchmarks. Our ICON outperforms the baseline methods in terms of a wide range of metrics. Notably, our ICON achieves about 10% relative improvement over the previous best model in terms of average false negative ratio (FNR), on six datasets. Codes and results are available at: https://github.com/mczhuge/ICON.

cs.CV↗

arXiv2022

Revisiting Deep Semi-supervised Learning: An Empirical Distribution Alignment Framework and Its Generalization Bound

In this work, we revisit the semi-supervised learning (SSL) problem from a new perspective of explicitly reducing empirical distribution mismatch between labeled and unlabeled samples. Benefited from this new perspective, we first propose a new deep semi-supervised learning framework called Semi-supervised Learning by Empirical Distribution Alignment (SLEDA), in which existing technologies from the domain adaptation community can be readily used to address the semi-supervised learning problem through reducing the empirical distribution distance between labeled and unlabeled data. Based on this framework, we also develop a new theoretical generalization bound for the research community to better understand the semi-supervised learning problem, in which we show the generalization error of semi-supervised learning can be effectively bounded by minimizing the training error on labeled data and the empirical distribution distance between labeled and unlabeled data. Building upon our new framework and the theoretical bound, we develop a simple and effective deep semi-supervised learning method called Augmented Distribution Alignment Network (ADA-Net) by simultaneously adopting the well-established adversarial training strategy from the domain adaptation community and a simple sample interpolation strategy for data augmentation. Additionally, we incorporate both strategies in our ADA-Net into two exiting SSL methods to further improve their generalization capability, which indicates that our new framework provides a complementary solution for solving the SSL problem. Our comprehensive experimental results on two benchmark datasets SVHN and CIFAR-10 for the semi-supervised image recognition task and another two benchmark datasets ModelNet40 and ShapeNet55 for the semi-supervised point cloud recognition task demonstrate the effectiveness of our proposed framework for SSL.

cs.CV↗

arXiv2022

Perturbative benchmark models for a dark shower search program

We provide five benchmark hidden valley models with perturbative parton showers, which span a wide range of dark shower phenomenology. We consider production through an $s$-channel, heavy mediator, which can be identified with the SM Higgs. By assuming a set of well-motivated decay portals, one can moreover fix both the branching ratios of the dark mesons and set a lower bound on their lifetime. We provide a public python tool which can be used to generate self-consistent PYTHIA 8 cards for our benchmark models.

hep-ph↗

arXiv2021

EndHiC: assemble large contigs into chromosomal-level scaffolds using the Hi-C links from contig ends

Motivation: The application of PacBio HiFi and ultra-long ONT reads have achieved huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaffolding software, which all compute the contact value between contigs using the Hi-C links from the whole contig regions. As the Hi-C links of two adjacent contigs concentrate only at the neighbor ends of the contigs, larger contig size will reduce the power to differentiate adjacent (signal) and non-adjacent (noise) contig linkages, leading to a higher rate of mis-assembly. Results: We present a software package EndHiC, which is suitable to assemble large contigs (> 1-Mb) into chromosomal-level scaffolds, using Hi-C links from only the contig end regions instead of the whole contig regions. Benefiting from the increased signal to noise ratio, EndHiC achieves much higher scaffolding accuracy compared to existing software LACHESIS, ALLHiC, and 3D-DNA. Moreover, EndHiC has few parameters, runs 10-1000 times faster than existing software, needs trivial memory, provides robustness evaluation, and allows graphic viewing of the scaffold results. The high scaffolding accuracy and user-friendly interface of EndHiC, liberate the users from labor-intensive manual checks and revision works. Availability and implementation: EndHiC is written in Perl, and is freely available at https://github.com/fanagislab/EndHiC. Contact: fanwei@caas.cn and milrazhang@163.com Supplementary information: Supplementary data are available at Bioinformatics online.

q-bio.GN↗

arXiv2021

Exotic Higgs Decays to Four Taus at Future Electron-Positron Colliders

We study the prospects for the exotic Higgs decay mode $h\to ss\to 4τ$ at planned electron-positron colliders in the case where the beyond-the-Standard Model particle $s$ is too light to decay into $b \bar b$ pairs. We find that with 5 ab$^{-1}$ of unpolarized collisions at 240 GeV, the branching ratio into this final state can be constrained to be below $\sim 1.3\times 10^{-4}$ at 95\% CL, depending on the mass of $s$ and the assumed tracking efficiency.

hep-ph↗

arXiv2021

FVC: A New Framework towards Deep Video Compression in Feature Space

Learning based video compression attracts increasing attention in the past few years. The previous hybrid coding approaches rely on pixel space operations to reduce spatial and temporal redundancy, which may suffer from inaccurate motion estimation or less effective motion compensation. In this work, we propose a feature-space video coding network (FVC) by performing all major operations (i.e., motion estimation, motion compression, motion compensation and residual compression) in the feature space. Specifically, in the proposed deformable compensation module, we first apply motion estimation in the feature space to produce motion information (i.e., the offset maps), which will be compressed by using the auto-encoder style network. Then we perform motion compensation by using deformable convolution and generate the predicted feature. After that, we compress the residual feature between the feature from the current frame and the predicted feature from our deformable compensation module. For better frame reconstruction, the reference features from multiple previous reconstructed frames are also fused by using the non-local attention mechanism in the multi-frame feature fusion module. Comprehensive experimental results demonstrate that the proposed framework achieves the state-of-the-art performance on four benchmark datasets including HEVC, UVG, VTL and MCL-JCV.

eess.IV↗

arXiv2021

NG+ : A Multi-Step Matrix-Product Natural Gradient Method for Deep Learning

In this paper, a novel second-order method called NG+ is proposed. By following the rule ``the shape of the gradient equals the shape of the parameter", we define a generalized fisher information matrix (GFIM) using the products of gradients in the matrix form rather than the traditional vectorization. Then, our generalized natural gradient direction is simply the inverse of the GFIM multiplies the gradient in the matrix form. Moreover, the GFIM and its inverse keeps the same for multiple steps so that the computational cost can be controlled and is comparable with the first-order methods. A global convergence is established under some mild conditions and a regret bound is also given for the online learning setting. Numerical results on image classification with ResNet50, quantum chemistry modeling with Schnet, neural machine translation with Transformer and recommendation system with DLRM illustrate that GN+ is competitive with the state-of-the-art methods.

math.OC↗