Xueying Wang

Ziyang Xu, Haitian Zhong, Bingrui He et al.

Phosphorylation is pivotal in numerous fundamental cellular processes and plays a significant role in the onset and progression of various diseases. The accurate identification of these phosphorylation sites is crucial for unraveling the molecular mechanisms within cells and during viral infections, potentially leading to the discovery of novel therapeutic targets. In this study, we develop PTransIPs, a new deep learning framework for the identification of phosphorylation sites. Independent testing results demonstrate that PTransIPs outperforms existing state-of-the-art (SOTA) methods, achieving AUCs of 0.9232 and 0.9660 for the identification of phosphorylated S/T and Y sites, respectively. PTransIPs contributes from three aspects. 1) PTransIPs is the first to apply protein pre-trained language model (PLM) embeddings to this task. It utilizes ProtTrans and EMBER2 to extract sequence and structure embeddings, respectively, as additional inputs into the model, effectively addressing issues of dataset size and overfitting, thus enhancing model performance; 2) PTransIPs is based on Transformer architecture, optimized through the integration of convolutional neural networks and TIM loss function, providing practical insights for model design and training; 3) The encoding of amino acids in PTransIPs enables it to serve as a universal framework for other peptide bioactivity tasks, with its excellent performance shown in extended experiments of this paper. Our code, data and models are publicly available at https://github.com/StatXzy7/PTransIPs.

Jianan Wang, Bin Li, Jingtao Qi et al.

Traditional robot simulators focus on physical process modeling and realistic rendering, often suffering from high computational costs, inefficiencies, and limited adaptability. To handle this issue, we concentrate on behavior simulation in robotics to analyze and validate the logic behind robot behaviors, aiming to achieve preliminary evaluation before deploying resource-intensive simulators and thus enhance simulation efficiency. In this paper, we propose BeSimulator, a modular and novel LLM-powered framework, as an attempt towards behavior simulation in the context of text-based environments. By constructing text-based virtual environments and performing semantic-level simulation, BeSimulator can generalize across scenarios and achieve long-horizon complex simulation. Inspired by human cognition paradigm, it employs a ``consider-decide-capture-transfer'' four-phase simulation process, termed Chain of Behavior Simulation (CBS), which excels at analyzing action feasibility and state transition. Additionally, BeSimulator incorporates code-driven reasoning to enable arithmetic operations and enhance reliability, and reflective feedback to refine simulation. Based on our manually constructed behavior-tree-based simulation benchmark, BTSIMBENCH, our experiments show a significant performance improvement in behavior simulation compared to baselines, ranging from 13.60% to 24.80%. Code and data are available at https://github.com/Dawn888888/BeSimulator.

Feng Zhang, Xueying Wang, Shilin Zhou et al.

Rotated object detection in aerial images has received increasing attention for a wide range of applications. However, it is also a challenging task due to the huge variations of scale, rotation, aspect ratio, and densely arranged targets. Most existing methods heavily rely on a large number of pre-defined anchors with different scales, angles, and aspect ratios, and are optimized with a distance loss. Therefore, these methods are sensitive to anchor hyper-parameters and easily suffer from performance degradation caused by boundary discontinuity. To handle this problem, in this paper, we propose a dense anchor-free rotated object detector (DARDet) for rotated object detection in aerial images. Our DARDet directly predicts five parameters of rotated boxes at each foreground pixel of feature maps. We design a new alignment convolution module to extracts aligned features and introduce a PIoU loss for precise and stable regression. Our method achieves state-of-the-art performance on three commonly used aerial objects datasets (i.e., DOTA, HRSC2016, and UCAS-AOD) while keeping high efficiency. Code is available at https://github.com/zf020114/DARDet.

Feng Zhang, Xueying Wang, Shilin Zhou et al.

Ship detection in remote sensing images plays a crucial role in various applications and has drawn increasing attention in recent years. However, existing arbitrary-oriented ship detection methods are generally developed on a set of predefined rotated anchor boxes. These predefined boxes not only lead to inaccurate angle predictions but also introduce extra hyper-parameters and high computational cost. Moreover, the prior knowledge of ship size has not been fully exploited by existing methods, which hinders the improvement of their detection accuracy. Aiming at solving the above issues, in this paper, we propose a center-head point extraction based detector (named CHPDet) to achieve arbitrary-oriented ship detection in remote sensing images. Our CHPDet formulates arbitrary-oriented ships as rotated boxes with head points which are used to determine the direction. And rotated Gaussian kernel is used to map the annotations into target heatmaps. Keypoint estimation is performed to find the center of ships. Then, the size and head point of the ships are regressed. The orientation-invariant model (OIM) is also used to produce orientation-invariant feature maps. Finally, we use the target size as prior to finetune the results. Moreover, we introduce a new dataset for multi-class arbitrary-oriented ship detection in remote sensing images at a fixed ground sample distance (GSD) which is named FGSD2021. Experimental results on FGSD2021 and two other widely used data sets, i.e., HRSC2016, and UCAS-AOD demonstrate that our CHPDet achieves state-of-the-art performance and can well distinguish between bow and stern. Code and FGSD2021 dataset are available at https://github.com/zf020114/CHPDet.

Xueying Wang, Yudong Guo, Bailin Deng et al.

Recently, 3D face reconstruction from a single image has achieved great success with the help of deep learning and shape prior knowledge, but they often fail to produce accurate geometry details. On the other hand, photometric stereo methods can recover reliable geometry details, but require dense inputs and need to solve a complex optimization problem. In this paper, we present a lightweight strategy that only requires sparse inputs or even a single image to recover high-fidelity face shapes with images captured under near-field lights. To this end, we construct a dataset containing 84 different subjects with 29 expressions under 3 different lights. Data augmentation is applied to enrich the data in terms of diversity in identity, lighting, expression, etc. With this constructed dataset, we propose a novel neural network specially designed for photometric stereo based 3D face reconstruction. Extensive experiments and comparisons demonstrate that our method can generate high-quality reconstruction results with one to three facial images captured under near-field lights. Our full framework is available at https://github.com/Juyong/FacePSNet.

Abhimanyu Talwar, Zudi Lin, Donglai Wei et al.

One of the essential tasks in connectomics is the morphology analysis of neurons and organelles like mitochondria to shed light on their biological properties. However, these biological objects often have tangled parts or complex branching patterns, which make it hard to abstract, categorize, and manipulate their morphology. In this paper, we develop a novel topological nomenclature system to name these objects like the appellation for chemical compounds to promote neuroscience analysis based on their skeletal structures. We first convert the volumetric representation into the topology-preserving reduced graph to untangle the objects. Next, we develop nomenclature rules for pyramidal neurons and mitochondria from the reduced graph and finally learn the feature embedding for shape manipulation. In ablation studies, we quantitatively show that graphs generated by our proposed method align with the perception of experts. On 3D shape retrieval and decomposition tasks, we qualitatively demonstrate that the encoded topological nomenclature features achieve better results than state-of-the-art shape descriptors. To advance neuroscience, we will release a 3D segmentation dataset of mitochondria and pyramidal neurons reconstructed from a 100um cube electron microscopy volume with their reduced graph and topological nomenclature annotations. Code is publicly available at https://github.com/donglaiw/ibexHelper.

Jinliang Shi, Shigang Li, Youxuan Xu et al.

Sparse Matrix-matrix Multiplication (SpMM) and Sampled Dense-dense Matrix Multiplication (SDDMM) are important sparse operators in scientific computing and deep learning. Tensor Core Units (TCUs) enhance modern accelerators with superior computing power, which is promising to boost the performance of matrix operators to a higher level. However, due to the irregularity of unstructured sparse data, it is difficult to deliver practical speedups on TCUs. To this end, we propose FlashSparse, a novel approach to bridge the gap between sparse workloads and the TCU architecture. Specifically, FlashSparse minimizes the sparse granularity for SpMM and SDDMM on TCUs through a novel swap-and-transpose matrix multiplication strategy. Benefiting from the minimum sparse granularity, the computation redundancy is remarkably reduced while the computing power of TCUs is fully utilized. Besides, FlashSparse is equipped with a memory-efficient thread mapping strategy for coalesced data access and a sparse matrix storage format to save memory footprint. Extensive experimental results on H100 and RTX 4090 GPUs show that FlashSparse sets a new state-of-the-art for sparse matrix multiplications (geometric mean 5.5x speedup over DTC-SpMM and 3.22x speedup over RoDe).

Minhui Zhu, Minyang Tian, Xiaocheng Yang et al.

While large language models (LLMs) with reasoning capabilities are progressing rapidly on high-school math competitions and coding, can they reason effectively through complex, open-ended challenges found in frontier physics research? And crucially, what kinds of reasoning tasks do physicists want LLMs to assist with? To address these questions, we present the CritPt (Complex Research using Integrated Thinking - Physics Test, pronounced "critical point"), the first benchmark designed to test LLMs on unpublished, research-level reasoning tasks that broadly covers modern physics research areas, including condensed matter, quantum physics, atomic, molecular & optical physics, astrophysics, high energy physics, mathematical physics, statistical physics, nuclear physics, nonlinear dynamics, fluid dynamics and biophysics. CritPt consists of 71 composite research challenges designed to simulate full-scale research projects at the entry level, which are also decomposed to 190 simpler checkpoint tasks for more fine-grained insights. All problems are newly created by 50+ active physics researchers based on their own research. Every problem is hand-curated to admit a guess-resistant and machine-verifiable answer and is evaluated by an automated grading pipeline heavily customized for advanced physics-specific output formats. We find that while current state-of-the-art LLMs show early promise on isolated checkpoints, they remain far from being able to reliably solve full research-scale challenges: the best average accuracy among base models is only 5.7%, achieved by GPT-5 (high), moderately rising to around 10% when equipped with coding tools. Through the realistic yet standardized evaluation offered by CritPt, we highlight a large disconnect between current model capabilities and realistic physics research demands, offering a foundation to guide the development of scientifically grounded AI tools.

Jinliang Shi, Shigang Li, Youxuan Xu et al.

Sparse matrix multiplication operators (i.e., SpMM and SDDMM) are widely used in deep learning and scientific computing. Modern accelerators are commonly equipped with Tensor cores and CUDA cores to accelerate sparse operators. The former brings superior computing power but only for structured matrix multiplication, while the latter has relatively lower performance but with higher programming flexibility. In this work, we discover that utilizing one resource alone leads to inferior performance for sparse matrix multiplication, due to their respective limitations. To this end, we propose Libra, a systematic approach that enables synergistic computation between CUDA and Tensor cores to achieve the best performance for sparse matrix multiplication. Specifically, we propose a 2D-aware workload distribution strategy to find out the sweet point of task mapping for different sparse operators, leveraging both the high performance of Tensor cores and the low computational redundancy on CUDA cores. In addition, Libra incorporates systematic optimizations for heterogeneous computing, including hybrid load-balancing, finely optimized kernel implementations, and GPU-accelerated preprocessing. Extensive experimental results on H100 and RTX 4090 GPUs show that Libra outperforms the state-of-the-art by on average 3.1x (up to 9.23x) over DTC-SpMM and 2.9x (up to 3.9x) for end-to-end GNN applications. Libra opens up a new perspective for sparse operator acceleration by fully exploiting the heterogeneous computing resources on GPUs.

Fu Li, Xueying Wang, Bin Li et al.

This paper presents an innovative exploration of the application potential of large language models (LLM) in addressing the challenging task of automatically generating behavior trees (BTs) for complex tasks. The conventional manual BT generation method is inefficient and heavily reliant on domain expertise. On the other hand, existing automatic BT generation technologies encounter bottlenecks related to task complexity, model adaptability, and reliability. In order to overcome these challenges, we propose a novel methodology that leverages the robust representation and reasoning abilities of LLMs. The core contribution of this paper lies in the design of a BT generation framework based on LLM, which encompasses the entire process, from data synthesis and model training to application developing and data verification. Synthetic data is introduced to train the BT generation model (BTGen model), enhancing its understanding and adaptability to various complex tasks, thereby significantly improving its overall performance. In order to ensure the effectiveness and executability of the generated BTs, we emphasize the importance of data verification and introduce a multilevel verification strategy. Additionally, we explore a range of agent design and development schemes with LLM as the central element. We hope that the work in this paper may provide a reference for the researchers who are interested in BT generation based on LLMs.

Xueying Wang, Juyong Zhang

Recently, the reconstruction of high-fidelity 3D head models from static portrait image has made great progress. However, most methods require multi-view or multi-illumination information, which therefore put forward high requirements for data acquisition. In this paper, we study the reconstruction of high-fidelity 3D head models from arbitrary monocular videos. Non-rigid structure from motion (NRSFM) methods have been widely used to solve such problems according to the two-dimensional correspondence between different frames. However, the inaccurate correspondence caused by high-complex hair structures and various facial expression changes would heavily influence the reconstruction accuracy. To tackle these problems, we propose a prior-guided dynamic implicit neural network. Specifically, we design a two-part dynamic deformation field to transform the current frame space to the canonical one. We further model the head geometry in the canonical space with a learnable signed distance field (SDF) and optimize it using the volumetric rendering with the guidance of two-main head priors to improve the reconstruction accuracy and robustness. Extensive ablation studies and comparisons with state-of-the-art methods demonstrate the effectiveness and robustness of our proposed method.

Zudi Lin, Donglai Wei, Mariela D. Petkova et al.

Segmenting 3D cell nuclei from microscopy image volumes is critical for biological and clinical analysis, enabling the study of cellular expression patterns and cell lineages. However, current datasets for neuronal nuclei usually contain volumes smaller than $10^{\text{-}3}\ mm^3$ with fewer than 500 instances per volume, unable to reveal the complexity in large brain regions and restrict the investigation of neuronal structures. In this paper, we have pushed the task forward to the sub-cubic millimeter scale and curated the NucMM dataset with two fully annotated volumes: one $0.1\ mm^3$ electron microscopy (EM) volume containing nearly the entire zebrafish brain with around 170,000 nuclei; and one $0.25\ mm^3$ micro-CT (uCT) volume containing part of a mouse visual cortex with about 7,000 nuclei. With two imaging modalities and significantly increased volume size and instance numbers, we discover a great diversity of neuronal nuclei in appearance and density, introducing new challenges to the field. We also perform a statistical analysis to illustrate those challenges quantitatively. To tackle the challenges, we propose a novel hybrid-representation learning model that combines the merits of foreground mask, contour map, and signed distance transform to produce high-quality 3D masks. The benchmark comparisons on the NucMM dataset show that our proposed method significantly outperforms state-of-the-art nuclei segmentation approaches. Code and data are available at https://connectomics-bazaar.github.io/proj/nucMM/index.html.

Donglai Wei, Kisuk Lee, Hanyu Li et al.

Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries. However, due to the complex morphology, an accurate reconstruction of cortical axons has become a major challenge. Worse still, there is no publicly available large-scale EM dataset from the cortex that provides dense ground truth segmentation for axons, making it difficult to develop and evaluate large-scale axon reconstruction methods. To address this, we introduce the AxonEM dataset, which consists of two 30x30x30 um^3 EM image volumes from the human and mouse cortex, respectively. We thoroughly proofread over 18,000 axon instances to provide dense 3D axon instance segmentation, enabling large-scale evaluation of axon reconstruction methods. In addition, we densely annotate nine ground truth subvolumes for training, per each data volume. With this, we reproduce two published state-of-the-art methods and provide their evaluation results as a baseline. We publicly release our code and data at https://connectomics-bazaar.github.io/proj/AxonEM/index.html to foster the development of advanced methods.

Xueying Wang, Yudong Guo, Zhongqi Yang et al.

Recovery of a 3D head model including the complete face and hair regions is still a challenging problem in computer vision and graphics. In this paper, we consider this problem using only a few multi-view portrait images as input. Previous multi-view stereo methods that have been based, either on optimization strategies or deep learning techniques, suffer from low-frequency geometric structures such as unclear head structures and inaccurate reconstruction in hair regions. To tackle this problem, we propose a prior-guided implicit neural rendering network. Specifically, we model the head geometry with a learnable signed distance field (SDF) and optimize it via an implicit differentiable renderer with the guidance of some human head priors, including the facial prior knowledge, head semantic segmentation information and 2D hair orientation maps. The utilization of these priors can improve the reconstruction accuracy and robustness, leading to a high-quality integrated 3D head model. Extensive ablation studies and comparisons with state-of-the-art methods demonstrate that our method can generate high-fidelity 3D head geometries with the guidance of these priors.

Felix Gonda, Xueying Wang, Johanna Beyer et al.

A connectivity graph of neurons at the resolution of single synapses provides scientists with a tool for understanding the nervous system in health and disease. Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain have made reconstructions of neurons possible at the nanometer scale. However, automatic segmentation sometimes struggles to segment large neurons correctly, requiring human effort to proofread its output. General proofreading involves inspecting large volumes to correct segmentation errors at the pixel level, a visually intensive and time-consuming process. This paper presents the design and implementation of an analytics framework that streamlines proofreading, focusing on connectivity-related errors. We accomplish this with automated likely-error detection and synapse clustering that drives the proofreading effort with highly interactive 3D visualizations. In particular, our strategy centers on proofreading the local circuit of a single cell to ensure a basic level of completeness. We demonstrate our framework's utility with a user study and report quantitative and subjective feedback from our users. Overall, users find the framework more efficient for proofreading, understanding evolving graphs, and sharing error correction strategies.

Jiansong Li, Xiao Dong, Guangli Li et al.

The training of deep neural networks (DNNs) is usually memory-hungry due to the limited device memory capacity of DNN accelerators. Characterizing the memory behaviors of DNN training is critical to optimize the device memory pressures. In this work, we pinpoint the memory behaviors of each device memory block of GPU during training by instrumenting the memory allocators of the runtime system. Our results show that the memory access patterns of device memory blocks are stable and follow an iterative fashion. These observations are useful for the future optimization of memory-efficient training from the perspective of raw memory access patterns.

Guangli Li, Xiu Ma, Xueying Wang et al.

The increasing computational cost of deep neural network models limits the applicability of intelligent applications on resource-constrained edge devices. While a number of neural network pruning methods have been proposed to compress the models, prevailing approaches focus only on parametric operators (e.g., convolution), which may miss optimization opportunities. In this paper, we present a novel fusion-catalyzed pruning approach, called FuPruner, which simultaneously optimizes the parametric and non-parametric operators for accelerating neural networks. We introduce an aggressive fusion method to equivalently transform a model, which extends the optimization space of pruning and enables non-parametric operators to be pruned in a similar manner as parametric operators, and a dynamic filter pruning method is applied to decrease the computational cost of models while retaining the accuracy requirement. Moreover, FuPruner provides configurable optimization options for controlling fusion and pruning, allowing much more flexible performance-accuracy trade-offs to be made. Evaluation with state-of-the-art residual neural networks on five representative intelligent edge platforms, Jetson TX2, Jetson Nano, Edge TPU, NCS, and NCS2, demonstrates the effectiveness of our approach, which can accelerate the inference of models on CIFAR-10 and ImageNet datasets.

Guangli Li, Lei Liu, Xueying Wang et al.

Accelerating deep convolutional neural networks has become an active topic and sparked an interest in academia and industry. In this paper, we propose an efficient low-precision quantized Winograd convolution algorithm, called LANCE, which combines the advantages of fast convolution and quantization techniques. By embedding linear quantization operations into the Winograd-domain, the fast convolution can be performed efficiently under low-precision computation on graphics processing units. We test neural network models with LANCE on representative image classification datasets, including SVHN, CIFAR, and ImageNet. The experimental results show that our 8-bit quantized Winograd convolution improves the performance by up to 2.40x over the full-precision convolution with trivial accuracy loss.

Xueying Wang, Lei Liu, Guangli Li et al.

Background subtraction is a significant component of computer vision systems. It is widely used in video surveillance, object tracking, anomaly detection, etc. A new data source for background subtraction appeared as the emergence of low-cost depth sensors like Microsof t Kinect, Asus Xtion PRO, etc. In this paper, we propose a background subtraction approach on depth videos, which is based on convolutional neural networks (CNNs), called BGSNet-D (BackGround Subtraction neural Networks for Depth videos). The method can be used in color unavailable scenarios like poor lighting situations, and can also be applied to combine with existing RGB background subtraction methods. A preprocessing strategy is designed to reduce the influences incurred by noise from depth sensors. The experimental results on the SBM-RGBD dataset show that the proposed method outperforms existing methods on depth data.

Guangli Li, Lei Liu, Xueying Wang et al.

Recently, deep neural networks (DNNs) have been widely applied in mobile intelligent applications. The inference for the DNNs is usually performed in the cloud. However, it leads to a large overhead of transmitting data via wireless network. In this paper, we demonstrate the advantages of the cloud-edge collaborative inference with quantization. By analyzing the characteristics of layers in DNNs, an auto-tuning neural network quantization framework for collaborative inference is proposed. We study the effectiveness of mixed-precision collaborative inference of state-of-the-art DNNs by using ImageNet dataset. The experimental results show that our framework can generate reasonable network partitions and reduce the storage on mobile devices with trivial loss of accuracy.

Zibang Zhang, Xueying Wang, Jingang Zhong

Fourier single-pixel imaging (FSI) has proven capable of reconstructing high-quality two-dimensional and three-dimensional images. The utilization of the sparsity of natural images in Fourier domain allows high-resolution images to be reconstructed from far fewer measurements than effective image pixels. However, applying original FSI in digital micro-mirror device (DMD) based high-speed imaging system turns out to be challenging, because the original FSI uses grayscale Fourier basis patterns for illumination while DMDs generate grayscale patterns at a relatively low rate. DMDs are a binary device which can only generate a black-and-white pattern at each instance. In this paper, we adopt binary Fourier patterns for illumination to achieve DMD-based high-speed single-pixel imaging. Binary Fourier patterns are generated by upsampling and then applying error diffusion based dithering to the grayscale patterns. Experiments demonstrate the proposed technique able to achieve static imaging with high quality and dynamic imaging in real time. The proposed technique potentially allows high-quality and high-speed imaging over broad wavebands.