arXiv subjects

Sheng Xu

Publications and source records attributed to Sheng Xu.

At least 73 records · Page 4Linked to original sources

arXiv2025

Fitness aligned structural modeling enables scalable virtual screening with AuroBind

Most human proteins remain undrugged, over 96% of human proteins remain unexploited by approved therapeutics. While structure-based virtual screening promises to expand the druggable proteome, existing methods lack atomic-level precision and fail to predict binding fitness, limiting translational impact. We present AuroBind, a scalable virtual screening framework that fine-tunes a custom atomic-level structural model on million-scale chemogenomic data. AuroBind integrates direct preference optimization, self-distillation from high-confidence complexes, and a teacher-student acceleration strategy to jointly predict ligand-bound structures and binding fitness. The proposed models outperform state-of-the-art models on structural and functional benchmarks while enabling 100,000-fold faster screening across ultra-large compound libraries. In a prospective screen across ten disease-relevant targets, AuroBind achieved experimental hit rates of 7-69%, with top compounds reaching sub-nanomolar to picomolar potency. For the orphan GPCRs GPR151 and GPR160, AuroBind identified both agonists and antagonists with success rates of 16-30%, and functional assays confirmed GPR160 modulation in liver and prostate cancer models. AuroBind offers a generalizable framework for structure-function learning and high-throughput molecular screening, bridging the gap between structure prediction and therapeutic discovery.

cs.LG↗

arXiv2025

SDRNET: Stacked Deep Residual Network for Accurate Semantic Segmentation of Fine-Resolution Remotely Sensed Images

Land cover maps generated from semantic segmentation of high-resolution remotely sensed images have drawn mucon in the photogrammetry and remote sensing research community. Currently, massive fine-resolution remotely sensed (FRRS) images acquired by improving sensing and imaging technologies become available. However, accurate semantic segmentation of such FRRS images is greatly affected by substantial class disparities, the invisibility of key ground objects due to occlusion, and object size variation. Despite the extraordinary potential in deep convolutional neural networks (DCNNs) in image feature learning and representation, extracting sufficient features from FRRS images for accurate semantic segmentation is still challenging. These challenges demand the deep learning models to learn robust features and generate sufficient feature descriptors. Specifically, learning multi-contextual features to guarantee adequate coverage of varied object sizes from the ground scene and harnessing global-local contexts to overcome class disparities challenge even profound networks. Deeper networks significantly lose spatial details due to gradual downsampling processes resulting in poor segmentation results and coarse boundaries. This article presents a stacked deep residual network (SDRNet) for semantic segmentation from FRRS images. The proposed framework utilizes two stacked encoder-decoder networks to harness long-range semantics yet preserve spatial information and dilated residual blocks (DRB) between each encoder and decoder network to capture sufficient global dependencies thus improving segmentation performance. Our experimental results obtained using the ISPRS Vaihingen and Potsdam datasets demonstrate that the SDRNet performs effectively and competitively against current DCNNs in semantic segmentation.

cs.CV↗

arXiv2025

Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing

Peptide sequencing-the process of identifying amino acid sequences from mass spectrometry data-is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional methods. Unlike autoregressive models, which generate tokens sequentially, NATs predict all positions simultaneously, leveraging bidirectional context through unmasked self-attention. However, existing NAT approaches often rely on Connectionist Temporal Classification (CTC) loss, which presents significant optimization challenges due to CTC's complexity and increases the risk of training failures. To address these issues, we propose an improved non-autoregressive peptide sequencing model that incorporates a structured protein sequence curriculum learning strategy. This approach adjusts protein's learning difficulty based on the model's estimated protein generational capabilities through a sampling process, progressively learning peptide generation from simple to complex sequences. Additionally, we introduce a self-refining inference-time module that iteratively enhances predictions using learned NAT token embeddings, improving sequence accuracy at a fine-grained level. Our curriculum learning strategy reduces NAT training failures frequency by more than 90% based on sampled training over various data distributions. Evaluations on nine benchmark species demonstrate that our approach outperforms all previous methods across multiple metrics and species.

q-bio.BM↗

arXiv2025

MaskGaussian: Adaptive 3D Gaussian Representation from Probabilistic Masks

While 3D Gaussian Splatting (3DGS) has demonstrated remarkable performance in novel view synthesis and real-time rendering, the high memory consumption due to the use of millions of Gaussians limits its practicality. To mitigate this issue, improvements have been made by pruning unnecessary Gaussians, either through a hand-crafted criterion or by using learned masks. However, these methods deterministically remove Gaussians based on a snapshot of the pruning moment, leading to sub-optimized reconstruction performance from a long-term perspective. To address this issue, we introduce MaskGaussian, which models Gaussians as probabilistic entities rather than permanently removing them, and utilize them according to their probability of existence. To achieve this, we propose a masked-rasterization technique that enables unused yet probabilistically existing Gaussians to receive gradients, allowing for dynamic assessment of their contribution to the evolving scene and adjustment of their probability of existence. Hence, the importance of Gaussians iteratively changes and the pruned Gaussians are selected diversely. Extensive experiments demonstrate the superiority of the proposed method in achieving better rendering quality with fewer Gaussians than previous pruning methods, pruning over 60% of Gaussians on average with only a 0.02 PSNR decline. Our code can be found at: https://github.com/kaikai23/MaskGaussian

cs.CV↗

arXiv2025

OmniTalker: One-shot Real-time Text-Driven Talking Audio-Video Generation With Multimodal Style Mimicking

Although significant progress has been made in audio-driven talking head generation, text-driven methods remain underexplored. In this work, we present OmniTalker, a unified framework that jointly generates synchronized talking audio-video content from input text while emulating the speaking and facial movement styles of the target identity, including speech characteristics, head motion, and facial dynamics. Our framework adopts a dual-branch diffusion transformer (DiT) architecture, with one branch dedicated to audio generation and the other to video synthesis. At the shallow layers, cross-modal fusion modules are introduced to integrate information between the two modalities. In deeper layers, each modality is processed independently, with the generated audio decoded by a vocoder and the video rendered using a GAN-based high-quality visual renderer. Leveraging the in-context learning capability of DiT through a masked-infilling strategy, our model can simultaneously capture both audio and visual styles without requiring explicit style extraction modules. Thanks to the efficiency of the DiT backbone and the optimized visual renderer, OmniTalker achieves real-time inference at 25 FPS. To the best of our knowledge, OmniTalker is the first one-shot framework capable of jointly modeling speech and facial styles in real time. Extensive experiments demonstrate its superiority over existing methods in terms of generation quality, particularly in preserving style consistency and ensuring precise audio-video synchronization, all while maintaining efficient inference.

cs.CV↗

arXiv2025

Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing

De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the first deep reranking framework that enhances de novo peptide sequencing by leveraging the complementary strengths of multiple sequencing models. RankNovo employs a list-wise reranking approach, modeling candidate peptides as multiple sequence alignments and utilizing axial attention to extract informative features across candidates. Additionally, we introduce two new metrics, PMD (Peptide Mass Deviation) and RMD (residual Mass Deviation), which offer delicate supervision by quantifying mass differences between peptides at both the sequence and residue levels. Extensive experiments demonstrate that RankNovo not only surpasses its base models used to generate training candidates for reranking pre-training, but also sets a new state-of-the-art benchmark. Moreover, RankNovo exhibits strong zero-shot generalization to unseen models whose generations were not exposed during training, highlighting its robustness and potential as a universal reranking framework for peptide sequencing. Our work presents a novel reranking strategy that fundamentally challenges existing single-model paradigms and advances the frontier of accurate de novo sequencing. Our source code is provided on GitHub.

cs.LG↗

arXiv2025

On the Performance Analysis of Momentum Method: A Frequency Domain Perspective

Momentum-based optimizers are widely adopted for training neural networks. However, the optimal selection of momentum coefficients remains elusive. This uncertainty impedes a clear understanding of the role of momentum in stochastic gradient methods. In this paper, we present a frequency domain analysis framework that interprets the momentum method as a time-variant filter for gradients, where adjustments to momentum coefficients modify the filter characteristics. Our experiments support this perspective and provide a deeper understanding of the mechanism involved. Moreover, our analysis reveals the following significant findings: high-frequency gradient components are undesired in the late stages of training; preserving the original gradient in the early stages, and gradually amplifying low-frequency gradient components during training both enhance performance. Based on these insights, we propose Frequency Stochastic Gradient Descent with Momentum (FSGDM), a heuristic optimizer that dynamically adjusts the momentum filtering characteristic with an empirically effective dynamic magnitude response. Experimental results demonstrate the superiority of FSGDM over conventional momentum optimizers.

cs.LG↗

arXiv2025

JANC: A cost-effective, differentiable compressible reacting flow solver featured with JAX-based adaptive mesh refinement

The compressible reacting flow numerical solver is an essential tool in the study of combustion, energy disciplines, as well as in the design of industrial power and propulsion devices. We have established the first JAX-based block-structured adaptive mesh refinement (AMR) framework, called JAX-AMR, and then developed a fully-differentiable solver for compressible reacting flows, named JANC. JANC is implemented in Python and features automatic differentiation capabilities, enabling an efficient integration of the solver with machine learning. Furthermore, benefited by multiple acceleration features such as XLA-powered JIT compilation, GPU/TPU computing, parallel computing, and AMR, the computational efficiency of JANC has been significantly improved. In a comparative test of a two-dimensional detonation tube case, the computational cost of the JANC core solver, running on a single A100 GPU, was reduced to 1% of that of OpenFOAM, which was parallelized across 384 CPU cores. When the AMR method is enabled for both solvers, JANC's computational cost can be reduced to 1-2% of that of OpenFOAM. The core solver of JANC has also been tested for parallel computation on a 4-card A100 setup, demonstrating its convenient and efficient parallel computing capability. JANC also shows strong compatibility with machine learning by combining adjoint optimization to make the whole dynamic trajectory efficiently differentiable. JANC provides a new generation of high-performance, cost-effective, and high-precision solver framework for large-scale numerical simulations of compressible reacting flows and related machine learning research. Now, the source codes have been available under the MIT license at https://github.com/JA4S/JAX-AMR and https://github.com/JA4S/JANC.

physics.flu-dyn↗

arXiv2025

Optimal Sensor Placement Using Combinations of Hybrid Measurements for Source Localization

This paper focuses on static source localization employing different combinations of measurements, including time-difference-of-arrival (TDOA), received-signal-strength (RSS), angle-of-arrival (AOA), and time-of-arrival (TOA) measurements. Since sensor-source geometry significantly impacts localization accuracy, the strategies of optimal sensor placement are proposed systematically using combinations of hybrid measurements. Firstly, the relationship between sensor placement and source estimation accuracy is formulated by a derived Cramér-Rao bound (CRB). Secondly, the A-optimality criterion, i.e., minimizing the trace of the CRB, is selected to calculate the smallest reachable estimation mean-squared-error (MSE) in a unified manner. Thirdly, the optimal sensor placement strategies are developed to achieve the optimal estimation bound. Specifically, the specific constraints of the optimal geometries deduced by specific measurement, i.e., TDOA, AOA, RSS, and TOA, are found and discussed theoretically. Finally, the new findings are verified by simulation studies.

eess.SP↗

arXiv2025

ChatAnyone: Stylized Real-time Portrait Video Generation with Hierarchical Motion Diffusion Model

Real-time interactive video-chat portraits have been increasingly recognized as the future trend, particularly due to the remarkable progress made in text and voice chat technologies. However, existing methods primarily focus on real-time generation of head movements, but struggle to produce synchronized body motions that match these head actions. Additionally, achieving fine-grained control over the speaking style and nuances of facial expressions remains a challenge. To address these limitations, we introduce a novel framework for stylized real-time portrait video generation, enabling expressive and flexible video chat that extends from talking head to upper-body interaction. Our approach consists of the following two stages. The first stage involves efficient hierarchical motion diffusion models, that take both explicit and implicit motion representations into account based on audio inputs, which can generate a diverse range of facial expressions with stylistic control and synchronization between head and body movements. The second stage aims to generate portrait video featuring upper-body movements, including hand gestures. We inject explicit hand control signals into the generator to produce more detailed hand movements, and further perform face refinement to enhance the overall realism and expressiveness of the portrait video. Additionally, our approach supports efficient and continuous generation of upper-body portrait video in maximum 512 * 768 resolution at up to 30fps on 4090 GPU, supporting interactive video-chat in real-time. Experimental results demonstrate the capability of our approach to produce portrait videos with rich expressiveness and natural upper-body movements.

cs.CV↗

arXiv2025

pFedLVM: A Large Vision Model (LVM)-Driven and Latent Feature-Based Personalized Federated Learning Framework in Autonomous Driving

Deep learning-based Autonomous Driving (AD) models often exhibit poor generalization due to data heterogeneity in an ever domain-shifting environment. While Federated Learning (FL) could improve the generalization of an AD model (known as FedAD system), conventional models often struggle with under-fitting as the amount of accumulated training data progressively increases. To address this issue, instead of conventional small models, employing Large Vision Models (LVMs) in FedAD is a viable option for better learning of representations from a vast volume of data. However, implementing LVMs in FedAD introduces three challenges: (I) the extremely high communication overheads associated with transmitting LVMs between participating vehicles and a central server; (II) lack of computing resource to deploy LVMs on each vehicle; (III) the performance drop due to LVM focusing on shared features but overlooking local vehicle characteristics. To overcome these challenges, we propose pFedLVM, a LVM-Driven, Latent Feature-Based Personalized Federated Learning framework. In this approach, the LVM is deployed only on central server, which effectively alleviates the computational burden on individual vehicles. Furthermore, the exchange between central server and vehicles are the learned features rather than the LVM parameters, which significantly reduces communication overhead. In addition, we utilize both shared features from all participating vehicles and individual characteristics from each vehicle to establish a personalized learning mechanism. This enables each vehicle's model to learn features from others while preserving its personalized characteristics, thereby outperforming globally shared models trained in general FL. Extensive experiments demonstrate that pFedLVM outperforms the existing state-of-the-art approaches.

cs.RO↗

arXiv2025

Extremely large magnetoresistance and chiral anomaly in the nodal-line semimetal ZrAs2

We performed the detailed magnetotransport measurements and first principle calculations to study the electronic properties of the transition metal dipnictides ZrAs2, which is a topological nodal-line semimetal. Extremely large unsaturated magnetoresistance (MR) which is up to 1.9 * 10^4 % at 2 K and 14 T was observed with magnetic field along the c-axis. The nonlinear magnetic field dependence of Hall resistivity indicates the multi-band features, and the electron and hole are nearly compensated according to the analysis of the two-band model, which may account for the extremely large unsaturated MR at low temperatures. The evident Shubnikov-de Haas (SdH) oscillations at low temperatures are observed and four distinct oscillation frequencies are extracted. The first principle calculations and angle-dependent SdH oscillations reveal that the Fermi surface consists of three pockets with different anisotropy. The observed twofold symmetry MR with electric field along the b-axis direction is consistent with our calculated Fermi surface structures. Furthermore, the negative magnetoresistance (NMR) with magnetic field in parallel with electric field is observed, which is an evident feature of the chiral anomaly.

cond-mat.mtrl-sci↗

arXiv2025

Multi-directional Backlighting Compressive Light Field Displays

We propose a compressive light field display of a wide viewing angle with a multi-directional backlight. Displayed layer images of sub-viewing zones are synchronized with the multi-directional backlight. Viewers can perceive a three-dimensional scene with a large viewing angle based on the persistence of vision.

physics.optics↗

arXiv2025

A Comprehensive Survey on Inverse Constrained Reinforcement Learning: Definitions, Progress and Challenges

Inverse Constrained Reinforcement Learning (ICRL) is the task of inferring the implicit constraints that expert agents adhere to, based on their demonstration data. As an emerging research topic, ICRL has received considerable attention in recent years. This article presents a categorical survey of the latest advances in ICRL. It serves as a comprehensive reference for machine learning researchers and practitioners, as well as starters seeking to comprehend the definitions, advancements, and important challenges in ICRL. We begin by formally defining the problem and outlining the algorithmic framework that facilitates constraint inference across various scenarios. These include deterministic or stochastic environments, environments with limited demonstrations, and multiple agents. For each context, we illustrate the critical challenges and introduce a series of fundamental methods to tackle these issues. This survey encompasses discrete, virtual, and realistic environments for evaluating ICRL agents. We also delve into the most pertinent applications of ICRL, such as autonomous driving, robot control, and sports analytics. To stimulate continuing research, we conclude the survey with a discussion of key unresolved questions in ICRL that can effectively foster a bridge between theoretical understanding and practical industrial applications. The papers referenced in this survey can be found at https://github.com/Jasonxu1225/Awesome-Constraint-Inference-in-RL.

cs.LG↗

arXiv2025

Giant Anomalous Hall Effect in Kagome Nodal Surface Semimetal Fe$_3$Ge

It is well known that the intrinsic anomalous Hall effect (AHE) arises from the integration of the non-zero Berry curvature (BC), conventionally observed in the Dirac/Weyl and nodal-line semimetals. Moreover, nodal surface semimetals are expected to exhibit more significant BC under the prevalence of degenerate points near the Fermi level. In this work, we report the detection of a giant AHE in the Kagome magnet Fe$_3$Ge with a two-dimensional (2D) nodal surface (NS) at $k_{z}=π$ plane, exhibiting an anomalous Hall conductivity (AHC) of 1500 $Ω^{-1}$cm$^{-1}$ at 160 K, the highest among all reported Kagome topological materials. This finding suggests a new platform for searching large AHC materials and facilitates potential room-temperature applications in spintronic devices and quantum computing.

cond-mat.mes-hall↗

arXiv2025

Generative AI in Education: From Foundational Insights to the Socratic Playground for Learning

This paper explores the synergy between human cognition and Large Language Models (LLMs), highlighting how generative AI can drive personalized learning at scale. We discuss parallels between LLMs and human cognition, emphasizing both the promise and new perspectives on integrating AI systems into education. After examining challenges in aligning technology with pedagogy, we review AutoTutor-one of the earliest Intelligent Tutoring Systems (ITS)-and detail its successes, limitations, and unfulfilled aspirations. We then introduce the Socratic Playground, a next-generation ITS that uses advanced transformer-based models to overcome AutoTutor's constraints and provide personalized, adaptive tutoring. To illustrate its evolving capabilities, we present a JSON-based tutoring prompt that systematically guides learner reflection while tracking misconceptions. Throughout, we underscore the importance of placing pedagogy at the forefront, ensuring that technology's power is harnessed to enhance teaching and learning rather than overshadow it.

cs.AI↗

arXiv2024

Spectral Convolutional Neural Network Chip for In-sensor Edge Computing of Incoherent Natural Light

Convolutional neural networks (CNNs) are representative models of artificial neural networks (ANNs). However, the considerable power consumption and limited computing speed of electrical computing platforms restrict further CNN development on edge devices. Optical neural networks are considered next-generation physical implementations of ANNs, but their capabilities are limited by on-chip integration scale and requirement for coherent light sources. This study proposes a spectral convolutional neural network (SCNN) of incoherent natural light by an optical convolutional layer (OCL) and a reconfigurable electrical backend. The OCL is implemented by integrating very large-scale, pixel-aligned spectral filters on a CMOS image sensor on a 12-inch wafer, facilitating highly parallel spectral vector-inner products of incident light. It accepts broadband incoherent natural light containing two spatial and one spectral dimension directly as input with the function of matter meta-imaging. This unique optoelectronic framework empowers in-sensor optical analog computing at extremely high energy efficiency because the OCL is driven by the energy of the information carrier, i. e. natural light. To the best of our knowledge, this is the first integrated optical computing utilizing natural light. We employ the same SCNN chip for completely different real-world complex tasks,and achieve accuracies of over 96% for pathological diagnosis and almost 100% for face anti-spoofing at video rates. The SCNN framework has an unprecedented new function of substance identification, provides a feasible optoelectronic and integrated optical CNN implementation for edge devices or cellphones, providing them with practical and powerful edge computing abilities and facilitating diverse applications, such as intelligent robotics, industrial automation, medical diagnosis, and remote sensing.

physics.optics↗

arXiv2024

BEACON: Benchmark for Comprehensive RNA Tasks and Language Models

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (\textbf{BE}nchm\textbf{A}rk for \textbf{CO}mprehensive R\textbf{N}A Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

q-bio.QM↗