arXiv subjects

Yunfan Liu

Publications and source records attributed to Yunfan Liu.

At least 19 recordsLinked to original sources

arXiv2026

Antineutron reconstruction in electromagnetic calorimeters with mixed-representation learning

A long-standing bottleneck in GeV-scale accelerator experiments lies in reconstructing long-lived neutral hadrons in conventional electromagnetic calorimeters (ECALs), where hadron--nucleus interactions fall outside the detector's native response regime. In this paper, we develop a physics-inspired representation approach for antineutron reconstruction using a large corpus of real collision data. Motivated by two distinct energy deposition patterns from the penetrating high energy antineutrons in ECALs, we propose a Mixed-representation Calorimetric Network (MrCAL) that integrates complementary visual and sequential representation branches within a unified object-detection architecture. This architecture jointly predicts particle identity, momentum direction, and momentum magnitude. Our approach improves the precision of antineutron momentum-direction reconstruction by up to 96% and, for the first time, enables direct measurement of momentum magnitude solely from ECAL readouts, achieving a momentum resolution of approximately 17% at 1 GeV/c. The model maintains robust performance through comprehensive generalization tests spanning a wide variety of physics processes and background environments. This work unlocks a novel measurement capability for legacy ECAL systems at large experimental facilities, broadening their scientific scope via innovative final-state neutral-hadron detection.

hep-ex↗

arXiv2026

Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation

Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficiency. However, single-cell sequencing is a destructive process, making it impossible to capture the same cell's phenotype before and after perturbation. Consequently, data collected under perturbed and unperturbed conditions are inherently unpaired, creating a critical yet unresolved problem in single-cell perturbation modeling. Moreover, the high dimensionality and sparsity of single-cell expression make direct modeling prone to focusing on zeros and neglecting meaningful patterns. To address these problems, we propose a new paradigm for single-cell perturbation modeling. Specifically, we leverage dual diffusion models to learn the control and perturbed distributions separately, and implicitly align them through a shared Gaussian latent space, without requiring explicit cell pairing. Furthermore, we introduce a sparsity masking strategy in which the mask model learns to predict zero-expressed genes, allowing the diffusion model to focus on capturing meaningful patterns among expressed genes and thereby preserving diversity in high-dimensional sparse data. We introduce \textbf{Doloris}, a generative framework that defines a new paradigm for modeling unpaired, high-dimensional, and sparse single-cell perturbation data. It leverages dual conditional diffusion models for separate learning of control and perturbed distributions, complemented by a sparsity masking strategy to enhance prediction of zero-valued genes. The results on publicly available datasets show that our model effectively captures the diversity of single-cell perturbations and achieves state-of-the-art performance. To facilitate reproducibility, we include the code in the supplementary materials.

cs.LG↗

arXiv2026

SkeletonAgent: An Agentic Interaction Framework for Skeleton-based Action Recognition

Recent advances in skeleton-based action recognition increasingly leverage semantic priors from Large Language Models (LLMs) to enrich skeletal representations. However, the LLM is typically queried in isolation from the recognition model and receives no performance feedback. As a result, it often fails to deliver the targeted discriminative cues critical to distinguish similar actions. To overcome these limitations, we propose SkeletonAgent, a novel framework that bridges the recognition model and the LLM through two cooperative agents, i.e., Questioner and Selector. Specifically, the Questioner identifies the most frequently confused classes and supplies them to the LLM as context for more targeted guidance. Conversely, the Selector parses the LLM's response to extract precise joint-level constraints and feeds them back to the recognizer, enabling finer-grained cross-modal alignment. Comprehensive evaluations on five benchmarks, including NTU RGB+D, NTU RGB+D 120, Kinetics-Skeleton, FineGYM, and UAV-Human, demonstrate that SkeletonAgent consistently outperforms state-of-the-art benchmark methods. The code is available at https://github.com/firework8/SkeletonAgent.

cs.CV↗

arXiv2026

Affinity Contrastive Learning for Skeleton-based Human Activity Understanding

In skeleton-based human activity understanding, existing methods often adopt the contrastive learning paradigm to construct a discriminative feature space. However, many of these approaches fail to exploit the structural inter-class similarities and overlook the impact of anomalous positive samples. In this study, we introduce ACLNet, an Affinity Contrastive Learning Network that explores the intricate clustering relationships among human activity classes to improve feature discrimination. Specifically, we propose an affinity metric to refine similarity measurements, thereby forming activity superclasses that provide more informative contrastive signals. A dynamic temperature schedule is also introduced to adaptively adjust the penalty strength for various superclasses. In addition, we employ a margin-based contrastive strategy to improve the separation of hard positive and negative samples within classes. Extensive experiments on NTU RGB+D 60, NTU RGB+D 120, Kinetics-Skeleton, PKU-MMD, FineGYM, and CASIA-B demonstrate the superiority of our method in skeleton-based action recognition, gait recognition, and person re-identification. The source code is available at https://github.com/firework8/ACLNet.

cs.CV↗

arXiv2026

VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention

Graph Transformer has demonstrated impressive capabilities in the field of graph representation learning. However, existing approaches face two critical challenges: (1) most models suffer from exponentially increasing computational complexity, making it difficult to scale to large graphs; (2) attention mechanisms based on node-level operations limit the flexibility of the model and result in poor generalization performance in out-of-distribution (OOD) scenarios. To address these issues, we propose \textbf{VecFormer} (the \textbf{Vec}tor Quantized Graph Trans\textbf{former}), an efficient and highly generalizable model for node classification, particularly under OOD settings. VecFormer adopts a two-stage training paradigm. In the first stage, two codebooks are used to reconstruct the node features and the graph structure, aiming to learn the rich semantic \texttt{Graph Codes}. In the second stage, attention mechanisms are performed at the \texttt{Graph Token} level based on the transformed cross codebook, reducing computational complexity while enhancing the model's generalization capability. Extensive experiments on datasets of various sizes demonstrate that VecFormer outperforms the existing Graph Transformer in both performance and speed.

cs.LG↗

arXiv2026

Balancing Understanding and Generation in Discrete Diffusion Models

In discrete generative modeling, two dominant paradigms demonstrate divergent capabilities: Masked Diffusion Language Models (MDLM) excel at semantic understanding and zero-shot generalization, whereas Uniform-noise Diffusion Language Models (UDLM) achieve strong few-step generation quality, yet neither attains balanced performance across both dimensions. To address this, we propose XDLM, which bridges the two paradigms via a stationary noise kernel. XDLM offers two key contributions: (1) it provides a principled theoretical unification of MDLM and UDLM, recovering each paradigm as a special case; and (2) an alleviated memory bottleneck enabled by an algebraic simplification of the posterior probabilities. Experiments demonstrate that XDLM advances the Pareto frontier between understanding capability and generation quality. Quantitatively, XDLM surpasses UDLM by 5.4 points on zero-shot text benchmarks and outperforms MDLM in few-step image generation (FID 54.1 vs. 80.8). When scaled to tune an 8B-parameter large language model, XDLM achieves 15.0 MBPP in just 32 steps, effectively doubling the baseline performance. Finally, analysis of training dynamics reveals XDLM's superior potential for long-term scaling. Code is available at https://github.com/MzeroMiko/XDLM

cs.CL↗

arXiv2026

Vision Calorimeter for Anti-neutron Reconstruction: A Baseline

In high-energy physics, anti-neutrons ($\bar{n}$) are fundamental particles that frequently appear as final-state particles, and the reconstruction of their kinematic properties provides an important probe for understanding the governing principles. However, this confronts significant challenges instrumentally with the electromagnetic calorimeter (EMC), a typical experimental sensor but recovering the information of incident $\bar{n}$ insufficiently. In this study, we introduce Vision Calorimeter (ViC), a baseline method for anti-neutron reconstruction that leverages deep learning detectors to analyze the implicit relationships between EMC responses and incident $\bar{n}$ characteristics. Our motivation lies in that energy distributions of $\bar{n}$ samples deposited in the EMC cell arrays embody rich contextual information. Converted to 2-D images, such contextual energy distributions can be used to predict the status of $\bar{n}$ ($i.e.$, incident position and momentum) through a deep learning detector along with pseudo bounding boxes and a specified training objective. Experimental results demonstrate that ViC substantially outperforms the conventional reconstruction approach, reducing the prediction error of incident position by 42.81% (from 17.31$^{\circ}$ to 9.90$^{\circ}$). More importantly, this study for the first time realizes the measurement of incident $\bar{n}$ momentum, underscoring the potential of deep learning detectors for particle reconstruction. Code is available at https://github.com/yuhongtian17/ViC.

hep-ex↗

arXiv2026

Vision Calorimeter for High-Energy Particle Detection

In high-energy physics, estimating anti-neutron parameters (position and momentum) using the electromagnetic calorimeter (EMC) is crucial but challenging. To conquer this challenge, we propose Vision Calorimeter (ViC), a framework that migrates visual object detectors to analyze particle images. The motivation lies in introducing a physics-inspired heat-conduction operator (HCO) into the detector's backbone and head to handle the discrete and sparse patterns of these images. Implemented via the Discrete Cosine Transform, HCO extracts frequency-domain features, bridging the distribution gap between natural and particle images. Experiments demonstrate that ViC significantly outperforms conventional methods, reducing the incident position prediction error by 46.16% (from 17.31° to 9.32°) and providing the first baseline result with an incident momentum regression error of 21.48%. This study underscores ViC's great potential as a reliable particle detector for high-energy physics. Code is available at https://github.com/yuhongtian17/ViC.

hep-ex↗

arXiv2025

Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schrödinger Bridges

Predicting single-cell perturbation outcomes directly advances gene function analysis and facilitates drug candidate selection, making it a key driver of both basic and translational biomedical research. However, a major bottleneck in this task is the unpaired nature of single-cell data, as the same cell cannot be observed both before and after perturbation due to the destructive nature of sequencing. Although some neural generative transport models attempt to tackle unpaired single-cell perturbation data, they either lack explicit conditioning or depend on prior spaces for indirect distribution alignment, limiting precise perturbation modeling. In this work, we approximate Schrödinger Bridge (SB), which defines stochastic dynamic mappings recovering the entropy-regularized optimal transport (OT), to directly align the distributions of control and perturbed single-cell populations across different perturbation conditions. Unlike prior SB approximations that rely on bidirectional modeling to infer optimal source-target sample coupling, we leverage Minibatch-OT based pairing to avoid such bidirectional inference and the associated ill-posedness of defining the reverse process. This pairing directly guides bridge learning, yielding a scalable approximation to the SB. We approximate two SB models, one modeling discrete gene activation states and the other continuous expression distributions. Joint training enables accurate perturbation modeling and captures single-cell heterogeneity. Experiments on public genetic and drug perturbation datasets show that our model effectively captures heterogeneous single-cell responses and achieves state-of-the-art performance.

cs.LG↗

arXiv2025

Expandable Residual Approximation for Knowledge Distillation

Knowledge distillation (KD) aims to transfer knowledge from a large-scale teacher model to a lightweight one, significantly reducing computational and storage requirements. However, the inherent learning capacity gap between the teacher and student often hinders the sufficient transfer of knowledge, motivating numerous studies to address this challenge. Inspired by the progressive approximation principle in the Stone-Weierstrass theorem, we propose Expandable Residual Approximation (ERA), a novel KD method that decomposes the approximation of residual knowledge into multiple steps, reducing the difficulty of mimicking the teacher's representation through a divide-and-conquer approach. Specifically, ERA employs a Multi-Branched Residual Network (MBRNet) to implement this residual knowledge decomposition. Additionally, a Teacher Weight Integration (TWI) strategy is introduced to mitigate the capacity disparity by reusing the teacher's head weights. Extensive experiments show that ERA improves the Top-1 accuracy on the ImageNet classification benchmark by 1.41% and the AP on the MS COCO object detection benchmark by 1.40, as well as achieving leading performance across computer vision tasks. Codes and models are available at https://github.com/Zhaoyi-Yan/ERA.

cs.CV↗

arXiv2025

Tokenizing Electron Cloud in Protein-Ligand Interaction Learning

The affinity and specificity of protein-molecule binding directly impact functional outcomes, uncovering the mechanisms underlying biological regulation and signal transduction. Most deep-learning-based prediction approaches focus on structures of atoms or fragments. However, quantum chemical properties, such as electronic structures, are the key to unveiling interaction patterns but remain largely underexplored. To bridge this gap, we propose ECBind, a method for tokenizing electron cloud signals into quantized embeddings, enabling their integration into downstream tasks such as binding affinity prediction. By incorporating electron densities, ECBind helps uncover binding modes that cannot be fully represented by atom-level models. Specifically, to remove the redundancy inherent in electron cloud signals, a structure-aware transformer and hierarchical codebooks encode 3D binding sites enriched with electron structures into tokens. These tokenized codes are then used for specific tasks with labels. To extend its applicability to a wider range of scenarios, we utilize knowledge distillation to develop an electron-cloud-agnostic prediction model. Experimentally, ECBind demonstrates state-of-the-art performance across multiple tasks, achieving improvements of 6.42\% and 15.58\% in per-structure Pearson and Spearman correlation coefficients, respectively.

cs.LG↗

arXiv2025

Building Vision Models upon Heat Conduction

Visual representation models leveraging attention mechanisms are challenged by significant computational overhead, particularly when pursuing large receptive fields. In this study, we aim to mitigate this challenge by introducing the Heat Conduction Operator (HCO) built upon the physical heat conduction principle. HCO conceptualizes image patches as heat sources and models their correlations through adaptive thermal energy diffusion, enabling robust visual representations. HCO enjoys a computational complexity of O(N^1.5), as it can be implemented using discrete cosine transformation (DCT) operations. HCO is plug-and-play, combining with deep learning backbones produces visual representation models (termed vHeat) with global receptive fields. Experiments across vision tasks demonstrate that, beyond the stronger performance, vHeat achieves up to a 3x throughput, 80% less GPU memory allocation, and 35% fewer computational FLOPs compared to the Swin-Transformer. Code is available at https://github.com/MzeroMiko/vHeat.

cs.CV↗

arXiv2025

Revealing Key Details to See Differences: A Novel Prototypical Perspective for Skeleton-based Action Recognition

In skeleton-based action recognition, a key challenge is distinguishing between actions with similar trajectories of joints due to the lack of image-level details in skeletal representations. Recognizing that the differentiation of similar actions relies on subtle motion details in specific body parts, we direct our approach to focus on the fine-grained motion of local skeleton components. To this end, we introduce ProtoGCN, a Graph Convolutional Network (GCN)-based model that breaks down the dynamics of entire skeleton sequences into a combination of learnable prototypes representing core motion patterns of action units. By contrasting the reconstruction of prototypes, ProtoGCN can effectively identify and enhance the discriminative representation of similar actions. Without bells and whistles, ProtoGCN achieves state-of-the-art performance on multiple benchmark datasets, including NTU RGB+D, NTU RGB+D 120, Kinetics-Skeleton, and FineGYM, which demonstrates the effectiveness of the proposed method. The code is available at https://github.com/firework8/ProtoGCN.

cs.CV↗

arXiv2025

CC-Diff: Enhancing Contextual Coherence in Remote Sensing Image Synthesis

Existing image synthesis methods for natural scenes focus primarily on foreground control, often reducing the background to simplistic textures. Consequently, these approaches tend to overlook the intrinsic correlation between foreground and background, which may lead to incoherent and unrealistic synthesis results in remote sensing (RS) scenarios. In this paper, we introduce CC-Diff, a $\underline{\textbf{Diff}}$usion Model-based approach for RS image generation with enhanced $\underline{\textbf{C}}$ontext $\underline{\textbf{C}}$oherence. Specifically, we propose a novel Dual Re-sampler for feature extraction, with a built-in `Context Bridge' to explicitly capture the intricate interdependency between foreground and background. Moreover, we reinforce their connection by employing a foreground-aware attention mechanism during the generation of background features, thereby enhancing the plausibility of the synthesized context. Extensive experiments show that CC-Diff outperforms state-of-the-art methods across critical quality metrics, excelling in the RS domain and effectively generalizing to natural images. Remarkably, CC-Diff also shows high trainability, boosting detection accuracy by 1.83 mAP on DOTA and 2.25 mAP on the COCO benchmark.

cs.CV↗

arXiv2025

A Simple yet Effective DDG Predictor is An Unsupervised Antibody Optimizer and Explainer

The proteins that exist today have been optimized over billions of years of natural evolution, during which nature creates random mutations and selects them. The discovery of functionally promising mutations is challenged by the limited evolutionary accessible regions, i.e., only a small region on the fitness landscape is beneficial. There have been numerous priors used to constrain protein evolution to regions of landscapes with high-fitness variants, among which the change in binding free energy (DDG) of protein complexes upon mutations is one of the most commonly used priors. However, the huge mutation space poses two challenges: (1) how to improve the efficiency of DDG prediction for fast mutation screening; and (2) how to explain mutation preferences and efficiently explore accessible evolutionary regions. To address these challenges, we propose a lightweight DDG predictor (Light-DDG), which adopts a structure-aware Transformer as the backbone and enhances it by knowledge distilled from existing powerful but computationally heavy DDG predictors. Additionally, we augmented, annotated, and released a large-scale dataset containing millions of mutation data for pre-training Light-DDG. We find that such a simple yet effective Light-DDG can serve as a good unsupervised antibody optimizer and explainer. For the target antibody, we propose a novel Mutation Explainer to learn mutation preferences, which accounts for the marginal benefit of each mutation per residue. To further explore accessible evolutionary regions, we conduct preference-guided antibody optimization and evaluate antibody candidates quickly using Light-DDG to identify desirable mutations.

q-bio.QM↗

arXiv2024

VMamba: Visual State Space Model

Designing computationally efficient network architectures remains an ongoing necessity in computer vision. In this paper, we adapt Mamba, a state-space language model, into VMamba, a vision backbone with linear time complexity. At the core of VMamba is a stack of Visual State-Space (VSS) blocks with the 2D Selective Scan (SS2D) module. By traversing along four scanning routes, SS2D bridges the gap between the ordered nature of 1D selective scan and the non-sequential structure of 2D vision data, which facilitates the collection of contextual information from various sources and perspectives. Based on the VSS blocks, we develop a family of VMamba architectures and accelerate them through a succession of architectural and implementation enhancements. Extensive experiments demonstrate VMamba's promising performance across diverse visual perception tasks, highlighting its superior input scaling efficiency compared to existing benchmark models. Source code is available at https://github.com/MzeroMiko/VMamba.

cs.CV↗

arXiv2024

Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization

Antibodies are Y-shaped proteins that protect the host by binding to specific antigens, and their binding is mainly determined by the Complementary Determining Regions (CDRs) in the antibody. Despite the great progress made in CDR design, existing computational methods still encounter several challenges: 1) poor capability of modeling complex CDRs with long sequences due to insufficient contextual information; 2) conditioned on pre-given antigenic epitopes and their static interaction with the target antibody; 3) neglect of specificity during antibody optimization leads to non-specific antibodies. In this paper, we take into account a variety of node features, edge features, and edge relations to include more contextual and geometric information. We propose a novel Relation-Aware Antibody Design (RAAD) framework, which dynamically models antigen-antibody interactions for co-designing the sequences and structures of antigen-specific CDRs. Furthermore, we propose a new evaluation metric to better measure antibody specificity and develop a contrasting specificity-enhancing constraint to optimize the specificity of antibodies. Extensive experiments have demonstrated the superior capability of RAAD in terms of antibody modeling, generation, and optimization across different CDR types, sequence lengths, pre-training strategies, and input contexts.

q-bio.QM↗

arXiv2024

Teach Harder, Learn Poorer: Rethinking Hard Sample Distillation for GNN-to-MLP Knowledge Distillation

To bridge the gaps between powerful Graph Neural Networks (GNNs) and lightweight Multi-Layer Perceptron (MLPs), GNN-to-MLP Knowledge Distillation (KD) proposes to distill knowledge from a well-trained teacher GNN into a student MLP. In this paper, we revisit the knowledge samples (nodes) in teacher GNNs from the perspective of hardness, and identify that hard sample distillation may be a major performance bottleneck of existing graph KD algorithms. The GNN-to-MLP KD involves two different types of hardness, one student-free knowledge hardness describing the inherent complexity of GNN knowledge, and the other student-dependent distillation hardness describing the difficulty of teacher-to-student distillation. However, most of the existing work focuses on only one of these aspects or regards them as one thing. This paper proposes a simple yet effective Hardness-aware GNN-to-MLP Distillation (HGMD) framework, which decouples the two hardnesses and estimates them using a non-parametric approach. Finally, two hardness-aware distillation schemes (i.e., HGMD-weight and HGMD-mixup) are further proposed to distill hardness-aware knowledge from teacher GNNs into the corresponding nodes of student MLPs. As non-parametric distillation, HGMD does not involve any additional learnable parameters beyond the student MLPs, but it still outperforms most of the state-of-the-art competitors. HGMD-mixup improves over the vanilla MLPs by 12.95% and outperforms its teacher GNNs by 2.48% averaged over seven real-world datasets.

cs.LG↗