Kun Xie

CV
h-index13
19papers
185citations
Novelty59%
AI Score61

19 Papers

AISep 29, 2022
Modeling driver's evasive behavior during safety-critical lane changes:Two-dimensional time-to-collision and deep reinforcement learning

Hongyu Guo, Kun Xie, Mehdi Keyvan-Ekbatani

Lane changes are complex driving behaviors and frequently involve safety-critical situations. This study aims to develop a lane-change-related evasive behavior model, which can facilitate the development of safety-aware traffic simulations and predictive collision avoidance systems. Large-scale connected vehicle data from the Safety Pilot Model Deployment (SPMD) program were used for this study. A new surrogate safety measure, two-dimensional time-to-collision (2D-TTC), was proposed to identify the safety-critical situations during lane changes. The validity of 2D-TTC was confirmed by showing a high correlation between the detected conflict risks and the archived crashes. A deep deterministic policy gradient (DDPG) algorithm, which could learn the sequential decision-making process over continuous action spaces, was used to model the evasive behaviors in the identified safety-critical situations. The results showed the superiority of the proposed model in replicating both the longitudinal and lateral evasive behaviors.

72.4CVMar 27Code
Seeing Like Radiologists: Context- and Gaze-Guided Vision-Language Pretraining for Chest X-rays

Kang Liu, Zhuoqi Ma, Siyu Liang et al.

Despite recent advances in medical vision-language pretraining, existing models still struggle to capture the diagnostic workflow: radiographs are typically treated as context-agnostic images, while radiologists' gaze -- a crucial cue for visual reasoning -- remains largely underexplored by existing methods. These limitations hinder the modeling of disease-specific patterns and weaken cross-modal alignment. To bridge this gap, we introduce CoGaze, a Context- and Gaze-guided vision-language pretraining framework for chest X-rays. We first propose a context-infused vision encoder that models how radiologists integrate clinical context -- including patient history, symptoms, and diagnostic intent -- to guide diagnostic reasoning. We then present a multi-level supervision paradigm that (1) enforces intra- and inter-modal semantic alignment through hybrid-positive contrastive learning, (2) injects diagnostic priors via disease-aware cross-modal representation learning, and (3) leverages radiologists' gaze as probabilistic priors to guide attention toward diagnostically salient regions. Extensive experiments demonstrate that CoGaze consistently outperforms state-of-the-art methods across diverse tasks, achieving up to +2.0% CheXbertF1 and +1.2% BLEU2 for free-text and structured report generation, +23.2% AUROC for zero-shot classification, and +12.2% Precision@1 for image-text retrieval. Code is available at https://github.com/mk-runner/CoGaze.

19.4AIMay 27
Modeling Vehicle-Type-Specific Pedestrian Crash Avoidance Behavior in Safety-Critical Interactions Using Smooth-Mamba Deep Reinforcement Learning

Qingwen Pu, Kun Xie, Hong Yang et al.

As automated vehicles (AVs) increasingly share roadways with human-driven vehicles (HDVs), understanding how pedestrians respond to different vehicle types in safety-critical interactions is essential for the safe deployment of automated driving technologies. This study extracts safety-critical pedestrian-vehicle interactions from the Argoverse 2 dataset to capture real-world crash avoidance behaviors in encounters involving AVs and HDVs. To model vehicle-type-specific pedestrian crash avoidance behavior, we develop a Smooth-Mamba Deep Deterministic Policy Gradient framework, termed SMamba-DDPG, which integrates smooth action constraints with efficient temporal representation learning. To quantify pedestrian behavioral differences, the framework trains separate crash avoidance policies for pedestrian interactions with AVs and HDVs. Results show that SMamba-DDPG outperforms baseline reinforcement learning and supervised learning models in reproducing pedestrian crash avoidance behaviors. Reconstructed trajectories demonstrate strong behavioral realism, accurately reproducing crash avoidance kinematics in both AV and HDV scenarios. Reaction time analysis shows that the model captures human-like response delays and reveals that pedestrians respond more quickly to AVs than to HDVs. Counterfactual analysis further indicates that pedestrians adopt lower crossing speeds when interacting with AVs. Large-scale safety analysis of model-generated data revealed that pedestrian-AV interactions consistently yielded lower conflict rates and higher pedestrian yielding rates compared to pedestrian-HDV interactions. The findings highlight the importance of incorporating vehicle-type-specific pedestrian behavioral models for safer automated driving system design and more realistic traffic simulations in mixed-traffic environments.

37.0CVApr 20
MEDN: Motion-Emotion Feature Decoupling Network for Micro-Expression Recognition

Chenxing Hu, Kun Xie, Qiguang Miao et al.

Unlike macro-expression, micro-expression does not follow a strictly consistent mapping rule between emotions and Action Units (AUs). As a result, some micro-expressions share identical AUs yet represent completely opposite emotional categories, making them highly visually similar. Existing microexpression recognition (MER) methods mostly rely on explicit facial motion cues (e.g., optical flow, frame differences, AU features) while ignoring implicit emotion information. To tackle this issue, this paper presents a Motion Emotion Feature Decoupling Network (MEDN) for MER. We design a dual-branch framework to separately extract motion and emotion features. In the motion branch, an AU-detection task restricts features to the explicit motion domain, and orthogonal loss is adopted to reduce motion emotion feature coupling. For implicit emotion modeling, we propose a Sparse Emotion Vision Transformer (SEVit) that sparsifies spatial tokens to highlight local temporal variations with multi-scale sparsity rates. A Collaborative Fusion Module (CoFM) is further developed to fuse disentangled motion and emotion features adaptively. Extensive experiments on three benchmark datasets validate that MEDN effectively decouples motion and emotion features and achieves superior recognition performance, offering a new perspective for enhancing recognition accuracy and generalization.

IVMay 15, 2024Code
Factual Serialization Enhancement: A Key Innovation for Chest X-ray Report Generation

Kang Liu, Zhuoqi Ma, Mengmeng Liu et al.

A radiology report comprises presentation-style vocabulary, which ensures clarity and organization, and factual vocabulary, which provides accurate and objective descriptions based on observable findings. While manually writing these reports is time-consuming and labor-intensive, automatic report generation offers a promising alternative. A critical step in this process is to align radiographs with their corresponding reports. However, existing methods often rely on complete reports for alignment, overlooking the impact of presentation-style vocabulary. To address this issue, we propose FSE, a two-stage Factual Serialization Enhancement method. In Stage 1, we introduce factuality-guided contrastive learning for visual representation by maximizing the semantic correspondence between radiographs and corresponding factual descriptions. In Stage 2, we present evidence-driven report generation that enhances diagnostic accuracy by integrating insights from similar historical cases structured as factual serialization. Experiments on MIMIC-CXR and IU X-ray datasets across specific and general scenarios demonstrate that FSE outperforms state-of-the-art approaches in both natural language generation and clinical efficacy metrics. Ablation studies further emphasize the positive effects of factual serialization in Stage 1 and Stage 2. The code is available at https://github.com/mk-runner/FSE.

50.5ROMay 17
Generating Realistic Safety-Critical Scenarios for Vehicle-Pedestrian Interactions

Qingwen Pu, Kun Xie, Yuan Zhu et al.

Automated driving system deployment requires rigorous validation across safety-critical vehicle-pedestrian interactions, yet real-world datasets rarely capture high-risk scenarios while simulation platforms lack realistic behavior. In response, this study proposes a three-stage framework that combines real-world grounding with adaptive simulation to generate behaviorally realistic safety-critical scenarios at scale. Stage 1 pre-trains multi-agent state-space Transformer-enhanced DDPG (MA-SST-DDPG) agents on real-world safety-critical data to learn human-like interactive evasive behaviors through data-driven learning. Stage 2 deploys pre-trained multi-agents in CARLA for online reinforcement learning to generalize across diverse scenarios, integrating real-world knowledge with simulation experience to produce a refined MA-SST-DDPG model. Stage 3 uses CARLA with the refined model to generate over 198,000 high-resolution interaction episodes from eight intersection scenarios, culminating in the Vehicle-Pedestrian Safety-Critical Interaction (VPSCI) dataset. The Refined MA-SST-DDPG model outperformed baseline methods in reproducing realistic evasive behaviors, achieving the lowest trajectory errors (ADE = 0.072 m, FDE = 0.142 m). Statistical comparison confirmed distributional equivalence between the generated and real-world data in both conflict severity and behavioral response. A Turing test confirmed that the three-stage framework generated evasive behaviors were indistinguishable from real-world interactions. These results demonstrate the framework's effectiveness in producing high-fidelity safety-critical data, offering valuable sources for the development of ADS and simulation-based safety evaluations.

CLJun 2, 2025Code
STORM-BORN: A Challenging Mathematical Derivations Dataset Curated via a Human-in-the-Loop Multi-Agent Framework

Wenhao Liu, Zhenyi Lu, Xinyu Hu et al.

High-quality math datasets are crucial for advancing the reasoning abilities of large language models (LLMs). However, existing datasets often suffer from three key issues: outdated and insufficient challenging content, neglecting human-like reasoning, and limited reliability due to single-LLM generation. To address these, we introduce STORM-BORN, an ultra-challenging dataset of mathematical derivations sourced from cutting-edge academic papers, which includes dense human-like approximations and heuristic cues. To ensure the reliability and quality, we propose a novel human-in-the-loop, multi-agent data generation framework, integrating reasoning-dense filters, multi-agent collaboration, and human mathematicians' evaluations. We curated a set of 2,000 synthetic samples and deliberately selected the 100 most difficult problems. Even most advanced models like GPT-o1 solved fewer than 5% of them. Fine-tuning on STORM-BORN boosts accuracy by 7.84% (LLaMA3-8B) and 9.12% (Qwen2.5-7B). As AI approaches mathematician-level reasoning, STORM-BORN provides both a high-difficulty benchmark and a human-like reasoning training resource. Our code and dataset are publicly available at https://github.com/lwhere/STORM-BORN.

69.3CYApr 28
TransResAI: A Compound AI System for Coastal Transportation Resilience

Qingwen Pu, Kun Xie, Chenyu Yan

Coastal flooding increasingly threatens transportation infrastructure, yet the analytical tools needed for resilience management remain difficult for many non-specialist practitioners to use. This study presents TransResAI, a compound AI system that supports analysis of flood-aware transportation resilience via natural-language interactions. The system integrates a locally deployable Large Language Model (LLM) with modules for task decomposition, secure code generation, geospatial analysis, retrieval-augmented generation, and interactive map rendering. TransResAI links MATSim flood-scenario simulation outputs, OpenStreetMap-derived flood-risk networks, equity-focused demographic indicators, and regional documents in Hampton Roads, Virginia. A structured user study with domain experts demonstrated that TransResAI reduced task completion time by 80-88% relative to conventional GIS workflows, compressing analytical tasks from a mean of 197.1 seconds to 29.7 seconds and visualization tasks from 364.0 seconds to 46.1 seconds, while maintaining mean accuracy of 4.60/5.00 and task completion rates exceeding 94%. These findings demonstrate that compound AI architectures bridge the gap between general-purpose language models and specialized domain knowledge, as well as the quantitative rigor required for infrastructure resilience, providing transportation agencies and communities with faster, more accessible analytical tools for decision-making under growing climate uncertainty.

AIJan 2
A Vision-and-Knowledge Enhanced Large Language Model for Generalizable Pedestrian Crossing Behavior Inference

Qingwen Pu, Kun Xie, Hong Yang et al.

Existing paradigms for inferring pedestrian crossing behavior, ranging from statistical models to supervised learning methods, demonstrate limited generalizability and perform inadequately on new sites. Recent advances in Large Language Models (LLMs) offer a shift from numerical pattern fitting to semantic, context-aware behavioral reasoning, yet existing LLM applications lack domain-specific adaptation and visual context. This study introduces Pedestrian Crossing LLM (PedX-LLM), a vision-and-knowledge enhanced framework designed to transform pedestrian crossing inference from site-specific pattern recognition to generalizable behavioral reasoning. By integrating LLaVA-extracted visual features with textual data and transportation domain knowledge, PedX-LLM fine-tunes a LLaMA-2-7B foundation model via Low-Rank Adaptation (LoRA) to infer crossing decisions. PedX-LLM achieves 82.0% balanced accuracy, outperforming the best statistical and supervised learning methods. Results demonstrate that the vision-augmented module contributes a 2.9% performance gain by capturing the built environment and integrating domain knowledge yields an additional 4.1% improvement. To evaluate generalizability across unseen environments, cross-site validation was conducted using site-based partitioning. The zero-shot PedX-LLM configuration achieves 66.9% balanced accuracy on five unseen test sites, outperforming the baseline data-driven methods by at least 18 percentage points. Incorporating just five validation examples via few-shot learning to PedX-LLM further elevates the balanced accuracy to 72.2%. PedX-LLM demonstrates strong generalizability to unseen scenarios, confirming that vision-and-knowledge-enhanced reasoning enables the model to mimic human-like decision logic and overcome the limitations of purely data-driven methods.

LGMay 25, 2025Code
Chi-Square Wavelet Graph Neural Networks for Heterogeneous Graph Anomaly Detection

Xiping Li, Xiangyu Dong, Xingyi Zhang et al.

Graph Anomaly Detection (GAD) in heterogeneous networks presents unique challenges due to node and edge heterogeneity. Existing Graph Neural Network (GNN) methods primarily focus on homogeneous GAD and thus fail to address three key issues: (C1) Capturing abnormal signal and rich semantics across diverse meta-paths; (C2) Retaining high-frequency content in HIN dimension alignment; and (C3) Learning effectively from difficult anomaly samples with class imbalance. To overcome these, we propose ChiGAD, a spectral GNN framework based on a novel Chi-Square filter, inspired by the wavelet effectiveness in diverse domains. Specifically, ChiGAD consists of: (1) Multi-Graph Chi-Square Filter, which captures anomalous information via applying dedicated Chi-Square filters to each meta-path graph; (2) Interactive Meta-Graph Convolution, which aligns features while preserving high-frequency information and incorporates heterogeneous messages by a unified Chi-Square Filter; and (3) Contribution-Informed Cross-Entropy Loss, which prioritizes difficult anomalies to address class imbalance. Extensive experiments on public and industrial datasets show that ChiGAD outperforms state-of-the-art models on multiple metrics. Additionally, its homogeneous variant, ChiGNN, excels on seven GAD datasets, validating the effectiveness of Chi-Square filters. Our code is available at https://github.com/HsipingLi/ChiGAD.

CVFeb 27, 2025
Enhanced Contrastive Learning with Multi-view Longitudinal Data for Chest X-ray Report Generation

Kang Liu, Zhuoqi Ma, Xiaolu Kang et al.

Automated radiology report generation offers an effective solution to alleviate radiologists' workload. However, most existing methods focus primarily on single or fixed-view images to model current disease conditions, which limits diagnostic accuracy and overlooks disease progression. Although some approaches utilize longitudinal data to track disease progression, they still rely on single images to analyze current visits. To address these issues, we propose enhanced contrastive learning with Multi-view Longitudinal data to facilitate chest X-ray Report Generation, named MLRG. Specifically, we introduce a multi-view longitudinal contrastive learning method that integrates spatial information from current multi-view images and temporal information from longitudinal data. This method also utilizes the inherent spatiotemporal information of radiology reports to supervise the pre-training of visual and textual representations. Subsequently, we present a tokenized absence encoding technique to flexibly handle missing patient-specific prior knowledge, allowing the model to produce more accurate radiology reports based on available prior knowledge. Extensive experiments on MIMIC-CXR, MIMIC-ABN, and Two-view CXR datasets demonstrate that our MLRG outperforms recent state-of-the-art methods, achieving a 2.3% BLEU-4 improvement on MIMIC-CXR, a 5.5% F1 score improvement on MIMIC-ABN, and a 2.7% F1 RadGraph improvement on Two-view CXR.

89.8SYApr 27
VLM-VPI: A Vision-Language Reasoning Framework for Improving Automated Vehicle-Pedestrian Interactions

Qingwen Pu, Kun Xie, Yuxiang Liu

Autonomous driving systems often infer pedestrian yielding behavior from geometric and kinematic cues alone, limiting their ability to reason about visual scene context and age-dependent behavioral variability. This limitation can produce delayed interventions in safety-critical encounters and unnecessary braking in benign interactions. This work introduces Vision-Language Model-based Vehicle-Pedestrian Interaction (VLM-VPI), a multimodal reasoning framework for pedestrian intent understanding and yielding-aware control in autonomous driving. The system combines three components: a multimodal perception layer that captures visual and kinematic observations, a reasoning layer that uses Qwen3-VL 8B for visual scene understanding and GPT-OSS 20B for few-shot intent reasoning, and a tiered safety controller that applies age-specific braking margins for children, adults, and seniors. In 112 CARLA scenarios, VLM-VPI achieves 92.3% intent classification accuracy, outperforming a rule-based baseline (78.4%), supervised trajectory models (73.5-82.4%), and a zero-shot LLM configuration (88.4%). Validation on 24 real-world PIE scenarios yields 87.5% accuracy, indicating functional sim-to-real transferability. Across 200 simulation cases, VLM-VPI reduces the false-alarm rate from 7.4% to 2.8% and mean intersection traversal time from 13.5 s to 11.8 s. Conflict occurrences decrease from 124 to 33, while mean minimum time-to-collision improves from 1.92 s to 4.47 s. Demographic-adaptive control further reduces conflicts by 60% for children and 54.5% for seniors compared with uniform control. These results show that an explicit vision-language reasoning layer can improve both safety and efficiency by linking pedestrian intent, demographic context, and vehicle control decisions.

CVNov 15, 2024
EVOKE: Elevating Chest X-ray Report Generation via Multi-View Contrastive Learning and Patient-Specific Knowledge

Qiguang Miao, Kang Liu, Zhuoqi Ma et al.

Radiology reports are crucial for planning treatment strategies and facilitating effective doctor-patient communication. However, the manual creation of these reports places a significant burden on radiologists. While automatic radiology report generation presents a promising solution, existing methods often rely on single-view radiographs, which constrain diagnostic accuracy. To address this challenge, we propose \textbf{EVOKE}, a novel chest X-ray report generation framework that incorporates multi-view contrastive learning and patient-specific knowledge. Specifically, we introduce a multi-view contrastive learning method that enhances visual representation by aligning multi-view radiographs with their corresponding report. After that, we present a knowledge-guided report generation module that integrates available patient-specific indications (e.g., symptom descriptions) to trigger the production of accurate and coherent radiology reports. To support research in multi-view report generation, we construct Multi-view CXR and Two-view CXR datasets using publicly available sources. Our proposed EVOKE surpasses recent state-of-the-art methods across multiple datasets, achieving a 2.9\% F\textsubscript{1} RadGraph improvement on MIMIC-CXR, a 7.3\% BLEU-1 improvement on MIMIC-ABN, a 3.1\% BLEU-4 improvement on Multi-view CXR, and an 8.2\% F\textsubscript{1,mic-14} CheXbert improvement on Two-view CXR.

SIMay 21, 2024
Rumor Detection on Social Media with Reinforcement Learning-based Key Propagation Graph Generator

Yusong Zhang, Kun Xie, Xingyi Zhang et al.

The spread of rumors on social media, particularly during significant events like the US elections and the COVID-19 pandemic, poses a serious threat to social stability and public health. Current rumor detection methods primarily rely on propagation graphs to improve the model performance. However, the effectiveness of these methods is often compromised by noisy and irrelevant structures in the propagation process. To tackle this issue, techniques such as weight adjustment and data augmentation have been proposed. However, they depend heavily on rich original propagation structures, limiting their effectiveness in handling rumors that lack sufficient propagation information, especially in the early stages of dissemination. In this work, we introduce the Key Propagation Graph Generator (KPG), a novel reinforcement learning-based framework, that generates contextually coherent and informative propagation patterns for events with insufficient topology information and identifies significant substructures in events with redundant and noisy propagation structures. KPG comprises two key components: the Candidate Response Generator (CRG) and the Ending Node Selector (ENS). CRG learns latent variable distributions from refined propagation patterns to eliminate noise and generate new candidates for ENS, while ENS identifies the most influential substructures in propagation graphs and provides training data for CRG. Furthermore, we develop an end-to-end framework that utilizes rewards derived from a pre-trained graph neural network to guide the training process. The resulting key propagation graphs are then employed in downstream rumor detection tasks. Extensive experiments conducted on four datasets demonstrate that KPG outperforms current state-of-the-art methods.

CVAug 7, 2025
PriorRG: Prior-Guided Contrastive Pre-training and Coarse-to-Fine Decoding for Chest X-ray Report Generation

Kang Liu, Zhuoqi Ma, Zikang Fang et al.

Chest X-ray report generation aims to reduce radiologists' workload by automatically producing high-quality preliminary reports. A critical yet underexplored aspect of this task is the effective use of patient-specific prior knowledge -- including clinical context (e.g., symptoms, medical history) and the most recent prior image -- which radiologists routinely rely on for diagnostic reasoning. Most existing methods generate reports from single images, neglecting this essential prior information and thus failing to capture diagnostic intent or disease progression. To bridge this gap, we propose PriorRG, a novel chest X-ray report generation framework that emulates real-world clinical workflows via a two-stage training pipeline. In Stage 1, we introduce a prior-guided contrastive pre-training scheme that leverages clinical context to guide spatiotemporal feature extraction, allowing the model to align more closely with the intrinsic spatiotemporal semantics in radiology reports. In Stage 2, we present a prior-aware coarse-to-fine decoding for report generation that progressively integrates patient-specific prior knowledge with the vision encoder's hidden states. This decoding allows the model to align with diagnostic focus and track disease progression, thereby enhancing the clinical accuracy and fluency of the generated reports. Extensive experiments on MIMIC-CXR and MIMIC-ABN datasets demonstrate that PriorRG outperforms state-of-the-art methods, achieving a 3.6% BLEU-4 and 3.8% F1 score improvement on MIMIC-CXR, and a 5.9% BLEU-1 gain on MIMIC-ABN. Code and checkpoints will be released upon acceptance.

BMFeb 11, 2025
Fast and Accurate Antibody Sequence Design via Structure Retrieval

Xingyi Zhang, Kun Xie, Ningqiao Huang et al.

Recent advancements in protein design have leveraged diffusion models to generate structural scaffolds, followed by a process known as protein inverse folding, which involves sequence inference on these scaffolds. However, these methodologies face significant challenges when applied to hyper-variable structures such as antibody Complementarity-Determining Regions (CDRs), where sequence inference frequently results in non-functional sequences due to hallucinations. Distinguished from prevailing protein inverse folding approaches, this paper introduces Igseek, a novel structure-retrieval framework that infers CDR sequences by retrieving similar structures from a natural antibody database. Specifically, Igseek employs a simple yet effective multi-channel equivariant graph neural network to generate high-quality geometric representations of CDR backbone structures. Subsequently, it aligns sequences of structurally similar CDRs and utilizes structurally conserved sequence motifs to enhance inference accuracy. Our experiments demonstrate that Igseek not only proves to be highly efficient in structural retrieval but also outperforms state-of-the-art approaches in sequence recovery for both antibodies and T-Cell Receptors, offering a new retrieval-based perspective for therapeutic protein design.

CLSep 25, 2025
Enhancing Molecular Property Prediction with Knowledge from Large Language Models

Peng Zhou, Lai Hou Tim, Zhixiang Cheng et al.

Predicting molecular properties is a critical component of drug discovery. Recent advances in deep learning, particularly Graph Neural Networks (GNNs), have enabled end-to-end learning from molecular structures, reducing reliance on manual feature engineering. However, while GNNs and self-supervised learning approaches have advanced molecular property prediction (MPP), the integration of human prior knowledge remains indispensable, as evidenced by recent methods that leverage large language models (LLMs) for knowledge extraction. Despite their strengths, LLMs are constrained by knowledge gaps and hallucinations, particularly for less-studied molecular properties. In this work, we propose a novel framework that, for the first time, integrates knowledge extracted from LLMs with structural features derived from pre-trained molecular models to enhance MPP. Our approach prompts LLMs to generate both domain-relevant knowledge and executable code for molecular vectorization, producing knowledge-based features that are subsequently fused with structural representations. We employ three state-of-the-art LLMs, GPT-4o, GPT-4.1, and DeepSeek-R1, for knowledge extraction. Extensive experiments demonstrate that our integrated method outperforms existing approaches, confirming that the combination of LLM-derived knowledge and structural information provides a robust and effective solution for MPP.

BMFeb 11, 2025
Towards More Accurate Full-Atom Antibody Co-Design

Jiayang Wu, Xingyi Zhang, Xiangyu Dong et al.

Antibody co-design represents a critical frontier in drug development, where accurate prediction of both 1D sequence and 3D structure of complementarity-determining regions (CDRs) is essential for targeting specific epitopes. Despite recent advances in equivariant graph neural networks for antibody design, current approaches often fall short in capturing the intricate interactions that govern antibody-antigen recognition and binding specificity. In this work, we present Igformer, a novel end-to-end framework that addresses these limitations through innovative modeling of antibody-antigen binding interfaces. Our approach refines the inter-graph representation by integrating personalized propagation with global attention mechanisms, enabling comprehensive capture of the intricate interplay between local chemical interactions and global conformational dependencies that characterize effective antibody-antigen binding. Through extensive validation on epitope-binding CDR design and structure prediction tasks, Igformer demonstrates significant improvements over existing methods, suggesting that explicit modeling of multi-scale residue interactions can substantially advance computational antibody design for therapeutic applications.

LGJun 10, 2021
Learning Based Proximity Matrix Factorization for Node Embedding

Xingyi Zhang, Kun Xie, Sibo Wang et al.

Node embedding learns a low-dimensional representation for each node in the graph. Recent progress on node embedding shows that proximity matrix factorization methods gain superb performance and scale to large graphs with millions of nodes. Existing approaches first define a proximity matrix and then learn the embeddings that fit the proximity by matrix factorization. Most existing matrix factorization methods adopt the same proximity for different tasks, while it is observed that different tasks and datasets may require different proximity, limiting their representation power. Motivated by this, we propose {\em Lemane}, a framework with trainable proximity measures, which can be learned to best suit the datasets and tasks at hand automatically. Our method is end-to-end, which incorporates differentiable SVD in the pipeline so that the parameters can be trained via backpropagation. However, this learning process is still expensive on large graphs. To improve the scalability, we train proximity measures only on carefully subsampled graphs, and then apply standard proximity matrix factorization on the original graph using the learned proximity. Note that, computing the learned proximities for each pair is still expensive for large graphs, and existing techniques for computing proximities are not applicable to the learned proximities. Thus, we present generalized push techniques to make our solution scalable to large graphs with millions of nodes. Extensive experiments show that our proposed solution outperforms existing solutions on both link prediction and node classification tasks on almost all datasets.