GenAI4ELab/papercli-papers huggingface dataset:
PDDFormer: Pairwise Distance Distribution Graph Transformer for Crystal Material Property Prediction
Authors: Xiangxiang Shen; Zheng Wan; Lingfeng Wen; Licheng Sun; Jian Yang; Xuan Tang; Shing-Ho J. Lin; Xiao He; Mingsong Chen; Xian Wei
Venue: IJCAI 2025 (main)

Abstract: Crystal structures can be simplified as a periodic point set that repeats across three-dimensional space along an underlying lattice. Traditionally, crystal representation methods rely on descriptors such as lattice parameters, symmetry, and space groups to characterize the structure. However, in reality, atoms in materials always vibrate above absolute zero, causing their positions to fluctuate continuously. This dynamic behavior disrupts the fundamental periodicity of the lattice, making crystal graphs based on static lattice parameters and conventional descriptors discontinuous under slight perturbations. Chemists proposed the pairwise distance distribution (PDD) method to address this. However, the completeness of PDD requires defining a large number of neighboring atoms, leading to high computational costs. Additionally, PDD does not account for atomic information, making it challenging to apply it directly to crystal material property prediction tasks. To tackle these challenges, we introduce the atom-weighted Pairwise Distance Distribution (WPDD) and Unit cell Pairwise Distance Distribution (UPDD) for the first time, applying them to the construction of multi-edge crystal graphs. We demonstrate the continuity and general completeness of crystal graphs under slight atomic position perturbations. Moreover, by modeling PDD as global information and integrating it into matrix-based message passing, we significantly reduce computational costs. Comprehensive evaluation results show that WPDDFormer achieves state-of-the-art predictive accuracy across tasks on benchmark datasets such as the Materials Project and JARVIS-DFT.
MTPNet: Multi-Grained Target Perception for Unified Activity Cliff Prediction
Authors: Zishan Shu; Yufan Deng; Hongyu Zhang; Zhiwei Nie; Jie Chen
Venue: IJCAI 2025 (main)

Abstract: Activity cliff prediction is a critical task in drug discovery and material design. Existing computational methods are limited to handling single binding targets, which restricts the applicability of these prediction models. In this paper, we present the Multi-Grained Target Perception network (MTPNet) to incorporate the prior knowledge of interactions between the molecules and their target proteins. Specifically, MTPNet is a unified framework for activity cliff prediction, which consists of two components: Macro-level Target Semantic (MTS) guidance and Micro-level Pocket Semantic (MPS) guidance. By this way, MTPNet dynamically optimizes molecular representations through multi-grained protein semantic conditions. To our knowledge, it is the first time to employ the receptor proteins as guiding information to effectively capture critical interaction details. Extensive experiments on 30 representative activity cliff datasets demonstrate that MTPNet significantly outperforms previous approaches, achieving an average RMSE improvement of 18.95% on top of several mainstream GNN architectures. Overall, MTPNet internalizes interaction patterns through conditional deep learning to achieve unified predictions of activity cliffs, helping to accelerate compound optimization and design. Codes are available at: https://github.com/ZishanShu/MTPNet.
LogiCase: Effective Test Case Generation from Logical Description in Competitive Programming
Authors: Sicheol Sung; Aditi; Dogyu Kim; Yo-Sub Han; Sang-Ki Ko
Venue: IJCAI 2025 (main)

Abstract: Automated Test Case Generation (ATCG) is crucial for evaluating software reliability, particularly in competitive programming where robust algorithm assessments depend on diverse and accurate test cases. However, existing ATCG methods often fail to meet complex specifications or generate effective corner cases, limiting their utility. In this work, we introduce Context-Free Grammars with Counters (CCFGs), a formalism that captures both syntactic and semantic structures in input specifications. Using a fine-tuned CodeT5 model, we translate natural language input specifications into CCFGs, enabling the systematic generation of high-quality test cases. Experiments on the CodeContests dataset demonstrate that CCFG-based test cases outperform baseline methods in identifying incorrect algorithms, achieving significant gains in validity and effectiveness. Our approach provides a scalable and reliable grammar-driven framework for enhancing automated competitive programming evaluations.
PeSANet: Physics-encoded Spectral Attention Network for Simulating PDE-Governed Complex Systems
Authors: Han Wan; Rui Zhang; Qi Wang; Yang Liu; Hao Sun
Venue: IJCAI 2025 (main)

Abstract: Accurately modeling and forecasting complex systems governed by partial differential equations (PDEs) is crucial in various scientific and engineering domains. However, traditional numerical methods struggle in real-world scenarios due to incomplete or unknown physical laws. Meanwhile, machine learning approaches often fail to generalize effectively when faced with scarce observational data and the challenge of capturing local and global features. To this end, we propose the Physics-encoded Spectral Attention Network (PeSANet), which integrates local and global information to forecast complex systems with limited data and incomplete physical priors. The model consists of two key components: a physics-encoded block that uses hard constraints to approximate local differential operators from limited data, and a spectral-enhanced block that captures long-range global dependencies in the frequency domain. Specifically, we introduce a novel spectral attention mechanism to model inter-spectrum relationships and learn long-range spatial features. Experimental results demonstrate that PeSANet outperforms existing methods across all metrics, particularly in long-term forecasting accuracy, providing a promising solution for simulating complex systems with limited data and incomplete physics.
Robust Misinformation Detection by Visiting Potential Commonsense Conflict
Authors: Bing Wang; Ximing Li; Changchun Li; Bingrui Zhao; Bo Fu; Renchu Guan; Shengsheng Wang
Venue: IJCAI 2025 (main)

Abstract: The development of Internet technology has led to an increased prevalence of misinformation, causing severe negative effects across diverse domains. To mitigate this challenge, Misinformation Detection (MD), aiming to detect online misinformation automatically, emerges as a rapidly growing research topic in the community. In this paper, we propose a novel plug-and-play augmentation method for the MD task, namely Misinformation Detection with Potential Commonsense Conflict (MD-PCC). We take inspiration from the prior studies indicating that fake articles are more likely to involve commonsense conflict. Accordingly, we construct commonsense expressions for articles, serving to express potential commonsense conflicts inferred by the difference between extracted commonsense triplet and golden ones inferred by the well-established commonsense reasoning tool COMET. These expressions are then specified for each article as augmentation. Any specific MD methods can be then trained on those commonsense-augmented articles. Besides, we also collect a novel commonsense-oriented dataset named CoMis, whose all fake articles are caused by commonsense conflict. We integrate MD-PCC with various existing MD backbones and compare them across both 4 public benchmark datasets and CoMis. Empirical results demonstrate that MD-PCC can consistently outperform the existing MD baselines.
Image-Enhanced Hybrid Encoding with Reinforced Contrastive Learning for Spatial Domain Identification in Spatial Transcriptomics
Authors: Daoyuan Wang; Lu Gao; Wenlan Chen; Cheng Liang; Fei Guo
Venue: IJCAI 2025 (main)

Abstract: Spatial transcriptomics integrates spatial, gene expression, and multichannel immunohistochemistry image data, enabling advanced insights into cellular organization. However, existing methods often struggle to effectively fuse these multimodal data, limiting their potential for accurate spatial domain identification. Here, we propose IE-HERCL (Image-Enhanced Hybrid Encoding with Reinforced Contrastive Learning), a novel framework designed to address this challenge. Specifically, IE-HERCL employs hybrid encoding to capture both the non-spatial features and spatial dependencies for both gene and image modalities via autoencoders and GraphSAGE, respectively. These features are then fused using cross-view attention mechanisms to generate the unified informative embedding. To enhance the representation learning capability, we introduce a reinforced contrastive learning strategy to mitigate the influences of false negative samples, where we detect potential positive counterparts with high-order random walks. In addition, the cluster alignment is dynamically refined through optimal transport, which ensures that the fused consensus representation is coherent and robust, enabling accurate spatial domain identification. Our approach achieves state-of-the-art performance on five image-enhanced spatial transcriptomics datasets, demonstrating its robustness and effectiveness in multimodal integration and spatial domain identification. IE-HERCL offers a powerful and innovative solution for advancing spatial transcriptomics analysis. The code is released on https://github.com/wdyi701/IE-HERCL.
ST-TAR: An Efficient Spatio-Temporal Learning Framework for Traffic Accident Risk Forecasting
Authors: Hongyu Wang; Lisi Chen; Shuo Shang; Peng Han; Christian S. Jensen
Venue: IJCAI 2025 (main)

Abstract: Traffic accidents represent a significant concern due to their devastating consequences. The ability to predict future traffic accident risks is of key importance to accident prevention activities in transportation systems. Although existing studies have made substantial efforts to model spatio-temporal correlations, they fall short when it comes to addressing the zero-inflated data issue and capturing spatio-temporal heterogeneity, which reduces their predictive abilities. In addition, improving efficiency is an urgent requirement for traffic accident forecasting. To overcome these limitations, we propose an efficient Spatio-Temporal learning framework for Traffic Accident Risk forecasting (ST-TAR). Taking long-term and short-term data as separate inputs, the ST-TAR model integrates hierarchical multi-view GCN and long short-term cross-attention mechanism to encode spatial dependencies and temporal patterns. We leverage long-term periodicity and short-term proximity for spatio-temporal contrastive learning to capture spatio-temporal heterogeneity. A tailored adaptive risk-level weighted loss function based on efficient locality-sensitive hashing is introduced to alleviate the zero-inflated issue. Extensive experiments on two real-world datasets offer evidence that ST-TAR is capable of advancing state-of-the-art forecasting accuracy with improved efficiency. This makes ST-TAR suitable for applications that require accurate real-time forecasting.
TESTN: A Triad-Enhanced Spatio-Temporal Network for Multi-Temporal POI Relationship Inference
Authors: Hongyu Wang; Lisi Chen; Shuo Shang
Venue: IJCAI 2025 (main)

Abstract: Multi-temporal Point-of-Interest (POI) relationship inference aims to identify evolving relationships among locations over time, providing critical insights for location-based services. While existing studies have made substantial efforts to model relationships with custom-designed graph neural networks, they face the challenge of leveraging POI contextual information characterized by spatial dependencies and temporal dynamics, as well as capturing the heterogeneity of multi-type relationships. To address these challenges, we propose a Triad-Enhanced Spatio-Temporal Network (TESTN), which conceptualizes triads as interactions between relationships for capturing potential interplay. Specifically, TESTN incorporates the spatial 2-hop aggregation layer to capture geographical and semantic information beyond first-order neighbors and the temporal context extractor to integrate relational dynamics within adjacent time segments. Furthermore, we introduce a self-supervised pairwise neighboring relation consistency detection scheme to preserve the heterogeneity of multi-type relationships. Extensive experiments on three real-world datasets demonstrate the superior performance of our TESTN framework.
Advancing Embodied Agent Security: From Safety Benchmarks to Input Moderation
Authors: Ning Wang; Zihan Yan; Weiyang Li; Chuan Ma; He Chen; Tao Xiang
Venue: IJCAI 2025 (main)

Abstract: Embodied agents exhibit immense potential across a multitude of domains, making the assurance of their behavioral safety a fundamental prerequisite for their widespread deployment. However, existing research predominantly concentrates on the security of general large language models, lacking specialized methodologies for establishing safety benchmarks and input moderation tailored to embodied agents. To bridge this gap, this paper introduces a novel input moderation framework, meticulously designed to safeguard embodied agents. This framework encompasses the entire pipeline, including taxonomy definition, dataset curation, moderator architecture, model training, and rigorous evaluation. Notably, we introduce EAsafetyBench, a meticulously crafted safety benchmark engineered to facilitate both the training and stringent assessment of moderators specifically designed for embodied agents. Furthermore, we propose Pinpoint, an innovative prompt-decoupled input moderation scheme that harnesses a masked attention mechanism to effectively isolate and mitigate the influence of functional prompts on moderation tasks. Extensive experiments conducted on diverse benchmark datasets and models validate the feasibility and efficacy of the proposed approach. The results demonstrate that our methodologies achieve an impressive average detection accuracy of 94.58%, surpassing the performance of existing state-of-the-art techniques, alongside an exceptional moderation processing time of merely 0.002 seconds per instance. The source code and datasets can be found at https://github.com/ZihanYan-CQU/EAsafetyBench.
Incorporating Legal Logic into Deep Learning: An Intelligent Approach to Probation Prediction
Authors: Qinghua Wang; Xu Zhang; Lingyan Yang; Rui Shao; Bonan Wang; Fang Wang; Cunquan Qu
Venue: IJCAI 2025 (main)

Abstract: Probation is a crucial institution in modern criminal law, embodying the principles of fairness and justice while contributing to the harmonious development of society. Despite its importance, the current Intelligent Judicial Assistant System (IJAS) lacks dedicated methods for probation prediction, and research on the underlying factors influencing probation eligibility remains limited. In addition, probation eligibility requires a comprehensive analysis of both criminal circumstances and remorse. Much of the existing research in IJAS relies primarily on data-driven methodologies, which often overlooks the legal logic underpinning judicial decision-making. To address this gap, we propose a novel approach that integrates legal logic into deep learning models for probation prediction, implemented in three distinct stages. First, we construct a specialized probation dataset that includes fact descriptions and probation legal elements (PLEs). Second, we design a distinct probation prediction model named the Multi-Task Dual-Theory Probation Prediction Model (MT-DT), which is grounded in the legal logic of probation and the Dual-Track Theory of Punishment. Finally, our experiments on the probation dataset demonstrate that the MT-DT model outperforms baseline models, and an analysis of the underlying legal logic further validates the effectiveness of the proposed approach.
POMP: Pathology-omics Multimodal Pre-training Framework for Cancer Survival Prediction
Authors: Suixue Wang; Shilin Zhang; Huiyuan Lai; Weiliang Huo; Qingchen Zhang
Venue: IJCAI 2025 (main)

Abstract: Cancer survival prediction is an important direction in precision medicine, aiming to help clinicians tailor treatment regimens for patients. With the rapid development of high-throughput sequencing and computational pathology technologies, survival prediction has shifted from clinical features to joint modeling of multi-omics data and pathology images. However, existing multimodal learning methods struggle to effectively learn pathology-omics interactions due to the lack of proper alignment of multimodal data before fusion. In this paper, we propose POMP, a pathology-omics multimodal pre-training framework jointly learned with three training tasks for integrating pathological images and omics data for cancer survival prediction. To better perform cross-modal learning, we introduce a pathology-omics contrastive learning method to align the pathology and omics information. POMP leverages the principle of pre-trained models and explores the benefit of aligning multimodal information from the same patient, achieving state-of-the-art results on six cancer datasets from the Cancer Genome Atlas (TCGA). We also show that our contrastive learning method allows us to exploit the cosine similarity of pathological images and omics data as the survival risk score, which can further boost prediction performance compared with other commonly used methods. The code is available at https://github.com/SuixueWang/POMP.
Attention-based Conditional Random Field for Financial Fraud Detection
Authors: Xiaoguang Wang; Chenxu Wang; Luyue Zhang; Xiaole Wang; Mengqin Wang; Huanlong Liu; Tao Qin
Venue: IJCAI 2025 (main)

Abstract: Financial fraud detection is critical for market transparency and regulatory compliance. Existing methods often ignore the temporal patterns in financial data, which are essential for understanding dynamic financial behaviors and detecting fraud. Moreover, they also treat companies as independent entities, overlooking the valuable interrelationships. To address these issues, we propose ACRF-RNN, a Recurrent Neural Network (RNN) with Attention-based Conditional Random Field (CRF) for fraud detection. Specifically, we use an RNN with a sliding window to capture temporal dependencies from historical data, and an attention-based CRF feature transformer to model inter-company relationships. This transforms raw financial data into optimized features, fed into a multi-layer perceptron for classification. Besides, we also use the focal loss to alleviate the class imbalance problem caused by rare fraudulent cases. This work presents a novel real-world dataset to evaluate the performance of ACRF-RNN. Extensive experiments show that ACRF-RNN outperforms the state-of-the-art methods by 15.28% in KS and 4.04% in Recall. Data and code are available at: https://github.com/XNetLab/ACRF-RNN.git.
ARMR: Adaptively Responsive Network for Medication Recommendation
Authors: Feiyue Wu; Tianxing Wu; Shenqi Jing
Venue: IJCAI 2025 (main)

Abstract: Medication recommendation is a crucial task in healthcare, especially for patients with complex medical conditions. However, existing methods often struggle to effectively balance the reuse of historical medications with the introduction of new drugs in response to the changing patient conditions. In order to address this challenge, we propose an Adaptively Responsive network for Medication Recommendation (ARMR), a new method which incorporates 1) a piecewise temporal learning component that distinguishes between recent and distant patient history, enabling more nuanced temporal understanding, and 2) an adaptively responsive mechanism that dynamically adjusts attention to new and existing drugs based on the patient's current health state and medication history. Experiments on the MIMIC-III and MIMIC-IV datasets indicate that ARMR has better performance compared with the state-of-the-art baselines in different evaluation metrics, which contributes to more personalized and accurate medication recommendations. The source code is publicly avaiable at: https://github.com/seucoin/armr2.
Electron Density-enhanced Molecular Geometry Learning
Authors: Hongxin Xiang; Jun Xia; Xin Jin; Wenjie Du; Li Zeng; Xiangxiang Zeng
Venue: IJCAI 2025 (main)

Abstract: Electron density (ED), which describes the probability distribution of electrons in space, is crucial for accurately understanding the energy and force distribution in molecular force fields (MFF). Existing machine learning force fields (MLFF) focus on mining appropriate physical quantities from the atom-level conformation to enhance the molecular geometry representation while ignoring the unique information from microscopic electrons. In this work, we propose an efficient Electronic Density representation framework to enhance molecular Geometric learning (called EDG), which leverages images rendered from ED to boost molecular geometric representations in MLFF. Specifically, we construct a novel image-based ED representation, which consists of 2 million 6-view images with RGB-D channels, and design an ED representation learning model, called ImageED, to learn ED-related knowledge from these images. We further propose an efficient ED-aware teacher and introduce a cross-modal distillation strategy to transfer knowledge from the image-based teacher to the geometry-based students. Extensive experiments on QM9 and rMD17 demonstrate that EDG can be directly integrated into existing geometry-based models and significantly improves the capabilities of these models (e.g., SchNet, EGNN, SphereNet, ViSNet) for geometry representation learning in MLFF with a maximum average performance increase of 33.7%. Code and appendix are available at https://github.com/HongxinXiang/EDG
Toward Reliable Scientific Hypothesis Generation: Evaluating Truthfulness and Hallucination in Large Language Models
Authors: Guangzhi Xiong; Eric Xie; Corey Williams; Myles Kim; Amir Hassan Shariatmadari; Sikun Guo; Stefan Bekiranov; Aidong Zhang
Venue: IJCAI 2025 (main)

Abstract: Large language models (LLMs) have shown significant potential in scientific disciplines such as biomedicine, particularly in hypothesis generation, where they can analyze vast literature, identify patterns, and suggest research directions. However, a key challenge lies in evaluating the truthfulness of generated hypotheses, as verifying their accuracy often requires substantial time and resources. Additionally, the hallucination problem in LLMs can lead to the generation of hypotheses that appear plausible but are ultimately incorrect, undermining their reliability. To facilitate the systematic study of these challenges, we introduce TruthHypo, a benchmark for assessing the capabilities of LLMs in generating truthful scientific hypotheses, and KnowHD, a knowledge-based hallucination detector to evaluate how well hypotheses are grounded in existing knowledge. Our results show that LLMs struggle to generate truthful hypotheses. By analyzing hallucinations in reasoning steps, we demonstrate that the groundedness scores provided by KnowHD serve as an effective metric for filtering truthful hypotheses from the diverse outputs of LLMs. Human evaluations further validate the utility of KnowHD in identifying truthful hypotheses and accelerating scientific discovery. Our data and source code are available at https://github.com/Teddy-XiongGZ/TruthHypo.