GenAI4ELab/papercli-papers huggingface dataset:
M^2LLM: Multi-view Molecular Representation Learning with Large Language Models
Authors: Jiaxin Ju; Yizhen Zheng; Huan Yee Koh; Can Wang; Shirui Pan
Venue: IJCAI 2025 (main)

Abstract: Accurate molecular property prediction is a critical challenge with wide-ranging applications in chemistry, materials science, and drug discovery. Molecular representation methods, including fingerprints and graph neural networks (GNNs), achieve state-of-the-art results by effectively deriving features from molecular structures. However, these methods often overlook decades of accumulated semantic and contextual knowledge. Recent advancements in large language models (LLMs) demonstrate remarkable reasoning abilities and prior knowledge across scientific domains, leading us to hypothesize that LLMs can generate rich molecular representations when guided to reason in multiple perspectives. To address these gaps, we propose M^2LLM, a multi-view framework that integrates three perspectives: the molecular structure view, the molecular task view, and the molecular rules view. These views are fused dynamically to adapt to task requirements, and experiments demonstrate that M^2LLM achieves state-of-the-art performance on multiple benchmarks across classification and regression tasks. Moreover, we demonstrate that representation derived from LLM achieves exceptional performance by leveraging two core functionalities: the generation of molecular embeddings through their encoding capabilities and the curation of molecular features through advanced reasoning processes.
Bridging Local and Global Knowledge via Transformer in Board Games
Authors: Yan-Ru Ju; Tai-Lin Wu; Chung-Chin Shih; Ti-Rong Wu
Venue: IJCAI 2025 (main)

Abstract: Although AlphaZero has achieved superhuman performance in board games, recent studies reveal its limitations in handling scenarios requiring a comprehensive understanding of the entire board, such as recognizing long-sequence patterns in Go. To address this challenge, we propose ResTNet, a network that interleaves residual and Transformer blocks to bridge local and global knowledge. ResTNet improves playing strength across multiple board games, increasing win rate from 54.6% to 60.8% in 9x9 Go, 53.6% to 60.9% in 19x19 Go, and 50.4% to 58.0% in 19x19 Hex. In addition, ResTNet effectively processes global information and tackles two long-sequence patterns in 19x19 Go, including circular pattern and ladder pattern. It reduces the mean square error for circular pattern recognition from 2.58 to 1.07 and lowers the attack probability against an adversary program from 70.44% to 23.91%. ResTNet also improves ladder pattern recognition accuracy from 59.15% to 80.01%. By visualizing attention maps, we demonstrate that ResTNet captures critical game concepts in both Go and Hex, offering insights into AlphaZero's decision-making process. Overall, ResTNet shows a promising approach to integrating local and global knowledge, paving the way for more effective AlphaZero-based algorithms in board games. Our code is available at https://rlg.iis.sinica.edu.tw/papers/restnet.
APIMig: A Project-Level Cross-Multi-Version API Migration Framework Based on Evolution Knowledge Graph
Authors: Li Kuang; Qi Xie; HaiYang Yang; Yang Yang; Xiang Wei; HaoYue Kang; YingJie Xia
Venue: IJCAI 2025 (main)

Abstract: API migration is essential for software maintenance due to the rapid evolution of third-party libraries where API elements may change continuously through updates. There are two main challenges for API migration at the project level, especially across multiple versions: 1) lack of specific library evolution knowledge across multi-version; 2) difficulty in identifying the chain of changes at the project level. This paper proposes a project-level cross-multi-version API migration framework APIMig. We first construct an API evolution knowledge graph (KG) to capture changes between adjacent library versions and then derive coherent cross-version API evolution knowledge by KG reasoning. Second, we design a chain exploration algorithm to track the chain of changes and aggregate the affected code segments. Finally, a large language model is employed in completing API migration by providing the API evolution knowledge and the chain of changes. We construct an evolution KG for the Lucene library from version 4.0.0 to 10.1.0 and evaluate our approach through project migration pairs that depend on different major versions. Our framework shows improvements over the baseline in migrating projects across 7 major versions, achieving average increases of 16.52% in CodeBLEU scores and 28.49% in VCEU scores in GPT-4o.
Contrastive Unlearning: A Contrastive Approach to Machine Unlearning
Authors: Hong kyu Lee; Qiuchen Zhang; Carl Yang; Jian Lou; Li Xiong
Venue: IJCAI 2025 (main)

Abstract: Machine unlearning aims to eliminate the influence of a subset of training samples (i.e., unlearning samples) from a trained model. Effectively and efficiently removing the unlearning samples without negatively impacting the overall model performance is challenging. Existing works mainly exploit input and output space and classification loss, which can result in ineffective unlearning or performance loss. In addition, they utilize unlearning or remaining samples ineffectively, sacrificing either unlearning efficacy or efficiency. Our main insight is that the direct optimization on the representation space utilizing both unlearning and remaining samples can effectively remove influence of unlearning samples while maintaining representations learned from remaining samples. We propose a contrastive unlearning framework, leveraging the concept of representation learning for more effective unlearning. It removes the influence of unlearning samples by contrasting their embeddings against the remaining samples' embeddings so that their embeddings are closer to the embeddings of unseen samples. Experiments on a variety of datasets and models on both class unlearning and sample unlearning showed that contrastive unlearning achieves the best unlearning effects and efficiency with the lowest performance loss compared with the state-of-the-art algorithms. In addition, it is generalizable to different contrastive frameworks and other models such as vision-language models. Our main code is available on github.com/Emory-AIMS/Contrastive-Unlearning
Secure and Efficient Watermarking for Latent Diffusion Models in Model Distribution Scenarios
Authors: Liangqi Lei; Keke Gai; Jing Yu; Liehuang Zhu; Qi Wu
Venue: IJCAI 2025 (main)

Abstract: Latent diffusion models have exhibited considerable potential in generative tasks. Watermarking is considered to be an alternative to safeguard the copyright of generative models and prevent their misuse. However, in the context of model distribution scenarios, the accessibility of models to large scale of model users brings new challenges to the security, efficiency and robustness of existing watermark solutions. To address these issues, we propose a secure and efficient watermarking solution. A new security mechanism is designed to prevent watermark leakage and watermark escape, which considers watermark randomness and watermark-model association as two constraints for mandatory watermark injection. To reduce the time cost of training the security module, watermark injection and the security mechanism are decoupled, ensuring that fine-tuning VAE only accomplishes the security mechanism without the burden of learning watermark patterns. A watermark distribution-based verification strategy is proposed to enhance the robustness against diverse attacks in the model distribution scenarios. Experimental results prove that our watermarking consistently outperforms existing six baselines on effectiveness and robustness against ten image processing attacks and adversarial attacks, while enhancing security in the distribution scenarios. The code is available at https://anonymous.4open.science/r/DistriMark-F11F/.
Diffusion Guided Propagation Augmentation for Popularity Prediction
Authors: Chaozhuo Li; Tianqi Yang; Litian Zhang; Xi Zhang
Venue: IJCAI 2025 (main)

Abstract: The prediction of information popularity propagation is critical for applications such as recommendation systems, targeted advertising, and social media trend analysis. Traditional approaches primarily rely on historical cascade data, often sacrificing timeliness for prediction accuracy. These methods capture aggregate diffusion patterns but fail to account for the complex temporal dynamics of early-stage propagation. In this paper, we introduce Diffusion Guided Propagation Augmentation(DGPA), a novel framework designed to improve early-stage popularity prediction. DGPA models cascade dynamics by leveraging a generative approach, where a temporal conditional interpolator serves as a noising process and forecasting as a denoising process. By iteratively generating cascade representations through a sampling procedure, DGPA effectively incorporates the evolving time steps of diffusion, significantly enhancing prediction timeliness and accuracy. Extensive experiments on benchmark datasets from Twitter, Weibo, and APS demonstrate that DGPA outperforms state-of-the-art methods in early-stage popularity prediction.
DASS: A Dual-Branch Attention-based Framework for Trajectory Similarity Learning with Spatial and Semantic Fusion
Authors: Jiayi Li; Junhua Fang; Pingfu Chao; Jiajie Xu; Pengpeng Zhao
Venue: IJCAI 2025 (main)

Abstract: Trajectory similarity aims to identify pairs of similar trajectories, serving as a crucial operation in spatial-temporal data mining. Although several approaches have been proposed, they encounter the following two issues: 1) An overemphasis on spatial similarity in road networks while the rich semantic information embedded in trajectories is not fully exploited; 2) Dependence on Recurrent Neural Network (RNN) architectures would struggle to capture long-term dependencies. To address these limitations, we propose a Dual-branch Attention-based framework with Spatial and Semantic information (DASS) based on self-supervised learning. Specifically, DASS comprises two core components: 1) A trajectory representation module that models spatial-temporal adjacent relationships in the form of graph and converts semantics into numerical embeddings. 2) A backbone encoder with a co-attention module to independently process two features before they are integrated. Extensive experiments on real-world datasets demonstrate that DASS outperforms state-of-the-art methods, establishing itself as a novel paradigm.
AlphaGAT: A Two-Stage Learning Approach for Adaptive Portfolio Selection
Authors: Shicheng Li; Jinshan  Zhang; Feng Wang
Venue: IJCAI 2025 (main)

Abstract: Portfolio selection is a critical task in finance, involving the allocation of resources across various assets. However, current methods often struggle to maintain robust performance due to the inherent low signal-to-noise ratio in raw financial data and shifts in data distribution. We propose AlphaGAT, a novel two-stage learning approach for portfolio selection, designed to adapt to different market scenarios. Inspired by the concept of alpha factors, which transform historical market data into actionable signals, the first stage introduces an advanced model named CATimeMixer for alpha factor generation with a novel loss function to improve the effectiveness and robustness. CATimeMixer integrates TimeMixer with Conv1D (C) and cross-asset Attention (A). Specifically, Conv1D enhances TimeMixer by capturing trend and seasonal features across different scales, while cross-asset attention enables TimeMixer to extract interrelationships between different assets. The second stage applies reinforcement learning to dynamically adjust weights, integrating alpha factors into trading signals. Recognizing the varying effectiveness of alpha factors across different periods, our RL agent innovatively transforms the alpha factors into graphs and employs graph attention networks (GAT) to discern the significance of different alpha factors, enhancing policy robustness. Extensive experiments on real-world market data show that our approach outperforms state-of-the-art methods.
RetroMoE: A Mixture-of-Experts Latent Translation Framework for Single-step Retrosynthesis
Authors: Xinjie Li; Abhinav Verma
Venue: IJCAI 2025 (main)

Abstract: Single-step retrosynthesis is a crucial task in organic synthesis, where the objective is to identify the reactants needed to produce a given product. In recent years, a variety of machine learning methods have been developed to tackle retrosynthesis prediction. In our study, we introduce RetroMoE, a novel generative model designed for the single-step retrosynthesis task. We start with a non-symmetric variational autoencoder (VAE) that incorporates a graph encoder to map molecular graphs into a latent space, followed by a transformer decoder for precise prediction of molecular SMILES strings. Additionally, we implement a simple yet effective mixture-of-experts (MoE) network to translate the product latent embedding into the reactant latent embedding. To our knowledge, this is the first approach that frames single-step retrosynthesis as a latent translation problem. Extensive experiments on the USPTO-50K and USPTO-MIT datasets demonstrate the superiority of our method, which not only surpasses most semi-template-based and template-free methods but also delivers competitive results against template-based methods. Notably, under the class-known setting on the USPTO-50K, our method achieves top-1 exact match accuracy comparable to the state-of-the-art template method, RetroKNN.
MTGIB-UNet: A Multi-Task Graph Information Bottleneck and Uncertainty Weighted Network for ADMET Prediction
Authors: Xuqiang Li; Wenjie Du; Jun Xia; Jianmin Wang; Xiaoqi Wang; Yang Yang; Yang Wang
Venue: IJCAI 2025 (main)

Abstract: Accurate prediction of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties is crucial in drug development, as these properties directly impact a drug's efficacy and safety. However, existing multi-task learning models often face challenges related to noise interference and task conflicts when dealing with complex molecular structures. To address these issues, we propose a novel multi-task Graph Neural Network (GNN) model, \textbf{MTGIB-UNet}. The model begins by encoding molecular graphs to capture intricate molecular structure information. Subsequently, based on the Graph Information Bottleneck (GIB) principle, the model compresses the information flow by extracting subgraphs, retaining task-relevant features while removing noise for each task. These embeddings are then fused through a gated network that dynamically adjusts the contribution weights of auxiliary tasks to the primary task. Specifically, an uncertainty weighting (UW) strategy is applied, with additional emphasis placed on the primary task, allowing dynamic adjustment of task weights while strengthening the influence of the primary task on model training. Experiments on standard ADMET datasets demonstrate that our model outperforms existing methods. Additionally, the model shows good interpretability by identifying key molecular substructures related to specific ADMET endpoints.
COGRASP: Co-Occurrence Graph Based Stock Price Forecasting
Authors: Zhengze Li; Zilin Song; Tingting Yuan; Xiaoming Fu
Venue: IJCAI 2025 (main)

Abstract: Forecasting stock prices is complex and challenging. Uncovering correlations among stocks has proven to enhance stock price forecasting. However, existing correlation discovery methods, such as concept-based methods, are slow, inaccurate, and limited by their reliance on predefined concepts and manual analysis. In this paper, we propose COGRASP, a novel approach for stock price forecasting that constructs stock co-occurrence graphs automatically by analyzing rapidly updated sources such as reports, newspapers, and social media. Besides, we aggregate forecasts across multiple timescales (i.e., long-, medium-, and short-term) to capture multi-timescale trends fluctuations, thereby enhancing price forecasting accuracy. In experiments with real-world open-source stock market data, COGRASP outperforms state-of-the-art methods.
KnowMDD: Knowledge-guided Cross Contrastive Learning for Major Depressive Disorder Diagnosis
Authors: Anchen Lin; Weikun Wang; Haijun Han; Fanwei Zhu; Qi Ma; Zengwei Zheng; Binbin Zhou
Venue: IJCAI 2025 (main)

Abstract: Major Depressive Disorder (MDD) is a prevalent and severe mental disease. Functional Magnetic Resonance Imaging (fMRI)-based diagnostic methods, which analyze Functional Connectivity (FC) to identify abnormal functional connections, have shown promise as biomarker-based approaches for diagnosing depression. However, the high costs of fMRI data result in small sample sizes, hindering the effective identification of abnormal FC patterns. Moreover, existing methods often overlook the potential benefits of incorporating domain knowledge into their models. In this paper, we propose KnowMDD, a novel knowledge-guided cross contrastive learning framework for MDD diagnosis. By incorporating domain knowledge and employing data augmentation, KnowMDD addresses data sparsity while improving robustness and interpretability. Specifically, multiple atlases are used to construct complementary brain graph representations. The default mode network, closely associated with depression, is introduced into the contrastive learning paradigm for diverse subgraph augmentations, while an attention mechanism captures global semantic relationships between brain regions. Based on them, a cross contrastive learning is designed to learn robust representations for accurate diagnosis. Extensive experiments demonstrate the effectiveness, robustness, and interpretability of KnowMDD, which outperforms state-of-the-art methods. We also develop a demonstration system to show its practical application.
PAMol: Pocket-Aware Drug Design Method with Hypergraph Representation of Protein Pocket Structure and Feature Fusion
Authors: Xiaoli Lin; Xiongwei Liao; Jun Pang; Bo Li; Xiaolong Zhang
Venue: IJCAI 2025 (main)

Abstract: Efficient generation of targeted drug molecules is crucial in the field of drug discovery. Most existing methods neglect the high-order information in the structure of protein pockets, limiting the performance of generated drug molecules. This paper proposes a pocket-aware drug design framework, namely PAMol, constructing the hypergraph to represent the spatial structure of protein pockets, effectively capturing high-order relations and neighborhood information within the pocket structures. This framework also fuses different modal embeddings from proteins and molecules, to generate high-quality molecules. In addition, a conditional molecule generation module uses the high-order structural information in protein pockets as constraints to more accurately generate molecules for specific targets. The performance of PAMol has been assessed by analyzing generated molecules in terms of vina score, high affinity, QED, SA, LogP, Lipinski, diversity, and time. Experimental results demonstrate the potential of PAMol for targeted drug design. The source code is available at https://github.com/YICHUANSYQ/PAMol.git.
Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning
Authors: Xuan Lin; Qingrui  Liu; Hongxin Xiang; Daojian Zeng; Xiangxiang Zeng
Venue: IJCAI 2025 (main)

Abstract: Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces two major challenges: (i) lacking a large-scale chemical synthesis-related instruction dataset; (ii) ignoring the close correlation between reaction and retrosynthesis prediction for the existing fine-tuning strategies. To address these challenges, we propose ChemDual, a novel LLM framework for accurate chemical synthesis. Specifically, considering the high cost of data acquisition for reaction and retrosynthesis, ChemDual regards the reaction-and-retrosynthesis of molecules as a related recombination-and-fragmentation process and constructs a large-scale of 4.4 million instruction dataset. Furthermore, ChemDual introduces an enhanced LLaMA, equipped with a multi-scale tokenizer and dual-task learning strategy, to jointly optimize the process of recombination and fragmentation as well as the tasks between reaction and retrosynthesis prediction. Extensive experiments on Mol-Instruction and USPTO-50K datasets demonstrate that ChemDual achieves state-of-the-art performance in both predictions of reaction and retrosynthesis, outperforming the existing conventional single-task approaches and the general open-source LLMs. Through molecular docking analysis, ChemDual generates compounds with diverse and strong protein binding affinity, further highlighting its strong potential in drug design.
Towards Generalizable Neural Simulators: Addressing Distribution Shifts Induced by Environmental and Temporal Variations
Authors: Jiaqi Liu; Jiaxu Cui; Shiang Sun; Yizhu Zhao; Bo Yang
Venue: IJCAI 2025 (main)

Abstract: With advancements in deep learning, neural simulators have become increasingly important for improving the efficiency and effectiveness of simulating complex dynamical systems in various scientific and technological fields. This paper presents a novel neural simulator called Context-informed Polymorphic Neural ODE Processes (CoPoNDP), aimed at addressing the challenges of modeling dynamical systems encountering concurrent environmental and temporal distribution shifts, which are common in real-world scenarios. CoPoNDP employs a context-driven neural stochastic process governed by a combination of basic differential equations in a time-sensitive manner to adaptively modulate the evolution of system states. This allows for flexible adaptation to changing temporal dynamics and generalization across different environments. Extensive experiments conducted on dynamical systems from ecology, chemistry, physics, and energy demonstrate that by effectively utilizing contextual information, CoPoNDP outperforms the state-of-the-art models in handling joint distribution shifts. It also shows robustness in sparse and noisy settings, making it a promising approach for modeling dynamical systems in complex real-world applications.
Asset Pricing with Contrastive Adversarial Variational Bayes
Authors: Ruirui Liu; Huichou Huang; Johannes Ruf
Venue: IJCAI 2025 (main)

Abstract: Machine learning techniques have gained considerable attention in the field of empirical asset pricing. Conditioning on a broad set of firm characteristics, one of the most popular no-arbitrage workhorses is a nonlinear conditional asset pricing model that consists of two modules within a neural network structure, i.e., factor and beta estimates, for which we propose a novel contrastive adversarial variational Bayes (CAVB) framework. To exploit the factor structure, we employ adversarial variational Bayes that transforms the maximum-likelihood problem into a zero-sum game between a variational autoencoder (VAE) and a generative adversarial network (GAN), where an auxiliary discriminative network brings in arbitrary expressiveness to the inference model. To tackle the problem of learning indistinguishable feature representations in the beta network, we introduce a contrastive loss to learn distinctive hidden features of the factor loadings in correspondence to conditional quantiles of return distributions. CAVB establishes a robust relation between the cross-section of asset returns and the common latent factors with nonlinear factor loadings. Extensive experiments show that CAVB not only significantly outperforms prominent models in the existing literature in terms of total and predictive R-squares, but also delivers superior Sharpe ratios after transaction costs for both long-only and long-short portfolios.