GenAI4ELab/papercli-papers huggingface dataset:
Comprehensive Review of Neural Differential Equations for Time Series Analysis
Authors: YongKyung Oh; Seungsu Kam; Jonghun Lee; Dong-Young Lim; Sungil Kim; Alex A. T. Bui
Venue: IJCAI 2025 (main)

Abstract: Time series modeling and analysis have become critical in various domains. Conventional methods such as RNNs and Transformers, while effective for discrete-time and regularly sampled data, face significant challenges in capturing the continuous dynamics and irregular sampling patterns inherent in real-world scenarios. Neural Differential Equations (NDEs) represent a paradigm shift by combining the flexibility of neural networks with the mathematical rigor of differential equations. This paper presents a comprehensive review of NDE-based methods for time series analysis, including neural ordinary differential equations, neural controlled differential equations, and neural stochastic differential equations. We provide a detailed discussion of their mathematical formulations, numerical methods, and applications, highlighting their ability to model continuous-time dynamics. Furthermore, we address key challenges and future research directions. This survey serves as a foundation for researchers and practitioners seeking to leverage NDEs for advanced time series analysis.
Image Captioning Evaluation in the Age of Multimodal LLMs: Challenges and Future Perspectives
Authors: Sara Sarto; Marcella Cornia; Rita Cucchiara
Venue: IJCAI 2025 (main)

Abstract: The evaluation of machine-generated captions is a complex and evolving challenge. With the advent of Multimodal Large Language Models (MLLMs), image captioning has become a core task, increasing the need for robust and reliable evaluation metrics. This survey provides a comprehensive overview of advancements in image captioning evaluation, analyzing the evolution, strengths, and limitations of existing metrics. We assess these metrics across multiple dimensions, including correlation with human judgment, ranking accuracy, and sensitivity to hallucinations. Additionally, we explore the challenges posed by the longer and more detailed captions generated by MLLMs and examine the adaptability of current metrics to these stylistic variations. Our analysis highlights some limitations of standard evaluation approaches and suggests promising directions for future research in image captioning assessment. For a comprehensive overview of captioning evaluation refer to our project page available at https://github.com/aimagelab/awesome-captioning-evaluation.
The Evolving Landscape of LLM- and VLM-Integrated Reinforcement Learning
Authors: Sheila Schoepp; Masoud Jafaripour; Yingyue Cao; Tianpei Yang; Fatemeh Abdollahi; Shadan Golestan; Zahin Sufiyan; Osmar R. Zaiane; Matthew E. Taylor
Venue: IJCAI 2025 (main)

Abstract: Reinforcement learning (RL) has shown impressive results in sequential decision-making tasks. Large Language Models (LLMs) and Vision-Language Models (VLMs) have recently emerged, exhibiting impressive capabilities in multimodal understanding and reasoning. These advances have led to a surge of research integrating LLMs and VLMs into RL. This survey reviews representative works in which LLMs and VLMs are used to overcome key challenges in RL, such as lack of prior knowledge, long-horizon planning, and reward design. We present a taxonomy that categorizes these LLM/VLM-assisted RL approaches into three roles: agent, planner, and reward. We conclude by exploring open problems, including grounding, bias mitigation, improved representations, and action advice. By consolidating existing research and identifying future directions, this survey establishes a framework for integrating LLMs and VLMs into RL, advancing approaches that unify natural language and visual understanding with sequential decision-making.
Multimodal Retina Image Analysis Survey: Datasets, Tasks and Methods
Authors: Hongwei Sheng; Heming Du; Xin Shen; Sen Wang; Xin Yu
Venue: IJCAI 2025 (main)

Abstract: Retina images provide a noninvasive view of the central nervous system and microvasculature, making it essential for clinical applications. Changes in the retina often indicate both ophthalmic and systemic diseases, aiding in diagnosis and early intervention. While deep learning algorithms have advanced retina image analysis, a comprehensive review of related datasets, tasks, and benchmarking is still lacking. In this survey, we systematically categorize existing retina image datasets based on their available data modalities, and review the tasks these datasets support in multimodal retina image analysis. We also explain key evaluation metrics used in various retina image analysis benchmarks. By thoroughly examining current datasets and methods, we highlight the challenges and limitations in existing benchmarks and discuss potential research topics in the field. We hope this work will guide future retina analysis methods and promote the shared use of existing data across different tasks.
A Survey of Structural Entropy: Theory, Methods, and Applications
Authors: Dingli Su; Hao Peng; Yicheng Pan; Angsheng Li
Venue: IJCAI 2025 (main)

Abstract: Classical information theory, a cornerstone of artificial intelligence, is fundamentally limited by its local perspective, often analyzing pairwise interactions while ignoring the larger, hierarchical architecture of complex systems. Structural entropy (SE) presents a paradigm shift, extending Shannon entropy to quantify information on a global scale and measure the uncertainty embedded in a system's organizational hierarchy. Although its applications have broadened significantly from its origins in community detection across diverse AI domains, a systematic synthesis of its theory, computational methods, and applications is currently lacking. This survey provides a comprehensive overview of SE to fill this critical void in the literature. We offer a detailed examination of its theoretical foundations, computational frameworks, and key learning paradigms, with a focus on its integration with graph learning and reinforcement learning. Through an exploration of its diverse applications, we highlight the power of SE to advance graph-based analysis and modeling. Finally, we discuss key challenges and future research opportunities for incorporating SE principles into the development of more interpretable and theoretically grounded AI systems.
Game Theory Meets Large Language Models: A Systematic Survey
Authors: Haoran Sun; Yusen Wu; Yukun Cheng; Xu Chu
Venue: IJCAI 2025 (main)

Abstract: Game theory establishes a fundamental framework for analyzing strategic interactions among rational decision-makers. The rapid advancement of large language models (LLMs) has sparked extensive research exploring the intersection of these two fields. Specifically, game-theoretic methods are being applied to evaluate and enhance LLM capabilities, while LLMs themselves are reshaping classic game models. This paper presents a comprehensive survey of the intersection of these fields, exploring a bidirectional relationship from three perspectives: (1) Establishing standardized game-based benchmarks for evaluating LLM behavior; (2) Leveraging game-theoretic methods to improve LLM performance through algorithmic innovations; (3) Characterizing the societal impacts of LLMs through game modeling. Among these three aspects, we also highlight how the equilibrium analysis for traditional game models is impacted by LLMs' advanced language understanding, which in turn extends the study of game theory. Finally, we identify key challenges and future research directions, assessing their feasibility based on the current state of the field. By bridging theoretical rigor with emerging AI capabilities, this survey aims to foster interdisciplinary collaboration and drive progress in this evolving research area.
Human-Centric Foundation Models: Perception, Generation and Agentic Modeling
Authors: Shixiang Tang; Yizhou Wang; Lu Chen; Yuan Wang; Sida Peng; Dan Xu; Wanli Ouyang
Venue: IJCAI 2025 (main)

Abstract: Human understanding and generation are critical for modeling digital humans and humanoid embodiments. Recently, Human-centric Foundation Models (HcFMs)—inspired by the success of generalist models such as large language and vision models—have emerged to unify diverse human-centric tasks into a single framework, surpassing traditional task-specific approaches. In this survey, we present a comprehensive overview of HcFMs by proposing a taxonomy that categorizes current approaches into four groups: (1) Human-centric Perception Foundation Models that capture fine-grained features for multi-modal 2D and 3D understanding; (2) Human-centric AIGC Foundation Models that generate high-fidelity, diverse human-related content; (3) Unified Perception and Generation Models that integrate these capabilities to enhance both human understanding and synthesis; and (4) Human-centric Agentic Foundation Models that extend beyond perception and generation to learn human-like intelligence and interactive behaviors for humanoid embodied tasks. We review state-of-the-art techniques, discuss emerging challenges and future research directions. This survey aims to serve as a roadmap for researchers and practitioners working towards more robust, versatile, and intelligent digital human and embodiments modeling. Website is https://github.com/HumanCentricModels/Awesome-Human-Centric-Foundation-Models/
Large Language Models for Causal Discovery: Current Landscape and Future Directions
Authors: Guangya Wan; Yunsheng Lu; Yuqi Wu; Mengxuan Hu; Sheng Li
Venue: IJCAI 2025 (main)

Abstract: Causal discovery (CD) and Large Language Models (LLMs) have emerged as transformative fields in artificial intelligence that have evolved largely independently. While CD specializes in uncovering cause-effect relationships from data, and LLMs excel at natural language processing and generation, their integration presents unique opportunities for advancing causal understanding. This survey examines how LLMs are transforming CD across three key dimensions: direct causal extraction from text, integration of domain knowledge into statistical methods, and refinement of causal structures. We systematically analyze approaches that leverage LLMs for CD tasks, highlighting their innovative use of metadata and natural language for causal inference. Our analysis reveals both LLMs' potential to enhance traditional CD methods and their current limitations as imperfect expert systems. We identify key research gaps, outline evaluation frameworks and benchmarks for LLM-based causal discovery, and advocate future research efforts for leveraging LLMs in causality research. As the first comprehensive examination of the synergy between LLMs and CD, this work lays the groundwork for future advances in the field.
Deep Learning for Multivariate Time Series Imputation: A Survey
Authors: Jun Wang; Wenjie Du; Yiyuan Yang; Linglong Qian; Wei Cao; Keli Zhang; Wenjia Wang; Yuxuan Liang; Qingsong Wen
Venue: IJCAI 2025 (main)

Abstract: Missing values are ubiquitous in multivariate time series (MTS) data, posing significant challenges for accurate analysis and downstream applications. In recent years, deep learning-based methods have successfully handled missing data by leveraging complex temporal dependencies and learned data distributions. In this survey, we provide a comprehensive summary of deep learning approaches for multivariate time series imputation (MTSI) tasks. We propose a novel taxonomy that categorizes existing methods based on two key perspectives: imputation uncertainty and neural network architecture. Furthermore, we summarize existing MTSI toolkits with a particular emphasis on the PyPOTS Ecosystem, which provides an integrated and standardized foundation for MTSI research. Finally, we discuss key challenges and future research directions, which give insight for further MTSI research. This survey aims to serve as a valuable resource for researchers and practitioners in the field of time series analysis and missing data imputation tasks. A well-maintained MTSI paper and tool list is available at https://github.com/WenjieDu/Awesome_Imputation.
An Empirical Study of Federated Prompt Learning for Vision Language Model
Authors: Zhihao Wang; Wenke Huang; Tian Chen; Zekun Shi; Guancheng Wan; Yu Qiao; Bin Yang; Jian Wang; Bing Li; Mang Ye
Venue: IJCAI 2025 (main)

Abstract: The Vision Language Model (VLM) excels in aligning vision and language representations, and prompt learning has emerged as a key technique for adapting such models to downstream tasks. However, the application of prompt learning with VLM in federated learning (FL) scenarios remains underexplored. This paper systematically investigates the behavioral differences between language prompt learning (LPT) and vision prompt learning (VPT) under data heterogeneity challenges, including label skew and domain shift. We conduct extensive experiments to evaluate the impact of various FL and prompt configurations, such as client scale, aggregation strategies, and prompt length, to assess the robustness of Federated Prompt Learning (FPL). Furthermore, we explore strategies for enhancing prompt learning in complex scenarios where label skew and domain shift coexist, including leveraging both prompt types when computational resources allow. Our findings offer practical insights into optimizing prompt learning in federated settings, contributing to the broader deployment of VLMs in privacy-preserving environments.
Safety of Embodied Navigation: A Survey
Authors: Zixia Wang; Jia Hu; Ronghui Mu
Venue: IJCAI 2025 (main)

Abstract: As large language models (LLMs) continue to advance and gain influence, the development of embodied AI has accelerated, drawing significant attention, particularly in navigation scenarios. Embodied navigation requires an agent to perceive, interact with, and adapt to its environment while moving toward a specified target in unfamiliar settings. However, the integration of embodied navigation into critical applications raises substantial safety concerns. Given their deployment in dynamic, real-world environments, ensuring the safety of such systems is critical. This survey provides a comprehensive analysis of safety in embodied navigation from multiple perspectives, encompassing attack strategies, defense mechanisms, and evaluation methodologies. Beyond conducting a comprehensive examination of existing safety challenges, mitigation technologies, and various datasets and metrics that assess effectiveness and robustness, we explore unresolved issues and future research directions in embodied navigation safety. These include potential attack methods, mitigation strategies, more reliable evaluation techniques, and the implementation of verification frameworks. By addressing these critical gaps, this survey aims to provide valuable insights that can guide future research toward the development of safer and more reliable embodied navigation systems. Furthermore, the findings of this study have broader implications for enhancing societal safety and increasing industrial efficiency.
Generative Multi-Agent Collaboration in Embodied AI: A Systematic Review
Authors: Di Wu; Xian Wei; Guang Chen; Hao Shen; Bo Jin
Venue: IJCAI 2025 (main)

Abstract: Embodied multi-agent systems (EMAS) have attracted growing attention for their potential to address complex, real-world challenges in areas such as logistics and robotics. Recent advances in foundation models pave the way for generative agents capable of richer communication and adaptive problem-solving. This survey provides a systematic examination of how EMAS can benefit from these generative capabilities. We propose a taxonomy that categorizes EMAS by system architectures and embodiment modalities, emphasizing how collaboration spans both physical and virtual contexts. Central building blocks, perception, planning, communication, and feedback, are then analyzed to illustrate how generative techniques bolster system robustness and flexibility. Through concrete examples, we demonstrate the transformative effects of integrating foundation models into embodied, multi-agent frameworks. Finally, we discuss challenges and future directions, underlining the significant promise of EMAS to reshape the landscape of AI-driven collaboration.
A Comprehensive and Systematic Review for Deep Learning-Based De Novo Peptide Sequencing
Authors: Jun Xia; Jingbo Zhou; Shaorong Chen; Tianze Ling; Stan Z. Li
Venue: IJCAI 2025 (main)

Abstract: Tandem mass spectrometry (MS/MS) has revolutionized the field of proteomics, enabling the high-throughput identification of proteins. However, one of the central challenges in mass spectrometry-based proteomics remains peptide identification, especially in the absence of a comprehensive peptide database. While traditional database search methods compare observed mass spectra to pre-existing protein databases, they are limited by the availability and completeness of these databases. \emph{De novo} peptide sequencing, which derives peptide sequences directly from mass spectra, has emerged as a crucial approach in such cases. In recent years, deep learning has made significant strides in this domain. These methods train deep neural networks for translating mass spectra into peptide sequences without relying on any pre-constructed databases. Despite significant progress, this field still lacks a comprehensive and systematic review. In this paper, we provide the first review of deep learning-based \emph{de novo} peptide sequencing techniques from the perspectives of data types, model architectures, decoding strategies, applications and evaluation metrics. We also identify key challenges and highlight promising avenues for future research, providing a valuable resource for the AI and scientific communities.
A Survey of Optimization Modeling Meets LLMs: Progress and Future Directions
Authors: Ziyang Xiao; Jingrong Xie; Lilin Xu; Shisi Guan; Jingyan Zhu; Xiongwei Han; Xiaojin Fu; WingYin Yu; Han Wu; Wei Shi; Qingcan Kang; Jiahui Duan; Tao Zhong; Mingxuan Yuan; Jia Zeng; Yuan Wang; Gang Chen; Dongxiang Zhang
Venue: IJCAI 2025 (main)

Abstract: By virtue of its great utility in solving real-world problems, optimization modeling has been widely employed for optimal decision-making across various sectors, but it requires substantial expertise from operations research professionals. With the advent of large language models (LLMs), new opportunities have emerged to automate the procedure of mathematical modeling. This survey presents a comprehensive and timely review of recent advancements that cover the entire technical stack, including data synthesis and fine-tuning for the base model, inference frameworks, benchmark datasets, and performance evaluation. In addition, we conducted an in-depth analysis on the quality of benchmark datasets, which was found to have a surprisingly high error rate. We cleaned the datasets and constructed a new leaderboard with fair performance evaluation in terms of base LLM model and datasets. We also build an online portal that integrates resources of cleaned datasets, code and paper repository to benefit the community. Finally, we identify limitations in current methodologies and outline future research opportunities.
A Survey of Pathology Foundation Model: Progress and Future Directions
Authors: Conghao Xiong; Hao Chen; Joseph J. Y. Sung
Venue: IJCAI 2025 (main)

Abstract: Computational pathology, which involves analyzing whole slide images for automated cancer diagnosis, relies on multiple instance learning, where performance depends heavily on the feature extractor and aggregator. Recent Pathology Foundation Models (PFMs), pretrained on large-scale histopathology data, have significantly enhanced both the extractor and aggregator, but they lack a systematic analysis framework. In this survey, we present a hierarchical taxonomy organizing PFMs through a top-down philosophy applicable to foundation model analysis in any domain: model scope, model pretraining, and model design. Additionally, we systematically categorize PFM evaluation tasks into slide-level, patch-level, multimodal, and biological tasks, providing comprehensive benchmarking criteria. Our analysis identifies critical challenges in both PFM development (pathology-specific methodology, end-to-end pretraining, data-model scalability) and utilization (effective adaptation, model maintenance), paving the way for future directions in this promising field. Resources referenced in this survey are available at https://github.com/BearCleverProud/AwesomeWSI.
Tensor Network: from the Perspective of AI4Science and Science4AI
Authors: Junchi Yan; Yehui Tang; Xinyu Ye; Hao Xiong; Xiaoqiu Zhong; Yuhan Wang; Yuan Qi
Venue: IJCAI 2025 (main)

Abstract: Tensor network has been a promising numerical tool for computational problems across science and AI. For their emerging and fast development especially in the intersection between AI and science, this paper tries to present a compact review, regarding both their applications and its own recent technical development including open-source tools. Specifically, we make the observations that tensor network plays a functional role in matrix compression and representation, information fusion, as well as quantum-inspired algorithms, which can be generally regarded as Science4AI in our survey. On the other hand, there is an emerging line of research in tensor network in AI4Science especially like learning quantum many-body physics by using e.g. neural network quantum state. Importantly, we unify tensorization methodologies across classical and modern architectures, and particularly show how tensorization bridges low-order parameter spaces to high-dimensional representations without exponential parameter growth, and further point out their potential use in scientific computing. We conclude the paper with outlook for future trends.
Neuro-Symbolic Artificial Intelligence: Towards Improving the Reasoning Abilities of Large Language Models
Authors: Xiao-Wen Yang; Jie-Jing Shao; Lan-Zhe Guo; Bo-Wen Zhang; Zhi Zhou; Lin-Han Jia; Wang-Zhou Dai; Yu-Feng Li
Venue: IJCAI 2025 (main)

Abstract: Large Language Models (LLMs) have shown promising results across various tasks, yet their reasoning capabilities remain a fundamental challenge. Developing AI systems with strong reasoning capabilities is regarded as a crucial milestone in the pursuit of Artificial General Intelligence (AGI) and has garnered considerable attention from both academia and industry. Various techniques have been explored to enhance the reasoning capabilities of LLMs, with neuro-symbolic approaches being a particularly promising way. This paper comprehensively reviews recent developments in neuro-symbolic approaches for enhancing LLM reasoning. We first present a formalization of reasoning tasks and give a brief introduction to the neuro-symbolic learning paradigm. Then, we discuss neuro-symbolic methods for improving the reasoning capabilities of LLMs from three perspectives: Symbolic->LLM, LLM->Symbolic, and LLM+Symbolic. Finally, we discuss several key challenges and promising future directions. We have also released a GitHub repository including papers and resources related to this survey: https://github.com/LAMDASZ-ML/Awesome-LLM-Reasoning-with-NeSy.