Yisen Gao

Jiaxin Bai, Yue Guo, Yifei Dong et al.

Text-agent environments are typically modeled as partially observable Markov decision processes (POMDPs), assuming that the simulator's latent state and transition dynamics are hidden from the agent. Yet little work has examined whether executable code can be induced to serve as a world model for prediction and planning under partial observability. We introduce PatchWorld, a gradient-free framework that turns offline trajectories into executable Python world models through counterexample-guided code repair. Instead of predicting the next observation with a black-box model, PatchWorld induces symbolic belief-state programs whose action updates can be inspected, replayed, and locally patched. Across seven AgentGym environments, PatchWorld-Simple achieves the highest code-based planning score among evaluated methods, reaching 76.4\% macro success in live one-step lookahead while invoking no LLM calls inside the world-model prediction module itself. We further find that a human-specified residual-memory bias improves surface observation fidelity but weakens decision utility. This exposes a tradeoff in executable world models, since improving observation fidelity can come at the expense of action-discriminative dynamics, and vice versa. Code is available at https://github.com/HKBU-KnowComp/PatchWorld.

Yufei Li, Yisen Gao, Jiaxuan Xiong et al.

Data critical to real-world decision-making is increasingly found within organizations. Such data is heterogeneous, constantly evolving, and only imperfectly captured. However, current data management systems remain largely passive, retrieving what is explicitly stored while offering limited support for uncovering implicit structure or reasoning under noise, incompleteness, and continuous updates. We argue that next-generation data management requires neural capabilities, which can uncover complex latent relationships, distinguish reliable signals from noise, and remain consistent as the underlying data state evolves. To support this direction, we introduce NGDBench, a benchmark across five domains that unifies structured and unstructured sources. NGDBench adopts a graph view because graphs provide a flexible abstraction for modeling complex systems, capturing latent relationships, and subsuming structured formats such as relational tables. Each instance pairs a clean latent graph with a realistically perturbed observed graph. NGDBench supports full Cypher queries and dynamic data management operations. Evaluations of state-of-the-art Text-to-Cypher by LLMs and GraphRAG pipelines reveal that current neural query methods remain sensitive to noise and struggle with dynamic state tracking, highlighting the need for resilient, inference-capable data management. Our code is available at https://github.com/HKUST-KnowComp/NGDBench.

Yisen Gao, Yixi Cai, Tianshi Zheng et al.

Abductive reasoning over knowledge graphs aims to generate logical hypotheses that explain observed entities or facts. Existing controllable hypothesis generation methods allow users to guide this process with explicit conditions, but they remain limited in interactive settings: they struggle to ground evolving natural-language intents across multi-turn dialogues and provide little fine-grained diagnosis when generated hypotheses fail. To address these limitations, we propose HypoAgent, an Agentic framework for interactive abductive Hypothesis Generation over knowledge graphs. HypoAgent integrates three agents: an Intent Recognition Agent that grounds user utterances and dialogue history into executable KG conditions, a Hypothesis Generation Agent that performs controllable hypothesis generation according to the extracted user intention, and a Root Cause Analysis Agent that diagnoses unreliable hypothesis fragments and leverages KG neighborhood probing to identify supported refinements. Experiments on commonsense and biomedical domain-specific knowledge graphs demonstrate that HypoAgent achieves state-of-the-art semantic similarity under single-turn, multi-turn, and unconditional settings. Our code is available at https://github.com/HKUST-KnowComp/HypoAgent.

Yisen Gao, Jiaxin Bai, Haoyu Huang et al.

Knowledge graph (KG) foundation models aim to generalize across graphs with unseen entities and relations by learning transferable relational structure. However, most existing methods primarily emphasize relation-level universality, while in-context learning, the other pillar of foundation models remains under-explored for KG reasoning. In KGs, context is inherently structured and heterogeneous: effective prediction requires conditioning on the local context around the query entities as well as the global context that summarizes how a relation behaves across many instances. We propose KGPFN, a KG foundation model using Prior-data Fitted Network that unifies transferable relational regularities with inference-time in-context learning from structured context. KGPFN first learns relation representations via message passing on relation graphs to capture cross-graph relational invariances. For query-specific reasoning, it encodes local neighborhoods using a multi-layer NBFNet as local context. To enable ICL at global scale, it constructs relation-specific global context by retrieving a large set of instances of the query relation together with their local neighborhoods, and aggregates them within a Prior-Data Fitted Network framework that combines feature-level and sample-level attention. Through multi-graph pretraining on diverse KGs, KGPFN learns when to instantiate reusable patterns and when to override them using contextual evidence. Experiments on 57 KG benchmarks demonstrate that KGPFN achieves strong adaptation to previously unseen graphs through in-context learning alone, consistently outperforming competitive fine-tuned KG foundation models. Our code is available at https://github.com/HKUST-KnowComp/KGPFN.

Yi Huang, Qingyun Sun, Yisen Gao et al.

The Information Bottleneck (IB) principle facilitates effective representation learning by preserving label-relevant information while compressing irrelevant information. However, its strong reliance on accurate labels makes it inherently vulnerable to label noise, prevalent in real-world scenarios, resulting in significant performance degradation and overfitting. To address this issue, we propose LaT-IB, a novel Label-Noise ResistanT Information Bottleneck method which introduces a "Minimal-Sufficient-Clean" (MSC) criterion. Instantiated as a mutual information regularizer to retain task-relevant information while discarding noise, MSC addresses standard IB's vulnerability to noisy label supervision. To achieve this, LaT-IB employs a noise-aware latent disentanglement that decomposes the latent representation into components aligned with to the clean label space and the noise space. Theoretically, we first derive mutual information bounds for each component of our objective including prediction, compression, and disentanglement, and moreover prove that optimizing it encourages representations invariant to input noise and separates clean and noisy label information. Furthermore, we design a three-phase training framework: Warmup, Knowledge Injection and Robust Training, to progressively guide the model toward noise-resistant representations. Extensive experiments demonstrate that LaT-IB achieves superior robustness and efficiency under label noise, significantly enhancing robustness and applicability in real-world scenarios with label noise.

Xingcheng Fu, Shengpeng Wang, Yisen Gao et al.

Knowledge Tracing (KT) diagnoses students' concept mastery through continuous learning state monitoring in education.Existing methods primarily focus on studying behavioral sequences based on ID or textual information.While existing methods rely on ID-based sequences or shallow textual features, they often fail to capture (1) the hierarchical evolution of cognitive states and (2) individualized problem difficulty perception due to limited semantic modeling. Therefore, this paper proposes a Large Language Model Hyperbolic Aligned Knowledge Tracing(L-HAKT). First, the teacher agent deeply parses question semantics and explicitly constructs hierarchical dependencies of knowledge points; the student agent simulates learning behaviors to generate synthetic data. Then, contrastive learning is performed between synthetic and real data in hyperbolic space to reduce distribution differences in key features such as question difficulty and forgetting patterns. Finally, by optimizing hyperbolic curvature, we explicitly model the tree-like hierarchical structure of knowledge points, precisely characterizing differences in learning curve morphology for knowledge points at different levels. Extensive experiments on four real-world educational datasets validate the effectiveness of our Large Language Model Hyperbolic Aligned Knowledge Tracing (L-HAKT) framework.

Zhongwei Xie, Jiaxin Bai, Shujie Liu et al.

Neural Graph Databases (NGDBs) facilitate complex logical reasoning over incomplete knowledge structures, yet their training efficiency and expressivity are constrained by rigid query-level batching and structure-exclusive embeddings. We present NGDB-Zoo, a unified framework that resolves these bottlenecks by synergizing operator-level training with semantic augmentation. By decoupling logical operators from query topologies, NGDB-Zoo transforms the training loop into a dynamically scheduled data-flow execution, enabling multi-stream parallelism and achieving a $1.8\times$ - $6.8\times$ throughput compared to baselines. Furthermore, we formalize a decoupled architecture to integrate high-dimensional semantic priors from Pre-trained Text Encoders (PTEs) without triggering I/O stalls or memory overflows. Extensive evaluations on six benchmarks, including massive graphs like ogbl-wikikg2 and ATLAS-Wiki, demonstrate that NGDB-Zoo maintains high GPU utilization across diverse logical patterns and significantly mitigates representation friction in hybrid neuro-symbolic reasoning.

Haoyu Huang, Jiaxin Bai, Shujie Liu et al.

Agent-compiled knowledge bases provide persistent external knowledge for large language model (LLM) agents in open-ended, knowledge-intensive downstream tasks. Yet their quality is systematically limited by \emph{incompleteness}, \emph{incorrectness}, and \emph{redundancy}, manifested as missing evidence or cross-document links, low-confidence or imprecise claims, and ambiguous or coreference resolution issues. Such defects compound under iterative use, degrading retrieval fidelity and downstream task performance. We present \textbf{DeepRefine}, a general LLM-based reasoning model for \emph{agent-compiled knowledge refinement} that improves the quality of any pre-constructed knowledge bases with user queries to make it more suitable for the downstream tasks. DeepRefine performs multi-turn interactions with the knowledge base and conducts abductive diagnosis over interaction history, localizes likely defects, and executes targeted refinement actions for incremental knowledge base updates. To optimize refinement policies of DeepRefine without gold references, we introduce a Gain-Beyond-Draft (GBD) reward and train the reasoning process end-to-end via reinforcement learning. Extensive experiments demonstrate consistent downstream gains over strong baselines.

Zihao Guo, Qingyun Sun, Haonan Yuan et al.

Real-world graphs have inherently complex and diverse topological patterns, known as topological heterogeneity. Most existing works learn graph representation in a single constant curvature space that is insufficient to match the complex geometric shapes, resulting in low-quality embeddings with high distortion. This also constitutes a critical challenge for graph foundation models, which are expected to uniformly handle a wide variety of diverse graph data. Recent studies have indicated that product manifold gains the possibility to address topological heterogeneity. However, the product manifold is still homogeneous, which is inadequate and inflexible for representing the mixed heterogeneous topology. In this paper, we propose a novel Graph Mixture of Riemannian Experts (GraphMoRE) framework to effectively tackle topological heterogeneity by personalized fine-grained topology geometry pattern preservation. Specifically, to minimize the embedding distortion, we propose a topology-aware gating mechanism to select the optimal embedding space for each node. By fusing the outputs of diverse Riemannian experts with learned gating weights, we construct personalized mixed curvature spaces for nodes, effectively embedding the graph into a heterogeneous manifold with varying curvatures at different points. Furthermore, to fairly measure pairwise distances between different embedding spaces, we present a concise and effective alignment strategy. Extensive experiments on real-world and synthetic datasets demonstrate that our method achieves superior performance with lower distortion, highlighting its potential for modeling complex graphs with topological heterogeneity, and providing a novel architectural perspective for graph foundation models.

Jiaxin Bai, Zihao Wang, Yukun Zhou et al. · tsinghua

Graph databases (GDBs) like Neo4j and TigerGraph excel at handling interconnected data but lack advanced inference capabilities. Neural Graph Databases (NGDBs) address this by integrating Graph Neural Networks (GNNs) for predictive analysis and reasoning over incomplete or noisy data. However, NGDBs rely on predefined queries and lack autonomy and adaptability. This paper introduces Agentic Neural Graph Databases (Agentic NGDBs), which extend NGDBs with three core functionalities: autonomous query construction, neural query execution, and continuous learning. We identify ten key challenges in realizing Agentic NGDBs: semantic unit representation, abductive reasoning, scalable query execution, and integration with foundation models like large language models (LLMs). By addressing these challenges, Agentic NGDBs can enable intelligent, self-improving systems for modern data-driven applications, paving the way for adaptable and autonomous data management solutions.

Yisen Gao, Jiaxin Bai, Tianshi Zheng et al.

Abductive reasoning in knowledge graphs aims to generate plausible logical hypotheses from observed entities, with broad applications in areas such as clinical diagnosis and scientific discovery. However, due to a lack of controllability, a single observation may yield numerous plausible but redundant or irrelevant hypotheses on large-scale knowledge graphs. To address this limitation, we introduce the task of controllable hypothesis generation to improve the practical utility of abductive reasoning. This task faces two key challenges when controlling for generating long and complex logical hypotheses: hypothesis space collapse and hypothesis oversensitivity. To address these challenges, we propose CtrlHGen, a Controllable logcial Hypothesis Generation framework for abductive reasoning over knowledge graphs, trained in a two-stage paradigm including supervised learning and subsequent reinforcement learning. To mitigate hypothesis space collapse, we design a dataset augmentation strategy based on sub-logical decomposition, enabling the model to learn complex logical structures by leveraging semantic patterns in simpler components. To address hypothesis oversensitivity, we incorporate smoothed semantic rewards including Dice and Overlap scores, and introduce a condition-adherence reward to guide the generation toward user-specified control constraints. Extensive experiments on three benchmark datasets demonstrate that our model not only better adheres to control conditions but also achieves superior semantic similarity performance compared to baselines.

Xingcheng Fu, Jian Wang, Yisen Gao et al.

Graph neural networks(GNNs) have been demonstrated to depend on whether the node effective information is sufficiently passing. Discrete curvature (Ricci curvature) is used to study graph connectivity and information propagation efficiency with a geometric perspective, and has been raised in recent years to explore the efficient message-passing structure of GNNs. However, most empirical studies are based on directly observed graph structures or heuristic topological assumptions and lack in-depth exploration of underlying optimal information transport structures for downstream tasks. We suggest that graph curvature optimization is more in-depth and essential than directly rewiring or learning for graph structure with richer message-passing characterization and better information transport interpretability. From both graph geometry and information theory perspectives, we propose the novel Discrete Curvature Graph Information Bottleneck (CurvGIB) framework to optimize the information transport structure and learn better node representations simultaneously. CurvGIB advances the Variational Information Bottleneck (VIB) principle for Ricci curvature optimization to learn the optimal information transport pattern for specific downstream tasks. The learned Ricci curvature is used to refine the optimal transport structure of the graph, and the node representation is fully and efficiently learned. Moreover, for the computational complexity of Ricci curvature differentiation, we combine Ricci flow and VIB to deduce a curvature optimization approximation to form a tractable IB objective function. Extensive experiments on various datasets demonstrate the superior effectiveness and interpretability of CurvGIB.

Xingcheng Fu, Yisen Gao, Beining Yang et al.

Dataset condensation has significantly improved model training efficiency, but its application on devices with different computing power brings new requirements for different data sizes. Thus, condensing multiple scale graphs simultaneously is the core of achieving efficient training in different on-device scenarios. Existing efficient works for multi-scale graph dataset condensation mainly perform efficient approximate computation in scale order (large-to-small or small-to-large scales). However, for non-Euclidean structures of sparse graph data, these two commonly used paradigms for multi-scale graph dataset condensation have serious scaling down degradation and scaling up collapse problems of a graph. The main bottleneck of the above paradigms is whether the effective information of the original graph is fully preserved when consenting to the primary sub-scale (the first of multiple scales), which determines the condensation effect and consistency of all scales. In this paper, we proposed a novel GNN-centric Bi-directional Multi-Scale Graph Dataset Condensation (BiMSGC) framework, to explore unifying paradigms by operating on both large-to-small and small-to-large for multi-scale graph condensation. Based on the mutual information theory, we estimate an optimal ``meso-scale'' to obtain the minimum necessary dense graph preserving the maximum utility information of the original graph, and then we achieve stable and consistent ``bi-directional'' condensation learning by optimizing graph eigenbasis matching with information bottleneck on other scales. Encouraging empirical results on several datasets demonstrates the significant superiority of the proposed framework in graph condensation at different scales.

Tianyu Chen, Xingcheng Fu, Yisen Gao et al.

Modern vision-language models (VLMs) develop patch embedding and convolution backbone within vector space, especially Euclidean ones, at the very founding. When expanding VLMs to a galaxy scale for understanding astronomical phenomena, the integration of spherical space for planetary orbits and hyperbolic spaces for black holes raises two formidable challenges. a) The current pre-training model is confined to Euclidean space rather than a comprehensive geometric embedding. b) The predominant architecture lacks suitable backbones for anisotropic physical geometries. In this paper, we introduced Galaxy-Walker, a geometry-aware VLM, for the universe-level vision understanding tasks. We proposed the geometry prompt that generates geometry tokens by random walks across diverse spaces on a multi-scale physical graph, along with a geometry adapter that compresses and reshapes the space anisotropy in a mixture-of-experts manner. Extensive experiments demonstrate the effectiveness of our approach, with Galaxy-Walker achieving state-of-the-art performance in both galaxy property estimation ($R^2$ scores up to $0.91$) and morphology classification tasks (up to $+0.17$ F1 improvement in challenging features), significantly outperforming both domain-specific models and general-purpose VLMs.

Yisen Gao, Jiaxin Bai, Yi Huang et al.

Deductive and abductive reasoning are two critical paradigms for analyzing knowledge graphs, enabling applications from financial query answering to scientific discovery. Deductive reasoning on knowledge graphs usually involves retrieving entities that satisfy a complex logical query, while abductive reasoning generates plausible logical hypotheses from observations. Despite their clear synergistic potential, where deduction can validate hypotheses and abduction can uncover deeper logical patterns, existing methods address them in isolation. To bridge this gap, we propose DARK, a unified framework for Deductive and Abductive Reasoning in Knowledge graphs. As a masked diffusion model capable of capturing the bidirectional relationship between queries and conclusions, DARK has two key innovations. First, to better leverage deduction for hypothesis refinement during abductive reasoning, we introduce a self-reflective denoising process that iteratively generates and validates candidate hypotheses against the observed conclusion. Second, to discover richer logical associations, we propose a logic-exploration reinforcement learning approach that simultaneously masks queries and conclusions, enabling the model to explore novel reasoning compositions. Extensive experiments on multiple benchmark knowledge graphs show that DARK achieves state-of-the-art performance on both deductive and abductive reasoning tasks, demonstrating the significant benefits of our unified approach.

Yisen Gao, Xingcheng Fu, Qingyun Sun et al.

Graph diffusion models have made significant progress in learning structured graph data and have demonstrated strong potential for predictive tasks. Existing approaches typically embed node, edge, and graph-level features into a unified latent space, modeling prediction tasks including classification and regression as a form of conditional generation. However, due to the non-Euclidean nature of graph data, features of different curvatures are entangled in the same latent space without releasing their geometric potential. To address this issue, we aim to construt an ideal Riemannian diffusion model to capture distinct manifold signatures of complex graph data and learn their distribution. This goal faces two challenges: numerical instability caused by exponential mapping during the encoding proces and manifold deviation during diffusion generation. To address these challenges, we propose GeoMancer: a novel Riemannian graph diffusion framework for both generation and prediction tasks. To mitigate numerical instability, we replace exponential mapping with an isometric-invariant Riemannian gyrokernel approach and decouple multi-level features onto their respective task-specific manifolds to learn optimal representations. To address manifold deviation, we introduce a manifold-constrained diffusion method and a self-guided strategy for unconditional generation, ensuring that the generated data remains aligned with the manifold signature. Extensive experiments validate the effectiveness of our approach, demonstrating superior performance across a variety of tasks.

Xingcheng Fu, Yisen Gao, Yuecen Wei et al.

Diffusion models have made significant contributions to computer vision, sparking a growing interest in the community recently regarding the application of them to graph generation. Existing discrete graph diffusion models exhibit heightened computational complexity and diminished training efficiency. A preferable and natural way is to directly diffuse the graph within the latent space. However, due to the non-Euclidean structure of graphs is not isotropic in the latent space, the existing latent diffusion models effectively make it difficult to capture and preserve the topological information of graphs. To address the above challenges, we propose a novel geometrically latent diffusion framework HypDiff. Specifically, we first establish a geometrically latent space with interpretability measures based on hyperbolic geometry, to define anisotropic latent diffusion processes for graphs. Then, we propose a geometrically latent diffusion process that is constrained by both radial and angular geometric properties, thereby ensuring the preservation of the original topological properties in the generative graphs. Extensive experimental results demonstrate the superior effectiveness of HypDiff for graph generation with various topologies.