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Yisen Gao

Publications and source records attributed to Yisen Gao.

At least 19 recordsLinked to original sources
arXiv2026

Safe, Persistent, and Evolving Agent Harness for Understanding Partially Observable Worlds

Large language model agents can invoke tools fluently, but enterprise workflows demand more than selecting the right tools: actions must strictly comply with organizational policies, tool feedback often conceals hidden side effects under partial observability, and long-horizon tasks require persistent state tracking across multiple records. To address these challenges, we introduce E-Ledger, a multi-agent harness for safe and persistent execution. E-Ledger employs a code approval layer that checks every proposed action against policy before execution, and maintains a world ledger of verified hidden rules alongside evidence-backed dynamic state. Because hidden rules are typically unknown a priori, we further propose WorldAbduct, an abductive, world-model-driven harness evolution framework. WorldAbduct diagnoses execution trajectories across four complementary views (state consistency, world-observation gap, policy-gate correctness, and goal judgment) to hypothesize latent rules, and verifies them through targeted abductive interactions before integrating them into the ledger. On the enterprise benchmark World of Workflows, E-Ledger with WorldAbduct improves safe task completion across four LLM backbones, outperforming the strongest evolution baseline by 5--15 percentage points. Experiments in ScienceWorld and DiscoveryWorld further show that abductive harness evolution carries over to scientific environments. Our code is available at https://github.com/HKUST-KnowComp/E-LEDGER-WorldAbduct.

cs.AI↗
arXiv2026

Towards In-Parameter Memory Augmentation for Large Language Models

Recently Large Language Models (LLMs) and LLM-based agents increasingly need to incorporate knowledge acquired after pretraining, e.g., domain facts, user preferences, documents, and interaction experience. In-context learning (ICL) and ICL-based agent harness remain flexible, but they consume context capacity and incur repeated discretized encoding cost that grows with context length. \textbf{In-parameter memory} offers a complementary substrate: reusable memory information is represented in model parameters, adapters, or other parameter-like objects that are composed into the forward pass at inference time. This survey focuses on methods that augment LLMs with such parametric memory at deployment: a memory-bearing parameter object is plugged into the forward pass during inference, whether it is acquired before or during deployment. We organize the landscape with two orthogonal axes: \textbf{Parameter Placement}, which includes Embedding, Attention, FFN layers, or Hybrid when two or more layers are used; and \textbf{Parameter Acquisition Time}, which distinguishes methods whose memory object is acquired during deployment (online) from those acquired before it (offline). We clarify boundaries, conduct comparisons, and discuss open directions in interference, safety, co-design with ICL, and recursive self-improvement.

cs.CL↗
arXiv2026

KGPFN: Unlocking the Potential of Knowledge Graph Foundation Model via In-Context Learning

Knowledge graph (KG) foundation models aim to generalize to graphs with unseen entities and relations by learning transferable relational structure. Most existing methods, however, focus on relation-level universality, leaving in-context learning, the other pillar of foundation models, largely unexplored for KG reasoning. Context in KGs is structured and heterogeneous: accurate prediction requires conditioning both on the local neighborhood of the query entities and on global context that summarizes how the query relation behaves across many instances. We propose KGPFN, a KG foundation model built on a Prior-Data Fitted Network (PFN) that combines transferable relational representations with inference-time in-context learning over structured context. KGPFN learns relation representations by message passing on relation graphs and extracts multi-scale local context from the intermediate head representations of a multi-layer NBFNet. It then builds relation-specific global context from positive and negative examples of the query relation, together with their local structural representations, and aggregates this context with feature-level and sample-level attention. Through multi-graph pretraining, KGPFN learns to combine structural representations with labeled contextual evidence without inference-time parameter updates. On 57 knowledge graphs, KGPFN achieves the best average MRR both without and with fine-tuning, and context sensitivity analyses highlight the value of negative context examples. Our code is available at https://github.com/HKUST-KnowComp/KGPFN.

cs.AI↗
arXiv2026

One Hypothesis Is Not Enough: Abductive Reasoning with Agentic Hypothesis Refinement over Knowledge Graphs

Abductive reasoning over knowledge graphs (KGs) seeks a first-order logic hypothesis whose answer set explains a given set of observed entities. Since many hypotheses can explain the same observations, controllable hypothesis generators condition generation on entities, relations, or logical patterns, but they treat generation as a single step. A generated hypothesis may be well-formed and satisfy the given conditions yet still fail to explain the observations, and the model has no mechanism to detect or correct this mismatch. Closing the abductive cycle requires revising a discrete, structured hypothesis, which large language models cannot do reliably, even though they iterate readily in natural language. We propose HypoAgent, an agentic hypothesis refinement framework that treats condition signals not only as expressions of user intent but also as operators that steer generation. A Hypothesis Proposal Agent calls a small trained generator to propose a hypothesis. Root-cause analysis then uses fragment-level coverage to locate branches worth inspecting and gathers neighborhood evidence from the training graph. A Hypothesis Refiner Agent combines this diagnosis with previously generated hypotheses to produce updated conditions and directly revised hypotheses. HypoAgent outperforms one-shot generation in single-turn and multi-turn settings on BioKG, PharmKG8k, and DBpedia50, and in the unconditional setting on DBpedia50. Our code is available at https://github.com/HKUST-KnowComp/HypoAgent.

cs.AI↗
arXiv2026

AgentIdeaBench: Benchmarking Scientific Ideation in the Agent Era

Scientific ideation is the capacity to formulate novel and testable hypotheses from scientific evidence, and autonomous AI scientists depend on it. Existing evaluations largely assess it by asking models to generate ideas from a static, curated set of reference papers. That passive setup departs from the retrieval-and-reasoning workflow of modern AI scientists, and it becomes less discriminative as models improve. We introduce AgentIdeaBench, a multidisciplinary benchmark that evaluates scientific ideation under two matched settings, static observation and active exploration. We report matched Static-Active evaluations for 33 LLMs across 40 densely scored subfields spanning five disciplines, using a multidimensional, literature-verified scoring framework whose critics assess originality against retrieved prior art. Active exploration reveals considerably more capability headroom, and that headroom is unevenly distributed across models. Performance scales about twice as fast as under static observation, and the exploration gain is capability-gated, favoring the strongest models over the weakest. The gain reflects better grounding, improving feasibility, clarity, and specificity while leaving measured originality unchanged under our critics. We further explore Scientific World Modeling, a generation-time loop that refines a draft hypothesis through structured thought experiments. It benefits mid-capability models, and its impact diminishes among frontier models that appear to have internalized such reasoning patterns already. AgentIdeaBench gives future work on scientific ideation a measurement basis suited to the agent era.

cs.AI↗
arXiv2026

DeepRefine: Agentic Knowledge Refinement via Reinforcement Learning

External knowledge enables large language model (LLM) agents to ground their actions and decisions beyond intrinsic parametric memory in open-ended, knowledge-intensive downstream tasks. Yet the quality of the underlying knowledge bases is systematically limited by incompleteness, incorrectness, or 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 reinforcement learning framework for agentic knowledge refinement that evolves the quality of any pre-constructed structured knowledge bases, e.g., knowledge graphs or LLM-Wikis, 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 the interaction history, localizes likely defects, and executes targeted refinement actions for incremental knowledge base updates. To further optimize refinement policies of DeepRefine without golden refinement trajectories, 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.

cs.CL↗
arXiv2026

Does More Retrieved Evidence Help Visual Retrieval-Augmented Generation with Diffusion Language Models?

Visual retrieval-augmented generation (RAG) commonly expands the retrieved evidence set to improve answer-page coverage, implicitly assuming that all available evidence should be passed to the generator. We show that this assumption does not hold for diffusion language models (DLMs): retrieving more pages increases answer-page recall, whereas unconditionally passing all retrieved pages to the generator often reduces answer accuracy, primarily because of semantic conflict. A latent-source analysis explains this mismatch through source-coherence loss in parallel denoising, where position-wise proposals can combine incompatible visual sources into unsupported answers. We further find that such interference is already visible in the first-step answer-block distribution, making it possible to assess evidence before decoding. To preserve retrieval coverage while limiting harmful visual exposure, we propose the Entropy-Based Candidate Filter (ECF), a training-free evidence-admission framework. To reduce irrelevant content within individual candidates, ECF constructs multi-granularity evidence units; to identify beneficial additional evidence, it uses blank-controlled block confidence and retrieval rank to determine whether and which candidate should enter the final context. Across three multimodal DLMs and five visual QA benchmarks, ECF improves answer accuracy by 2.62 percentage points on average over the strongest fixed top-$k$ input and, with LLaDA2.0-Uni, by 2.37 percentage points on average over the best competing training-free result for each dataset. These results show that broader retrieval benefits visual DLM-RAG through selective evidence admission rather than unconditional evidence expansion. Code is publicly available at https://github.com/wjkuser/ECF.

cs.CL↗
arXiv2026

MAFIA: Query-Only Memory Attacks via Probing and Factual Injection against Audited LLM Agents

Memory-augmented LLM agents rely on rich context for long-horizon reasoning and acting, yet their memory modules expose a persistent attack surface for malicious records, making the study of memory poisoning threats imperative. However, existing query-only attacks often fail to remain effective in two realistic and prevalent settings: large-scale benign memory pools and active input auditing. Consequently, current approaches fall short when facing the dual challenges of high retrieval competitiveness and rigorous semantic checks. To overcome these limitations, we propose MAFIA, a query-only Memory Attack framework via probing and Factual Injection against Audit, tailored to this extended threat model. Specifically, MAFIA introduces: (1) a placement strategy that ensures retrieval-competitive injection via memory probing, budget allocation, and scheduling; and (2) a payload design that bypasses audits using compact factual cloaks, preserving malicious effects while maintaining high semantic similarity. Extensive evaluations reveal that MAFIA achieves up to a 90.7% attack success rate while suppressing audit detection from a peak of 83.3% to at most 7.4%, exposing critical vulnerabilities across agentic memory systems. Code will be made publicly available at https://github.com/JiamingChen1234/MAFIA.

cs.AI↗
arXiv2026

PatchWorld: Gradient-Free Optimization of Executable World Models for Agent Environments

World models for interactive text agents must typically be learned from observation-action trajectories alone. Specifically, the environment returns text observations after each action, but does not expose a ground-truth latent state nor an inspectable transition model.A research gap remains in how to induce executable code as a world model in this black-box setting for prediction and agent decision making. 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 decision-making score among evaluated methods (76.4% macro success in live one-step lookahead), matching or exceeding LLM-based 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 agent decision-making utility. This reveals 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.

cs.CL↗
arXiv2026

SING: Synthetic Intention Graph for Scalable Active Tool Discovery in LLM Agents

Large language model (LLM) agents increasingly rely on agent harnesses that manage context, tools, and multi-turn execution, making tools a central interface for acting in realistic digital environments. As harness-connected tool ecosystems expand to hundreds or thousands of APIs, services, and task-specific skills, exhaustive tool schema injection becomes costly and imposes a closed-world assumption that limits agents to a predefined static inventory. Retrieval-augmented tool selection offers a natural alternative, but existing one-shot retrieval methods often fail to align isolated tool descriptions with the agent's true task intention, especially in long-horizon tasks where required capabilities emerge through decomposition, observations, and newly induced subgoals. We propose SING, an intention-aware active tool discovery framework that builds an intention-tool graph linking user intentions, tool capabilities, and tool collaboration patterns, and dynamically retrieves tools according to evolving task states. Using a unified corpus of 7,471 tools, we evaluate SING on three real-world tool-use benchmarks. SING improves Global Recall@5 by up to 59.8% and downstream success rate by up to 28.9% over baselines, while reducing full-corpus tool-schema exposure by 99.8%, demonstrating that intention-aware graph structure enables more accurate and context-efficient tool discovery in large-scale agentic ecosystems.

cs.CL↗
arXiv2026

NGDBench: Towards Neural Graph Data Management

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.

cs.DB↗
arXiv2026

Controllable Logical Hypothesis Generation for Abductive Reasoning in Knowledge Graphs

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. Our code is available at https://github.com/HKUST-KnowComp/CtrlHGen.

cs.AI↗
arXiv2026

Towards LLM-Empowered Knowledge Tracing via LLM-Student Hierarchical Behavior Alignment in Hyperbolic Space

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.

cs.AI↗
arXiv2026

NGDB-Zoo: Towards Efficient and Scalable Neural Graph Databases Training

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.

cs.LG↗
arXiv2026

Unifying Deductive and Abductive Reasoning in Knowledge Graphs with Masked Diffusion Model

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.

cs.AI↗
arXiv2025

Toward a Unified Geometry Understanding: Riemannian Diffusion Framework for Graph Generation and Prediction

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.

cs.LG↗
arXiv2025

Is the Information Bottleneck Robust Enough? Towards Label-Noise Resistant Information Bottleneck Learning

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.

cs.LG↗
arXiv2025

Galaxy Walker: Geometry-aware VLMs For Galaxy-scale Understanding

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.

cs.LG↗