arXiv subjects

Yuan He

Publications and source records attributed to Yuan He.

At least 37 records · Page 2Linked to original sources

arXiv2026

What Breaks Knowledge Graph based RAG? Benchmarking and Empirical Insights into Reasoning under Incomplete Knowledge

Knowledge Graph-based Retrieval-Augmented Generation (KG-RAG) is an increasingly explored approach for combining the reasoning capabilities of large language models with the structured evidence of knowledge graphs. However, current evaluation practices fall short: existing benchmarks often include questions that can be directly answered using existing triples in KG, making it unclear whether models perform reasoning or simply retrieve answers directly. Moreover, inconsistent evaluation metrics and lenient answer matching criteria further obscure meaningful comparisons. In this work, we introduce a general method for constructing benchmarks and present BRINK (Benchmark for Reasoning under Incomplete Knowledge) to systematically assess KG-RAG methods under knowledge incompleteness. Our empirical results show that current KG-RAG methods have limited reasoning ability under missing knowledge, often rely on internal memorization, and exhibit varying degrees of generalization depending on their design.

cs.AI↗

arXiv2025

Necking of epithelial tissues with cellular topological transition

As the cover of embryos and adult organisms, epithelial tissues are subjected to substantial mechanical forces in tissue morphogenesis. However, the finite deformation behaviors of epithelial tissues remain largely unexplored. This study combines discrete vertex simulations with a multiscale constitutive model to investigate the necking behavior of epithelial tissues. In the multiscale model, the shape changes and topological transitions of single cells are mapped to the elastic and inelastic tissue deformations via a mean-field formulation. Our results show that the necking bifurcation of a stretched tissue arises from cellular topological transitions. The bifurcation condition and the steady state of necking propagation are predicted from the constitutive model and validated by vertex simulations. Furthermore, we find that topological defects in disordered tissues facilitate necking bifurcation but impede its propagation. These defects also induce the necked region to collapse into a thin thread, as observed in real tissues. Together, our work provides valuable insights into the deformation behaviors of epithelial tissues.

physics.bio-ph↗

arXiv2025

GR-Agent: Adaptive Graph Reasoning Agent under Incomplete Knowledge

Large language models (LLMs) achieve strong results on knowledge graph question answering (KGQA), but most benchmarks assume complete knowledge graphs (KGs) where direct supporting triples exist. This reduces evaluation to shallow retrieval and overlooks the reality of incomplete KGs, where many facts are missing and answers must be inferred from existing facts. We bridge this gap by proposing a methodology for constructing benchmarks under KG incompleteness, which removes direct supporting triples while ensuring that alternative reasoning paths required to infer the answer remain. Experiments on benchmarks constructed using our methodology show that existing methods suffer consistent performance degradation under incompleteness, highlighting their limited reasoning ability. To overcome this limitation, we present the Adaptive Graph Reasoning Agent (GR-Agent). It first constructs an interactive environment from the KG, and then formalizes KGQA as agent environment interaction within this environment. GR-Agent operates over an action space comprising graph reasoning tools and maintains a memory of potential supporting reasoning evidence, including relevant relations and reasoning paths. Extensive experiments demonstrate that GR-Agent outperforms non-training baselines and performs comparably to training-based methods under both complete and incomplete settings.

cs.AI↗

arXiv2025

Conceptual Design of the Muonium-to-Antimuonium Conversion Experiment (MACE)

The spontaneous conversion of muonium to antimuonium is one of the interesting charged lepton flavor violation phenomena offering a sensitive probe of potential new physics and serving as a tool to constrain the parameter space beyond the Standard Model. The Muonium-to-Antimuonium Conversion Experiment (MACE) is designed to utilize a high-intensity muon beam, a Michel electron magnetic spectrometer, a positron transport system, and a positron detection system, to either discover or constrain this rare process with a conversion probability of $\mathcal{O}(10^{-13})$. This article presents an overview of the theoretical framework as well as a detailed description of the experimental design for the search for muonium-to-antimuonium conversion.

hep-ex↗

arXiv2025

Self-Exploring Language Models for Explainable Link Forecasting on Temporal Graphs via Reinforcement Learning

Forecasting future links is a central task in temporal graph (TG) reasoning, requiring models to leverage historical interactions to predict upcoming ones. Traditional neural approaches, such as temporal graph neural networks, achieve strong performance but lack explainability and cannot be applied to unseen graphs without retraining. Recent studies have begun to explore using large language models (LLMs) for graph reasoning, but most of them are constrained to static graphs or small synthetic TGs and lack the evaluation of the quality of reasoning traces generated by LLMs. In this work, we present Reasoning-Enhanced Learning for Temporal Graphs (ReaL-TG), a reinforcement learning framework that fine-tunes LLMs to perform explainable link forecasting on real-world TGs. ReaL-TG uses outcome-based reward to encourage models to self-explore reasoning strategies from graph structure and to produce explanations that directly justify their predictions. To enable evaluation on LLM-generated reasoning traces, we propose a new evaluation protocol combining ranking metrics with an LLM-as-a-Judge system that assesses both the quality of reasoning and the impact of hallucinations. Experiments with ReaL-TG-4B, obtained by fine-tuning Qwen3-4B under our framework, show that it outperforms much larger frontier LLMs, including GPT-5 mini, on ranking metrics, while producing high-quality explanations confirmed by both the LLM judge and human evaluation.

cs.AI↗

arXiv2025

A Deep Learning System for Rapid and Accurate Warning of Acute Aortic Syndrome on Non-contrast CT in China

The accurate and timely diagnosis of acute aortic syndromes (AAS) in patients presenting with acute chest pain remains a clinical challenge. Aortic CT angiography (CTA) is the imaging protocol of choice in patients with suspected AAS. However, due to economic and workflow constraints in China, the majority of suspected patients initially undergo non-contrast CT as the initial imaging testing, and CTA is reserved for those at higher risk. In this work, we present an artificial intelligence-based warning system, iAorta, using non-contrast CT for AAS identification in China, which demonstrates remarkably high accuracy and provides clinicians with interpretable warnings. iAorta was evaluated through a comprehensive step-wise study. In the multi-center retrospective study (n = 20,750), iAorta achieved a mean area under the receiver operating curve (AUC) of 0.958 (95% CI 0.950-0.967). In the large-scale real-world study (n = 137,525), iAorta demonstrated consistently high performance across various non-contrast CT protocols, achieving a sensitivity of 0.913-0.942 and a specificity of 0.991-0.993. In the prospective comparative study (n = 13,846), iAorta demonstrated the capability to significantly shorten the time to correct diagnostic pathway. For the prospective pilot deployment that we conducted, iAorta correctly identified 21 out of 22 patients with AAS among 15,584 consecutive patients presenting with acute chest pain and under non-contrast CT protocol in the emergency department (ED) and enabled the average diagnostic time of these 21 AAS positive patients to be 102.1 (75-133) mins. Last, the iAorta can help avoid delayed or missed diagnosis of AAS in settings where non-contrast CT remains the unavoidable the initial or only imaging test in resource-constrained regions and in patients who cannot or did not receive intravenous contrast.

eess.IV↗

arXiv2025

Schema Generation for Large Knowledge Graphs Using Large Language Models

Schemas play a vital role in ensuring data quality and supporting usability in the Semantic Web and natural language processing. Traditionally, their creation demands substantial involvement from knowledge engineers and domain experts. Leveraging the impressive capabilities of large language models (LLMs) in tasks like ontology engineering, we explore schema generation using LLMs. To bridge the resource gap, we introduce two datasets: YAGO Schema and Wikidata EntitySchema, along with novel evaluation metrics. The LLM-based pipelines utilize local and global information from knowledge graphs (KGs) to generate schemas in Shape Expressions (ShEx). Experiments demonstrate LLMs' strong potential in producing high-quality ShEx schemas, paving the way for scalable, automated schema generation for large KGs. Furthermore, our benchmark introduces a new challenge for structured generation, pushing the limits of LLMs on syntactically rich formalisms.

cs.AI↗

arXiv2025

Merging Bodies, Dividing Conflict: Body-Swapping in Mixed Reality Increases Closeness Yet Weakens the Joint Simon Effect

Mixed Reality (MR) presents novel opportunities to investigate how individuals perceive themselves and others during shared, augmented experiences within a common physical environment. Previous research has demonstrated that users can embody avatars in MR, temporarily extending their sense of self. However, there has been limited exploration of body-swapping, a condition in which two individuals simultaneously inhabit each other's avatars, and its potential effects on social interaction in immersive environments. To address this gap, we adapted the Joint Simon Task (JST), a well-established implicit paradigm, to examine how body-swapping influences the cognitive and perceptual boundaries between self and other. Our results indicate that body-swapping led participants to experience themselves and their partner as functioning like a single, unified system, as in two bodies operating as one agent. This suggests possible cognitive and perceptual changes that go beyond simple collaboration. Our findings have significant implications for the design of MR systems intended to support collaboration, empathy, social learning, and therapeutic interventions through shared embodiment.

cs.HC↗

arXiv2025

Evaluating Knowledge Graph Based Retrieval Augmented Generation Methods under Knowledge Incompleteness

Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) is a technique that enhances Large Language Model (LLM) inference in tasks like Question Answering (QA) by retrieving relevant information from knowledge graphs (KGs). However, real-world KGs are often incomplete, meaning that essential information for answering questions may be missing. Existing benchmarks do not adequately capture the impact of KG incompleteness on KG-RAG performance. In this paper, we systematically evaluate KG-RAG methods under incomplete KGs by removing triples using different methods and analyzing the resulting effects. We demonstrate that KG-RAG methods are sensitive to KG incompleteness, highlighting the need for more robust approaches in realistic settings.

cs.AI↗

arXiv2025

ArgRAG: Explainable Retrieval Augmented Generation using Quantitative Bipolar Argumentation

Retrieval-Augmented Generation (RAG) enhances large language models by incorporating external knowledge, yet suffers from critical limitations in high-stakes domains -- namely, sensitivity to noisy or contradictory evidence and opaque, stochastic decision-making. We propose ArgRAG, an explainable, and contestable alternative that replaces black-box reasoning with structured inference using a Quantitative Bipolar Argumentation Framework (QBAF). ArgRAG constructs a QBAF from retrieved documents and performs deterministic reasoning under gradual semantics. This allows faithfully explaining and contesting decisions. Evaluated on two fact verification benchmarks, PubHealth and RAGuard, ArgRAG achieves strong accuracy while significantly improving transparency.

cs.AI↗

arXiv2025

Multibeam High Throughput Satellite: Hardware Foundation, Resource Allocation, and Precoding

With its wide coverage and uninterrupted service, satellite communication is a critical technology for next-generation 6G communications. High throughput satellite (HTS) systems, utilizing multipoint beam and frequency multiplexing techniques, enable satellite communication capacity of up to Tbps to meet the growing traffic demand. Therefore, it is imperative to review the-state-of-the-art of multibeam HTS systems and identify their associated challenges and perspectives. Firstly, we summarize the multibeam HTS hardware foundations, including ground station systems, on-board payloads, and user terminals. Subsequently, we review the flexible on-board radio resource allocation approaches of bandwidth, power, time slot, and joint allocation schemes of HTS systems to optimize resource utilization and cater to non-uniform service demand. Additionally, we survey multibeam precoding methods for the HTS system to achieve full-frequency reuse and interference cancellation, which are classified according to different deployments such as single gateway precoding, multiple gateway precoding, on-board precoding, and hybrid on-board/on-ground precoding. Finally, we disscuss the challenges related to Q/V band link outage, time and frequency synchronization of gateways, the accuracy of channel state information (CSI), payload light-weight development, and the application of deep learning (DL). Research on these topics will contribute to enhancing the performance of HTS systems and finally delivering high-speed data to areas underserved by terrestrial networks.

eess.SP↗

arXiv2025

Language Models as Ontology Encoders

OWL (Web Ontology Language) ontologies which are able to formally represent complex knowledge and support semantic reasoning have been widely adopted across various domains such as healthcare and bioinformatics. Recently, ontology embeddings have gained wide attention due to its potential to infer plausible new knowledge and approximate complex reasoning. However, existing methods face notable limitations: geometric model-based embeddings typically overlook valuable textual information, resulting in suboptimal performance, while the approaches that incorporate text, which are often based on language models, fail to preserve the logical structure. In this work, we propose a new ontology embedding method OnT, which tunes a Pretrained Language Model (PLM) via geometric modeling in a hyperbolic space for effectively incorporating textual labels and simultaneously preserving class hierarchies and other logical relationships of Description Logic EL. Extensive experiments on four real-world ontologies show that OnT consistently outperforms the baselines including the state-of-the-art across both tasks of prediction and inference of axioms. OnT also demonstrates strong potential in real-world applications, indicated by its robust transfer learning abilities and effectiveness in real cases of constructing a new ontology from SNOMED CT. Data and code are available at https://github.com/HuiYang1997/OnT.

cs.AI↗

arXiv2025

Supposedly Equivalent Facts That Aren't? Entity Frequency in Pre-training Induces Asymmetry in LLMs

Understanding and mitigating hallucinations in Large Language Models (LLMs) is crucial for ensuring reliable content generation. While previous research has primarily focused on "when" LLMs hallucinate, our work explains "why" and directly links model behaviour to the pre-training data that forms their prior knowledge. Specifically, we demonstrate that an asymmetry exists in the recognition of logically equivalent facts, which can be attributed to frequency discrepancies of entities appearing as subjects versus objects. Given that most pre-training datasets are inaccessible, we leverage the fully open-source OLMo series by indexing its Dolma dataset to estimate entity frequencies. Using relational facts (represented as triples) from Wikidata5M, we construct probing datasets to isolate this effect. Our experiments reveal that facts with a high-frequency subject and a low-frequency object are better recognised than their inverse, despite their logical equivalence. The pattern reverses in low-to-high frequency settings, and no statistically significant asymmetry emerges when both entities are high-frequency. These findings highlight the influential role of pre-training data in shaping model predictions and provide insights for inferring the characteristics of pre-training data in closed or partially closed LLMs.

cs.CL↗

arXiv2025

Distilling Tool Knowledge into Language Models via Back-Translated Traces

Large language models (LLMs) often struggle with mathematical problems that require exact computation or multi-step algebraic reasoning. Tool-integrated reasoning (TIR) offers a promising solution by leveraging external tools such as code interpreters to ensure correctness, but it introduces inference-time dependencies that hinder scalability and deployment. In this work, we propose a new paradigm for distilling tool knowledge into LLMs purely through natural language. We first construct a Solver Agent that solves math problems by interleaving planning, symbolic tool calls, and reflective reasoning. Then, using a back-translation pipeline powered by multiple LLM-based agents, we convert interleaved TIR traces into natural language reasoning traces. A Translator Agent generates explanations for individual tool calls, while a Rephrase Agent merges them into a fluent and globally coherent narrative. Empirically, we show that fine-tuning a small open-source model on these synthesized traces enables it to internalize both tool knowledge and structured reasoning patterns, yielding gains on competition-level math benchmarks without requiring tool access at inference.

cs.LG↗

arXiv2025

DyGMamba: Efficiently Modeling Long-Term Temporal Dependency on Continuous-Time Dynamic Graphs with State Space Models

Learning useful representations for continuous-time dynamic graphs (CTDGs) is challenging, due to the concurrent need to span long node interaction histories and grasp nuanced temporal details. In particular, two problems emerge: (1) Encoding longer histories requires more computational resources, making it crucial for CTDG models to maintain low computational complexity to ensure efficiency; (2) Meanwhile, more powerful models are needed to identify and select the most critical temporal information within the extended context provided by longer histories. To address these problems, we propose a CTDG representation learning model named DyGMamba, originating from the popular Mamba state space model (SSM). DyGMamba first leverages a node-level SSM to encode the sequence of historical node interactions. Another time-level SSM is then employed to exploit the temporal patterns hidden in the historical graph, where its output is used to dynamically select the critical information from the interaction history. We validate DyGMamba experimentally on the dynamic link prediction task. The results show that our model achieves state-of-the-art in most cases. DyGMamba also maintains high efficiency in terms of computational resources, making it possible to capture long temporal dependencies with a limited computation budget.

cs.LG↗

arXiv2025

Predicate-Conditional Conformalized Answer Sets for Knowledge Graph Embeddings

Uncertainty quantification in Knowledge Graph Embedding (KGE) methods is crucial for ensuring the reliability of downstream applications. A recent work applies conformal prediction to KGE methods, providing uncertainty estimates by generating a set of answers that is guaranteed to include the true answer with a predefined confidence level. However, existing methods provide probabilistic guarantees averaged over a reference set of queries and answers (marginal coverage guarantee). In high-stakes applications such as medical diagnosis, a stronger guarantee is often required: the predicted sets must provide consistent coverage per query (conditional coverage guarantee). We propose CondKGCP, a novel method that approximates predicate-conditional coverage guarantees while maintaining compact prediction sets. CondKGCP merges predicates with similar vector representations and augments calibration with rank information. We prove the theoretical guarantees and demonstrate empirical effectiveness of CondKGCP by comprehensive evaluations.

cs.AI↗

arXiv2025

Preserving phase coherence and linearity in cat qubits with exponential bit-flip suppression

Cat qubits, a type of bosonic qubit encoded in a harmonic oscillator, can exhibit an exponential noise bias against bit-flip errors with increasing mean photon number. Here, we focus on cat qubits stabilized by two-photon dissipation, where pairs of photons are added and removed from a harmonic oscillator by an auxiliary, lossy buffer mode. This process requires a large loss rate and strong nonlinearities of the buffer mode that must not degrade the coherence and linearity of the oscillator. In this work, we show how to overcome this challenge by coloring the loss environment of the buffer mode with a multi-pole filter and optimizing the circuit to take into account additional inductances in the buffer mode. Using these techniques, we achieve near-ideal enhancement of cat-qubit bit-flip times with increasing photon number, reaching over $0.1$ seconds with a mean photon number of only $4$. Concurrently, our cat qubit remains highly phase coherent, with phase-flip times corresponding to an effective lifetime of $T_{1,\text{eff}} \simeq 70$ $μ$s, comparable with the bare oscillator lifetime. We achieve this performance even in the presence of an ancilla transmon, used for reading out the cat qubit states, by engineering a tunable oscillator-ancilla dispersive coupling. Furthermore, the low nonlinearity of the harmonic oscillator mode allows us to perform pulsed cat-qubit stabilization, an important control primitive, where the stabilization can remain off for a significant fraction (e.g., two thirds) of a $3~\mathrm{μs}$ cycle without degrading bit-flip times. These advances are important for the realization of scalable error-correction with cat qubits, where large noise bias and low phase-flip error rate enable the use of hardware-efficient outer error-correcting codes.

quant-ph↗

arXiv2025

BIFROST: Reinventing WiFi Signals Based on Dispersion Effect for Accurate Indoor Localization

WiFi-based device localization is a key enabling technology for smart applications, which has attracted numerous research studies in the past decade. Most of the existing approaches rely on Line-of-Sight (LoS) signals to work, while a critical problem is often neglected: In the real-world indoor environments, WiFi signals are everywhere, but very few of them are usable for accurate localization. As a result, the localization accuracy in practice is far from being satisfactory. This paper presents BIFROST, a novel hardware-software co-design for accurate indoor localization. The core idea of BIFROST is to reinvent WiFi signals, so as to provide sufficient LoS signals for localization. This is realized by exploiting the dispersion effect of signals emitted by the leaky wave antenna (LWA). We present a low-cost plug-in design of LWA that can generate orthogonal polarized signals: On one hand, LWA disperses signals of different frequencies to different angles, thus providing Angle-of-Arrival (AoA) information for the localized target. On the other hand, the target further leverages the antenna polarization mismatch to distinguish AoAs from different LWAs. In the software layer, fine-grained information in Channel State Information (CSI) is exploited to cope with multipath and noise. We implement BIFROST and evaluate its performance under various settings. The results show that the median localization error of BIFROST is 0.81m, which is 52.35% less than that of SpotFi, a state-of-the-art approach. SpotFi, when combined with BIFROST to work in the realistic settings, can reduce the localization error by 33.54%.

cs.ET↗