arXiv subjects

Siyuan Li

Publications and source records attributed to Siyuan Li.

At least 73 records · Page 4Linked to original sources

arXiv2026

Vibe Medicine: Redefining Biomedical Research Through Human-AI Co-Work

With the emergence of large language models (LLMs) and AI agent frameworks, the human-AI co-work paradigm known as Vibe Coding is changing how people code, making it more accessible and productive. In scientific research, where workflows are more complex and the burden of specialized labor limits independent researchers and those in low-resource areas, the potential impact is even greater, particularly in biomedicine, which involves heterogeneous data modalities and multi-step analytical pipelines. In this paper, we introduce Vibe Medicine, a co-work paradigm in which clinicians and researchers direct skill-augmented AI agents through natural language to execute complex, multi-step biomedical workflows, while retaining the role of research director who specifies objectives, reviews intermediate results, and makes domain-informed decisions. The enabling infrastructure consists of three layers: capable LLMs, agent frameworks such as OpenClaw and Hermes Agent, and the OpenClaw medical skills collection, which includes more than 1,000 curated skills from multiple open-source repositories. We analyze the architecture and skill categories of this collection across ten biomedical domains, and present case studies covering rare disease diagnosis, drug repurposing, and clinical trial design that demonstrate end-to-end workflows in practice. We also identify the principal risks, such as hallucination, data privacy, and over-reliance, and outline directions toward more reliable, trustworthy, and clinically integrated agent-assisted research that advances research and technological equity and reduces health care resource disparities.

cs.AI↗

arXiv2026

Evolving Beyond Snapshots: Harmonizing Structure and Sequence via Entity State Tuning for Temporal Knowledge Graph Forecasting

Temporal knowledge graph (TKG) forecasting requires predicting future facts by jointly modeling structural dependencies within each snapshot and temporal evolution across snapshots. However, most existing methods are stateless: they recompute entity representations at each timestamp from a limited query window, leading to episodic amnesia and rapid decay of long-term dependencies. To address this limitation, we propose Entity State Tuning (EST), an encoder-agnostic framework that endows TKG forecasters with persistent and continuously evolving entity states. EST maintains a global state buffer and progressively aligns structural evidence with sequential signals via a closed-loop design. Specifically, a topology-aware state perceiver first injects entity-state priors into structural encoding. Then, a unified temporal context module aggregates the state-enhanced events with a pluggable sequence backbone. Subsequently, a dual-track evolution mechanism writes the updated context back to the global entity state memory, balancing plasticity against stability. Experiments on multiple benchmarks show that EST consistently improves diverse backbones and achieves state-of-the-art performance, highlighting the importance of state persistence for long-horizon TKG forecasting.

cs.AI↗

arXiv2026

CoopGuard: Stateful Cooperative Agents Safeguarding LLMs Against Evolving Multi-Round Attacks

As Large Language Models (LLMs) are increasingly deployed in complex applications, their vulnerability to adversarial attacks raises urgent safety concerns, especially those evolving over multi-round interactions. Existing defenses are largely reactive and struggle to adapt as adversaries refine strategies across rounds. In this work, we propose CoopGuard , a stateful multi-round LLM defense framework based on cooperative agents that maintains and updates an internal defense state to counter evolving attacks. It employs three specialized agents (Deferring Agent, Tempting Agent, and Forensic Agent) for complementary round-level strategies, coordinated by System Agent, which conditions decisions on the evolving defense state (interaction history) and orchestrates agents over time. To evaluate evolving threats, we introduce the EMRA benchmark with 5,200 adversarial samples across 8 attack types, simulating progressively LLM multi-round attacks. Experiments show that CoopGuard reduces attack success rate by 78.9% over state-of-the-art defenses, while improving deceptive rate by 186% and reducing attack efficiency by 167.9%, offering a more comprehensive assessment of multi-round defense. These results demonstrate that CoopGuard provides robust protection for LLMs in multi-round adversarial scenarios.

cs.CR↗

arXiv2026

SAM 3: Segment Anything with Concepts

We present Segment Anything Model (SAM) 3, a unified model that detects, segments, and tracks objects in images and videos based on concept prompts, which we define as either short noun phrases (e.g., "yellow school bus"), image exemplars, or a combination of both. Promptable Concept Segmentation (PCS) takes such prompts and returns segmentation masks and unique identities for all matching object instances. To advance PCS, we build a scalable data engine that produces a high-quality dataset with 4M unique concept labels, including hard negatives, across images and videos. Our model consists of an image-level detector and a memory-based video tracker that share a single backbone. Recognition and localization are decoupled with a presence head, which boosts detection accuracy. SAM 3 doubles the accuracy of existing systems in both image and video PCS, and improves previous SAM capabilities on visual segmentation tasks. We open source SAM 3 along with our new Segment Anything with Concepts (SA-Co) benchmark for promptable concept segmentation.

cs.CV↗

arXiv2026

$2^{++}$ Light Tensor Hybrid Meson from QCD Laplace Sum Rules

We present an analysis of the light tensor ($J^{PC}=2^{++}$) hybrid meson mass and coupling from QCD Laplace Sum Rules where the next-to-leading order (NLO) perturbative (PT) corrections and the contributions of the non-perturbative (NP) condensates up to dimension-six ($D=6$) are included. NLO leading-logarithms corrections due to the condensates which contribute in the chiral limit are considered. We obtain the mass $M_{2^+}= (2038\pm 190)$ MeV and a relatively small coupling $f_{2^+}=(10.5\pm 2.9)$ MeV normalized as $f_π=93$ MeV. Our results suggest that the $f_2(1950)$ or/and the $f'_2(2010)$ may have a sizeable $\bar qqg$ hybrid component. We also compute the tensor hybrid topological charge (value of the two-point function at zero momentum) and find (for the first time) at NLO: $Π_{qg}(0)=(2.41\pm 0.43) \times 10^{-4}{\rm GeV}^6$ which could be checked from some lattice QCD or/and low energy theorems (LET).

hep-ph↗

arXiv2026

Hierarchical Decision-Making under Uncertainty: A Hybrid MDP and Chance-Constrained MPC Approach

This paper presents a hierarchical decision-making framework for autonomous systems operating under uncertainty, demonstrated through autonomous driving as a representative application. Surrounding agents are modeled using Hybrid Markov Decision Processes (HMDPs) that jointly capture maneuver-level and dynamic-level uncertainties, enabling the multi-modal environmental prediction. The ego agent is modeled using a separate HMDP and integrated into a Model Predictive Control (MPC) framework that unifies maneuver selection with dynamic feasibility within a single optimization. A set of joint chance constraints serves as the bridge between environmental prediction and optimization, incorporating multi-modal environment predictions into the MPC formulation and ensuring safety across all plausible interaction scenarios. The proposed framework provides theoretical guarantees on recursive feasibility and asymptotic stability, and its benefits in terms of safety and efficiency are validated through comprehensive evaluations in highway and urban environments, together with comparisons against a rule-based baseline.

eess.SY↗

arXiv2026

An HMDP-MPC Decision-making Framework with Adaptive Safety Margins and Hysteresis for Autonomous Driving

This paper presents a unified decision-making framework that integrates Hybrid Markov Decision Processes (HMDPs) with Model Predictive Control (MPC), augmented by velocity-dependent safety margins and a prediction-aware hysteresis mechanism. Both the ego and surrounding vehicles are modeled as HMDPs, allowing discrete maneuver transition and kinematic evolution to be jointly considered within the MPC optimization. Safety margins derived from the Intelligent Driver Model (IDM) adapt to traffic context but vary with speed, which can cause oscillatory decisions and velocity fluctuations. To mitigate this, we propose a frozen-release hysteresis mechanism with distinct trigger and release thresholds, effectively enlarging the reaction buffer and suppressing oscillations. Decision continuity is further safeguarded by a two-layer recovery scheme: a global bounded relaxation tied to IDM margins and a deterministic fallback policy. The framework is evaluated through a case study, an ablation against a no-hysteresis baseline, and largescale randomized experiments across 18 traffic settings. Across 8,050 trials, it achieves a collision rate of only 0.05%, with 98.77% of decisions resolved by nominal MPC and minimal reliance on relaxation or fallback. These results demonstrate the robustness and adaptability of the proposed decision-making framework in heterogeneous traffic conditions.

eess.SY↗

arXiv2026

TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling

The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we propose TrinityDNA, a novel DNA foundational model designed to address these challenges. The model integrates biologically informed components, including Groove Fusion for capturing DNA's structural features and Gated Reverse Complement (GRC) to handle the inherent symmetry of DNA sequences. Additionally, we introduce a multi-scale attention mechanism that allows the model to attend to varying levels of sequence dependencies, and an evolutionary training strategy that progressively adapts the model to both prokaryotic and eukaryotic genomes. TrinityDNA provides a more accurate and efficient approach to genomic sequence modeling, offering significant improvements in gene function prediction, regulatory mechanism discovery, and other genomics applications. Our model bridges the gap between machine learning techniques and biological insights, paving the way for more effective analysis of genomic data. Additionally, we introduced a new DNA long-sequence CDS annotation benchmark to make evaluations more comprehensive and oriented toward practical applications.

cs.CE↗

arXiv2026

Beyond Prefixes: Graph-as-Memory Cross-Attention for Knowledge Graph Completion with Large Language Models

Fusing Knowledge Graphs with Large Language Models (LLMs) is crucial for knowledge-intensive tasks like knowledge graph completion. Existing LLM-based approaches typically inject graph information via prefix concatenation, resulting in shallow interactions that fail to support fine-grained evidence retrieval during generation. Beyond prefixes, we propose Graph-as-Memory Tuning (GMT), a new paradigm that represents local graph structure as explicit graph memory and injects it into LLMs via deep, token-wise cross-attention. Specifically, GMT first employs a Semantic Graph Module to encode context-aware semantics from local neighborhoods guided by knowledge-enhanced relations, and compresses them into a fixed number of graph memory tokens. A Graph-as-Memory Cross-Attention Fusion Module then integrates these tokens into multiple Transformer layers, allowing LLM hidden state to dynamically retrieve relevant graph evidence. To enable efficient adaptation, GMT applies LoRA only to the memory cross-attention while keeping the base LLM frozen. Extensive experiments show that GMT significantly outperforms prefix-tuning and other strong baselines, providing more potent signals for robust reasoning. The code is published at https://github.com/tongruiliu/GMT.

cs.AI↗

arXiv2026

Progressive Refinement Regulation for Accelerating Diffusion Language Model Decoding

Diffusion language models generate text through iterative denoising under a uniform refinement rule applied to all tokens. However, tokens stabilize at different rates in practice, leading to substantial redundant refinement and motivating refinement control over the denoising process. Existing approaches typically assess refinement necessity from instantaneous, step-level signals under a fixed decoding process. In contrast, whether a token has converged is defined by how its prediction changes along its future refinement trajectory. Moreover, changing the refinement rule reshapes future refinement trajectories, which in turn determine how refinement rules should be formulated, making refinement control inherently dynamic. We propose \emph{Progressive Refinement Regulation} (PRR), a progressive, trajectory-grounded refinement control framework that derives a token-level notion of empirical convergence progress from full decoding rollouts. Based on this signal, PRR learns a lightweight token-wise controller to regulate refinement via temperature-based distribution shaping under a progressive self-evolving training scheme. Experiments show that PRR substantially accelerates diffusion language model decoding while preserving generation quality.

cs.AI↗

arXiv2026

The Trinity of Consistency as a Defining Principle for General World Models

The construction of World Models capable of learning, simulating, and reasoning about objective physical laws constitutes a foundational challenge in the pursuit of Artificial General Intelligence. Recent advancements represented by video generation models like Sora have demonstrated the potential of data-driven scaling laws to approximate physical dynamics, while the emerging Unified Multimodal Model (UMM) offers a promising architectural paradigm for integrating perception, language, and reasoning. Despite these advances, the field still lacks a principled theoretical framework that defines the essential properties requisite for a General World Model. In this paper, we propose that a World Model must be grounded in the Trinity of Consistency: Modal Consistency as the semantic interface, Spatial Consistency as the geometric basis, and Temporal Consistency as the causal engine. Through this tripartite lens, we systematically review the evolution of multimodal learning, revealing a trajectory from loosely coupled specialized modules toward unified architectures that enable the synergistic emergence of internal world simulators. To complement this conceptual framework, we introduce CoW-Bench, a benchmark centered on multi-frame reasoning and generation scenarios. CoW-Bench evaluates both video generation models and UMMs under a unified evaluation protocol. Our work establishes a principled pathway toward general world models, clarifying both the limitations of current systems and the architectural requirements for future progress.

cs.AI↗

arXiv2026

MergeMix: A Unified Augmentation Paradigm for Visual and Multi-Modal Understanding

Vision-language alignment in multi-modal large language models (MLLMs) relies on supervised fine-tuning (SFT) or reinforcement learning (RL). To align multi-modal large language models (MLLMs) in the post-training stage, supervised fine-tuning (SFT) is a stable choice but requires human annotations and lacks task generalizations, while Reinforcement Learning (RL) searches for better answers from reward signals but suffers from computational overhead and instability. To achieve balance among scalability, efficiency, and alignment generalizations, we propose MergeMix, a unified paradigm that bridges SFT and RL with an efficient Token Merge based Mixup augmentation. As for the Mixup policy, we generate contextual aligned mixed images with the corresponding labels according to the merged attention maps with cluster regions. Then, we enhance the preference-driven paradigm for MLLMs by building preference pairs with raw images and MergeMix-generated ones and optimizing the soft preference margin with the mixed SimPO loss. Extensive experiments demonstrate that MergeMix not only achieves dominant classification accuracy as an augmentation method but also improves generalization abilities and alignment of MLLMs, providing a new learning paradigm for preference alignment with training efficiency and stability.

cs.CV↗

arXiv2026

VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention

Graph Transformer has demonstrated impressive capabilities in the field of graph representation learning. However, existing approaches face two critical challenges: (1) most models suffer from exponentially increasing computational complexity, making it difficult to scale to large graphs; (2) attention mechanisms based on node-level operations limit the flexibility of the model and result in poor generalization performance in out-of-distribution (OOD) scenarios. To address these issues, we propose \textbf{VecFormer} (the \textbf{Vec}tor Quantized Graph Trans\textbf{former}), an efficient and highly generalizable model for node classification, particularly under OOD settings. VecFormer adopts a two-stage training paradigm. In the first stage, two codebooks are used to reconstruct the node features and the graph structure, aiming to learn the rich semantic \texttt{Graph Codes}. In the second stage, attention mechanisms are performed at the \texttt{Graph Token} level based on the transformed cross codebook, reducing computational complexity while enhancing the model's generalization capability. Extensive experiments on datasets of various sizes demonstrate that VecFormer outperforms the existing Graph Transformer in both performance and speed.

cs.LG↗

arXiv2026

GlobeDiff: State Diffusion Process for Partial Observability in Multi-Agent Systems

In the realm of multi-agent systems, the challenge of \emph{partial observability} is a critical barrier to effective coordination and decision-making. Existing approaches, such as belief state estimation and inter-agent communication, often fall short. Belief-based methods are limited by their focus on past experiences without fully leveraging global information, while communication methods often lack a robust model to effectively utilize the auxiliary information they provide. To solve this issue, we propose Global State Diffusion Algorithm~(GlobeDiff) to infer the global state based on the local observations. By formulating the state inference process as a multi-modal diffusion process, GlobeDiff overcomes ambiguities in state estimation while simultaneously inferring the global state with high fidelity. We prove that the estimation error of GlobeDiff under both unimodal and multi-modal distributions can be bounded. Extensive experimental results demonstrate that GlobeDiff achieves superior performance and is capable of accurately inferring the global state.

cs.AI↗

arXiv2026

Zooming without Zooming: Region-to-Image Distillation for Fine-Grained Multimodal Perception

Multimodal Large Language Models (MLLMs) excel at broad visual understanding but still struggle with fine-grained perception, where decisive evidence is small and easily overwhelmed by global context. Recent "Thinking-with-Images" methods alleviate this by iteratively zooming in and out regions of interest during inference, but incur high latency due to repeated tool calls and visual re-encoding. To address this, we propose Region-to-Image Distillation, which transforms zooming from an inference-time tool into a training-time primitive, thereby internalizing the benefits of agentic zooming into a single forward pass of an MLLM. In particular, we first zoom in to micro-cropped regions to let strong teacher models generate high-quality VQA data, and then distill this region-grounded supervision back to the full image. After training on such data, the smaller student model improves "single-glance" fine-grained perception without tool use. To rigorously evaluate this capability, we further present ZoomBench, a hybrid-annotated benchmark of 845 VQA data spanning six fine-grained perceptual dimensions, together with a dual-view protocol that quantifies the global--regional "zooming gap". Experiments show that our models achieve leading performance across multiple fine-grained perception benchmarks, and also improve general multimodal cognition on benchmarks such as visual reasoning and GUI agents. We further discuss when "Thinking-with-Images" is necessary versus when its gains can be distilled into a single forward pass. Our code is available at https://github.com/inclusionAI/Zooming-without-Zooming.

cs.CV↗

arXiv2026

Hierarchical Audio-Visual-Proprioceptive Fusion for Precise Robotic Manipulation

Existing robotic manipulation methods primarily rely on visual and proprioceptive observations, which may struggle to infer contact-related interaction states in partially observable real-world environments. Acoustic cues, by contrast, naturally encode rich interaction dynamics during contact, yet remain underexploited in current multimodal fusion literature. Most multimodal fusion approaches implicitly assume homogeneous roles across modalities, and thus design flat and symmetric fusion structures. However, this assumption is ill-suited for acoustic signals, which are inherently sparse and contact-driven. To achieve precise robotic manipulation through acoustic-informed perception, we propose a hierarchical representation fusion framework that progressively integrates audio, vision, and proprioception. Our approach first conditions visual and proprioceptive representations on acoustic cues, and then explicitly models higher-order cross-modal interactions to capture complementary dependencies among modalities. The fused representation is leveraged by a diffusion-based policy to directly generate continuous robot actions from multimodal observations. The combination of end-to-end learning and hierarchical fusion structure enables the policy to exploit task-relevant acoustic information while mitigating interference from less informative modalities. The proposed method has been evaluated on real-world robotic manipulation tasks, including liquid pouring and cabinet opening. Extensive experiment results demonstrate that our approach consistently outperforms state-of-the-art multimodal fusion frameworks, particularly in scenarios where acoustic cues provide task-relevant information not readily available from visual observations alone. Furthermore, a mutual information analysis is conducted to interpret the effect of audio cues in robotic manipulation via multimodal fusion.

cs.RO↗

arXiv2026

Canvas-of-Thought: Grounding Reasoning via Mutable Structured States

While Chain-of-Thought (CoT) prompting has significantly advanced the reasoning capabilities of Multimodal Large Language Models (MLLMs), relying solely on linear text sequences remains a bottleneck for complex tasks. We observe that even when auxiliary visual elements are interleaved, they are often treated as static snapshots within a one-dimensional, unstructured reasoning chain. We argue that such approaches treat reasoning history as an immutable stream: correcting a local error necessitates either generating verbose downstream corrections or regenerating the entire context. This forces the model to implicitly maintain and track state updates, significantly increasing token consumption and cognitive load. This limitation is particularly acute in high-dimensional domains, such as geometry and SVG design, where the textual expression of CoT lacks explicit visual guidance, further constraining the model's reasoning precision. To bridge this gap, we introduce \textbf{Canvas-of-Thought (Canvas-CoT)}. By leveraging a HTML Canvas as an external reasoning substrate, Canvas-CoT empowers the model to perform atomic, DOM-based CRUD operations. This architecture enables in-place state revisions without disrupting the surrounding context, allowing the model to explicitly maintain the "ground truth". Furthermore, we integrate a rendering-based critique loop that serves as a hard constraint validator, providing explicit visual feedback to resolve complex tasks that are difficult to articulate through text alone. Extensive experiments on VCode, RBench-V, and MathVista demonstrate that Canvas-CoT significantly outperforms existing baselines, establishing a new paradigm for context-efficient multimodal reasoning.

cs.CL↗

arXiv2026

Dense Feature Learning via Linear Structure Preservation in Medical Data

Deep learning models for medical data are typically trained using task specific objectives that encourage representations to collapse onto a small number of discriminative directions. While effective for individual prediction problems, this paradigm underutilizes the rich structure of clinical data and limits the transferability, stability, and interpretability of learned features. In this work, we propose dense feature learning, a representation centric framework that explicitly shapes the linear structure of medical embeddings. Our approach operates directly on embedding matrices, encouraging spectral balance, subspace consistency, and feature orthogonality through objectives defined entirely in terms of linear algebraic properties. Without relying on labels or generative reconstruction, dense feature learning produces representations with higher effective rank, improved conditioning, and greater stability across time. Empirical evaluations across longitudinal EHR data, clinical text, and multimodal patient representations demonstrate consistent improvements in downstream linear performance, robustness, and subspace alignment compared to supervised and self supervised baselines. These results suggest that learning to span clinical variation may be as important as learning to predict clinical outcomes, and position representation geometry as a first class objective in medical AI.

cs.LG↗