arXiv subjects

Yuan Cheng

Publications and source records attributed to Yuan Cheng.

At least 55 records · Page 3Linked to original sources

arXiv2026

Towards a Science of Collective AI: LLM-based Multi-Agent Systems Need a Transition from Blind Trial-and-Error to Rigorous Science

Recent advancements in Large Language Models (LLMs) have greatly extended the capabilities of Multi-Agent Systems (MAS), demonstrating significant effectiveness across a wide range of complex and open-ended domains. However, despite this rapid progress, the field still relies heavily on empirical trial-and-error. It lacks a unified and principled scientific framework necessary for systematic optimization and improvement. This bottleneck stems from the ambiguity of attribution: first, the absence of a structured taxonomy of factors leaves researchers restricted to unguided adjustments; second, the lack of a unified metric fails to distinguish genuine collaboration gain from mere resource accumulation. In this paper, we advocate for a transition to design science through an integrated framework. We advocate to establish the collaboration gain metric ($Γ$) as the scientific standard to isolate intrinsic gains from increased budgets. Leveraging $Γ$, we propose a factor attribution paradigm to systematically identify collaboration-driving factors. To support this, we construct a systematic MAS factor library, structuring the design space into control-level presets and information-level dynamics. Ultimately, this framework facilitates the transition from blind experimentation to rigorous science, paving the way towards a true science of Collective AI.

cs.CL↗

arXiv2026

Disco: Densely-overlapping Cell Instance Segmentation via Adjacency-aware Collaborative Coloring

Accurate cell instance segmentation is foundational for digital pathology analysis. Existing methods based on contour detection and distance mapping still face significant challenges in processing complex and dense cellular regions. Graph coloring-based methods provide a new paradigm for this task, yet the effectiveness of this paradigm in real-world scenarios with dense overlaps and complex topologies has not been verified. Addressing this issue, we release a large-scale dataset GBC-FS 2025, which contains highly complex and dense sub-cellular nuclear arrangements. We conduct the first systematic analysis of the chromatic properties of cell adjacency graphs across four diverse datasets and reveal an important discovery: most real-world cell graphs are non-bipartite, with a high prevalence of odd-length cycles (predominantly triangles). This makes simple 2-coloring theory insufficient for handling complex tissues, while higher-chromaticity models would cause representational redundancy and optimization difficulties. Building on this observation of complex real-world contexts, we propose Disco (Densely-overlapping Cell Instance Segmentation via Adjacency-aware COllaborative Coloring), an adjacency-aware framework based on the "divide and conquer" principle. It uniquely combines a data-driven topological labeling strategy with a constrained deep learning system to resolve complex adjacency conflicts. First, "Explicit Marking" strategy transforms the topological challenge into a learnable classification task by recursively decomposing the cell graph and isolating a "conflict set." Second, "Implicit Disambiguation" mechanism resolves ambiguities in conflict regions by enforcing feature dissimilarity between different instances, enabling the model to learn separable feature representations.

cs.CV↗

arXiv2026

Topology-Aware Revival for Efficient Sparse Training

Static sparse training is a promising route to efficient learning by committing to a fixed mask pattern, yet the constrained structure reduces robustness. Early pruning decisions can lock the network into a brittle structure that is difficult to escape, especially in deep reinforcement learning (RL) where the evolving policy continually shifts the training distribution. We propose Topology-Aware Revival (TAR), a lightweight one-shot post-pruning procedure that improves static sparsity without dynamic rewiring. After static pruning, TAR performs a single revival step by allocating a small reserve budget across layers according to topology needs, randomly uniformly reactivating a few previously pruned connections within each layer, and then keeping the resulting connectivity fixed for the remainder of training. Across multiple continuous-control tasks with SAC and TD3, TAR improves final return over static sparse baselines by up to +37.9% and also outperforms dynamic sparse training baselines with a median gain of +13.5%.

cs.LG↗

arXiv2026

PRPO: Aligning Process Reward with Outcome Reward in Policy Optimization

Policy optimization for large language models often suffers from sparse reward signals in multi-step reasoning tasks. Critic-free methods like GRPO assign a single normalized outcome reward to all tokens, providing limited guidance for intermediate reasoning . While Process Reward Models (PRMs) offer dense feedback, they risk premature collapse when used alone, as early low-reward tokens can drive policies toward truncated outputs. We introduce Process Relative Policy Optimization (PRPO), which combines outcome reliability with process-level guidance in a critic-free framework. PRPO segments reasoning sequences based on semantic clues, normalizes PRM scores into token-level advantages, and aligns their distribution with outcome advantages through location-parameter shift. On MATH500, PRPO improves Qwen2.5-Math-1.5B accuracy from 61.2% to 64.4% over GRPO using only eight rollouts and no value network, demonstrating efficient fine-grained credit assignment within critic-free optimization. Code is available at: https://github.com/SchumiDing/srpocode

cs.LG↗

arXiv2026

SAES-SVD: Self-Adaptive Suppression of Accumulated and Local Errors for SVD-based LLM Compression

The rapid growth in the parameter scale of large language models (LLMs) has created a high demand for efficient compression techniques. As a hardware-agnostic and highly compatible technique, low-rank compression has been widely adopted. However, existing methods typically compress each layer independently by minimizing per-layer reconstruction error, overlooking a critical limitation: the reconstruction error propagates and accumulates through the network, which leads to amplified global deviations from the full-precision baseline. To address this, we propose Self-Adaptive Error Suppression SVD (SAES-SVD), a LLMs compression framework that jointly optimizes intra-layer reconstruction and inter-layer error compensation. SAES-SVD is composed of two novel components: (1) Cumulative Error-Aware Layer Compression (CEALC), which formulates the compression objective as a combination of local reconstruction and weighted cumulative error compensation. Based on it, we derive a closed-form low-rank solution relied on second-order activation statistics, which explicitly aligns each layer's output with its full-precision counterpart to compensate for accumulated errors. (2) Adaptive Collaborative Error Suppression (ACES), which automatically adjusts the weighting coefficient to enhance the low-rank structure of the compression objective in CEALC. Specifically, the coefficient is optimized to maximize the ratio between the Frobenius norm of the compressed layer's output and that of the compression objective under a fixed rank, thus ensuring that the rank budget is utilized effectively. Extensive experiments across multiple LLM architectures and tasks show that, without fine-tuning or mixed-rank strategies, SAES-SVD consistently improves post-compression performance.

cs.CL↗

arXiv2026

Spectra: Rethinking Optimizers for LLMs Under Spectral Anisotropy

Gradient signals in LLM training are highly anisotropic: recurrent linguistic structure concentrates energy into a small set of dominant spectral directions, while context specific information resides in a long tail. We show that this spike tail separation persists throughout training, with the spike occupying only about 1.5% of directions yet dominating optimizer statistics. This dominance suppresses tail learning by contracting tail updates through second moment normalization and tightening the globally stable learning rate bound. Motivated by this analysis, we propose Spectra, a spike aware optimizer that suppresses the dominant low rank spike subspace without amplifying the noise sensitive spectral tail. Spectra tracks the spike subspace via cached, warm started power iteration and applies low rank spectral shaping with negligible overhead and substantially reduced optimizer state memory. On LLaMA3 8B trained on 50B tokens, Spectra reaches the same target loss 30% faster than AdamW, reduces per step end to end overhead by 0.7%, cuts optimizer state memory by 49.25%, and improves average downstream accuracy by 1.62%. Compared to Muon, Spectra is 5.1x faster in optimizer processing time, achieves a lower final loss, and improves average accuracy by 0.66%.

cs.LG↗

arXiv2026

Demystifying the Slash Pattern in Attention: The Role of RoPE

Large Language Models (LLMs) often exhibit slash attention patterns, where attention scores concentrate along the $Δ$-th sub-diagonal for some offset $Δ$. These patterns play a key role in passing information across tokens. But why do they emerge? In this paper, we demystify the emergence of these Slash-Dominant Heads (SDHs) from both empirical and theoretical perspectives. First, by analyzing open-source LLMs, we find that SDHs are intrinsic to models and generalize to out-of-distribution prompts. To explain the intrinsic emergence, we analyze the queries, keys, and Rotary Position Embedding (RoPE), which jointly determine attention scores. Our empirical analysis reveals two characteristic conditions of SDHs: (1) Queries and keys are almost rank-one, and (2) RoPE is dominated by medium- and high-frequency components. Under these conditions, queries and keys are nearly identical across tokens, and interactions between medium- and high-frequency components of RoPE give rise to SDHs. Beyond empirical evidence, we theoretically show that these conditions are sufficient to ensure the emergence of SDHs by formalizing them as our modeling assumptions. Particularly, we analyze the training dynamics of a shallow Transformer equipped with RoPE under these conditions, and prove that models trained via gradient descent exhibit SDHs. The SDHs generalize to out-of-distribution prompts.

cs.LG↗

arXiv2026

Structure-based RNA Design by Step-wise Optimization of Latent Diffusion Model

RNA inverse folding, designing sequences to form specific 3D structures, is critical for therapeutics, gene regulation, and synthetic biology. Current methods, focused on sequence recovery, struggle to address structural objectives like secondary structure consistency (SS), minimum free energy (MFE), and local distance difference test (LDDT), leading to suboptimal structural accuracy. To tackle this, we propose a reinforcement learning (RL) framework integrated with a latent diffusion model (LDM). Drawing inspiration from the success of diffusion models in RNA inverse folding, which adeptly model complex sequence-structure interactions, we develop an LDM incorporating pre-trained RNA-FM embeddings from a large-scale RNA model. These embeddings capture co-evolutionary patterns, markedly improving sequence recovery accuracy. However, existing approaches, including diffusion-based methods, cannot effectively handle non-differentiable structural objectives. By contrast, RL excels in this task by using policy-driven reward optimization to navigate complex, non-gradient-based objectives, offering a significant advantage over traditional methods. In summary, we propose the Step-wise Optimization of Latent Diffusion Model (SOLD), a novel RL framework that optimizes single-step noise without sampling the full diffusion trajectory, achieving efficient refinement of multiple structural objectives. Experimental results demonstrate SOLD surpasses its LDM baseline and state-of-the-art methods across all metrics, establishing a robust framework for RNA inverse folding with profound implications for biotechnological and therapeutic applications.

cs.LG↗

arXiv2025

Tracing the Heart's Pathways: ECG Representation Learning from a Cardiac Conduction Perspective

The multi-lead electrocardiogram (ECG) stands as a cornerstone of cardiac diagnosis. Recent strides in electrocardiogram self-supervised learning (eSSL) have brightened prospects for enhancing representation learning without relying on high-quality annotations. Yet earlier eSSL methods suffer a key limitation: they focus on consistent patterns across leads and beats, overlooking the inherent differences in heartbeats rooted in cardiac conduction processes, while subtle but significant variations carry unique physiological signatures. Moreover, representation learning for ECG analysis should align with ECG diagnostic guidelines, which progress from individual heartbeats to single leads and ultimately to lead combinations. This sequential logic, however, is often neglected when applying pre-trained models to downstream tasks. To address these gaps, we propose CLEAR-HUG, a two-stage framework designed to capture subtle variations in cardiac conduction across leads while adhering to ECG diagnostic guidelines. In the first stage, we introduce an eSSL model termed Conduction-LEAd Reconstructor (CLEAR), which captures both specific variations and general commonalities across heartbeats. Treating each heartbeat as a distinct entity, CLEAR employs a simple yet effective sparse attention mechanism to reconstruct signals without interference from other heartbeats. In the second stage, we implement a Hierarchical lead-Unified Group head (HUG) for disease diagnosis, mirroring clinical workflow. Experimental results across six tasks show a 6.84% improvement, validating the effectiveness of CLEAR-HUG. This highlights its ability to enhance representations of cardiac conduction and align patterns with expert diagnostic guidelines.

cs.LG↗

arXiv2025

DART: Difficulty-Adaptive Reasoning Truncation for Efficient Large Language Models

Adaptive reasoning is essential for aligning the computational effort of large language models (LLMs) with the intrinsic difficulty of problems. Current chain-of-thought methods boost reasoning ability but indiscriminately generate long explanations, leading to evident inefficiency. However, existing reinforcement learning approaches to adaptive thinking remain unstable and heavily reward-dependent. Here we propose \textbf{DART}, a supervised \textbf{D}ifficulty-\textbf{A}daptive \textbf{R}easoning \textbf{T}runcation framework that adjusts thinking length according to problem difficulty. By distilling concise reasoning patterns from stronger models, interpolating them into a continuum of reasoning styles, and curating optimal training data that balances correctness and compactness, DART learns when to ``stop thinking''. Across multiple mathematical benchmarks, experimental results demonstrate its remarkable efficiency while preserving or improving accuracy, achieving a significant 81.2\% reasoning truncation (DeepSeek-R1-Distill-Qwen-7B on GSM8K dataset) with 5.33$\times$ computational acceleration. DART provides a stable and general paradigm for efficient reasoning, advancing the development of adaptive intelligence in LLMs.

cs.AI↗

arXiv2025

Rethinking Intracranial Aneurysm Vessel Segmentation: A Perspective from Computational Fluid Dynamics Applications

The precise segmentation of intracranial aneurysms and their parent vessels (IA-Vessel) is a critical step for hemodynamic analyses, which mainly depends on computational fluid dynamics (CFD). However, current segmentation methods predominantly focus on image-based evaluation metrics, often neglecting their practical effectiveness in subsequent CFD applications. To address this deficiency, we present the Intracranial Aneurysm Vessel Segmentation (IAVS) dataset, the first comprehensive, multi-center collection comprising 641 3D MRA images with 587 annotations of aneurysms and IA-Vessels. In addition to image-mask pairs, IAVS dataset includes detailed hemodynamic analysis outcomes, addressing the limitations of existing datasets that neglect topological integrity and CFD applicability. To facilitate the development and evaluation of clinically relevant techniques, we construct two evaluation benchmarks including global localization of aneurysms (Stage I) and fine-grained segmentation of IA-Vessel (Stage II) and develop a simple and effective two-stage framework, which can be used as a out-of-the-box method and strong baseline. For comprehensive evaluation of applicability of segmentation results, we establish a standardized CFD applicability evaluation system that enables the automated and consistent conversion of segmentation masks into CFD models, offering an applicability-focused assessment of segmentation outcomes. The dataset, code, and model will be public available at https://github.com/AbsoluteResonance/IAVS.

cs.CV↗

arXiv2025

PET2Rep: Towards Vision-Language Model-Drived Automated Radiology Report Generation for Positron Emission Tomography

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficacy metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

eess.IV↗

arXiv2025

Transformers Provably Learn Directed Acyclic Graphs via Kernel-Guided Mutual Information

Uncovering hidden graph structures underlying real-world data is a critical challenge with broad applications across scientific domains. Recently, transformer-based models leveraging the attention mechanism have demonstrated strong empirical success in capturing complex dependencies within graphs. However, the theoretical understanding of their training dynamics has been limited to tree-like graphs, where each node depends on a single parent. Extending provable guarantees to more general directed acyclic graphs (DAGs) -- which involve multiple parents per node -- remains challenging, primarily due to the difficulty in designing training objectives that enable different attention heads to separately learn multiple different parent relationships. In this work, we address this problem by introducing a novel information-theoretic metric: the kernel-guided mutual information (KG-MI), based on the $f$-divergence. Our objective combines KG-MI with a multi-head attention framework, where each head is associated with a distinct marginal transition kernel to model diverse parent-child dependencies effectively. We prove that, given sequences generated by a $K$-parent DAG, training a single-layer, multi-head transformer via gradient ascent converges to the global optimum in polynomial time. Furthermore, we characterize the attention score patterns at convergence. In addition, when particularizing the $f$-divergence to the KL divergence, the learned attention scores accurately reflect the ground-truth adjacency matrix, thereby provably recovering the underlying graph structure. Experimental results validate our theoretical findings.

cs.LG↗

arXiv2025

ChromFound: Towards A Universal Foundation Model for Single-Cell Chromatin Accessibility Data

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

q-bio.GN↗

arXiv2025

Adaptive Reasoning Executor: A Collaborative Agent System for Efficient Reasoning

Recent advances in Large Language Models (LLMs) demonstrate that chain-of-thought prompting and deep reasoning substantially enhance performance on complex tasks, and multi-agent systems can further improve accuracy by enabling model debates. However, applying deep reasoning to all problems is computationally expensive. To mitigate these costs, we propose a complementary agent system integrating small and large LLMs. The small LLM first generates an initial answer, which is then verified by the large LLM. If correct, the answer is adopted directly; otherwise, the large LLM performs in-depth reasoning. Experimental results show that, for simple problems, our approach reduces the computational cost of the large LLM by more than 50% with negligible accuracy loss, while consistently maintaining robust performance on complex tasks.

cs.AI↗

arXiv2025

Metis: Training LLMs with FP4 Quantization

This work identifies anisotropy in the singular value spectra of parameters, activations, and gradients as the fundamental barrier to low-bit training of large language models (LLMs). These spectra are dominated by a small fraction of large singular values, inducing wide numerical ranges that cause quantization bias and severe spectral distortion, ultimately degrading training performance. This work presents Metis, a spectral-domain quantization framework that partitions anisotropic spectra into narrower sub-distributions for independent quantization, thereby reducing errors and preserving spectral structure. To minimize overhead, Metis leverages two key properties of the dominant spectral subspace: preservation via sparsely random sampling and preservation via random projection, reducing decomposition cost to a negligible level. On LLaMA-3 8B trained with 100B tokens, Metis enables robust W4A4G4 training with FP4 quantization of weights, activations, and gradients, yielding only a 0.4% training loss gap and a 0.1% degradation in downstream accuracy relative to BF16. Beyond matching BF16 fidelity, Metis also surpasses our implementation of Nvidia's recently announced (yet to be publicly released) FP4 recipe, consistently achieving lower loss and higher downstream accuracy while incurring significantly lower computational overhead. The code implementation for Metis is available at: https://anonymous.4open.science/r/Metis-quantization-644B.

cs.LG↗

arXiv2025

LIMI: Less is More for Agency

We define Agency as the emergent capacity of AI systems to function as autonomous agents actively discovering problems, formulating hypotheses, and executing solutions through self-directed engagement with environments and tools. This fundamental capability marks the dawn of the Age of AI Agency, driven by a critical industry shift: the urgent need for AI systems that don't just think, but work. While current AI excels at reasoning and generating responses, industries demand autonomous agents that can execute tasks, operate tools, and drive real-world outcomes. As agentic intelligence becomes the defining characteristic separating cognitive systems from productive workers, efficiently cultivating machine autonomy becomes paramount. Current approaches assume that more data yields better agency, following traditional scaling laws from language modeling. We fundamentally challenge this paradigm. LIMI (Less Is More for Intelligent Agency) demonstrates that agency follows radically different development principles. Through strategic focus on collaborative software development and scientific research workflows, we show that sophisticated agentic intelligence can emerge from minimal but strategically curated demonstrations of autonomous behavior. Using only 78 carefully designed training samples, LIMI achieves 73.5% on comprehensive agency benchmarks, dramatically outperforming state-of-the-art models: Kimi-K2-Instruct (24.1%), DeepSeek-V3.1 (11.9%), Qwen3-235B-A22B-Instruct (27.5%), and GLM-4.5 (45.1%). Most strikingly, LIMI demonstrates 53.7% improvement over models trained on 10,000 samples-achieving superior agentic intelligence with 128 times fewer samples. Our findings establish the Agency Efficiency Principle: machine autonomy emerges not from data abundance but from strategic curation of high-quality agentic demonstrations.

cs.AI↗

arXiv2025

Minimal Semantic Sufficiency Meets Unsupervised Domain Generalization

The generalization ability of deep learning has been extensively studied in supervised settings, yet it remains less explored in unsupervised scenarios. Recently, the Unsupervised Domain Generalization (UDG) task has been proposed to enhance the generalization of models trained with prevalent unsupervised learning techniques, such as Self-Supervised Learning (SSL). UDG confronts the challenge of distinguishing semantics from variations without category labels. Although some recent methods have employed domain labels to tackle this issue, such domain labels are often unavailable in real-world contexts. In this paper, we address these limitations by formalizing UDG as the task of learning a Minimal Sufficient Semantic Representation: a representation that (i) preserves all semantic information shared across augmented views (sufficiency), and (ii) maximally removes information irrelevant to semantics (minimality). We theoretically ground these objectives from the perspective of information theory, demonstrating that optimizing representations to achieve sufficiency and minimality directly reduces out-of-distribution risk. Practically, we implement this optimization through Minimal-Sufficient UDG (MS-UDG), a learnable model by integrating (a) an InfoNCE-based objective to achieve sufficiency; (b) two complementary components to promote minimality: a novel semantic-variation disentanglement loss and a reconstruction-based mechanism for capturing adequate variation. Empirically, MS-UDG sets a new state-of-the-art on popular unsupervised domain-generalization benchmarks, consistently outperforming existing SSL and UDG methods, without category or domain labels during representation learning.

cs.CV↗