arXiv subjects

Qiang Ye

Publications and source records attributed to Qiang Ye.

At least 19 recordsLinked to original sources

arXiv2026

OmicSync: Reliability-Aware Spatial Multi-Omics Clustering with Evidence-Constrained LLM Reasoning

Spatial multi-omics technologies jointly profile gene expression, surface proteins, and histology at each tissue spot, yet most spatial domain discovery methods provide only cluster assignments, without indicating assignment reliability, modality contributions, or why a domain decision should be trusted. We present OmicSync, a reliability-aware spatial multi-omics framework that couples unsupervised domain clustering with evidence-constrained LLM reasoning using model-derived per-spot signals, including assignment confidence, epistemic routing uncertainty, and modality-routing weights. These signals are converted into structured evidence dictionaries and used to generate standard, stepwise, counterfactual, contrastive, and uncertainty-focused explanations. OmicSync integrates a KAN-GCN backbone with spatial encoding, cross-modal fusion, uncertainty-aware routing, cell-type supervision, and missing-modality imputation. We further introduce OmicSync-R, which closes the reasoning-clustering loop by using automatically computed reasoning-quality scores as REINFORCE rewards, allowing reasoning coherence to shape the latent structure without backpropagating through the language model. Across four 10x CytAssist FFPE spatial proteomics benchmarks, OmicSync achieves the best average rank on Human Tonsil (1.44), Glioblastoma (1.78), and Tonsil Add-on (1.22), and second-best on Human Breast Cancer (2.33). OmicSync-R further improves ARI on Human Breast Cancer from 45.73 to 46.72 and outperforms existing methods on six of nine clustering metrics. Together, OmicSync and OmicSync-R enable reliability-aware, spot-level auditable spatial domain discovery guided by evidence-constrained reasoning.

cs.CV↗

arXiv2026

FL-MAESTRO: Multi-Agent LLM Orchestration for Resource-Constrained Federated Learning

In Federated Learning (FL), the communication topology is a runtime variable rather than a fixed design choice, since links and edge devices drop in and out during training. Each round, the server must commit three coupled decisions, namely the communication topology, per-client resource allocation, and the aggregation rule for combining local updates. Recent agentic systems have begun bringing large language models (LLM) into FL, but the existing line of work either operates at setup time or handles a single runtime dimension such as client selection. We propose FL-MAESTRO, a multi-agent orchestrator that makes the joint runtime FL decision directly through three specialist LLM agents, one per decision dimension. A coordinator combines their analyses into a single decision, and a non-LLM feasibility check confirms it before the round executes. Because the orchestrator consumes the server's predicted-failure list, it withholds clients whose updates would never be aggregated, which removes the dominant source of wasted round energy in classical FL on volatile edge networks. Because client state is read as natural-text profiles, the same orchestrator extends to heterogeneous device classes without per-class energy models. On a non-IID CIFAR-10 benchmark, FL-MAESTRO matches the accuracy of the strongest energy-aware baseline while cutting wasted round energy from over a third to near zero. Code is available at https://github.com/denoslab/FL-MAESTRO.

cs.AI↗

arXiv2026

GenED-SC: Generative Editing Semantic Communication with Integrated Multi-Modal LLMs

Deep learning-based joint source-channel coding has recently demonstrated strong potential for semantic communication (SemComm). However, most existing approaches focus on optimizing visual-fidelity metrics, which can lead to reduced perceptual quality. Generative model-based SemComm leverages rich prior knowledge from large-scale pre-training to enhance perceptual quality, but often at the cost of increased distortion and unreliability. This paper addresses the above issues by proposing a two-stage semantic image transmission framework, integrating a multimodal large language model (MLLM) for generative editing. In the first stage, a JSCC-based discriminative transmission selectively prioritizes semantically important regions, preserving scene layout and object integrity under limited bandwidth. In the second phase, MLLM-driven generative editing refines missing details based on the textual descriptions, enhancing semantic fidelity and perceptual quality. Extensive experiments show that the proposed framework achieves state-of-the-art performance in semantic preservation, perceptual quality, and visual fidelity across a wide range of channel conditions, especially in low-SNR regimes.

eess.SP↗

arXiv2026

AI/ML for mobile networks: Current status in Rel. 19 and challenges ahead

The transformative power of artificial intelligence (AI) and machine learning (ML) is recognized as a key enabler for sixth generation (6G) mobile networks by both academia and industry. Research on AI/ML in mobile networks has been ongoing for years, and the 3rd generation partnership project (3GPP) launched standardization efforts to integrate AI into mobile networks. However, a comprehensive review of the current status and challenges of the standardization of AI/ML for mobile networks is still missing. To this end, we provided a comprehensive review of the standardization efforts by 3GPP on AI/ML for mobile networks. This includes an overview of the general AI/ML framework, representative use cases (i.e., CSI feedback, beam management and positioning), and corresponding evaluation matrices. We emphasized the key research challenges on dataset preparation, generalization evaluation and baseline AI/ML models selection. Using CSI feedback as a case study, given the test dataset 2, we demonstrated that the pre-training-fine-tuning paradigm (i.e., pre-training using dataset 1 and fine-tuning using dataset 2) outperforms training on dataset 2. Moreover, we observed the highest performance enhancements in Transformer-based models through fine-tuning, showing its great generalization potential at large floating-point operations (FLOPs). Finally, we outlined future research directions for the application of AI/ML in mobile networks.

eess.SP↗

arXiv2026

CrossLLM-Mamba: Multimodal State Space Fusion of LLMs for RNA Interaction Prediction

Accurate prediction of RNA-associated interactions is essential for understanding cellular regulation and advancing drug discovery. While Biological Large Language Models (BioLLMs) such as ESM-2 and RiNALMo provide powerful sequence representations, existing methods rely on static fusion strategies that fail to capture the dynamic, context-dependent nature of molecular binding. We introduce CrossLLM-Mamba, a novel framework that reformulates interaction prediction as a state-space alignment problem. By leveraging bidirectional Mamba encoders, our approach enables deep ``crosstalk'' between modality-specific embeddings through hidden state propagation, modeling interactions as dynamic sequence transitions rather than static feature overlaps. The framework maintains linear computational complexity, making it scalable to high-dimensional BioLLM embeddings. We further incorporate Gaussian noise injection and Focal Loss to enhance robustness against hard-negative samples. Comprehensive experiments across three interaction categories, RNA-protein, RNA-small molecule, and RNA-RNA demonstrate that CrossLLM-Mamba achieves state-of-the-art performance. On the RPI1460 benchmark, our model attains an MCC of 0.892, surpassing the previous best by 5.2\%. For binding affinity prediction, we achieve Pearson correlations exceeding 0.95 on riboswitch and repeat RNA subtypes. These results establish state-space modeling as a powerful paradigm for multi-modal biological interaction prediction.

q-bio.GN↗

arXiv2025

Design Criteria for SGD Preconditioners: Local Conditioning, Noise Floors, and Basin Stability

Stochastic Gradient Descent (SGD) often slows in the late stage of training due to anisotropic curvature and gradient noise. We analyze preconditioned SGD in the geometry induced by a symmetric positive definite matrix $\mathbf{M}$, deriving bounds in which both the convergence rate and the stochastic noise floor are governed by $\mathbf{M}$-dependent quantities: the rate through an effective condition number in the $\mathbf{M}$-metric, and the floor through the product of that condition number and the preconditioned noise level. For nonconvex objectives, we establish a preconditioner-dependent basin-stability guarantee: when smoothness and basin size are measured in the $\mathbf{M}$-norm, the probability that the iterates remain in a well-behaved local region admits an explicit lower bound. This perspective is particularly relevant in Scientific Machine Learning (SciML), where achieving small training loss under stochastic updates is closely tied to physical fidelity, numerical stability, and constraint satisfaction. The framework applies to both diagonal/adaptive and curvature-aware preconditioners and yields a simple design principle: choose $\mathbf{M}$ to improve local conditioning while attenuating noise. Experiments on a quadratic diagnostic and three SciML benchmarks validate the predicted rate-floor behavior.

math.NA↗

arXiv2025

Joint Computation Offloading and Resource Allocation for Maritime MEC with Energy Harvesting

In this paper, we establish a multi-access edge computing (MEC)-enabled sea lane monitoring network (MSLMN) architecture with energy harvesting (EH) to support dynamic ship tracking, accident forensics, and anti-fouling through real-time maritime traffic scene monitoring. Under this architecture, the computation offloading and resource allocation are jointly optimized to maximize the long-term average throughput of MSLMN. Due to the dynamic environment and unavailable future network information, we employ the Lyapunov optimization technique to tackle the optimization problem with large state and action spaces and formulate a stochastic optimization program subject to queue stability and energy consumption constraints. We transform the formulated problem into a deterministic one and decouple the temporal and spatial variables to obtain asymptotically optimal solutions. Under the premise of queue stability, we develop a joint computation offloading and resource allocation (JCORA) algorithm to maximize the long-term average throughput by optimizing task offloading, subchannel allocation, computing resource allocation, and task migration decisions. Simulation results demonstrate the effectiveness of the proposed scheme over existing approaches.

cs.NI↗

arXiv2025

Large-scale Multi-sequence Pretraining for Generalizable MRI Analysis in Versatile Clinical Applications

Multi-sequence Magnetic Resonance Imaging (MRI) offers remarkable versatility, enabling the distinct visualization of different tissue types. Nevertheless, the inherent heterogeneity among MRI sequences poses significant challenges to the generalization capability of deep learning models. These challenges undermine model performance when faced with varying acquisition parameters, thereby severely restricting their clinical utility. In this study, we present PRISM, a foundation model PRe-trained with large-scale multI-Sequence MRI. We collected a total of 64 datasets from both public and private sources, encompassing a wide range of whole-body anatomical structures, with scans spanning diverse MRI sequences. Among them, 336,476 volumetric MRI scans from 34 datasets (8 public and 26 private) were curated to construct the largest multi-organ multi-sequence MRI pretraining corpus to date. We propose a novel pretraining paradigm that disentangles anatomically invariant features from sequence-specific variations in MRI, while preserving high-level semantic representations. We established a benchmark comprising 44 downstream tasks, including disease diagnosis, image segmentation, registration, progression prediction, and report generation. These tasks were evaluated on 32 public datasets and 5 private cohorts. PRISM consistently outperformed both non-pretrained models and existing foundation models, achieving first-rank results in 39 out of 44 downstream benchmarks with statistical significance improvements. These results underscore its ability to learn robust and generalizable representations across unseen data acquired under diverse MRI protocols. PRISM provides a scalable framework for multi-sequence MRI analysis, thereby enhancing the translational potential of AI in radiology. It delivers consistent performance across diverse imaging protocols, reinforcing its clinical applicability.

eess.IV↗

arXiv2025

MolSnap: Snap-Fast Molecular Generation with Latent Variational Mean Flow

Molecular generation conditioned on textual descriptions is a fundamental task in computational chemistry and drug discovery. Existing methods often struggle to simultaneously ensure high-quality, diverse generation and fast inference. In this work, we propose a novel causality-aware framework that addresses these challenges through two key innovations. First, we introduce a Causality-Aware Transformer (CAT) that jointly encodes molecular graph tokens and text instructions while enforcing causal dependencies during generation. Second, we develop a Variational Mean Flow (VMF) framework that generalizes existing flow-based methods by modeling the latent space as a mixture of Gaussians, enhancing expressiveness beyond unimodal priors. VMF enables efficient one-step inference while maintaining strong generation quality and diversity. Extensive experiments on four standard molecular benchmarks demonstrate that our model outperforms state-of-the-art baselines, achieving higher novelty (up to 74.5\%), diversity (up to 70.3\%), and 100\% validity across all datasets. Moreover, VMF requires only one number of function evaluation (NFE) during conditional generation and up to five NFEs for unconditional generation, offering substantial computational efficiency over diffusion-based methods.

cs.LG↗

arXiv2025

RefiDiff: Progressive Refinement Diffusion for Efficient Missing Data Imputation

Missing values in high-dimensional, mixed-type datasets pose significant challenges for data imputation, particularly under Missing Not At Random (MNAR) mechanisms. Existing methods struggle to integrate local and global data characteristics, limiting performance in MNAR and high-dimensional settings. We propose an innovative framework, RefiDiff, combining local machine learning predictions with a novel Mamba-based denoising network efficiently capturing long-range dependencies among features and samples with low computational complexity. RefiDiff bridges the predictive and generative paradigms of imputation, leveraging pre-refinement for initial warm-up imputations and post-refinement to polish results, enhancing stability and accuracy. By encoding mixed-type data into unified tokens, RefiDiff enables robust imputation without architectural or hyperparameter tuning. RefiDiff outperforms state-of-the-art (SOTA) methods across missing-value settings, demonstrating strong performance in MNAR settings and superior out-of-sample generalization. Extensive evaluations on nine real-world datasets demonstrate its robustness, scalability, and effectiveness in handling complex missingness patterns.

cs.LG↗

arXiv2025

Joint stochastic localization and applications

Stochastic localization is a pathwise analysis technique that has emerged as a powerful tool in high-dimensional probability and sampling. In this work, we extend stochastic localization to a joint framework for coupling probability measures and explore its applications in distributional data analysis. We first unify existing stochastic localization processes under Eldan's $\alpha$-scheme and characterize their localization rates. Building on this, we introduce a joint scheme to couple probability measures via concurrent $\alpha$-schemes driven by a shared Brownian motion. This construction is canonical and induces a family of metrics on the space of probability measures, which we call Eldan's $\alpha$-distance. Alternative variants that extrapolate optimal Gaussian couplings to log-concave measures are also discussed. We study the theoretical properties of Eldan's $\alpha$-distance, including its restriction to Gaussian measures and its behavior under affine transformations. For $\alpha = 0$, we show it is topologically equivalent to the $2$-Wasserstein distance for measures supported on a common compact set; we also relate its weighted variants to linearized optimal transport in Wiener space and to score-matching objectives in training diffusion models. Computationally, we develop efficient estimators for Eldan's $\alpha$-distance in the cases $\alpha=0$ and $\alpha=1/2$, with rigorous error guarantees for log-concave and finitely supported measures in the former setting and Gaussian measures in the latter. Finally, we apply Eldan's $\alpha$-distance as a scalable surrogate for the $2$-Wasserstein distance to enable fast pairwise distance estimation and approximate computation of Wasserstein barycenters.

math.ST↗

arXiv2025

Compact Recurrent Transformer with Persistent Memory

The Transformer architecture has shown significant success in many language processing and visual tasks. However, the method faces challenges in efficiently scaling to long sequences because the self-attention computation is quadratic with respect to the input length. To overcome this limitation, several approaches scale to longer sequences by breaking long sequences into a series of segments, restricting self-attention to local dependencies between tokens within each segment and using a memory mechanism to manage information flow between segments. However, these approached generally introduce additional compute overhead that restricts them from being used for applications where limited compute memory and power are of great concern (such as edge computing). We propose a novel and efficient Compact Recurrent Transformer (CRT), which combines shallow Transformer models that process short local segments with recurrent neural networks to compress and manage a single persistent memory vector that summarizes long-range global information between segments. We evaluate CRT on WordPTB and WikiText-103 for next-token-prediction tasks, as well as on the Toyota Smarthome video dataset for classification. CRT achieves comparable or superior prediction results to full-length Transformers in the language datasets while using significantly shorter segments (half or quarter size) and substantially reduced FLOPs. Our approach also demonstrates state-of-the-art performance on the Toyota Smarthome video dataset.

cs.LG↗

arXiv2025

Mol-CADiff: Causality-Aware Autoregressive Diffusion for Molecule Generation

The design of novel molecules with desired properties is a key challenge in drug discovery and materials science. Traditional methods rely on trial-and-error, while recent deep learning approaches have accelerated molecular generation. However, existing models struggle with generating molecules based on specific textual descriptions. We introduce Mol-CADiff, a novel diffusion-based framework that uses causal attention mechanisms for text-conditional molecular generation. Our approach explicitly models the causal relationship between textual prompts and molecular structures, overcoming key limitations in existing methods. We enhance dependency modeling both within and across modalities, enabling precise control over the generation process. Our extensive experiments demonstrate that Mol-CADiff outperforms state-of-the-art methods in generating diverse, novel, and chemically valid molecules, with better alignment to specified properties, enabling more intuitive language-driven molecular design.

cs.LG↗

arXiv2025

GraphMinNet: Learning Dependencies in Graphs with Light Complexity Minimal Architecture

Graph Neural Networks (GNNs) have demonstrated remarkable success in various applications, yet they often struggle to capture long-range dependencies (LRD) effectively. This paper introduces GraphMinNet, a novel GNN architecture that generalizes the idea of minimal Gated Recurrent Units to graph-structured data. Our approach achieves efficient LRD modeling with linear computational complexity while maintaining permutation equivariance and stability. The model incorporates both structural and positional information through a unique combination of feature and positional encodings, leading to provably stronger expressiveness than the 1-WL test. Theoretical analysis establishes that GraphMinNet maintains non-decaying gradients over long distances, ensuring effective long-range information propagation. Extensive experiments on ten diverse datasets, including molecular graphs, image graphs, and synthetic networks, demonstrate that GraphMinNet achieves state-of-the-art performance while being computationally efficient. Our results show superior performance on 6 out of 10 datasets and competitive results on the others, validating the effectiveness of our approach in capturing both local and global graph structures.

cs.LG↗

arXiv2024

Preconditioning for Accelerated Gradient Descent Optimization and Regularization

Accelerated training algorithms, such as adaptive learning rates (or preconditioning) and various normalization methods, are widely used but not fully understood. When regularization is introduced, standard optimizers like adaptive learning rates may not perform effectively. This raises the need for alternative regularization approaches such as AdamW and the question of how to properly combine regularization with preconditioning. In this paper, we address these challenges using the theory of preconditioning as follows: (1) We explain how AdaGrad, RMSProp, and Adam accelerates training through improving Hessian conditioning; (2) We explore the interaction between $L_2$-regularization and preconditioning, demonstrating that AdamW amounts to selecting the underlying intrinsic parameters for regularization, and we derive a generalization for the $L_1$-regularization; and (3) We demonstrate how various normalization methods such as input data normalization, batch normalization, and layer normalization accelerate training by improving Hessian conditioning. Our analysis offers a unified mathematical framework for understanding various acceleration techniques or deriving appropriate regularization schemes.

cs.LG↗

arXiv2024

Model-Assisted Learning for Adaptive Cooperative Perception of Connected Autonomous Vehicles

Cooperative perception (CP) is a key technology to facilitate consistent and accurate situational awareness for connected and autonomous vehicles (CAVs). To tackle the network resource inefficiency issue in traditional broadcast-based CP, unicast-based CP has been proposed to associate CAV pairs for cooperative perception via vehicle-to-vehicle transmission. In this paper, we investigate unicast-based CP among CAV pairs. With the consideration of dynamic perception workloads and channel conditions due to vehicle mobility and dynamic radio resource availability, we propose an adaptive cooperative perception scheme for CAV pairs in a mixed-traffic autonomous driving scenario with both CAVs and human-driven vehicles. We aim to determine when to switch between cooperative perception and stand-alone perception for each CAV pair, and allocate communication and computing resources to cooperative CAV pairs for maximizing the computing efficiency gain under perception task delay requirements. A model-assisted multi-agent reinforcement learning (MARL) solution is developed, which integrates MARL for an adaptive CAV cooperation decision and an optimization model for communication and computing resource allocation. Simulation results demonstrate the effectiveness of the proposed scheme in achieving high computing efficiency gain, as compared with benchmark schemes.

cs.NI↗

arXiv2023

Millimeter Wave Full-Duplex Networks: MAC Design and Throughput Optimization

Full-duplex (FD) technique can remarkably boost the network capacity in the millimeter wave (mmWave) bands by enabling simultaneous transmission and reception. However, due to directional transmission and large bandwidth, the throughput and fairness performance of a mmWave FD network are affected by deafness and directional hidden-node (HN) problems and severe residual self-interference (RSI). To address these challenges, this paper proposes a directional FD medium access control protocol, named DFDMAC to support typical directional FD transmission modes by exploiting FD to transmit control frames to reduce signaling overhead. Furthermore, a novel busy-tone mechanism is designed to avoid deafness and directional HN problems and improve the fairness of channel access. To reduce the impact of RSI on link throughput, we formulate a throughput maximization problem for different FD transmission modes and propose a power control algorithm to obtain the optimal transmit power. Simulation results show that the proposed DFDMAC can improve the network throughput and fairness by over 60% and 32%, respectively, compared with the existing MAC protocol in IEEE 802.11ay. Moreover, the proposed power control algorithm can effectively enhance the network throughput.

cs.NI↗

arXiv2022

SCP-GAN: Self-Correcting Discriminator Optimization for Training Consistency Preserving Metric GAN on Speech Enhancement Tasks

In recent years, Generative Adversarial Networks (GANs) have produced significantly improved results in speech enhancement (SE) tasks. They are difficult to train, however. In this work, we introduce several improvements to the GAN training schemes, which can be applied to most GAN-based SE models. We propose using consistency loss functions, which target the inconsistency in time and time-frequency domains caused by Fourier and Inverse Fourier Transforms. We also present self-correcting optimization for training a GAN discriminator on SE tasks, which helps avoid "harmful" training directions for parts of the discriminator loss function. We have tested our proposed methods on several state-of-the-art GAN-based SE models and obtained consistent improvements, including new state-of-the-art results for the Voice Bank+DEMAND dataset.

cs.SD↗