arXiv subjects

Zhengyi Lu

Publications and source records attributed to Zhengyi Lu.

16 recordsLinked to original sources

arXiv2026

HybridSB-MoE: Dual-Domain Schr\"odinger Bridges with Scene-Adaptive Expert Routing for Speech Enhancement

Generative speech enhancement faces three gaps: spectral models capture harmonic structure but often disrupt phase, waveform models preserve phase but miss harmonics, and Schr\"odinger Bridges (SB) shorten transport from noise to clean speech but leave inference cost only loosely tied to training. We propose HybridSB-MoE, a dual-domain framework that fills these gaps through three contributions unified by a single asymmetric design principle. (i) Asymmetric uncertainty fusion: The spectral path captures epistemic uncertainty via expert disagreement, while the waveform bridge models aleatoric variance through stochastic dynamics. We fuse them asymmetrically, allowing the mixing weight to adapt to distinct error regimes rather than average predictions. (ii) Heterogeneous MoE with top-k=2 routing across five distinct architectural archetypes, where architectural diversity makes the epistemic signal indicate which inductive bias fails rather than small perturbations among similar experts. (iii) Discretization bound (Theorem 1): path-consistency and trajectory regularizers together bound the K-step bridge sampling error in 2-Wasserstein distance at rate K-alpha, making small-K inference an objective-level guarantee rather than an empirical claim. On VoiceBank+DEMAND, HybridSB-MoE outperforms diffusion- and SB-based baselines at their step budgets while remaining competitive with consistency-distilled few-step methods.

cs.SD↗

arXiv2026

SAGEAgent: A Self-Evolving Agent for Cost-Aware Modality Acquisition in Multimodal Survival Prediction

Does every cancer patient truly need a complete diagnostic workup for accurate survival prediction? In multimodal clinical oncology, diagnostic modalities follow a clinically mandated order of escalating burden -- from demographics collected at intake to genomic profiling requiring specialized tissue analysis. Current multimodal survival methods either assume all modalities are available or passively handle missing data, but none actively reason about whether acquiring the next modality is justified for a given patient along this ordered workflow. We formulate this as a sequential decision problem and propose SAGEAgent (Sequential Acquisition Guided by Experience), a self-evolving LLM-based clinical agent that decides which diagnostic modalities to acquire for each patient, balancing predictive accuracy against clinical invasiveness. SAGEAgent reasons about each patient's evolving diagnostic state through clinical tools that translate numerical predictions into text, an episodic memory that retrieves similar past cases, and a semantic memory that accumulates reusable decision patterns from experience. Experiments on a glioma cohort combining TCGA-LGG, TCGA-GBM, and BraTS with four diagnostic modalities demonstrate that SAGEAgent achieves competitive survival prediction accuracy while reducing average acquisition burden by 55%.

cs.AI↗

arXiv2026

Multi-level Self-supervised Pretraining on Compositional Hierarchical Graph for Molecular Property Prediction

Self-supervised pretraining on molecular graphs has emerged as a promising approach for molecular property prediction, yet most existing methods operate at a single structural granularity and treat bond information as auxiliary edge attributes rather than as an independent semantic layer. In this work, we propose MolCHG, a multi-level self-supervised pretraining framework built upon a novel Compositional Hierarchical Graph that organizes molecular structure into four types of nodes across three semantic levels. By introducing a bond graph that operates in parallel with the atom graph, our architecture elevates bond-level information to independently evolving node representations, enabling fragment nodes to aggregate atom-level and bond-level semantics on an equal footing. We design three level-specific pretraining objectives: an atom-bond cross-view contrastive task that aligns the atom-view and bond-view representations within each fragment, a fragment-level functional group prediction task to inject domain-relevant chemical knowledge, and graph-level structure prediction tasks to encode global molecular topology. Experiments on nine MoleculeNet benchmarks demonstrate that MolCHG achieves the best performance on seven datasets across both classification and regression tasks, remaining competitive with the strongest baselines on the rest. Ablation studies further confirm that the multi-level supervision signals are complementary and that each component contributes to the overall performance.

cs.LG↗

arXiv2026

DUET: Dual-Paradigm Adaptive Expert Triage with Single-cell Inductive Prior for Spatial Transcriptomics Prediction

Inferring spatially resolved gene expression from histology images offers a cost-effective complement to spatial transcriptomics (ST). However, existing methods reduce this task to a simple morphology-to-expression mapping, where visual similarity does not guarantee molecular consistency. Meanwhile, single-cell data has amassed rich resources far surpassing the scale of ST data, yet it remains underexplored in vision-omics modeling. Furthermore, current approaches commit to a monolithic paradigm with bottlenecks, unable to balance expressive flexibility with biological fidelity. To bridge these gaps, we propose DUET, a novel dual-paradigm framework that synergizes parametric prediction and memory-based retrieval under cellular inductive priors. DUET implements a parallel regression-retrieval paradigm, adaptively reconciling the outputs of its complementary pathways. To mitigate aleatoric vision ambiguity, we incorporate large-scale single-cell references to impose molecular states as biological constraints for faithful learning. Building upon structural refinement, we further design a lightweight adapter to dynamically assign branch preference across spatial contexts to achieve optimal performance. Extensive experiments on three public datasets across varied gene scales demonstrate that DUET achieves SOTA performance, with consistent gains contributed by each proposed component. Code is available at https://github.com/Junchao-Zhu/DUET

cs.CV↗

arXiv2026

Four Limit Cycles in Three-Dimensional Competitive Lotka-Volterra Systems of Class 28 in Zeeman's Classification

In this paper, a three-dimensional competitive Lotka-Volterra system with four limit cycles is constructed for class 28 in Zeeman's classification. Combined with existing results -- from Gyllenberg and Yan (2009) for class 27, from Wang, Huang and Wu (2011) for class 29, and from Yu, Han and Xiao (2016) for class 26 -- our finding indicates that there exist systems with at least four limit cycles for each class among classes 26 $-$ 29.

math.DS↗

arXiv2026

Explainable Pathomics Feature Visualization via Correlation-aware Conditional Feature Editing

Pathomics is a recent approach that offers rich quantitative features beyond what black-box deep learning can provide, supporting more reproducible and explainable biomarkers in digital pathology. However, many derived features (e.g., "second-order moment") remain difficult to interpret, especially across different clinical contexts, which limits their practical adoption. Conditional diffusion models show promise for explainability through feature editing, but they typically assume feature independence**--**an assumption violated by intrinsically correlated pathomics features. Consequently, editing one feature while fixing others can push the model off the biological manifold and produce unrealistic artifacts. To address this, we propose a Manifold-Aware Diffusion (MAD) framework for controllable and biologically plausible cell nuclei editing. Unlike existing approaches, our method regularizes feature trajectories within a disentangled latent space learned by a variational auto-encoder (VAE). This ensures that manipulating a target feature automatically adjusts correlated attributes to remain within the learned distribution of real cells. These optimized features then guide a conditional diffusion model to synthesize high-fidelity images. Experiments demonstrate that our approach is able to navigate the manifold of pathomics features when editing those features. The proposed method outperforms baseline methods in conditional feature editing while preserving structural coherence.

cs.CV↗

arXiv2026

Local-Global Multimodal Contrastive Learning for Molecular Property Prediction

Accurate molecular property prediction requires integrating complementary information from molecular structure and chemical semantics. In this work, we propose LGM-CL, a local-global multimodal contrastive learning framework that jointly models molecular graphs and textual representations derived from SMILES and chemistry-aware augmented texts. Local functional group information and global molecular topology are captured using AttentiveFP and Graph Transformer encoders, respectively, and aligned through self-supervised contrastive learning. In addition, chemically enriched textual descriptions are contrasted with original SMILES to incorporate physicochemical semantics in a task-agnostic manner. During fine-tuning, molecular fingerprints are further integrated via Dual Cross-attention multimodal fusion. Extensive experiments on MoleculeNet benchmarks demonstrate that LGM-CL achieves consistent and competitive performance across both classification and regression tasks, validating the effectiveness of unified local-global and multimodal representation learning.

cs.LG↗

arXiv2026

AdaFuse: Adaptive Multimodal Fusion for Lung Cancer Risk Prediction via Reinforcement Learning

Multimodal fusion has emerged as a promising paradigm for disease diagnosis and prognosis, integrating complementary information from heterogeneous data sources such as medical images, clinical records, and radiology reports. However, existing fusion methods process all available modalities through the network, either treating them equally or learning to assign different contribution weights, leaving a fundamental question unaddressed: for a given patient, should certain modalities be used at all? We present AdaFuse, an adaptive multimodal fusion framework that leverages reinforcement learning (RL) to learn patient-specific modality selection and fusion strategies for lung cancer risk prediction. AdaFuse formulates multimodal fusion as a sequential decision process, where the policy network iteratively decides whether to incorporate an additional modality or proceed to prediction based on the information already acquired. This sequential formulation enables the model to condition each selection on previously observed modalities and terminate early when sufficient information is available, rather than committing to a fixed subset upfront. We evaluate AdaFuse on the National Lung Screening Trial (NLST) dataset. Experimental results demonstrate that AdaFuse achieves the highest AUC (0.762) compared to the best single-modality baseline (0.732), the best fixed fusion strategy (0.759), and adaptive baselines including DynMM (0.754) and MoE (0.742), while using fewer FLOPs than all triple-modality methods. Our work demonstrates the potential of reinforcement learning for personalized multimodal fusion in medical imaging, representing a shift from uniform fusion strategies toward adaptive diagnostic pipelines that learn when to consult additional modalities and when existing information suffices for accurate prediction.

cs.CV↗

arXiv2026

MASC: Metal-Aware Sampling and Correction via Reinforcement Learning for Accelerated MRI

Metal implants in MRI cause severe artifacts that degrade image quality and hinder clinical diagnosis. Traditional approaches address metal artifact reduction (MAR) and accelerated MRI acquisition as separate problems. We propose MASC, a unified reinforcement learning framework that jointly optimizes metal-aware k-space sampling and artifact correction for accelerated MRI. To enable supervised training, we construct a paired MRI dataset using physics-based simulation, generating k-space data and reconstructions for phantoms with and without metal implants. This paired dataset provides simulated 3D MRI scans with and without metal implants, where each metal-corrupted sample has an exactly matched clean reference, enabling direct supervision for both artifact reduction and acquisition policy learning. We formulate active MRI acquisition as a sequential decision-making problem, where an artifact-aware Proximal Policy Optimization (PPO) agent learns to select k-space phase-encoding lines under a limited acquisition budget. The agent operates on undersampled reconstructions processed through a U-Net-based MAR network, learning patterns that maximize reconstruction quality. We further propose an end-to-end training scheme where the acquisition policy learns to select k-space lines that best support artifact removal while the MAR network simultaneously adapts to the resulting undersampling patterns. Experiments demonstrate that MASC's learned policies outperform conventional sampling strategies, and end-to-end training improves performance compared to using a frozen pre-trained MAR network, validating the benefit of joint optimization. Cross-dataset experiments on FastMRI with physics-based artifact simulation further confirm generalization to realistic clinical MRI data. The code and models of MASC have been made publicly available: https://github.com/hrlblab/masc

cs.CV↗

arXiv2026

Disparate Quantum Corrections to Conduction in Carbon Nanotube Bundles

Quantum interference effects such as weak localization (WL) and universal conductance fluctuations (UCF) normally yield consistent electronic phase-coherence lengths in homogeneous conductors. Here we show that in individual carbon nanotube bundles exfoliated from highly conductive solution-spun fibers, different probes, including the field scales and magnitudes of WL and UCF and nonlocal magnetoconductance, lead to strikingly disparate estimates of coherence lengths. WL magnetoconductance measured in a perpendicular magnetic field yields a phase-coherence length of approximately 50 nm. In contrast, UCF amplitudes are comparable to e squared over h even for an 8 micrometer long segment, and nonlocal magnetoconductance persists across a 4 micrometer separation of electrodes, revealing phase-coherent transport over micrometer length scales within a single bundle. The coexistence of short- and long-range coherence implies that locally diffusive electrons remain partially phase-correlated among nanotubes within the same bundle. These findings challenge the conventional single-scale picture of mesoscopic coherence and establish carbon nanotube bundles as a model platform for emergent, network-level quantum transport.

cond-mat.mes-hall↗

arXiv2025

SCR2-ST: Combine Single Cell with Spatial Transcriptomics for Efficient Active Sampling via Reinforcement Learning

Spatial transcriptomics (ST) is an emerging technology that enables researchers to investigate the molecular relationships underlying tissue morphology. However, acquiring ST data remains prohibitively expensive, and traditional fixed-grid sampling strategies lead to redundant measurements of morphologically similar or biologically uninformative regions, thus resulting in scarce data that constrain current methods. The well-established single-cell sequencing field, however, could provide rich biological data as an effective auxiliary source to mitigate this limitation. To bridge these gaps, we introduce SCR2-ST, a unified framework that leverages single-cell prior knowledge to guide efficient data acquisition and accurate expression prediction. SCR2-ST integrates a single-cell guided reinforcement learning-based (SCRL) active sampling and a hybrid regression-retrieval prediction network SCR2Net. SCRL combines single-cell foundation model embeddings with spatial density information to construct biologically grounded reward signals, enabling selective acquisition of informative tissue regions under constrained sequencing budgets. SCR2Net then leverages the actively sampled data through a hybrid architecture combining regression-based modeling with retrieval-augmented inference, where a majority cell-type filtering mechanism suppresses noisy matches and retrieved expression profiles serve as soft labels for auxiliary supervision. We evaluated SCR2-ST on three public ST datasets, demonstrating SOTA performance in both sampling efficiency and prediction accuracy, particularly under low-budget scenarios. Code is publicly available at: https://github.com/hrlblab/SCR2ST

cs.CV↗

arXiv2025

Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models

Accurate cell nuclei segmentation is critical for downstream tasks in kidney pathology and remains a major challenge due to the morphological diversity and imaging variability of renal tissues. While our prior work has evaluated early-generation AI cell foundation models in this domain, the effectiveness of recent cell foundation models remains unclear. In this study, we benchmark advanced AI cell foundation models (2025), including CellViT++ variants and Cellpose-SAM, against three widely used cell foundation models developed prior to 2024, using a diverse large-scale set of kidney image patches within a human-in-the-loop rating framework. We further performed fusion-based ensemble evaluation and model agreement analysis to assess the segmentation capabilities of the different models. Our results show that CellViT++ [Virchow] yields the highest standalone performance with 40.3% of predictions rated as "Good" on a curated set of 2,091 challenging samples, outperforming all prior models. In addition, our fused model achieves 62.2% "Good" predictions and only 0.4% "Bad", substantially reducing segmentation errors. Notably, the fusion model (2025) successfully resolved the majority of challenging cases that remained unaddressed in our previous study. These findings demonstrate the potential of AI cell foundation model development in renal pathology and provide a curated dataset of challenging samples to support future kidney-specific model refinement.

q-bio.QM↗

arXiv2025

CASC-AI: Consensus-aware Self-corrective Learning for Noise Cell Segmentation

Multi-class cell segmentation in high-resolution gigapixel whole slide images (WSIs) is crucial for various clinical applications. However, training such models typically requires labor-intensive, pixel-wise annotations by domain experts. Recent efforts have democratized this process by involving lay annotators without medical expertise. However, conventional non-corrective approaches struggle to handle annotation noise adaptively because they lack mechanisms to mitigate false positives (FP) and false negatives (FN) at both the image-feature and pixel levels. In this paper, we propose a consensus-aware self-corrective AI agent that leverages the Consensus Matrix to guide its learning process. The Consensus Matrix defines regions where both the AI and annotators agree on cell and non-cell annotations, which are prioritized with stronger supervision. Conversely, areas of disagreement are adaptively weighted based on their feature similarity to high-confidence consensus regions, with more similar regions receiving greater attention. Additionally, contrastive learning is employed to separate features of noisy regions from those of reliable consensus regions by maximizing their dissimilarity. This paradigm enables the model to iteratively refine noisy labels, enhancing its robustness. Validated on one real-world lay-annotated cell dataset and two reasoning-guided simulated noisy datasets, our method demonstrates improved segmentation performance, effectively correcting FP and FN errors and showcasing its potential for training robust models on noisy datasets. The official implementation and cell annotations are publicly available at https://github.com/ddrrnn123/CASC-AI.

cs.CV↗

arXiv2025

Fast-RF-Shimming: Accelerate RF Shimming in 7T MRI using Deep Learning

Ultrahigh field (UHF) Magnetic Resonance Imaging (MRI) offers an elevated signal-to-noise ratio (SNR), enabling exceptionally high spatial resolution that benefits both clinical diagnostics and advanced research. However, the jump to higher fields introduces complications, particularly transmit radiofrequency (RF) field ($B_{1}^{+}$) inhomogeneities, manifesting as uneven flip angles and image intensity irregularities. These artifacts can degrade image quality and impede broader clinical adoption. Traditional RF shimming methods, such as Magnitude Least Squares (MLS) optimization, effectively mitigate $B_{1}^{+}$ inhomogeneity, but remain time-consuming. Recent machine learning approaches, including RF Shim Prediction by Iteratively Projected Ridge Regression and other deep learning architectures, suggest alternative pathways. Although these approaches show promise, challenges such as extensive training periods, limited network complexity, and practical data requirements persist. In this paper, we introduce a holistic learning-based framework called Fast-RF-Shimming, which achieves a 5000x speed-up compared to the traditional MLS method. In the initial phase, we employ random-initialized Adaptive Moment Estimation (Adam) to derive the desired reference shimming weights from multi-channel $B_{1}^{+}$ fields. Next, we train a Residual Network (ResNet) to map $B_{1}^{+}$ fields directly to the ultimate RF shimming outputs, incorporating the confidence parameter into its loss function. Finally, we design Non-uniformity Field Detector (NFD), an optional post-processing step, to ensure the extreme non-uniform outcomes are identified. Comparative evaluations with standard MLS optimization underscore notable gains in both processing speed and predictive accuracy, which indicates that our technique shows a promising solution for addressing persistent inhomogeneity challenges.

cs.CV↗

arXiv2024

Optimizing Transmit Field Inhomogeneity of Parallel RF Transmit Design in 7T MRI using Deep Learning

Ultrahigh field (UHF) Magnetic Resonance Imaging (MRI) provides a higher signal-to-noise ratio and, thereby, higher spatial resolution. However, UHF MRI introduces challenges such as transmit radiofrequency (RF) field (B1+) inhomogeneities, leading to uneven flip angles and image intensity anomalies. These issues can significantly degrade imaging quality and its medical applications. This study addresses B1+ field homogeneity through a novel deep learning-based strategy. Traditional methods like Magnitude Least Squares (MLS) optimization have been effective but are time-consuming and dependent on the patient's presence. Recent machine learning approaches, such as RF Shim Prediction by Iteratively Projected Ridge Regression and deep learning frameworks, have shown promise but face limitations like extensive training times and oversimplified architectures. We propose a two-step deep learning strategy. First, we obtain the desired reference RF shimming weights from multi-channel B1+ fields using random-initialized Adaptive Moment Estimation. Then, we employ Residual Networks (ResNets) to train a model that maps B1+ fields to target RF shimming outputs. Our approach does not rely on pre-calculated reference optimizations for the testing process and efficiently learns residual functions. Comparative studies with traditional MLS optimization demonstrate our method's advantages in terms of speed and accuracy. The proposed strategy achieves a faster and more efficient RF shimming design, significantly improving imaging quality at UHF. This advancement holds potential for broader applications in medical imaging and diagnostics.

cs.CV↗

arXiv2023

Four limit cycles in three-dimensional Lotka-Volterra competitive systems with classes 28, 30 and 31 in Zeemans classification via automatic search

Four limit cycles are constructed for classes 28, 30 and 31 in Zeeman's classification, together with the results in [5 ] for class 27, [20] for class 29 and [22] for class 26 which indicate that for each class among classes 26-31, there exist at least four limit cycles. This gives a partial answer to a problem proposed in [22] as well as in [7].

math.DS↗