arXiv subjects
Publications and source records attributed to Zhengyi Lu.
This paper proposes a generalized AHU algorithm based on tree isomorphism theory and applies it to the complete classification of n-dimensional stably dissipative Lotka-Volterra systems.
Spatial transcriptomics (ST) platforms simultaneously measure gene expression and capture cell nucleus images at single-cell resolution. A fundamental property of tissue preparation introduces a confounding relationship between the two measurement modalities: sectioning a three-dimensional tissue into a thin slice produces a two-dimensional cross-section whose area depends on the cutting angle. Larger cross-sections expose more cytoplasm, yielding higher mRNA counts, while pathomics features such as nuclear area are measured directly from the same 2D boundary. This sectioning geometry creates an apparent correlation between gene expression and pathomics that reflects the measurement process rather than independent biology. Existing gene-to-image methods generate cell images from gene features but do not support condition-driven editing of existing images across both omics layers. We apply the Manifold-Aware Diffusion (MAD) framework to this dual-omics editing setting, enabling targeted modification of one feature group while preserving the other. Evaluated on podocyte cells from CosMx SMI kidney tissue, MAD achieves MAE=0.6636 and FID=25.19 for pathomics editing, outperforming all compared baselines. A controlled simulation study further confirms that the VAE component in MAD better preserves cross-group independence than CCDM (MAD without VAE).
Spatial transcriptomics (ST) enables joint characterization of tissue morphology and gene expression. However, 3D volumetric ST acquisition remains expensive. AI-driven methods offer a low-cost alternative but remain limited in accuracy, while recent 2D section-wise ST acquisition still rely on dense grid sampling, resulting in redundant measurements and undersampling of biologically informative regions. To bridge the gap, we propose STRATA, a reinforcement-driven active sampling framework with tri-paradigm adaptation for reconstructing dense 3D transcriptomic maps from sparse voxel-wise ST acquisition. STRATA constructs a 3D graph integrating H&E morphology with single-cell priors and employs a reinforcement learning agent to estimate morphological sparsity and transcriptomic informativeness, enabling budget-aware selection of informative spots. Given these sparse measurements, an adaptive tri-paradigm predictor combines retrieval, regression, and cross-layer imputation through lightweight fusion, dynamically weighting their contributions. Experiments across datasets demonstrate improved sampling efficiency and accuracy, particularly under low-budget settings. Code is available at https://github.com/Junchao-Zhu/STRATA.
Materials improvements in transmon qubits have yielded remarkable advances in qubit lifetimes (T1)and coherence times (T2). However, state-of-the-art superconducting qubits experience temporal fluctuations in their performance, which limit gate fidelities and quantum processor performance. We observe correlated increases in qubit relaxation and dephasing rates that last for minutes to hours, which we call T1 and T2 excursions. Using interleaved lifetime and coherence time measurements, noise spectroscopy, and two-level-system (TLS) spectroscopy, we find that these excursions are caused by single or few strongly-coupled TLS defects that spectrally diffuse into resonance with the qubit frequency. Our measurement protocol provides a powerful tool for understanding the noise sources that cause temporal fluctuations in superconducting qubit performance.
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
Vision-Language Models (VLMs) are far more reliable at recognizing what appears in a video than at reasoning about its spatial and temporal properties, such as metric distances, object dimensions, and consistent object identities across frames. We present Geometric Code, a perception-to-geometry pipeline that computes explicit spatial structure from video and supplies it to VLMs as context to augment reasoning. A perception layer segments and classifies objects and recovers depth, camera pose, and intrinsics from monocular RGB video. A deterministic geometric engine then back-projects, merges, and cleans these outputs into a spatial code, including per-object positions, dimensions, counts, inter-object distances, appearance order, and room geometry. The code is serialized into VLMs' prompts, either alongside the video or replacing it entirely. Specifically, there is no component trained or fine-tuned in our approach. On VSI-Bench, augmenting 2B and 4B open models with the spatial code improves average accuracy by +4.1 points over the frames-only baseline, with the largest gains on numeric estimation tasks such as absolute distance (+24.1 points). The results suggest that explicitly computed geometry, delivered through the language channel, recovers spatial competence that small VLMs cannot extract from pixels alone.
Metal implants corrupt MRI measurements throughout $k$-space, yet existing accelerated MRI methods assume clean data and most metal artifact reduction approaches assume fully sampled acquisitions. No public dataset provides paired $k$-space and images with and without metal for the same anatomy, and no framework jointly addresses artifact-aware acquisition and reconstruction across sampling trajectories. We present OpenMASC, an open-source pipeline covering the full workflow from data generation to deployment. A physics-based data generation module converts public CT volumes into paired clean and metal-corrupted MRI data in both Cartesian and radial formats. MA-VarNet, an unrolled reconstruction network with a per-cascade DC Rectifier, corrects artifacts that data-consistency steps reintroduce from corrupted measurements. A reinforcement learning agent actively selects $k$-space readouts and co-trains with the reconstruction network through a decoupled three-stage procedure. The framework is trajectory-agnostic except for the data-consistency operator, supporting both Cartesian and radial acquisition without architectural changes. Experiments on two datasets at $4\times$ and $8\times$ acceleration demonstrate consistent improvements over conventional and learned baselines on both trajectories.
Generative speech enhancement faces three gaps: spectral models capture harmonic structure but often disrupt phase, waveform models preserve phase but miss harmonics, and Schrödinger 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.
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%.
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.
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
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.
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.
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
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.
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.
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.
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.