arXiv subjects

Xiaoqi Sheng

Publications and source records attributed to Xiaoqi Sheng.

8 recordsLinked to original sources

arXiv2026

DeMixPert: Decomposed Response Modeling with Gaussian Mixtures for OOD Single-Cell Perturbation Prediction

Predicting transcriptome-wide responses to unseen genetic perturbations remains a major computational challenge because accurate prediction requires recovering both perturbation-specific transcriptional shifts and heterogeneous cellular responses. Existing methods often entangle deterministic response structure with stochastic population-level variation, causing dominant shared patterns to mask weaker perturbation-specific signals and impair distributional modeling. To address these challenges, we propose \textbf{DeMixPert}, an approach for Decomposed response Modeling with Gaussian Mixtures for Out-Of-Distribution (OOD) single-cell Perturbation prediction. DeMixPert decomposes perturbation-induced changes into a basal-state-dependent systematic response, a perturbation-specific response, and population-level variation. The systematic component is derived from the basal state encoded from control-cell expression, whereas the perturbation-specific component is inferred from pretrained target embeddings for unseen-target generalization. DeMixPert models population-level variation using a Gaussian prototype Invertible Network and adaptively combines reusable Gaussian prototypes according to the basal state and perturbation condition. The resulting mixture is mapped to a condition-specific variation distribution. Sampled variations are integrated with the systematic and perturbation-specific components, followed by joint decoding with the basal state to reconstruct perturbed-cell gene expression. Experimental results show that DeMixPert effectively captures heterogeneous single-cell perturbation responses and achieves superior performance across unseen-perturbation settings. The source code is made publicly available upon publication.

cs.LG↗

arXiv2026

S$^3$-Diff: Structural Semantic Synergy Diffusion Model for High Fidelity Super Resolution of Pathological Images

Digital pathology relies on high-resolution whole slide images for accurate diagnosis, yet limitations in imaging devices, storage, and transmission often make lower-resolution pathology images more common in clinical workflows. Current super-resolution techniques often tend to smooth diagnostically relevant morphology, leading to over-smoothed textures and semantic drift that compromise downstream clinical interpretation. To this end, we develop the Structural Semantic Synergy Diffusion Model (S3-Diff), a diffusion framework for high-fidelity super-resolution of pathological images. The core of S3-Diff is Specimen-aware Structural Anchoring (SSA), which combines prognosis-aware tissue support extracted by a fixed SAM with LR-HR gradient discrepancies to generate a specimen-specific structural anchor to preserve pathological morphology. Concurrently, we introduce Structure-guided Semantic Fidelity Tuning (SSFT) to adapt DINOv3 representations using SSA-derived structural supervision. SSFT combines the adapted semantic energy with LR-derived edge and grayscale cues. The resulting control guides denoising to suppress stochastic artifacts and maintain structural consistency. Extensive experimental results demonstrate that S3-Diff consistently outperforms state-of-the-art methods in both reconstruction quality and downstream survival analysis performance. The source code will be made public.

cs.CV↗

arXiv2026

Morphology-Aware Implicit Super-Resolution Network for Pathological Images

Accurate diagnosis in Digital Pathology (DP) relies on high-resolution whole-slide images, yet clinical deployment is often limited by hardware costs. Super-Resolution (SR) offers a promising alternative by computationally enhancing low-resolution acquisitions. However, existing SR methods frequently struggle to preserve fine-grained cellular morphology, leading to texture oversmoothing and blurred structural boundaries under complex tissue variability. To address this issue, we propose Morph-ISR, a morphology-aware implicit super-resolution framework for DP that restores diagnostically relevant details with sub-pixel precision. Morph-ISR reformulates SR as a continuous coordinate-based reconstruction problem and integrates an Implicit Position-aware Kernel Generator (IPKG) to adaptively model spatially varying tissue morphology. To further enhance structural fidelity, a Morphological Fidelity Prior (MFP) is introduced, leveraging semantic guidance from a pre-trained cell segmentation network to enforce boundary-preserving and region-aware reconstruction, thereby improving the representation of critical cellular boundaries and nuclear textures. Experiments on TCGA and SurGen datasets show that Morph-ISR achieves the best LPIPS and ST-LPIPS among the evaluated methods, reducing them by up to 38.37% and 39.55%, respectively, over the second-best methods while maintaining strong PSNR and SSIM. These results demonstrate superior preservation of diagnostically relevant cellular boundaries and nuclear textures, while compact parameterization and high throughput support efficient edge deployment. Code and trained models will be released upon publication.

cs.CV↗

arXiv2026

CHM-Net: Center Heatmap-driven Macro-Micro Modeling Network for MRI-based Microbial Density Stratification

Microbial density is clinically important for tumor assessment and treatment decision-making, and recent advances in deep learning suggest that it can be non-invasively inferred from multimodal MRI. In this work, MRI-based Microbial Density Stratification (MRI-MDS) is first investigated as a patient-level representation learning task, and Center Heatmap-driven Macro-micro modeling Network (CHM-Net) is introduced for this task. CHM-Net first establishes the link between imaging phenotypes and microbial states through center heatmap-guided small-lesion response localization. Building upon this, it constructs patient-level macro-micro evidence from localized heatmap responses for microbial density prediction. Experiments on the novel GBNPC 2026 dataset constructed for MRI-MDS demonstrate the effectiveness of CHM-Net, achieving superior performance over representative baselines with a 12.06% absolute ACC gain over the strongest competing result. Additionally, auxiliary validation on two 3D medical image datasets further verifies its robustness across volumetric medical image classification scenarios. The project is available at https://anonymous.4open.science/r/CHM-Net-942E/.

eess.IV↗

arXiv2025

DB-KAUNet: An Adaptive Dual Branch Kolmogorov-Arnold UNet for Retinal Vessel Segmentation

Accurate segmentation of retinal vessels is crucial for the clinical diagnosis of numerous ophthalmic and systemic diseases. However, traditional Convolutional Neural Network (CNN) methods exhibit inherent limitations, struggling to capture long-range dependencies and complex nonlinear relationships. To address the above limitations, an Adaptive Dual Branch Kolmogorov-Arnold UNet (DB-KAUNet) is proposed for retinal vessel segmentation. In DB-KAUNet, we design a Heterogeneous Dual-Branch Encoder (HDBE) that features parallel CNN and Transformer pathways. The HDBE strategically interleaves standard CNN and Transformer blocks with novel KANConv and KAT blocks, enabling the model to form a comprehensive feature representation. To optimize feature processing, we integrate several critical components into the HDBE. First, a Cross-Branch Channel Interaction (CCI) module is embedded to facilitate efficient interaction of channel features between the parallel pathways. Second, an attention-based Spatial Feature Enhancement (SFE) module is employed to enhance spatial features and fuse the outputs from both branches. Building upon the SFE module, an advanced Spatial Feature Enhancement with Geometrically Adaptive Fusion (SFE-GAF) module is subsequently developed. In the SFE-GAF module, adaptive sampling is utilized to focus on true vessel morphology precisely. The adaptive process strengthens salient vascular features while significantly reducing background noise and computational overhead. Extensive experiments on the DRIVE, STARE, and CHASE_DB1 datasets validate that DB-KAUNet achieves leading segmentation performance and demonstrates exceptional robustness.

cs.CV↗

arXiv2025

MM-UNet: Morph Mamba U-shaped Convolutional Networks for Retinal Vessel Segmentation

Accurate detection of retinal vessels plays a critical role in reflecting a wide range of health status indicators in the clinical diagnosis of ocular diseases. Recently, advances in deep learning have led to a surge in retinal vessel segmentation methods, which have significantly contributed to the quantitative analysis of vascular morphology. However, retinal vasculature differs significantly from conventional segmentation targets in that it consists of extremely thin and branching structures, whose global morphology varies greatly across images. These characteristics continue to pose challenges to segmentation precision and robustness. To address these issues, we propose MM-UNet, a novel architecture tailored for efficient retinal vessel segmentation. The model incorporates Morph Mamba Convolution layers, which replace pointwise convolutions to enhance branching topological perception through morph, state-aware feature sampling. Additionally, Reverse Selective State Guidance modules integrate reverse guidance theory with state-space modeling to improve geometric boundary awareness and decoding efficiency. Extensive experiments conducted on two public retinal vessel segmentation datasets demonstrate the superior performance of the proposed method in segmentation accuracy. Compared to the existing approaches, MM-UNet achieves F1-score gains of 1.64 % on DRIVE and 1.25 % on STARE, demonstrating its effectiveness and advancement. The project code is public via https://github.com/liujiawen-jpg/MM-UNet.

cs.CV↗

arXiv2025

Evolvable Graph Diffusion Optimal Transport with Pattern-Specific Alignment for Brain Connectome Modeling

Network analysis of human brain connectivity indicates that individual differences in cognitive abilities arise from neurobiological mechanisms inherent in structural and functional brain networks. Existing studies routinely treat structural connectivity (SC) as optimal or fixed topological scaffolds for functional connectivity (FC), often overlooking higher-order dependencies between brain regions and limiting the modeling of complex cognitive processes. Besides, the distinct spatial organizations of SC and FC complicate direct integration, as naive alignment may distort intrinsic nonlinear patterns of brain connectivity. In this study, we propose a novel framework called Evolvable Graph Diffusion Optimal Transport with Pattern-Specific Alignment (EDT-PA), designed to identify disease-specific connectome patterns and classify brain disorders. To accurately model high-order structural dependencies, EDT-PA incorporates a spectrum of evolvable modeling blocks to dynamically capture high-order dependencies across brain regions. Additionally, a Pattern-Specific Alignment mechanism employs optimal transport to align structural and functional representations in a geometry-aware manner. By incorporating a Kolmogorov-Arnold network for flexible node aggregation, EDT-PA is capable of modeling complex nonlinear interactions among brain regions for downstream classification. Extensive evaluations on the REST-meta-MDD and ADNI datasets demonstrate that EDT-PA outperforms state-of-the-art methods, offering a more effective framework for revealing structure-function misalignments and disorder-specific subnetworks in brain disorders. The project of this work is released via this link.

q-bio.NC↗

arXiv2025

HWA-UNETR: Hierarchical Window Aggregate UNETR for 3D Multimodal Gastric Lesion Segmentation

Multimodal medical image segmentation faces significant challenges in the context of gastric cancer lesion analysis. This clinical context is defined by the scarcity of independent multimodal datasets and the imperative to amalgamate inherently misaligned modalities. As a result, algorithms are constrained to train on approximate data and depend on application migration, leading to substantial resource expenditure and a potential decline in analysis accuracy. To address those challenges, we have made two major contributions: First, we publicly disseminate the GCM 2025 dataset, which serves as the first large-scale, open-source collection of gastric cancer multimodal MRI scans, featuring professionally annotated FS-T2W, CE-T1W, and ADC images from 500 patients. Second, we introduce HWA-UNETR, a novel 3D segmentation framework that employs an original HWA block with learnable window aggregation layers to establish dynamic feature correspondences between different modalities' anatomical structures, and leverages the innovative tri-orientated fusion mamba mechanism for context modeling and capturing long-range spatial dependencies. Extensive experiments on our GCM 2025 dataset and the publicly BraTS 2021 dataset validate the performance of our framework, demonstrating that the new approach surpasses existing methods by up to 1.68\% in the Dice score while maintaining solid robustness. The dataset and code are public via https://github.com/JeMing-creater/HWA-UNETR.

eess.IV↗