arXiv subjects

Yilei Shi

Publications and source records attributed to Yilei Shi.

At least 37 records · Page 2Linked to original sources

arXiv2025

High-Order Progressive Trajectory Matching for Medical Image Dataset Distillation

Medical image analysis faces significant challenges in data sharing due to privacy regulations and complex institutional protocols. Dataset distillation offers a solution to address these challenges by synthesizing compact datasets that capture essential information from real, large medical datasets. Trajectory matching has emerged as a promising methodology for dataset distillation; however, existing methods primarily focus on terminal states, overlooking crucial information in intermediate optimization states. We address this limitation by proposing a shape-wise potential that captures the geometric structure of parameter trajectories, and an easy-to-complex matching strategy that progressively addresses parameters based on their complexity. Experiments on medical image classification tasks demonstrate that our method improves distillation performance while preserving privacy and maintaining model accuracy comparable to training on the original datasets. Our code is available at https://github.com/Bian-jh/HoP-TM.

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arXiv2025

BRepFormer: Transformer-Based B-rep Geometric Feature Recognition

Recognizing geometric features on B-rep models is a cornerstone technique for multimedia content-based retrieval and has been widely applied in intelligent manufacturing. However, previous research often merely focused on Machining Feature Recognition (MFR), falling short in effectively capturing the intricate topological and geometric characteristics of complex geometry features. In this paper, we propose BRepFormer, a novel transformer-based model to recognize both machining feature and complex CAD models' features. BRepFormer encodes and fuses the geometric and topological features of the models. Afterwards, BRepFormer utilizes a transformer architecture for feature propagation and a recognition head to identify geometry features. During each iteration of the transformer, we incorporate a bias that combines edge features and topology features to reinforce geometric constraints on each face. In addition, we also proposed a dataset named Complex B-rep Feature Dataset (CBF), comprising 20,000 B-rep models. By covering more complex B-rep models, it is better aligned with industrial applications. The experimental results demonstrate that BRepFormer achieves state-of-the-art accuracy on the MFInstSeg, MFTRCAD, and our CBF datasets.

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arXiv2025

Multimodal Large Language Models for Medical Report Generation via Customized Prompt Tuning

Medical report generation from imaging data remains a challenging task in clinical practice. While large language models (LLMs) show great promise in addressing this challenge, their effective integration with medical imaging data still deserves in-depth exploration. In this paper, we present MRG-LLM, a novel multimodal large language model (MLLM) that combines a frozen LLM with a learnable visual encoder and introduces a dynamic prompt customization mechanism. Our key innovation lies in generating instance-specific prompts tailored to individual medical images through conditional affine transformations derived from visual features. We propose two implementations: prompt-wise and promptbook-wise customization, enabling precise and targeted report generation. Extensive experiments on IU X-ray and MIMIC-CXR datasets demonstrate that MRG-LLM achieves state-of-the-art performance in medical report generation. Our code will be made publicly available.

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arXiv2025

Taming Stable Diffusion for Computed Tomography Blind Super-Resolution

High-resolution computed tomography (CT) imaging is essential for medical diagnosis but requires increased radiation exposure, creating a critical trade-off between image quality and patient safety. While deep learning methods have shown promise in CT super-resolution, they face challenges with complex degradations and limited medical training data. Meanwhile, large-scale pre-trained diffusion models, particularly Stable Diffusion, have demonstrated remarkable capabilities in synthesizing fine details across various vision tasks. Motivated by this, we propose a novel framework that adapts Stable Diffusion for CT blind super-resolution. We employ a practical degradation model to synthesize realistic low-quality images and leverage a pre-trained vision-language model to generate corresponding descriptions. Subsequently, we perform super-resolution using Stable Diffusion with a specialized controlling strategy, conditioned on both low-resolution inputs and the generated text descriptions. Extensive experiments show that our method outperforms existing approaches, demonstrating its potential for achieving high-quality CT imaging at reduced radiation doses. Our code will be made publicly available.

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arXiv2025

GlobalBuildingAtlas: An Open Global and Complete Dataset of Building Polygons, Heights and LoD1 3D Models

We introduce GlobalBuildingAtlas, a publicly available dataset providing global and complete coverage of building polygons, heights and Level of Detail 1 (LoD1) 3D building models. This is the first open dataset to offer high quality, consistent, and complete building data in 2D and 3D form at the individual building level on a global scale. Towards this dataset, we developed machine learning-based pipelines to derive building polygons and heights (called GBA.Height) from global PlanetScope satellite data, respectively. Also a quality-based fusion strategy was employed to generate higher-quality polygons (called GBA.Polygon) based on existing open building polygons, including our own derived one. With more than 2.75 billion buildings worldwide, GBA.Polygon surpasses the most comprehensive database to date by more than 1 billion buildings. GBA.Height offers the most detailed and accurate global 3D building height maps to date, achieving a spatial resolution of 3x3 meters-30 times finer than previous global products (90 m), enabling a high-resolution and reliable analysis of building volumes at both local and global scales. Finally, we generated a global LoD1 building model (called GBA.LoD1) from the resulting GBA.Polygon and GBA.Height. GBA.LoD1 represents the first complete global LoD1 building models, including 2.68 billion building instances with predicted heights, i.e., with a height completeness of more than 97%, achieving RMSEs ranging from 1.5 m to 8.9 m across different continents. With its height accuracy, comprehensive global coverage and rich spatial details, GlobalBuildingAltas offers novel insights on the status quo of global buildings, which unlocks unprecedented geospatial analysis possibilities, as showcased by a better illustration of where people live and a more comprehensive monitoring of the progress on the 11th Sustainable Development Goal of the United Nations.

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arXiv2025

Global Collinearity-aware Polygonizer for Polygonal Building Mapping in Remote Sensing

This paper addresses the challenge of mapping polygonal buildings from remote sensing images and introduces a novel algorithm, the Global Collinearity-aware Polygonizer (GCP). GCP, built upon an instance segmentation framework, processes binary masks produced by any instance segmentation model. The algorithm begins by collecting polylines sampled along the contours of the binary masks. These polylines undergo a refinement process using a transformer-based regression module to ensure they accurately fit the contours of the targeted building instances. Subsequently, a collinearity-aware polygon simplification module simplifies these refined polylines and generate the final polygon representation. This module employs dynamic programming technique to optimize an objective function that balances the simplicity and fidelity of the polygons, achieving globally optimal solutions. Furthermore, the optimized collinearity-aware objective is seamlessly integrated into network training, enhancing the cohesiveness of the entire pipeline. The effectiveness of GCP has been validated on two public benchmarks for polygonal building mapping. Further experiments reveal that applying the collinearity-aware polygon simplification module to arbitrary polylines, without prior knowledge, enhances accuracy over traditional methods such as the Douglas-Peucker algorithm. This finding underscores the broad applicability of GCP. The code for the proposed method will be made available at https://github.com/zhu-xlab.

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arXiv2025

UniCrossAdapter: Multimodal Adaptation of CLIP for Radiology Report Generation

Automated radiology report generation aims to expedite the tedious and error-prone reporting process for radiologists. While recent works have made progress, learning to align medical images and textual findings remains challenging due to the relative scarcity of labeled medical data. For example, datasets for this task are much smaller than those used for image captioning in computer vision. In this work, we propose to transfer representations from CLIP, a large-scale pre-trained vision-language model, to better capture cross-modal semantics between images and texts. However, directly applying CLIP is suboptimal due to the domain gap between natural images and radiology. To enable efficient adaptation, we introduce UniCrossAdapter, lightweight adapter modules that are incorporated into CLIP and fine-tuned on the target task while keeping base parameters fixed. The adapters are distributed across modalities and their interaction to enhance vision-language alignment. Experiments on two public datasets demonstrate the effectiveness of our approach, advancing state-of-the-art in radiology report generation. The proposed transfer learning framework provides a means of harnessing semantic knowledge from large-scale pre-trained models to tackle data-scarce medical vision-language tasks. Code is available at https://github.com/chauncey-tow/MRG-CLIP.

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arXiv2025

CausalCLIPSeg: Unlocking CLIP's Potential in Referring Medical Image Segmentation with Causal Intervention

Referring medical image segmentation targets delineating lesions indicated by textual descriptions. Aligning visual and textual cues is challenging due to their distinct data properties. Inspired by large-scale pre-trained vision-language models, we propose CausalCLIPSeg, an end-to-end framework for referring medical image segmentation that leverages CLIP. Despite not being trained on medical data, we enforce CLIP's rich semantic space onto the medical domain by a tailored cross-modal decoding method to achieve text-to-pixel alignment. Furthermore, to mitigate confounding bias that may cause the model to learn spurious correlations instead of meaningful causal relationships, CausalCLIPSeg introduces a causal intervention module which self-annotates confounders and excavates causal features from inputs for segmentation judgments. We also devise an adversarial min-max game to optimize causal features while penalizing confounding ones. Extensive experiments demonstrate the state-of-the-art performance of our proposed method. Code is available at https://github.com/WUTCM-Lab/CausalCLIPSeg.

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arXiv2025

Reducing Annotation Burden: Exploiting Image Knowledge for Few-Shot Medical Video Object Segmentation via Spatiotemporal Consistency Relearning

Few-shot video object segmentation aims to reduce annotation costs; however, existing methods still require abundant dense frame annotations for training, which are scarce in the medical domain. We investigate an extremely low-data regime that utilizes annotations from only a few video frames and leverages existing labeled images to minimize costly video annotations. Specifically, we propose a two-phase framework. First, we learn a few-shot segmentation model using labeled images. Subsequently, to improve performance without full supervision, we introduce a spatiotemporal consistency relearning approach on medical videos that enforces consistency between consecutive frames. Constraints are also enforced between the image model and relearning model at both feature and prediction levels. Experiments demonstrate the superiority of our approach over state-of-the-art few-shot segmentation methods. Our model bridges the gap between abundant annotated medical images and scarce, sparsely labeled medical videos to achieve strong video segmentation performance in this low data regime. Code is available at https://github.com/MedAITech/RAB.

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arXiv2025

Ultrasound Image-to-Video Synthesis via Latent Dynamic Diffusion Models

Ultrasound video classification enables automated diagnosis and has emerged as an important research area. However, publicly available ultrasound video datasets remain scarce, hindering progress in developing effective video classification models. We propose addressing this shortage by synthesizing plausible ultrasound videos from readily available, abundant ultrasound images. To this end, we introduce a latent dynamic diffusion model (LDDM) to efficiently translate static images to dynamic sequences with realistic video characteristics. We demonstrate strong quantitative results and visually appealing synthesized videos on the BUSV benchmark. Notably, training video classification models on combinations of real and LDDM-synthesized videos substantially improves performance over using real data alone, indicating our method successfully emulates dynamics critical for discrimination. Our image-to-video approach provides an effective data augmentation solution to advance ultrasound video analysis. Code is available at https://github.com/MedAITech/U_I2V.

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arXiv2025

One-Shot Medical Video Object Segmentation via Temporal Contrastive Memory Networks

Video object segmentation is crucial for the efficient analysis of complex medical video data, yet it faces significant challenges in data availability and annotation. We introduce the task of one-shot medical video object segmentation, which requires separating foreground and background pixels throughout a video given only the mask annotation of the first frame. To address this problem, we propose a temporal contrastive memory network comprising image and mask encoders to learn feature representations, a temporal contrastive memory bank that aligns embeddings from adjacent frames while pushing apart distant ones to explicitly model inter-frame relationships and stores these features, and a decoder that fuses encoded image features and memory readouts for segmentation. We also collect a diverse, multi-source medical video dataset spanning various modalities and anatomies to benchmark this task. Extensive experiments demonstrate state-of-the-art performance in segmenting both seen and unseen structures from a single exemplar, showing ability to generalize from scarce labels. This highlights the potential to alleviate annotation burdens for medical video analysis. Code is available at https://github.com/MedAITech/TCMN.

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arXiv2025

Scale-Aware Contrastive Reverse Distillation for Unsupervised Medical Anomaly Detection

Unsupervised anomaly detection using deep learning has garnered significant research attention due to its broad applicability, particularly in medical imaging where labeled anomalous data are scarce. While earlier approaches leverage generative models like autoencoders and generative adversarial networks (GANs), they often fall short due to overgeneralization. Recent methods explore various strategies, including memory banks, normalizing flows, self-supervised learning, and knowledge distillation, to enhance discrimination. Among these, knowledge distillation, particularly reverse distillation, has shown promise. Following this paradigm, we propose a novel scale-aware contrastive reverse distillation model that addresses two key limitations of existing reverse distillation methods: insufficient feature discriminability and inability to handle anomaly scale variations. Specifically, we introduce a contrastive student-teacher learning approach to derive more discriminative representations by generating and exploring out-of-normal distributions. Further, we design a scale adaptation mechanism to softly weight contrastive distillation losses at different scales to account for the scale variation issue. Extensive experiments on benchmark datasets demonstrate state-of-the-art performance, validating the efficacy of the proposed method. Code is available at https://github.com/MedAITech/SCRD4AD.

cs.CV↗

arXiv2025

Striving for Simplicity: Simple Yet Effective Prior-Aware Pseudo-Labeling for Semi-Supervised Ultrasound Image Segmentation

Medical ultrasound imaging is ubiquitous, but manual analysis struggles to keep pace. Automated segmentation can help but requires large labeled datasets, which are scarce. Semi-supervised learning leveraging both unlabeled and limited labeled data is a promising approach. State-of-the-art methods use consistency regularization or pseudo-labeling but grow increasingly complex. Without sufficient labels, these models often latch onto artifacts or allow anatomically implausible segmentations. In this paper, we present a simple yet effective pseudo-labeling method with an adversarially learned shape prior to regularize segmentations. Specifically, we devise an encoder-twin-decoder network where the shape prior acts as an implicit shape model, penalizing anatomically implausible but not ground-truth-deviating predictions. Without bells and whistles, our simple approach achieves state-of-the-art performance on two benchmarks under different partition protocols. We provide a strong baseline for future semi-supervised medical image segmentation. Code is available at https://github.com/WUTCM-Lab/Shape-Prior-Semi-Seg.

eess.IV↗

arXiv2025

Rethinking Cell Counting Methods: Decoupling Counting and Localization

Cell counting in microscopy images is vital in medicine and biology but extremely tedious and time-consuming to perform manually. While automated methods have advanced in recent years, state-of-the-art approaches tend to increasingly complex model designs. In this paper, we propose a conceptually simple yet effective decoupled learning scheme for automated cell counting, consisting of separate counter and localizer networks. In contrast to jointly learning counting and density map estimation, we show that decoupling these objectives surprisingly improves results. The counter operates on intermediate feature maps rather than pixel space to leverage global context and produce count estimates, while also generating coarse density maps. The localizer then reconstructs high-resolution density maps that precisely localize individual cells, conditional on the original images and coarse density maps from the counter. Besides, to boost counting accuracy, we further introduce a global message passing module to integrate cross-region patterns. Extensive experiments on four datasets demonstrate that our approach, despite its simplicity, challenges common practice and achieves state-of-the-art performance by significant margins. Our key insight is that decoupled learning alleviates the need to learn counting on high-resolution density maps directly, allowing the model to focus on global features critical for accurate estimates. Code is available at https://github.com/MedAITech/DCL.

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arXiv2025

Q-PART: Quasi-Periodic Adaptive Regression with Test-time Training for Pediatric Left Ventricular Ejection Fraction Regression

In this work, we address the challenge of adaptive pediatric Left Ventricular Ejection Fraction (LVEF) assessment. While Test-time Training (TTT) approaches show promise for this task, they suffer from two significant limitations. Existing TTT works are primarily designed for classification tasks rather than continuous value regression, and they lack mechanisms to handle the quasi-periodic nature of cardiac signals. To tackle these issues, we propose a novel \textbf{Q}uasi-\textbf{P}eriodic \textbf{A}daptive \textbf{R}egression with \textbf{T}est-time Training (Q-PART) framework. In the training stage, the proposed Quasi-Period Network decomposes the echocardiogram into periodic and aperiodic components within latent space by combining parameterized helix trajectories with Neural Controlled Differential Equations. During inference, our framework further employs a variance minimization strategy across image augmentations that simulate common quality issues in echocardiogram acquisition, along with differential adaptation rates for periodic and aperiodic components. Theoretical analysis is provided to demonstrate that our variance minimization objective effectively bounds the regression error under mild conditions. Furthermore, extensive experiments across three pediatric age groups demonstrate that Q-PART not only significantly outperforms existing approaches in pediatric LVEF prediction, but also exhibits strong clinical screening capability with high mAUROC scores (up to 0.9747) and maintains gender-fair performance across all metrics, validating its robustness and practical utility in pediatric echocardiography analysis.

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arXiv2024

Beyond Grid Data: Exploring Graph Neural Networks for Earth Observation

Earth Observation (EO) data analysis has been significantly revolutionized by deep learning (DL), with applications typically limited to grid-like data structures. Graph Neural Networks (GNNs) emerge as an important innovation, propelling DL into the non-Euclidean domain. Naturally, GNNs can effectively tackle the challenges posed by diverse modalities, multiple sensors, and the heterogeneous nature of EO data. To introduce GNNs in the related domains, our review begins by offering fundamental knowledge on GNNs. Then, we summarize the generic problems in EO, to which GNNs can offer potential solutions. Following this, we explore a broad spectrum of GNNs' applications to scientific problems in Earth systems, covering areas such as weather and climate analysis, disaster management, air quality monitoring, agriculture, land cover classification, hydrological process modeling, and urban modeling. The rationale behind adopting GNNs in these fields is explained, alongside methodologies for organizing graphs and designing favorable architectures for various tasks. Furthermore, we highlight methodological challenges of implementing GNNs in these domains and possible solutions that could guide future research. While acknowledging that GNNs are not a universal solution, we conclude the paper by comparing them with other popular architectures like transformers and analyzing their potential synergies.

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arXiv2024

PolyGNN: Polyhedron-based Graph Neural Network for 3D Building Reconstruction from Point Clouds

We present PolyGNN, a polyhedron-based graph neural network for 3D building reconstruction from point clouds. PolyGNN learns to assemble primitives obtained by polyhedral decomposition via graph node classification, achieving a watertight and compact reconstruction. To effectively represent arbitrary-shaped polyhedra in the neural network, we propose a skeleton-based sampling strategy to generate polyhedron-wise queries. These queries are then incorporated with inter-polyhedron adjacency to enhance the classification. PolyGNN is end-to-end optimizable and is designed to accommodate variable-size input points, polyhedra, and queries with an index-driven batching technique. To address the abstraction gap between existing city-building models and the underlying instances, and provide a fair evaluation of the proposed method, we develop our method on a large-scale synthetic dataset with well-defined ground truths of polyhedral labels. We further conduct a transferability analysis across cities and on real-world point clouds. Both qualitative and quantitative results demonstrate the effectiveness of our method, particularly its efficiency for large-scale reconstructions. The source code and data are available at https://github.com/chenzhaiyu/polygnn.

cs.CV↗

arXiv2024

Multi-Modal and Multi-Resolution Data Fusion for High-Resolution Cloud Removal: A Novel Baseline and Benchmark

Cloud removal is a significant and challenging problem in remote sensing, and in recent years, there have been notable advancements in this area. However, two major issues remain hindering the development of cloud removal: the unavailability of high-resolution imagery for existing datasets and the absence of evaluation regarding the semantic meaningfulness of the generated structures. In this paper, we introduce M3R-CR, a benchmark dataset for high-resolution Cloud Removal with Multi-Modal and Multi-Resolution data fusion. With this dataset, we consider the problem of cloud removal in high-resolution optical remote sensing imagery by integrating multi-modal and multi-resolution information. In this context, we have to take into account the alignment errors caused by the multi-resolution nature, along with the more pronounced misalignment issues in high-resolution images due to inherent imaging mechanism differences and other factors. Existing multi-modal data fusion based methods, which assume the image pairs are aligned accurately at pixel-level, are thus not appropriate for this problem. To this end, we design a new baseline named Align-CR to perform the low-resolution SAR image guided high-resolution optical image cloud removal. It gradually warps and fuses the features of the multi-modal and multi-resolution data during the reconstruction process, effectively mitigating concerns associated with misalignment. In the experiments, we evaluate the performance of cloud removal by analyzing the quality of visually pleasing textures using image reconstruction metrics and further analyze the generation of semantically meaningful structures using a well-established semantic segmentation task. The proposed Align-CR method is superior to other baseline methods in both areas.

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