Shiqi Huang

Shiqi Huang, Yipei Wang, Natasha Thorley et al.

Foundation models leverage large-scale pretraining to capture extensive knowledge, demonstrating generalization in a wide range of language tasks. By comparison, vision foundation models (VFMs) often exhibit uneven improvements across downstream tasks, despite substantial computational investment. We postulate that this limitation arises from a mismatch between pretraining objectives and the demands of downstream vision-and-imaging tasks. Pretraining strategies like masked image reconstruction or contrastive learning shape representations for tasks such as recovery of generic visual patterns or global semantic structures, which may not align with the task-specific requirements of downstream applications including segmentation, classification, or image synthesis. To investigate this in a concrete real-world clinical area, we assess two VFMs, a reconstruction-focused MAE-based model (ProFound) and a contrastive-learning-based model (ProViCNet), on five prostate multiparametric MR imaging tasks, examining how such task alignment influences transfer performance, i.e., from pretraining to fine-tuning. Our findings indicate that better alignment between pretraining and downstream tasks, measured by simple divergence metrics such as maximum-mean-discrepancy (MMD) between the same features before and after fine-tuning, correlates with greater performance improvements and faster convergence, emphasizing the importance of designing and analyzing pretraining objectives with downstream applicability in mind.

Wen Yan, Yipei Wang, Shiqi Huang et al.

Label variability is a major challenge for prostate lesion segmentation. In multi-site datasets, annotations often reflect centre-specific contouring protocols, causing segmentation networks to overfit to local styles and generalise poorly to unseen sites in inference. We treat each observed annotation as a noisy observation of an underlying latent 'clean' lesion mask, and propose a hierarchical expectation-maximisation (HierEM) framework that alternates between: (1) inferring a voxel-wise posterior distribution over the latent mask, and (2) training a CNN using this posterior as a soft target and estimate site-specific sensitivity and specificity under a hierarchical prior. This hierarchical prior decomposes label-quality into a global mean with site- and case-level deviations, reducing site-specific bias by penalising the likelihood term contributed only by site deviations. Experiments on three cohorts demonstrate that the proposed hierarchical EM framework enhances cross-site generalisation compared to state-of-the-art methods. For pooled-dataset evaluation, the per-site mean DSC ranges from 29.50% to 39.69%; for leave-one-site-out generalisation, it ranges from 27.91% to 32.67%, yielding statistically significant improvements over comparison methods (p<0.039). The method also produces interpretable per-site latent label-quality estimates (sensitivity alpha ranges from 31.5% to 47.3% at specificity beta approximates 0.99), supporting post-hoc analyses of cross-site annotation variability. These results indicate that explicitly modelling site-dependent annotation can improve cross-site generalisation.

Shiqi Huang, Ziyue Wang, Zhongrong Zuo et al.

Recent Video Large Language Models (Video-LLMs) have demonstrated strong capabilities in video reasoning through reinforcement learning (RL). However, existing RL pipelines rely heavily on human-annotated tasks and solutions, making them costly to scale and fundamentally constrained by human expertise. Self-evolving frameworks have recently emerged as a promising alternative through autonomous Questioner-Solver self-play. Unfortunately, these approaches are primarily designed for static modalities such as text and images, fundamentally failing to capture the temporal dynamics that are central to video reasoning. In this work, we propose $\textbf{EvoVid}$, a temporal-centric self-evolving framework that enables Video-LLMs to improve directly from raw, unannotated videos. Specifically, we introduce two complementary temporal-centric rewards: a temporal-aware Questioner reward that encourages temporally dependent question generation through temporal perturbation sensitivity, and a temporal-grounded Solver reward that provides automatic temporal supervision via inherent video segment localization. Extensive experiments across four base models and six benchmarks demonstrate consistent improvements over both base models and existing self-evolving baselines, achieving competitive performance with supervised methods. These results highlight temporal-centric self-evolution as an effective and scalable paradigm for video understanding and reasoning.

Yuheng Fan, Hanxi Liao, Shiqi Huang et al.

Diffusion probabilistic models (DPMs) which employ explicit likelihood characterization and a gradual sampling process to synthesize data, have gained increasing research interest. Despite their huge computational burdens due to the large number of steps involved during sampling, DPMs are widely appreciated in various medical imaging tasks for their high-quality and diversity of generation. Magnetic resonance imaging (MRI) is an important medical imaging modality with excellent soft tissue contrast and superb spatial resolution, which possesses unique opportunities for DPMs. Although there is a recent surge of studies exploring DPMs in MRI, a survey paper of DPMs specifically designed for MRI applications is still lacking. This review article aims to help researchers in the MRI community to grasp the advances of DPMs in different applications. We first introduce the theory of two dominant kinds of DPMs, categorized according to whether the diffusion time step is discrete or continuous, and then provide a comprehensive review of emerging DPMs in MRI, including reconstruction, image generation, image translation, segmentation, anomaly detection, and further research topics. Finally, we discuss the general limitations as well as limitations specific to the MRI tasks of DPMs and point out potential areas that are worth further exploration.

Shiqi Huang, Shuting He, Bihan Wen

Instance segmentation algorithms in remote sensing are typically based on conventional methods, limiting their application to seen scenarios and closed-set predictions. In this work, we propose a novel task called zero-shot remote sensing instance segmentation, aimed at identifying aerial objects that are absent from training data. Challenges arise when classifying aerial categories with high inter-class similarity and intra-class variance. Besides, the domain gap between vision-language models' pretraining datasets and remote sensing datasets hinders the zero-shot capabilities of the pretrained model when it is directly applied to remote sensing images. To address these challenges, we propose a $\textbf{Z}$ero-Sh$\textbf{o}$t $\textbf{R}$emote Sensing $\textbf{I}$nstance Segmentation framework, dubbed $\textbf{ZoRI}$. Our approach features a discrimination-enhanced classifier that uses refined textual embeddings to increase the awareness of class disparities. Instead of direct fine-tuning, we propose a knowledge-maintained adaptation strategy that decouples semantic-related information to preserve the pretrained vision-language alignment while adjusting features to capture remote sensing domain-specific visual cues. Additionally, we introduce a prior-injected prediction with cache bank of aerial visual prototypes to supplement the semantic richness of text embeddings and seamlessly integrate aerial representations, adapting to the remote sensing domain. We establish new experimental protocols and benchmarks, and extensive experiments convincingly demonstrate that ZoRI achieves the state-of-art performance on the zero-shot remote sensing instance segmentation task. Our code is available at https://github.com/HuangShiqi128/ZoRI.

Shiqi Huang, Tingfa Xu, Ziyi Shen et al.

This paper describes a new spatial correspondence representation based on paired regions-of-interest (ROIs), for medical image registration. The distinct properties of the proposed ROI-based correspondence are discussed, in the context of potential benefits in clinical applications following image registration, compared with alternative correspondence-representing approaches, such as those based on sampled displacements and spatial transformation functions. These benefits include a clear connection between learning-based image registration and segmentation, which in turn motivates two cases of image registration approaches using (pre-)trained segmentation networks. Based on the segment anything model (SAM), a vision foundation model for segmentation, we develop a new registration algorithm SAMReg, which does not require any training (or training data), gradient-based fine-tuning or prompt engineering. The proposed SAMReg models are evaluated across five real-world applications, including intra-subject registration tasks with cardiac MR and lung CT, challenging inter-subject registration scenarios with prostate MR and retinal imaging, and an additional evaluation with a non-clinical example with aerial image registration. The proposed methods outperform both intensity-based iterative algorithms and DDF-predicting learning-based networks across tested metrics including Dice and target registration errors on anatomical structures, and further demonstrates competitive performance compared to weakly-supervised registration approaches that rely on fully-segmented training data. Open source code and examples are available at: https://github.com/sqhuang0103/SAMReg.git.

Shiqi Huang, Shuting He, Huaiyuan Qin et al.

Most existing remote sensing instance segmentation approaches are designed for close-vocabulary prediction, limiting their ability to recognize novel categories or generalize across datasets. This restricts their applicability in diverse Earth observation scenarios. To address this, we introduce open-vocabulary (OV) learning for remote sensing instance segmentation. While current OV segmentation models perform well on natural image datasets, their direct application to remote sensing faces challenges such as diverse landscapes, seasonal variations, and the presence of small or ambiguous objects in aerial imagery. To overcome these challenges, we propose $\textbf{SCORE}$ ($\textbf{S}$cene $\textbf{C}$ontext matters in $\textbf{O}$pen-vocabulary $\textbf{RE}$mote sensing instance segmentation), a framework that integrates multi-granularity scene context, i.e., regional context and global context, to enhance both visual and textual representations. Specifically, we introduce Region-Aware Integration, which refines class embeddings with regional context to improve object distinguishability. Additionally, we propose Global Context Adaptation, which enriches naive text embeddings with remote sensing global context, creating a more adaptable and expressive linguistic latent space for the classifier. We establish new benchmarks for OV remote sensing instance segmentation across diverse datasets. Experimental results demonstrate that, our proposed method achieves SOTA performance, which provides a robust solution for large-scale, real-world geospatial analysis. Our code is available at https://github.com/HuangShiqi128/SCORE.

Wen Yan, Qianye Yang, Shiqi Huang et al.

Spatial correspondence can be represented by pairs of segmented regions, such that the image registration networks aim to segment corresponding regions rather than predicting displacement fields or transformation parameters. In this work, we show that such a corresponding region pair can be predicted by the same language prompt on two different images using the pre-trained large multimodal models based on GroundingDINO and SAM. This enables a fully automated and training-free registration algorithm, potentially generalisable to a wide range of image registration tasks. In this paper, we present experimental results using one of the challenging tasks, registering inter-subject prostate MR images, which involves both highly variable intensity and morphology between patients. Tell2Reg is training-free, eliminating the need for costly and time-consuming data curation and labelling that was previously required for this registration task. This approach outperforms unsupervised learning-based registration methods tested, and has a performance comparable to weakly-supervised methods. Additional qualitative results are also presented to suggest that, for the first time, there is a potential correlation between language semantics and spatial correspondence, including the spatial invariance in language-prompted regions and the difference in language prompts between the obtained local and global correspondences. Code is available at https://github.com/yanwenCi/Tell2Reg.git.

Shiqi Huang, Shuting He, Bihan Wen

Remote Sensing Visual Grounding (RSVG) aims to localize target objects in large-scale aerial imagery based on natural language descriptions. Owing to the vast spatial scale and high semantic ambiguity of remote sensing scenes, these descriptions often rely heavily on positional cues, posing unique challenges for Multimodal Large Language Models (MLLMs) in spatial reasoning. To leverage this unique feature, we propose a reasoning-guided, position-aware post-training framework, dubbed \textbf{RSGround-R1}, to progressively enhance spatial understanding. Specifically, we first introduce Chain-of-Thought Supervised Fine-Tuning (CoT-SFT) using synthetically generated RSVG reasoning data to establish explicit position awareness. Reinforcement Fine-Tuning (RFT) is then applied, augmented by our newly designed positional reward that provides continuous and distance-aware guidance toward accurate localization. Moreover, to mitigate incoherent localization behaviors across rollouts, we introduce a spatial consistency guided optimization scheme that dynamically adjusts policy updates based on their spatial coherence, ensuring stable and robust convergence. Extensive experiments on RSVG benchmarks demonstrate superior performance and generalization of our model.

Shiqi Huang, Tingfa Xu, Ziyi Shen et al.

The goal of image registration is to establish spatial correspondence between two or more images, traditionally through dense displacement fields (DDFs) or parametric transformations (e.g., rigid, affine, and splines). Rethinking the existing paradigms of achieving alignment via spatial transformations, we uncover an alternative but more intuitive correspondence representation: a set of corresponding regions-of-interest (ROI) pairs, which we demonstrate to have sufficient representational capability as other correspondence representation methods.Further, it is neither necessary nor sufficient for these ROIs to hold specific anatomical or semantic significance. In turn, we formulate image registration as searching for the same set of corresponding ROIs from both moving and fixed images - in other words, two multi-class segmentation tasks on a pair of images. For a general-purpose and practical implementation, we integrate the segment anything model (SAM) into our proposed algorithms, resulting in a SAM-enabled registration (SAMReg) that does not require any training data, gradient-based fine-tuning or engineered prompts. We experimentally show that the proposed SAMReg is capable of segmenting and matching multiple ROI pairs, which establish sufficiently accurate correspondences, in three clinical applications of registering prostate MR, cardiac MR and abdominal CT images. Based on metrics including Dice and target registration errors on anatomical structures, the proposed registration outperforms both intensity-based iterative algorithms and DDF-predicting learning-based networks, even yielding competitive performance with weakly-supervised registration which requires fully-segmented training data.

Shiqi Huang, Tingfa Xu, Wen Yan et al.

Establishing pixel/voxel-level or region-level correspondences is the core challenge in image registration. The latter, also known as region-based correspondence representation, leverages paired regions of interest (ROIs) to enable regional matching while preserving fine-grained capability at pixel/voxel level. Traditionally, this representation is implemented via two steps: segmenting ROIs in each image then matching them between the two images. In this paper, we simplify this into one step by directly "searching for corresponding prompts", using extensively pre-trained segmentation models (e.g., SAM) for a training-free registration approach, PromptReg. Firstly, we introduce the "corresponding prompt problem", which aims to identify a corresponding Prompt Y in Image Y for any given visual Prompt X in Image X, such that the two respectively prompt-conditioned segmentations are a pair of corresponding ROIs from the two images. Secondly, we present an "inverse prompt" solution that generates primary and optionally auxiliary prompts, inverting Prompt X into the prompt space of Image Y. Thirdly, we propose a novel registration algorithm that identifies multiple paired corresponding ROIs by marginalizing the inverted Prompt X across both prompt and spatial dimensions. Comprehensive experiments are conducted on five applications of registering 3D prostate MR, 3D abdomen MR, 3D lung CT, 2D histopathology and, as a non-medical example, 2D aerial images. Based on metrics including Dice and target registration errors on anatomical structures, the proposed registration outperforms both intensity-based iterative algorithms and learning-based DDF-predicting networks, even yielding competitive performance with weakly-supervised approaches that require fully-segmented training data.

Shiqi Huang, Jianan Li, Yuze Xiao et al.

Automatic diabetic retinopathy (DR) lesions segmentation makes great sense of assisting ophthalmologists in diagnosis. Although many researches have been conducted on this task, most prior works paid too much attention to the designs of networks instead of considering the pathological association for lesions. Through investigating the pathogenic causes of DR lesions in advance, we found that certain lesions are closed to specific vessels and present relative patterns to each other. Motivated by the observation, we propose a relation transformer block (RTB) to incorporate attention mechanisms at two main levels: a self-attention transformer exploits global dependencies among lesion features, while a cross-attention transformer allows interactions between lesion and vessel features by integrating valuable vascular information to alleviate ambiguity in lesion detection caused by complex fundus structures. In addition, to capture the small lesion patterns first, we propose a global transformer block (GTB) which preserves detailed information in deep network. By integrating the above blocks of dual-branches, our network segments the four kinds of lesions simultaneously. Comprehensive experiments on IDRiD and DDR datasets well demonstrate the superiority of our approach, which achieves competitive performance compared to state-of-the-arts.