arXiv subjects

Qian Tao

Publications and source records attributed to Qian Tao.

At least 37 records · Page 2Linked to original sources

arXiv2025

Recurrent Inference Machine for Medical Image Registration

Image registration is essential for medical image applications where alignment of voxels across multiple images is needed for qualitative or quantitative analysis. With recent advancements in deep neural networks and parallel computing, deep learning-based medical image registration methods become competitive with their flexible modelling and fast inference capabilities. However, compared to traditional optimization-based registration methods, the speed advantage may come at the cost of registration performance at inference time. Besides, deep neural networks ideally demand large training datasets while optimization-based methods are training-free. To improve registration accuracy and data efficiency, we propose a novel image registration method, termed Recurrent Inference Image Registration (RIIR) network. RIIR is formulated as a meta-learning solver to the registration problem in an iterative manner. RIIR addresses the accuracy and data efficiency issues, by learning the update rule of optimization, with implicit regularization combined with explicit gradient input. We evaluated RIIR extensively on brain MRI and quantitative cardiac MRI datasets, in terms of both registration accuracy and training data efficiency. Our experiments showed that RIIR outperformed a range of deep learning-based methods, even with only $5\%$ of the training data, demonstrating high data efficiency. Key findings from our ablation studies highlighted the important added value of the hidden states introduced in the recurrent inference framework for meta-learning. Our proposed RIIR offers a highly data-efficient framework for deep learning-based medical image registration.

eess.IV↗

arXiv2025

Bridging Classical and Learning-based Iterative Registration through Deep Equilibrium Models

Deformable medical image registration is traditionally formulated as an optimization problem. While classical methods solve this problem iteratively, recent learning-based approaches use recurrent neural networks (RNNs) to mimic this process by unrolling the prediction of deformation fields in a fixed number of steps. However, classical methods typically converge after sufficient iterations, but learning-based unrolling methods lack a theoretical convergence guarantee and show instability empirically. In addition, unrolling methods have a practical bottleneck at training time: GPU memory usage grows linearly with the unrolling steps due to backpropagation through time (BPTT). To address both theoretical and practical challenges, we propose DEQReg, a novel registration framework based on Deep Equilibrium Models (DEQ), which formulates registration as an equilibrium-seeking problem, establishing a natural connection between classical optimization and learning-based unrolling methods. DEQReg maintains constant memory usage, enabling theoretically unlimited iteration steps. Through extensive evaluation on the public brain MRI and lung CT datasets, we show that DEQReg can achieve competitive registration performance, while substantially reducing memory consumption compared to state-of-the-art unrolling methods. We also reveal an intriguing phenomenon: the performance of existing unrolling methods first increases slightly then degrades irreversibly when the inference steps go beyond the training configuration. In contrast, DEQReg achieves stable convergence with its inbuilt equilibrium-seeking mechanism, bridging the gap between classical optimization-based and modern learning-based registration methods.

eess.IV↗

arXiv2025

Physics-Informed Neural ODEs for Temporal Dynamics Modeling in Cardiac T1 Mapping

Spin-lattice relaxation time ($T_1$) is an important biomarker in cardiac parametric mapping for characterizing myocardial tissue and diagnosing cardiomyopathies. Conventional Modified Look-Locker Inversion Recovery (MOLLI) acquires 11 breath-hold baseline images with interleaved rest periods to ensure mapping accuracy. However, prolonged scanning can be challenging for patients with poor breathholds, often leading to motion artifacts that degrade image quality. In addition, $T_1$ mapping requires voxel-wise nonlinear fitting to a signal recovery model involving an iterative estimation process. Recent studies have proposed deep-learning approaches for rapid $T_1$ mapping using shortened sequences to reduce acquisition time for patient comfort. Nevertheless, existing methods overlook important physics constraints, limiting interpretability and generalization. In this work, we present an accelerated, end-to-end $T_1$ mapping framework leveraging Physics-Informed Neural Ordinary Differential Equations (ODEs) to model temporal dynamics and address these challenges. Our method achieves high-accuracy $T_1$ estimation from a sparse subset of baseline images and ensures efficient null index estimation at test time. Specifically, we develop a continuous-time LSTM-ODE model to enable selective Look-Locker (LL) data acquisition with arbitrary time lags. Experimental results show superior performance in $T_1$ estimation for both native and post-contrast sequences and demonstrate the strong benefit of our physics-based formulation over direct data-driven $T_1$ priors.

eess.IV↗

arXiv2025

GastCoCo: Graph Storage and Coroutine-Based Prefetch Co-Design for Dynamic Graph Processing

An efficient data structure is fundamental to meeting the growing demands in dynamic graph processing. However, the dual requirements for graph computation efficiency (with contiguous structures) and graph update efficiency (with linked list-like structures) present a conflict in the design principles of graph structures. After experimental studies of existing state-of-the-art dynamic graph structures, we observe that the overhead of cache misses accounts for a major portion of the graph computation time. This paper presents GastCoCo, a system with graph storage and coroutine-based prefetch co-design. By employing software prefetching via stackless coroutines and introducing a prefetch-friendly data structure CBList, GastCoCo significantly alleviates the performance degradation caused by cache misses. Our results show that GastCoCo outperforms state-of-the-art graph storage systems by 1.3x - 180x in graph updates and 1.4x - 41.1x in graph computation.

cs.DB↗

arXiv2025

Extremely large magnetoresistance and chiral anomaly in the nodal-line semimetal ZrAs2

We performed the detailed magnetotransport measurements and first principle calculations to study the electronic properties of the transition metal dipnictides ZrAs2, which is a topological nodal-line semimetal. Extremely large unsaturated magnetoresistance (MR) which is up to 1.9 * 10^4 % at 2 K and 14 T was observed with magnetic field along the c-axis. The nonlinear magnetic field dependence of Hall resistivity indicates the multi-band features, and the electron and hole are nearly compensated according to the analysis of the two-band model, which may account for the extremely large unsaturated MR at low temperatures. The evident Shubnikov-de Haas (SdH) oscillations at low temperatures are observed and four distinct oscillation frequencies are extracted. The first principle calculations and angle-dependent SdH oscillations reveal that the Fermi surface consists of three pockets with different anisotropy. The observed twofold symmetry MR with electric field along the b-axis direction is consistent with our calculated Fermi surface structures. Furthermore, the negative magnetoresistance (NMR) with magnetic field in parallel with electric field is observed, which is an evident feature of the chiral anomaly.

cond-mat.mtrl-sci↗

arXiv2025

Giant Anomalous Hall Effect in Kagome Nodal Surface Semimetal Fe$_3$Ge

It is well known that the intrinsic anomalous Hall effect (AHE) arises from the integration of the non-zero Berry curvature (BC), conventionally observed in the Dirac/Weyl and nodal-line semimetals. Moreover, nodal surface semimetals are expected to exhibit more significant BC under the prevalence of degenerate points near the Fermi level. In this work, we report the detection of a giant AHE in the Kagome magnet Fe$_3$Ge with a two-dimensional (2D) nodal surface (NS) at $k_{z}=π$ plane, exhibiting an anomalous Hall conductivity (AHC) of 1500 $Ω^{-1}$cm$^{-1}$ at 160 K, the highest among all reported Kagome topological materials. This finding suggests a new platform for searching large AHC materials and facilitates potential room-temperature applications in spintronic devices and quantum computing.

cond-mat.mes-hall↗

arXiv2025

Combining Knowledge Graph and LLMs for Enhanced Zero-shot Visual Question Answering

Zero-shot visual question answering (ZS-VQA), an emerged critical research area, intends to answer visual questions without providing training samples. Existing research in ZS-VQA has proposed to leverage knowledge graphs or large language models (LLMs), respectively, as external information sources to help VQA model comprehend images and questions. However, LLMs often struggle in accurately interpreting specific question meanings. Meanwhile, although knowledge graph has rich entity relationships, it is challenging to effectively connect entities to individual image content for visual question answers. In this paper, we propose a novel design to combine knowledge graph and LLMs for zero-shot visual question answer. Our approach uses LLMs' powerful understanding capabilities to accurately interpret image content through a strategic question search mechanism. Meanwhile, the knowledge graph is used to expand and connect users' queries to the image content for better visual question answering. An optimization algorithm is further used to determine the optimal weights for the loss functions derived from different information sources, towards a globally optimal set of candidate answers. Experimental results on two benchmark datasets demonstrate that our model achieves state-of-the-art (SOTA) performance. Both source code and benchmark data will be released for public access.

cs.CV↗

arXiv2024

Exact Acceleration of Subgraph Graph Neural Networks by Eliminating Computation Redundancy

Graph neural networks (GNNs) have become a prevalent framework for graph tasks. Many recent studies have proposed the use of graph convolution methods over the numerous subgraphs of each graph, a concept known as subgraph graph neural networks (subgraph GNNs), to enhance GNNs' ability to distinguish non-isomorphic graphs. To maximize the expressiveness, subgraph GNNs often require each subgraph to have equal size to the original graph. Despite their impressive performance, subgraph GNNs face challenges due to the vast number and large size of subgraphs which lead to a surge in training data, resulting in both storage and computational inefficiencies. In response to this problem, this paper introduces Ego-Nets-Fit-All (ENFA), a model that uniformly takes the smaller ego nets as subgraphs, thereby providing greater storage and computational efficiency, while at the same time guarantees identical outputs to the original subgraph GNNs even taking the whole graph as subgraphs. The key is to identify and eliminate the redundant computation among subgraphs. For example, a node $v_i$ may appear in multiple subgraphs but is far away from all of their centers (the unsymmetric part between subgraphs). Therefore, its first few rounds of message passing within each subgraph can be computed once in the original graph instead of being computed multiple times within each subgraph. Such strategy enables our ENFA to accelerate subgraph GNNs in an exact way, unlike previous sampling approaches that often lose the performance. Extensive experiments across various datasets reveal that compared with the conventional subgraph GNNs, ENFA can reduce storage space by 29.0% to 84.5% and improve training efficiency by up to 1.66x.

cs.AI↗

arXiv2024

GL-Fusion: Rethinking the Combination of Graph Neural Network and Large Language model

Recent research on integrating Large Language Models (LLMs) with Graph Neural Networks (GNNs) typically follows two approaches: LLM-centered models, which convert graph data into tokens for LLM processing, and GNN-centered models, which use LLMs to encode text features into node and edge representations for GNN input. LLM-centered models often struggle to capture graph structures effectively, while GNN-centered models compress variable-length textual data into fixed-size vectors, limiting their ability to understand complex semantics. Additionally, GNN-centered approaches require converting tasks into a uniform, manually-designed format, restricting them to classification tasks and preventing language output. To address these limitations, we introduce a new architecture that deeply integrates GNN with LLM, featuring three key innovations: (1) Structure-Aware Transformers, which incorporate GNN's message-passing capabilities directly into LLM's transformer layers, allowing simultaneous processing of textual and structural information and generating outputs from both GNN and LLM; (2) Graph-Text Cross-Attention, which processes full, uncompressed text from graph nodes and edges, ensuring complete semantic integration; and (3) GNN-LLM Twin Predictor, enabling LLM's flexible autoregressive generation alongside GNN's scalable one-pass prediction. GL-Fusion achieves outstand performance on various tasks. Notably, it achieves state-of-the-art performance on OGBN-Arxiv and OGBG-Code2.

cs.LG↗

arXiv2024

LSMGraph: A High-Performance Dynamic Graph Storage System with Multi-Level CSR

The growing volume of graph data may exhaust the main memory. It is crucial to design a disk-based graph storage system to ingest updates and analyze graphs efficiently. However, existing dynamic graph storage systems suffer from read or write amplification and face the challenge of optimizing both read and write performance simultaneously. To address this challenge, we propose LSMGraph, a novel dynamic graph storage system that combines the write-friendly LSM-tree and the read-friendly CSR. It leverages the multi-level structure of LSM-trees to optimize write performance while utilizing the compact CSR structures embedded in the LSM-trees to boost read performance. LSMGraph uses a new memory structure, MemGraph, to efficiently cache graph updates and uses a multi-level index to speed up reads within the multi-level structure. Furthermore, LSMGraph incorporates a vertex-grained version control mechanism to mitigate the impact of LSM-tree compaction on read performance and ensure the correctness of concurrent read and write operations. Our evaluation shows that LSMGraph significantly outperforms state-of-the-art (graph) storage systems on both graph update and graph analytical workloads.

cs.DB↗

arXiv2024

Improving Instance Optimization in Deformable Image Registration with Gradient Projection

Deformable image registration is inherently a multi-objective optimization (MOO) problem, requiring a delicate balance between image similarity and deformation regularity. These conflicting objectives often lead to poor optimization outcomes, such as being trapped in unsatisfactory local minima or experiencing slow convergence. Deep learning methods have recently gained popularity in this domain due to their efficiency in processing large datasets and achieving high accuracy. However, they often underperform during test time compared to traditional optimization techniques, which further explore iterative, instance-specific gradient-based optimization. This performance gap is more pronounced when a distribution shift between training and test data exists. To address this issue, we focus on the instance optimization (IO) paradigm, which involves additional optimization for test-time instances based on a pre-trained model. IO effectively combines the generalization capabilities of deep learning with the fine-tuning advantages of instance-specific optimization. Within this framework, we emphasize the use of gradient projection to mitigate conflicting updates in MOO. This technique projects conflicting gradients into a common space, better aligning the dual objectives and enhancing optimization stability. We validate our method using a state-of-the-art foundation model on the 3D Brain inter-subject registration task (LUMIR) from the Learn2Reg 2024 Challenge. Our results show significant improvements over standard gradient descent, leading to more accurate and reliable registration results.

cs.CV↗

arXiv2024

AsymKV: Enabling 1-Bit Quantization of KV Cache with Layer-Wise Asymmetric Quantization Configurations

Large language models have shown exceptional capabilities in a wide range of tasks, such as text generation and video generation, among others. However, due to their massive parameter count, these models often require substantial storage space, imposing significant constraints on the machines deploying LLMs. To overcome this limitation, one research direction proposes to compress the models using integer replacements for floating-point numbers, in a process known as Quantization. Some recent studies suggest quantizing the key and value cache (KV Cache) of LLMs, and designing quantization techniques that treat the key and value matrices equivalently. This work delves deeper into the asymmetric structural roles of KV Cache, a phenomenon where the transformer's output loss is more sensitive to the quantization of key matrices. We conduct a systematic examination of the attention output error resulting from key and value quantization. The phenomenon inspires us to propose an asymmetric quantization strategy. Our approach allows for 1-bit quantization of the KV cache by implementing distinct configurations for key and value matrices. We carry out experiments across a variety of datasets, demonstrating that our proposed model allows for the quantization of up to 75% decoder layers with 1 bit, while simultaneously maintaining performance levels comparable to those of the models with floating parameters.

cs.LG↗

arXiv2024

Lost in Tracking: Uncertainty-guided Cardiac Cine MRI Segmentation at Right Ventricle Base

Accurate biventricular segmentation of cardiac magnetic resonance (CMR) cine images is essential for the clinical evaluation of heart function. However, compared to left ventricle (LV), right ventricle (RV) segmentation is still more challenging and less reproducible. Degenerate performance frequently occurs at the RV base, where the in-plane anatomical structures are complex (with atria, valve, and aorta) and vary due to the strong interplanar motion. In this work, we propose to address the currently unsolved issues in CMR segmentation, specifically at the RV base, with two strategies: first, we complemented the public resource by reannotating the RV base in the ACDC dataset, with refined delineation of the right ventricle outflow tract (RVOT), under the guidance of an expert cardiologist. Second, we proposed a novel dual encoder U-Net architecture that leverages temporal incoherence to inform the segmentation when interplanar motions occur. The inter-planar motion is characterized by loss-of-tracking, via Bayesian uncertainty of a motion-tracking model. Our experiments showed that our method significantly improved RV base segmentation taking into account temporal incoherence. Furthermore, we investigated the reproducibility of deep learning-based segmentation and showed that the combination of consistent annotation and loss of tracking could enhance the reproducibility of RV segmentation, potentially facilitating a large number of clinical studies focusing on RV.

eess.IV↗

arXiv2024

Annealing-induced long-range charge density wave order in magnetic kagome FeGe: fluctuations and disordered structure

Charge density wave (CDW) in kagome materials with the geometric frustration is able to carry unconventional characteristics. Recently, a CDW has been observed below the antiferromagnetic order in kagome FeGe, in which magnetism and CDW are intertwined to form an emergent quantum ground state. However, the CDW is only short-ranged and the structural modulation originating from it has yet to be determined experimentally. Here we realize a long-range CDW order by post-annealing process, and resolve the structure model through single crystal x-ray diffraction. Occupational disorder of Ge resulting from short-range CDW correlations above $T_\mathrm{CDW}$ is identified from structure refinements. The partial dimerization of Ge along the $c$ axis is unveiled to be the dominant distortion for the CDW. Occupational disorder of Ge is also proved to exist in the CDW phase due to the random selection of partially dimerized Ge sites. Our work provides useful insights for understanding the unconventional nature of the CDW in FeGe.

cond-mat.str-el↗

arXiv2024

Bayesian Uncertainty Estimation by Hamiltonian Monte Carlo: Applications to Cardiac MRI Segmentation

Deep learning (DL)-based methods have achieved state-of-the-art performance for many medical image segmentation tasks. Nevertheless, recent studies show that deep neural networks (DNNs) can be miscalibrated and overconfident, leading to "silent failures" that are risky for clinical applications. Bayesian DL provides an intuitive approach to DL failure detection, based on posterior probability estimation. However, the posterior is intractable for large medical image segmentation DNNs. To tackle this challenge, we propose a Bayesian learning framework using Hamiltonian Monte Carlo (HMC), tempered by cold posterior (CP) to accommodate medical data augmentation, named HMC-CP. For HMC computation, we further propose a cyclical annealing strategy, capturing both local and global geometries of the posterior distribution, enabling highly efficient Bayesian DNN training with the same computational budget as training a single DNN. The resulting Bayesian DNN outputs an ensemble segmentation along with the segmentation uncertainty. We evaluate the proposed HMC-CP extensively on cardiac magnetic resonance image (MRI) segmentation, using in-domain steady-state free precession (SSFP) cine images as well as out-of-domain datasets of quantitative T1 and T2 mapping. Our results show that the proposed method improves both segmentation accuracy and uncertainty estimation for in- and out-of-domain data, compared with well-established baseline methods such as Monte Carlo Dropout and Deep Ensembles. Additionally, we establish a conceptual link between HMC and the commonly known stochastic gradient descent (SGD) and provide general insight into the uncertainty of DL. This uncertainty is implicitly encoded in the training dynamics but often overlooked. With reliable uncertainty estimation, our method provides a promising direction toward trustworthy DL in clinical applications.

eess.IV↗

arXiv2024

Deep-learning-based groupwise registration for motion correction of cardiac $T_1$ mapping

Quantitative $T_1$ mapping by MRI is an increasingly important tool for clinical assessment of cardiovascular diseases. The cardiac $T_1$ map is derived by fitting a known signal model to a series of baseline images, while the quality of this map can be deteriorated by involuntary respiratory and cardiac motion. To correct motion, a template image is often needed to register all baseline images, but the choice of template is nontrivial, leading to inconsistent performance sensitive to image contrast. In this work, we propose a novel deep-learning-based groupwise registration framework, which omits the need for a template, and registers all baseline images simultaneously. We design two groupwise losses for this registration framework: the first is a linear principal component analysis (PCA) loss that enforces alignment of baseline images irrespective of the intensity variation, and the second is an auxiliary relaxometry loss that enforces adherence of intensity profile to the signal model. We extensively evaluated our method, termed ``PCA-Relax'', and other baseline methods on an in-house cardiac MRI dataset including both pre- and post-contrast $T_1$ sequences. All methods were evaluated under three distinct training-and-evaluation strategies, namely, standard, one-shot, and test-time-adaptation. The proposed PCA-Relax showed further improved performance of registration and mapping over well-established baselines. The proposed groupwise framework is generic and can be adapted to applications involving multiple images.

eess.IV↗

arXiv2024

COT Flow: Learning Optimal-Transport Image Sampling and Editing by Contrastive Pairs

Diffusion models have demonstrated strong performance in sampling and editing multi-modal data with high generation quality, yet they suffer from the iterative generation process which is computationally expensive and slow. In addition, most methods are constrained to generate data from Gaussian noise, which limits their sampling and editing flexibility. To overcome both disadvantages, we present Contrastive Optimal Transport Flow (COT Flow), a new method that achieves fast and high-quality generation with improved zero-shot editing flexibility compared to previous diffusion models. Benefiting from optimal transport (OT), our method has no limitation on the prior distribution, enabling unpaired image-to-image (I2I) translation and doubling the editable space (at both the start and end of the trajectory) compared to other zero-shot editing methods. In terms of quality, COT Flow can generate competitive results in merely one step compared to previous state-of-the-art unpaired image-to-image (I2I) translation methods. To highlight the advantages of COT Flow through the introduction of OT, we introduce the COT Editor to perform user-guided editing with excellent flexibility and quality. The code will be released at https://github.com/zuxinrui/cot_flow.

cs.CV↗

arXiv2024

Efficient Bayesian Uncertainty Estimation for nnU-Net

The self-configuring nnU-Net has achieved leading performance in a large range of medical image segmentation challenges. It is widely considered as the model of choice and a strong baseline for medical image segmentation. However, despite its extraordinary performance, nnU-Net does not supply a measure of uncertainty to indicate its possible failure. This can be problematic for large-scale image segmentation applications, where data are heterogeneous and nnU-Net may fail without notice. In this work, we introduce a novel method to estimate nnU-Net uncertainty for medical image segmentation. We propose a highly effective scheme for posterior sampling of weight space for Bayesian uncertainty estimation. Different from previous baseline methods such as Monte Carlo Dropout and mean-field Bayesian Neural Networks, our proposed method does not require a variational architecture and keeps the original nnU-Net architecture intact, thereby preserving its excellent performance and ease of use. Additionally, we boost the segmentation performance over the original nnU-Net via marginalizing multi-modal posterior models. We applied our method on the public ACDC and M&M datasets of cardiac MRI and demonstrated improved uncertainty estimation over a range of baseline methods. The proposed method further strengthens nnU-Net for medical image segmentation in terms of both segmentation accuracy and quality control.

cs.CV↗