arXiv subjects

Chen Zhao

Publications and source records attributed to Chen Zhao.

At least 217 records · Page 12Linked to original sources

arXiv2024

MsMorph: An Unsupervised pyramid learning network for brain image registration

In the field of medical image analysis, image registration is a crucial technique. Despite the numerous registration models that have been proposed, existing methods still fall short in terms of accuracy and interpretability. In this paper, we present MsMorph, a deep learning-based image registration framework aimed at mimicking the manual process of registering image pairs to achieve more similar deformations, where the registered image pairs exhibit consistency or similarity in features. By extracting the feature differences between image pairs across various as-pects using gradients, the framework decodes semantic information at different scales and continuously compen-sates for the predicted deformation field, driving the optimization of parameters to significantly improve registration accuracy. The proposed method simulates the manual approach to registration, focusing on different regions of the image pairs and their neighborhoods to predict the deformation field between the two images, which provides strong interpretability. We compared several existing registration methods on two public brain MRI datasets, including LPBA and Mindboggle. The experimental results show that our method consistently outperforms state of the art in terms of metrics such as Dice score, Hausdorff distance, average symmetric surface distance, and non-Jacobian. The source code is publicly available at https://github.com/GaodengFan/MsMorph

cs.CV↗

arXiv2024

SGUQ: Staged Graph Convolution Neural Network for Alzheimer's Disease Diagnosis using Multi-Omics Data

Alzheimer's disease (AD) is a chronic neurodegenerative disorder and the leading cause of dementia, significantly impacting cost, mortality, and burden worldwide. The advent of high-throughput omics technologies, such as genomics, transcriptomics, proteomics, and epigenomics, has revolutionized the molecular understanding of AD. Conventional AI approaches typically require the completion of all omics data at the outset to achieve optimal AD diagnosis, which are inefficient and may be unnecessary. To reduce the clinical cost and improve the accuracy of AD diagnosis using multi-omics data, we propose a novel staged graph convolutional network with uncertainty quantification (SGUQ). SGUQ begins with mRNA and progressively incorporates DNA methylation and miRNA data only when necessary, reducing overall costs and exposure to harmful tests. Experimental results indicate that 46.23% of the samples can be reliably predicted using only single-modal omics data (mRNA), while an additional 16.04% of the samples can achieve reliable predictions when combining two omics data types (mRNA + DNA methylation). In addition, the proposed staged SGUQ achieved an accuracy of 0.858 on ROSMAP dataset, which outperformed existing methods significantly. The proposed SGUQ can not only be applied to AD diagnosis using multi-omics data but also has the potential for clinical decision-making using multi-viewed data. Our implementation is publicly available at https://github.com/chenzhao2023/multiomicsuncertainty.

cs.IR↗

arXiv2024

Energy Bands of Incommensurate Systems

Energy band theory is a fundamental cornerstone of condensed matter physics. According to conventional wisdom, discrete translational symmetry is mandatory for defining energy bands. Here, we illustrate that, in fact, the concept of energy band can be generalized to incommensurate systems lacking such symmetry, thus transcending the traditional paradigm of energy band. The validity of our theory is verified by extensive numerical calculations in the celebrated Aubry-André-Harper model and a two-dimensional incommensurate model of graphene. Building upon the proposed concept of incommensurate energy bands, we further develop a theory of angle-resolved photoemission spectroscopy (ARPES) for incommensurate systems, providing a clear physical picture for the incommensurate ARPES spectra. Our work establishes a comprehensive energy band theory for incommensurate systems.

cond-mat.mes-hall↗

arXiv2024

Variational Quantum Imaginary Time Evolution for Matrix Product State Ansatz with Tests on Transcorrelated Hamiltonians

The matrix product state (MPS) ansatz offers a promising approach for finding the ground state of molecular Hamiltonians and solving quantum chemistry problems. Building on this concept, the proposed technique of quantum circuit MPS (QCMPS) enables the simulation of chemical systems using a relatively small number of qubits. In this study, we enhance the optimization performance of the QCMPS ansatz by employing the variational quantum imaginary time evolution (VarQITE) approach. Guided by McLachlan's variational principle, the VarQITE method provides analytical metrics and gradients, resulting in improved convergence efficiency and robustness of the QCMPS. We validate these improvements numerically through simulations of $\rm H_2$, $\rm H_4$, and $\rm LiH$ molecules. Additionally, given that VarQITE is applicable to non-Hermitian Hamiltonians, we evaluate its effectiveness in preparing the ground state of transcorrelated (TC) Hamiltonians. This approach yields energy estimates comparable to the complete basis set (CBS) limit while using even fewer qubits. Specifically, we perform simulations of the beryllium atom and $\rm LiH$ molecule using only three qubits, maintaining high fidelity with the CBS ground state energy of these systems. This qubit reduction is achieved through the combined advantages of both the QCMPS ansatz and transcorrelation. Our findings demonstrate the potential practicality of this quantum chemistry algorithm on near-term quantum devices.

quant-ph↗

arXiv2024

SynTQA: Synergistic Table-based Question Answering via Mixture of Text-to-SQL and E2E TQA

Text-to-SQL parsing and end-to-end question answering (E2E TQA) are two main approaches for Table-based Question Answering task. Despite success on multiple benchmarks, they have yet to be compared and their synergy remains unexplored. In this paper, we identify different strengths and weaknesses through evaluating state-of-the-art models on benchmark datasets: Text-to-SQL demonstrates superiority in handling questions involving arithmetic operations and long tables; E2E TQA excels in addressing ambiguous questions, non-standard table schema, and complex table contents. To combine both strengths, we propose a Synergistic Table-based Question Answering approach that integrate different models via answer selection, which is agnostic to any model types. Further experiments validate that ensembling models by either feature-based or LLM-based answer selector significantly improves the performance over individual models.

cs.CL↗

arXiv2024

Ego-Exo4D: Understanding Skilled Human Activity from First- and Third-Person Perspectives

We present Ego-Exo4D, a diverse, large-scale multimodal multiview video dataset and benchmark challenge. Ego-Exo4D centers around simultaneously-captured egocentric and exocentric video of skilled human activities (e.g., sports, music, dance, bike repair). 740 participants from 13 cities worldwide performed these activities in 123 different natural scene contexts, yielding long-form captures from 1 to 42 minutes each and 1,286 hours of video combined. The multimodal nature of the dataset is unprecedented: the video is accompanied by multichannel audio, eye gaze, 3D point clouds, camera poses, IMU, and multiple paired language descriptions -- including a novel "expert commentary" done by coaches and teachers and tailored to the skilled-activity domain. To push the frontier of first-person video understanding of skilled human activity, we also present a suite of benchmark tasks and their annotations, including fine-grained activity understanding, proficiency estimation, cross-view translation, and 3D hand/body pose. All resources are open sourced to fuel new research in the community. Project page: http://ego-exo4d-data.org/

cs.CV↗

arXiv2024

3D Lymphoma Segmentation on PET/CT Images via Multi-Scale Information Fusion with Cross-Attention

Background: Accurate segmentation of diffuse large B-cell lymphoma (DLBCL) lesions is challenging due to their complex patterns in medical imaging. Objective: This study aims to develop a precise segmentation method for DLBCL using 18F-Fluorodeoxyglucose (FDG) positron emission tomography (PET) and computed tomography (CT) images. Methods: We propose a 3D dual-branch encoder segmentation method using shifted window transformers and a Multi-Scale Information Fusion (MSIF) module. To enhance feature integration, the MSIF module performs multi-scale feature fusion using cross-attention mechanisms with a shifted window framework. A gated neural network within the MSIF module dynamically balances the contributions from each modality. The model was optimized using the Dice Similarity Coefficient (DSC) loss function. Additionally, we computed the total metabolic tumor volume (TMTV) and performed statistical analyses. Results: The model was trained and validated on a dataset of 165 DLBCL patients using 5-fold cross-validation, achieving a DSC of 0.7512. Statistical analysis showed a significant improvement over comparative methods (p < 0.05). Additionally, a Pearson correlation coefficient of 0.91 and an R^2 of 0.89 were observed when comparing manual annotations to segmentation results for TMTV measurement. Conclusion: This study presents an effective automatic segmentation method for DLBCL that leverages the complementary strengths of PET and CT imaging. Our method has the potential to improve diagnostic interpretations and assist in treatment planning for DLBCL patients.

eess.IV↗

arXiv2024

Minimal extension property of direct images

Given a projective morphism $f:X\to Y$ from a complex space to a complex manifold, we prove the Griffiths semi-positivity and minimal extension property of the direct image sheaf $f_\ast(\mathscr{F})$. Here, $\mathscr{F}$ is a coherent sheaf on $X$, which consists of the Grauert-Riemenschneider dualizing sheaf, a multiplier ideal sheaf, and a variation of Hodge structure (or more generally, a tame harmonic bundle).

math.AG↗

arXiv2024

Causal Diffusion Autoencoders: Toward Counterfactual Generation via Diffusion Probabilistic Models

Diffusion probabilistic models (DPMs) have become the state-of-the-art in high-quality image generation. However, DPMs have an arbitrary noisy latent space with no interpretable or controllable semantics. Although there has been significant research effort to improve image sample quality, there is little work on representation-controlled generation using diffusion models. Specifically, causal modeling and controllable counterfactual generation using DPMs is an underexplored area. In this work, we propose CausalDiffAE, a diffusion-based causal representation learning framework to enable counterfactual generation according to a specified causal model. Our key idea is to use an encoder to extract high-level semantically meaningful causal variables from high-dimensional data and model stochastic variation using reverse diffusion. We propose a causal encoding mechanism that maps high-dimensional data to causally related latent factors and parameterize the causal mechanisms among latent factors using neural networks. To enforce the disentanglement of causal variables, we formulate a variational objective and leverage auxiliary label information in a prior to regularize the latent space. We propose a DDIM-based counterfactual generation procedure subject to do-interventions. Finally, to address the limited label supervision scenario, we also study the application of CausalDiffAE when a part of the training data is unlabeled, which also enables granular control over the strength of interventions in generating counterfactuals during inference. We empirically show that CausalDiffAE learns a disentangled latent space and is capable of generating high-quality counterfactual images.

cs.LG↗

arXiv2024

O-Mamba: O-shape State-Space Model for Underwater Image Enhancement

Underwater image enhancement (UIE) face significant challenges due to complex underwater lighting conditions. Recently, mamba-based methods have achieved promising results in image enhancement tasks. However, these methods commonly rely on Vmamba, which focuses only on spatial information modeling and struggles to deal with the cross-color channel dependency problem in underwater images caused by the differential attenuation of light wavelengths, limiting the effective use of deep networks. In this paper, we propose a novel UIE framework called O-mamba. O-mamba employs an O-shaped dual-branch network to separately model spatial and cross-channel information, utilizing the efficient global receptive field of state-space models optimized for underwater images. To enhance information interaction between the two branches and effectively utilize multi-scale information, we design a Multi-scale Bi-mutual Promotion Module. This branch includes MS-MoE for fusing multi-scale information within branches, Mutual Promotion module for interaction between spatial and channel information across branches, and Cyclic Multi-scale optimization strategy to maximize the use of multi-scale information. Extensive experiments demonstrate that our method achieves state-of-the-art (SOTA) results.The code is available at https://github.com/chenydong/O-Mamba.

cs.CV↗

arXiv2024

BURExtract-Llama: An LLM for Clinical Concept Extraction in Breast Ultrasound Reports

Breast ultrasound is essential for detecting and diagnosing abnormalities, with radiology reports summarizing key findings like lesion characteristics and malignancy assessments. Extracting this critical information is challenging due to the unstructured nature of these reports, with varied linguistic styles and inconsistent formatting. While proprietary LLMs like GPT-4 are effective, they are costly and raise privacy concerns when handling protected health information. This study presents a pipeline for developing an in-house LLM to extract clinical information from radiology reports. We first use GPT-4 to create a small labeled dataset, then fine-tune a Llama3-8B model on it. Evaluated on clinician-annotated reports, our model achieves an average F1 score of 84.6%, which is on par with GPT-4. Our findings demonstrate the feasibility of developing an in-house LLM that not only matches GPT-4's performance but also offers cost reductions and enhanced data privacy.

cs.CL↗

arXiv2024

CO2Wounds-V2: Extended Chronic Wounds Dataset From Leprosy Patients

Chronic wounds pose an ongoing health concern globally, largely due to the prevalence of conditions such as diabetes and leprosy's disease. The standard method of monitoring these wounds involves visual inspection by healthcare professionals, a practice that could present challenges for patients in remote areas with inadequate transportation and healthcare infrastructure. This has led to the development of algorithms designed for the analysis and follow-up of wound images, which perform image-processing tasks such as classification, detection, and segmentation. However, the effectiveness of these algorithms heavily depends on the availability of comprehensive and varied wound image data, which is usually scarce. This paper introduces the CO2Wounds-V2 dataset, an extended collection of RGB wound images from leprosy patients with their corresponding semantic segmentation annotations, aiming to enhance the development and testing of image-processing algorithms in the medical field.

eess.IV↗

arXiv2024

$\rm SP^3$: Enhancing Structured Pruning via PCA Projection

Structured pruning is a widely used technique for reducing the size of pre-trained language models (PLMs), but current methods often overlook the potential of compressing the hidden dimension (d) in PLMs, a dimension critical to model size and efficiency. This paper introduces a novel structured pruning approach, Structured Pruning with PCA Projection (SP3), targeting the effective reduction of d by projecting features into a space defined by principal components before masking. Extensive experiments on benchmarks (GLUE and SQuAD) show that SP3 can reduce d by 70%, compress 94% of the BERTbase model, maintain over 96% accuracy, and outperform other methods that compress d by 6% in accuracy at the same compression ratio. SP3 has also proven effective with other models, including OPT and Llama. Our data and code are available at an anonymous repo.

cs.CL↗

arXiv2024

Learning Fair Invariant Representations under Covariate and Correlation Shifts Simultaneously

Achieving the generalization of an invariant classifier from training domains to shifted test domains while simultaneously considering model fairness is a substantial and complex challenge in machine learning. Existing methods address the problem of fairness-aware domain generalization, focusing on either covariate shift or correlation shift, but rarely consider both at the same time. In this paper, we introduce a novel approach that focuses on learning a fairness-aware domain-invariant predictor within a framework addressing both covariate and correlation shifts simultaneously, ensuring its generalization to unknown test domains inaccessible during training. In our approach, data are first disentangled into content and style factors in latent spaces. Furthermore, fairness-aware domain-invariant content representations can be learned by mitigating sensitive information and retaining as much other information as possible. Extensive empirical studies on benchmark datasets demonstrate that our approach surpasses state-of-the-art methods with respect to model accuracy as well as both group and individual fairness.

cs.LG↗

arXiv2024

GIR: 3D Gaussian Inverse Rendering for Relightable Scene Factorization

This paper presents a 3D Gaussian Inverse Rendering (GIR) method, employing 3D Gaussian representations to effectively factorize the scene into material properties, light, and geometry. The key contributions lie in three-fold. We compute the normal of each 3D Gaussian using the shortest eigenvector, with a directional masking scheme forcing accurate normal estimation without external supervision. We adopt an efficient voxel-based indirect illumination tracing scheme that stores direction-aware outgoing radiance in each 3D Gaussian to disentangle secondary illumination for approximating multi-bounce light transport. To further enhance the illumination disentanglement, we represent a high-resolution environmental map with a learnable low-resolution map and a lightweight, fully convolutional network. Our method achieves state-of-the-art performance in both relighting and novel view synthesis tasks among the recently proposed inverse rendering methods while achieving real-time rendering. This substantiates our proposed method's efficacy and broad applicability, highlighting its potential as an influential tool in various real-time interactive graphics applications such as material editing and relighting. The code will be released at https://github.com/guduxiaolang/GIR.

cs.CV↗

arXiv2024

Multi-graph Graph Matching for Coronary Artery Semantic Labeling

Coronary artery disease (CAD) stands as the leading cause of death worldwide, and invasive coronary angiography (ICA) remains the gold standard for assessing vascular anatomical information. However, deep learning-based methods encounter challenges in generating semantic labels for arterial segments, primarily due to the morphological similarity between arterial branches and varying anatomy of arterial system between different projection view angles and patients. To address this challenge, we model the vascular tree as a graph and propose a multi-graph graph matching (MGM) algorithm for coronary artery semantic labeling. The MGM algorithm assesses the similarity between arterials in multiple vascular tree graphs, considering the cycle consistency between each pair of graphs. As a result, the unannotated arterial segments are appropriately labeled by matching them with annotated segments. Through the incorporation of anatomical graph structure, radiomics features, and semantic mapping, the proposed MGM model achieves an impressive accuracy of 0.9471 for coronary artery semantic labeling using our multi-site dataset with 718 ICAs. With the semantic labeled arteries, an overall accuracy of 0.9155 was achieved for stenosis detection. The proposed MGM presents a novel tool for coronary artery analysis using multiple ICA-derived graphs, offering valuable insights into vascular health and pathology.

cs.CV↗

arXiv2024

FinanceMath: Knowledge-Intensive Math Reasoning in Finance Domains

We introduce FinanceMath, a novel benchmark designed to evaluate LLMs' capabilities in solving knowledge-intensive math reasoning problems. Compared to prior works, this study features three core advancements. First, FinanceMath includes 1,200 problems with a hybrid of textual and tabular content. These problems require college-level knowledge in the finance domain for effective resolution. Second, we provide expert-annotated, detailed solution references in Python program format, ensuring a high-quality benchmark for LLM assessment. We also construct a finance-domain knowledge bank and investigate various knowledge integration strategies. Finally, we evaluate a wide spectrum of 44 LLMs with both Chain-of-Thought and Program-of-Thought prompting methods. Our experimental results reveal that the current best-performing system (i.e., GPT-4o) achieves only 60.9% accuracy using CoT prompting, leaving substantial room for improvement. Moreover, while augmenting LLMs with external knowledge can improve model performance (e.g., from 47.5% to 54.5% for Gemini-1.5-Pro), their accuracy remains significantly lower than the estimated human expert performance of 92%. We believe that FinanceMath can advance future research in the area of domain-specific knowledge retrieval and integration, particularly within the context of solving reasoning-intensive tasks.

cs.CL↗

arXiv2024

Harnessing Temporal Causality for Advanced Temporal Action Detection

As a fundamental task in long-form video understanding, temporal action detection (TAD) aims to capture inherent temporal relations in untrimmed videos and identify candidate actions with precise boundaries. Over the years, various networks, including convolutions, graphs, and transformers, have been explored for effective temporal modeling for TAD. However, these modules typically treat past and future information equally, overlooking the crucial fact that changes in action boundaries are essentially causal events. Inspired by this insight, we propose leveraging the temporal causality of actions to enhance TAD representation by restricting the model's access to only past or future context. We introduce CausalTAD, which combines causal attention and causal Mamba to achieve state-of-the-art performance on multiple benchmarks. Notably, with CausalTAD, we ranked 1st in the Action Recognition, Action Detection, and Audio-Based Interaction Detection tracks at the EPIC-Kitchens Challenge 2024, as well as 1st in the Moment Queries track at the Ego4D Challenge 2024. Our code is available at https://github.com/sming256/OpenTAD/.

cs.CV↗