arXiv subjects

Yi Guo

Publications and source records attributed to Yi Guo.

At least 73 records · Page 4Linked to original sources

arXiv2025

VAP-Diffusion: Enriching Descriptions with MLLMs for Enhanced Medical Image Generation

As the appearance of medical images is influenced by multiple underlying factors, generative models require rich attribute information beyond labels to produce realistic and diverse images. For instance, generating an image of skin lesion with specific patterns demands descriptions that go beyond diagnosis, such as shape, size, texture, and color. However, such detailed descriptions are not always accessible. To address this, we explore a framework, termed Visual Attribute Prompts (VAP)-Diffusion, to leverage external knowledge from pre-trained Multi-modal Large Language Models (MLLMs) to improve the quality and diversity of medical image generation. First, to derive descriptions from MLLMs without hallucination, we design a series of prompts following Chain-of-Thoughts for common medical imaging tasks, including dermatologic, colorectal, and chest X-ray images. Generated descriptions are utilized during training and stored across different categories. During testing, descriptions are randomly retrieved from the corresponding category for inference. Moreover, to make the generator robust to unseen combination of descriptions at the test time, we propose a Prototype Condition Mechanism that restricts test embeddings to be similar to those from training. Experiments on three common types of medical imaging across four datasets verify the effectiveness of VAP-Diffusion.

cs.CV↗

arXiv2025

Scale-Invariance Drives Convergence in AI and Brain Representations

Despite variations in architecture and pretraining strategies, recent studies indicate that large-scale AI models often converge toward similar internal representations that also align with neural activity. We propose that scale-invariance, a fundamental structural principle in natural systems, is a key driver of this convergence. In this work, we propose a multi-scale analytical framework to quantify two core aspects of scale-invariance in AI representations: dimensional stability and structural similarity across scales. We further investigate whether these properties can predict alignment performance with functional Magnetic Resonance Imaging (fMRI) responses in the visual cortex. Our analysis reveals that embeddings with more consistent dimension and higher structural similarity across scales align better with fMRI data. Furthermore, we find that the manifold structure of fMRI data is more concentrated, with most features dissipating at smaller scales. Embeddings with similar scale patterns align more closely with fMRI data. We also show that larger pretraining datasets and the inclusion of language modalities enhance the scale-invariance properties of embeddings, further improving neural alignment. Our findings indicate that scale-invariance is a fundamental structural principle that bridges artificial and biological representations, providing a new framework for evaluating the structural quality of human-like AI systems.

q-bio.NC↗

arXiv2025

A Pre-trained Framework for Multilingual Brain Decoding Using Non-invasive Recordings

Brain-computer interfaces (BCIs) with speech decoding from brain recordings have broad application potential in fields such as clinical rehabilitation and cognitive neuroscience. However, current decoding methods remain limited to single-language, single-subject, and single neuroimaging modality settings, restricting their clinical applicability and generalizability. Here we propose a joint multilingual, multi-subject and multimodal decoding framework. It maps diverse brain recordings into a unified semantic space defined by a pre-trained multilingual model (PMM), enabling decoding across multiple languages, multiple subjects and multiple neuroimaging modalities. The proposed framework is validated using non-invasive brain recordings from 159 participants across four languages. Experimental results show that it exhibits strong generalization across multilingual, multi-subject, and multimodal settings. More importantly, the proposed framework can promote linguistic fairness, which is vital for underrepresented languages in BCI applications. The unified semantic space enables cross-lingual mapping enhancement, allowing the framework to boost the decoding performance of underrepresented languages, thereby promoting linguistic fairness. Overall, the proposed framework establishes a new potential paradigm for brain decoding, opening new paths for broader applications of BCI.

q-bio.NC↗

arXiv2025

Towards the Efficient Inference by Incorporating Automated Computational Phenotypes under Covariate Shift

Collecting gold-standard phenotype data via manual extraction is typically labor-intensive and slow, whereas automated computational phenotypes (ACPs) offer a systematic and much faster alternative. However, simply replacing the gold-standard with ACPs, without acknowledging their differences, could lead to biased results and misleading conclusions. Motivated by the complexity of incorporating ACPs while maintaining the validity of downstream analyses, in this paper, we consider a semi-supervised learning setting that consists of both labeled data (with gold-standard) and unlabeled data (without gold-standard), under the covariate shift framework. We develop doubly robust and semiparametrically efficient estimators that leverage ACPs for general target parameters in the unlabeled and combined populations. In addition, we carefully analyze the efficiency gains achieved by incorporating ACPs, comparing scenarios with and without their inclusion. Notably, we identify that ACPs for the unlabeled data, instead of for the labeled data, drive the enhanced efficiency gains. To validate our theoretical findings, we conduct comprehensive synthetic experiments and apply our method to multiple real-world datasets, confirming the practical advantages of our approach. \hfill{\texttt{Code}: \href{https://github.com/brucejunjin/ICML2025-ACPCS}{\faGithub}}

stat.ME↗

arXiv2025

Causal Discovery in Symmetric Dynamic Systems with Convergent Cross Mapping

This paper systematically discusses how the inherent properties of chaotic attractors influence the results of discovering causality from time series using convergent cross mapping, particularly how convergent cross mapping misleads bidirectional causality as unidirectional when the chaotic attractor exhibits symmetry. We propose a novel method based on the k-means clustering method to address the challenges when the chaotic attractor exhibits two-fold rotation symmetry. This method is demonstrated to recover the symmetry of the latent chaotic attractor and discover the correct causality between time series without introducing information from other variables. We validate the accuracy of this method using time series derived from low-dimension and high-dimensional chaotic symmetric attractors for which convergent cross mapping may conclude erroneous results.

math.DS↗

arXiv2025

Physics-informed Deep Diffusion MRI Reconstruction with Synthetic Data: Break Training Data Bottleneck in Artificial Intelligence

Diffusion magnetic resonance imaging (MRI) is the only imaging modality for non-invasive movement detection of in vivo water molecules, with significant clinical and research applications. Diffusion weighted imaging (DWI) MRI acquired by multi-shot techniques can achieve higher resolution, better signal-to-noise ratio, and lower geometric distortion than single-shot, but suffers from inter-shot motion-induced artifacts. These artifacts cannot be removed prospectively, leading to the absence of artifact-free training labels. Thus, the potential of deep learning in multi-shot DWI reconstruction remains largely untapped. To break the training data bottleneck, here, we propose a Physics-Informed Deep DWI reconstruction method (PIDD) to synthesize high-quality paired training data by leveraging the physical diffusion model (magnitude synthesis) and inter-shot motion-induced phase model (motion phase synthesis). The network is trained only once with 100,000 synthetic samples, achieving encouraging results on multiple realistic in vivo data reconstructions. Advantages over conventional methods include: (a) Better motion artifact suppression and reconstruction stability; (b) Outstanding generalization to multi-scenario reconstructions, including multi-resolution, multi-b-value, multi-under-sampling, multi-vendor, and multi-center; (c) Excellent clinical adaptability to patients with verifications by seven experienced doctors (p<0.001). In conclusion, PIDD presents a novel deep learning framework by exploiting the power of MRI physics, providing a cost-effective and explainable way to break the data bottleneck in deep learning medical imaging.

eess.IV↗

arXiv2025

Learning Modality-Aware Representations: Adaptive Group-wise Interaction Network for Multimodal MRI Synthesis

Multimodal MR image synthesis aims to generate missing modality images by effectively fusing and mapping from a subset of available MRI modalities. Most existing methods adopt an image-to-image translation paradigm, treating multiple modalities as input channels. However, these approaches often yield sub-optimal results due to the inherent difficulty in achieving precise feature- or semantic-level alignment across modalities. To address these challenges, we propose an Adaptive Group-wise Interaction Network (AGI-Net) that explicitly models both inter-modality and intra-modality relationships for multimodal MR image synthesis. Specifically, feature channels are first partitioned into predefined groups, after which an adaptive rolling mechanism is applied to conventional convolutional kernels to better capture feature and semantic correspondences between different modalities. In parallel, a cross-group attention module is introduced to enable effective feature fusion across groups, thereby enhancing the network's representational capacity. We validate the proposed AGI-Net on the publicly available IXI and BraTS2023 datasets. Experimental results demonstrate that AGI-Net achieves state-of-the-art performance in multimodal MR image synthesis tasks, confirming the effectiveness of its modality-aware interaction design. We release the relevant code at: https://github.com/zunzhumu/Adaptive-Group-wise-Interaction-Network-for-Multimodal-MRI-Synthesis.git.

eess.IV↗

arXiv2025

Self-Consistent Nested Diffusion Bridge for Accelerated MRI Reconstruction

Accelerated MRI reconstruction plays a vital role in reducing scan time while preserving image quality. While most existing methods rely on complex-valued image-space or k-space data, these formats are often inaccessible in clinical practice due to proprietary reconstruction pipelines, leaving only magnitude images stored in DICOM files. To address this gap, we focus on the underexplored task of magnitude-image-based MRI reconstruction. Recent advancements in diffusion models, particularly denoising diffusion probabilistic models (DDPMs), have demonstrated strong capabilities in modeling image priors. However, their task-agnostic denoising nature limits performance in source-to-target image translation tasks, such as MRI reconstruction. In this work, we propose a novel Self-Consistent Nested Diffusion Bridge (SC-NDB) framework that models accelerated MRI reconstruction as a bi-directional image translation process between under-sampled and fully-sampled magnitude MRI images. SC-NDB introduces a nested diffusion architecture with a self-consistency constraint and reverse bridge diffusion pathways to improve intermediate prediction fidelity and better capture the explicit priors of source images. Furthermore, we incorporate a Contour Decomposition Embedding Module (CDEM) to inject structural and textural knowledge by leveraging Laplacian pyramids and directional filter banks. Extensive experiments on the fastMRI and IXI datasets demonstrate that our method achieves state-of-the-art performance compared to both magnitude-based and non-magnitude-based diffusion models, confirming the effectiveness and clinical relevance of SC-NDB.

eess.IV↗

arXiv2025

Deep Learning-Based Direct Leaf Area Estimation using Two RGBD Datasets for Model Development

Estimation of a single leaf area can be a measure of crop growth and a phenotypic trait to breed new varieties. It has also been used to measure leaf area index and total leaf area. Some studies have used hand-held cameras, image processing 3D reconstruction and unsupervised learning-based methods to estimate the leaf area in plant images. Deep learning works well for object detection and segmentation tasks; however, direct area estimation of objects has not been explored. This work investigates deep learning-based leaf area estimation, for RGBD images taken using a mobile camera setup in real-world scenarios. A dataset for attached leaves captured with a top angle view and a dataset for detached single leaves were collected for model development and testing. First, image processing-based area estimation was tested on manually segmented leaves. Then a Mask R-CNN-based model was investigated, and modified to accept RGBD images and to estimate the leaf area. The detached-leaf data set was then mixed with the attached-leaf plant data set to estimate the single leaf area for plant images, and another network design with two backbones was proposed: one for segmentation and the other for area estimation. Instead of trying all possibilities or random values, an agile approach was used in hyperparameter tuning. The final model was cross-validated with 5-folds and tested with two unseen datasets: detached and attached leaves. The F1 score with 90% IoA for segmentation result on unseen detached-leaf data was 1.0, while R-squared of area estimation was 0.81. For unseen plant data segmentation, the F1 score with 90% IoA was 0.59, while the R-squared score was 0.57. The research suggests using attached leaves with ground truth area to improve the results.

cs.CV↗

arXiv2025

Optimal PMU Placement for Kalman Filtering of DAE Power System Models

Optimal sensor placement is essential for minimizing costs and ensuring accurate state estimation in power systems. This paper introduces a novel method for optimal sensor placement for dynamic state estimation of power systems modeled by differential-algebraic equations. The method identifies optimal sensor locations by minimizing the steady-state covariance matrix of the Kalman filter, thus minimizing the error of joint differential and algebraic state estimation. The problem is reformulated as a mixed-integer semidefinite program and effectively solved using off-the-shelf numerical solvers. Numerical results demonstrate the merits of the proposed approach by benchmarking its performance in phasor measurement unit placement in comparison to greedy algorithms.

eess.SY↗

arXiv2025

EEG-ReMinD: Enhancing Neurodegenerative EEG Decoding through Self-Supervised State Reconstruction-Primed Riemannian Dynamics

The development of EEG decoding algorithms confronts challenges such as data sparsity, subject variability, and the need for precise annotations, all of which are vital for advancing brain-computer interfaces and enhancing the diagnosis of diseases. To address these issues, we propose a novel two-stage approach named Self-Supervised State Reconstruction-Primed Riemannian Dynamics (EEG-ReMinD) , which mitigates reliance on supervised learning and integrates inherent geometric features. This approach efficiently handles EEG data corruptions and reduces the dependency on labels. EEG-ReMinD utilizes self-supervised and geometric learning techniques, along with an attention mechanism, to analyze the temporal dynamics of EEG features within the framework of Riemannian geometry, referred to as Riemannian dynamics. Comparative analyses on both intact and corrupted datasets from two different neurodegenerative disorders underscore the enhanced performance of EEG-ReMinD.

eess.SP↗

arXiv2024

Defensive Dual Masking for Robust Adversarial Defense

The field of textual adversarial defenses has gained considerable attention in recent years due to the increasing vulnerability of natural language processing (NLP) models to adversarial attacks, which exploit subtle perturbations in input text to deceive models. This paper introduces the Defensive Dual Masking (DDM) algorithm, a novel approach designed to enhance model robustness against such attacks. DDM utilizes a unique adversarial training strategy where [MASK] tokens are strategically inserted into training samples to prepare the model to handle adversarial perturbations more effectively. During inference, potentially adversarial tokens are dynamically replaced with [MASK] tokens to neutralize potential threats while preserving the core semantics of the input. The theoretical foundation of our approach is explored, demonstrating how the selective masking mechanism strengthens the model's ability to identify and mitigate adversarial manipulations. Our empirical evaluation across a diverse set of benchmark datasets and attack mechanisms consistently shows that DDM outperforms state-of-the-art defense techniques, improving model accuracy and robustness. Moreover, when applied to Large Language Models (LLMs), DDM also enhances their resilience to adversarial attacks, providing a scalable defense mechanism for large-scale NLP applications.

cs.CL↗

arXiv2024

SAM-MPA: Applying SAM to Few-shot Medical Image Segmentation using Mask Propagation and Auto-prompting

Medical image segmentation often faces the challenge of prohibitively expensive annotation costs. While few-shot learning offers a promising solution to alleviate this burden, conventional approaches still rely heavily on pre-training with large volumes of labeled data from known categories. To address this issue, we propose leveraging the Segment Anything Model (SAM), pre-trained on over 1 billion masks, thus circumventing the need for extensive domain-specific annotated data. In light of this, we developed SAM-MPA, an innovative SAM-based framework for few-shot medical image segmentation using Mask Propagation-based Auto-prompting. Initially, we employ k-centroid clustering to select the most representative examples for labelling to construct the support set. These annotated examples are registered to other images yielding deformation fields that facilitate the propagation of the mask knowledge to obtain coarse masks across the dataset. Subsequently, we automatically generate visual prompts based on the region and boundary expansion of the coarse mask, including points, box and a coarse mask. Finally, we can obtain the segmentation predictions by inputting these prompts into SAM and refine the results by post refinement module. We validate the performance of the proposed framework through extensive experiments conducted on two medical image datasets with different modalities. Our method achieves Dices of 74.53%, 94.36% on Breast US, Chest X-ray, respectively. Experimental results substantiate that SAM-MPA yields high-accuracy segmentations within 10 labeled examples, outperforming other state-of-the-art few-shot auto-segmentation methods. Our method enables the customization of SAM for any medical image dataset with a small number of labeled examples.

cs.CV↗

arXiv2024

Diff-CXR: Report-to-CXR generation through a disease-knowledge enhanced diffusion model

Text-To-Image (TTI) generation is significant for controlled and diverse image generation with broad potential applications. Although current medical TTI methods have made some progress in report-to-Chest-Xray (CXR) generation, their generation performance may be limited due to the intrinsic characteristics of medical data. In this paper, we propose a novel disease-knowledge enhanced Diffusion-based TTI learning framework, named Diff-CXR, for medical report-to-CXR generation. First, to minimize the negative impacts of noisy data on generation, we devise a Latent Noise Filtering Strategy that gradually learns the general patterns of anomalies and removes them in the latent space. Then, an Adaptive Vision-Aware Textual Learning Strategy is designed to learn concise and important report embeddings in a domain-specific Vision-Language Model, providing textual guidance for Chest-Xray generation. Finally, by incorporating the general disease knowledge into the pretrained TTI model via a delicate control adapter, a disease-knowledge enhanced diffusion model is introduced to achieve realistic and precise report-to-CXR generation. Experimentally, our Diff-CXR outperforms previous SOTA medical TTI methods by 33.4\% / 8.0\% and 23.8\% / 56.4\% in the FID and mAUC score on MIMIC-CXR and IU-Xray, with the lowest computational complexity at 29.641 GFLOPs. Downstream experiments on three thorax disease classification benchmarks and one CXR-report generation benchmark demonstrate that Diff-CXR is effective in improving classical CXR analysis methods. Notably, models trained on the combination of 1\% real data and synthetic data can achieve a competitive mAUC score compared to models trained on all data, presenting promising clinical applications.

cs.CV↗

arXiv2024

When Graph Neural Networks Meet Dynamic Mode Decomposition

Graph Neural Networks (GNNs) have emerged as fundamental tools for a wide range of prediction tasks on graph-structured data. Recent studies have drawn analogies between GNN feature propagation and diffusion processes, which can be interpreted as dynamical systems. In this paper, we delve deeper into this perspective by connecting the dynamics in GNNs to modern Koopman theory and its numerical method, Dynamic Mode Decomposition (DMD). We illustrate how DMD can estimate a low-rank, finite-dimensional linear operator based on multiple states of the system, effectively approximating potential nonlinear interactions between nodes in the graph. This approach allows us to capture complex dynamics within the graph accurately and efficiently. We theoretically establish a connection between the DMD-estimated operator and the original dynamic operator between system states. Building upon this foundation, we introduce a family of DMD-GNN models that effectively leverage the low-rank eigenfunctions provided by the DMD algorithm. We further discuss the potential of enhancing our approach by incorporating domain-specific constraints such as symmetry into the DMD computation, allowing the corresponding GNN models to respect known physical properties of the underlying system. Our work paves the path for applying advanced dynamical system analysis tools via GNNs. We validate our approach through extensive experiments on various learning tasks, including directed graphs, large-scale graphs, long-range interactions, and spatial-temporal graphs. We also empirically verify that our proposed models can serve as powerful encoders for link prediction tasks. The results demonstrate that our DMD-enhanced GNNs achieve state-of-the-art performance, highlighting the effectiveness of integrating DMD into GNN frameworks.

cs.LG↗

arXiv2024

Quantifying and Optimizing the Time-Coupled Flexibilities at the Distribution-Level for TSO-DSO Coordination

The flexibilities provided by the distributed energy resources (DERs) in distribution systems enable the coordination of transmission system operator (TSO) and distribution system operators (DSOs). At the distribution level, the flexibilities should be optimized for participation in the transmission system operation. This paper first proposes a flexibility quantification method that quantifies the costs of providing flexibilities and their values to the DSO in the TSO-DSO coordination. Compared with traditional power-range-based quantification approaches that are mainly suitable for generators, the proposed method can directly capture the time-coupling characteristics of DERs' individual and aggregated flexibility regions. Based on the quantification method, we further propose a DSO optimization model to activate the flexibilities from DER aggregators in the distribution system for energy arbitrage and ancillary services provision in the transmission system, along with a revenue allocation strategy that ensures a non-profit DSO. Numerical tests on the IEEE test system verify the proposed methods.

eess.SY↗

arXiv2024

Seed-ASR: Understanding Diverse Speech and Contexts with LLM-based Speech Recognition

Modern automatic speech recognition (ASR) model is required to accurately transcribe diverse speech signals (from different domains, languages, accents, etc) given the specific contextual information in various application scenarios. Classic end-to-end models fused with extra language models perform well, but mainly in data matching scenarios and are gradually approaching a bottleneck. In this work, we introduce Seed-ASR, a large language model (LLM) based speech recognition model. Seed-ASR is developed based on the framework of audio conditioned LLM (AcLLM), leveraging the capabilities of LLMs by inputting continuous speech representations together with contextual information into the LLM. Through stage-wise large-scale training and the elicitation of context-aware capabilities in LLM, Seed-ASR demonstrates significant improvement over end-to-end models on comprehensive evaluation sets, including multiple domains, accents/dialects and languages. Additionally, Seed-ASR can be further deployed to support specific needs in various scenarios without requiring extra language models. Compared to recently released large ASR models, Seed-ASR achieves 10%-40% reduction in word (or character, for Chinese) error rates on Chinese and English public test sets, further demonstrating its powerful performance.

eess.AS↗

arXiv2024

Chest-Diffusion: A Light-Weight Text-to-Image Model for Report-to-CXR Generation

Text-to-image generation has important implications for generation of diverse and controllable images. Several attempts have been made to adapt Stable Diffusion (SD) to the medical domain. However, the large distribution difference between medical reports and natural texts, as well as high computational complexity in common stable diffusion limit the authenticity and feasibility of the generated medical images. To solve above problems, we propose a novel light-weight transformer-based diffusion model learning framework, Chest-Diffusion, for report-to-CXR generation. Chest-Diffusion employs a domain-specific text encoder to obtain accurate and expressive text features to guide image generation, improving the authenticity of the generated images. Meanwhile, we introduce a light-weight transformer architecture as the denoising model, reducing the computational complexity of the diffusion model. Experiments demonstrate that our Chest-Diffusion achieves the lowest FID score 24.456, under the computation budget of 118.918 GFLOPs, which is nearly one-third of the computational complexity of SD.

cs.CV↗