arXiv subjects

Yudong Yao

Publications and source records attributed to Yudong Yao.

At least 19 recordsLinked to original sources

arXiv2026

Spatial-Code-Domain Grouped Index Modulation: Fluid-Antenna-Assisted System Design and BER Performance Analysis

Fluid antenna systems (FASs) provide reconfigurable spatial resources within compact apertures. In this paper, we introduce code-domain grouped index modulation (CGIM) and its spatial-code-domain extension, termed SCGIM, for FA-assisted transceivers. CGIM partitions the available orthogonal spreading codes into multiple subsets and jointly maps information onto their in-phase and quadrature indices and constellation symbols. In an Rx-FAS-assisted single-input multiple-output (SIMO) link, group-wise despreading separates the orthogonal code groups for parallel detection, while receive-port selection provides spatial diversity. SCGIM further associates interleaved Tx-FA port subsets with the code subsets, with the Tx-FAS conveying spatial-index information and the Rx-FAS providing selection diversity in a multiple-input multiple-output (MIMO) link. For SCGIM, we develop maximum-likelihood (ML), staged greedy (GD), and cross-domain index message-passing (CD-IMPD) detectors. CD-IMPD exchanges soft information over a cycle-free factor graph to account for the coupling between the spatial and code indices, requiring only one inward and one outward message pass. For CGIM, the BER is derived from the joint decision regions of the despread-domain observations and averaged over the Rx-FAS selected-gain distribution under Rayleigh, Nakagami-m, and additive white Gaussian noise channels. For SCGIM, an average-BER approximation is derived from a full-pair union bound using the selected-gain density ratio and exponentially tilted quadratic-form Laplace transforms. Simulation results validate the BER analysis and show that the proposed schemes achieve lower BER and higher throughput than the considered IM schemes, while CD-IMPD achieves near-ML BER performance with lower detection complexity.

cs.IT↗

arXiv2026

MatMind: A Structure-Activity Knowledge-Driven Generative Foundation Model for Materials Science

Progress in AI-driven crystal materials science has so far been carried by narrow architectures purpose-built for individual tasks -- graph neural networks for property prediction, diffusion and flow-matching models for crystal generation -- each excelling within its niche yet unable to act as a shared backbone across the full spectrum of materials problems. Generative large language models offer a fundamentally different paradigm, in which structural representation, quantitative prediction, and structure-activity reasoning can be unified within one model, but the materials community has yet to see this paradigm realized at a level competitive with established narrow specialists. Here we present MatMind, a generative foundation model purpose-built for crystal materials science under this paradigm, developed through the coordinated activation of structure-activity knowledge and physics-informed feedback within a progressive training framework -- combining structure-activity knowledge injection, a dual-head architecture that jointly trains language reasoning and numerical regression in a shared representation space, and multi-objective physics-informed reinforcement learning over stability, novelty, and structural diversity. Across three task families, MatMind attains the lowest mean absolute error on energy above hull, bulk modulus, and band gap -- surpassing graph neural network predictors purpose-built for these tasks -- reaches an S.U.N. rate of 65.3% on unconditional crystal generation, and achieves a comparable multiplicative improvement on magnetization-density-conditioned generation, where only 21 positive samples exist within over 600000 training entries. By matching or surpassing narrow specialists on their own ground while operating within a single unified model, MatMind shows that the LLM-based paradigm can serve as a viable backbone for crystal materials science going forward.

cond-mat.mtrl-sci↗

arXiv2025

CF-CAM: Cluster Filter Class Activation Mapping for Reliable Gradient-Based Interpretability

As deep learning continues to advance, the transparency of neural network decision-making remains a critical challenge, limiting trust and applicability in high-stakes domains. Class Activation Mapping (CAM) techniques have emerged as a key approach toward visualizing model decisions, yet existing methods face inherent trade-offs. Gradient-based CAM variants suffer from sensitivity to gradient perturbations due to gradient noise, leading to unstable and unreliable explanations. Conversely, gradient-free approaches mitigate gradient instability but incur significant computational overhead and inference latency. To address these limitations, we propose a Cluster Filter Class Activation Map (CF-CAM) technique, a novel framework that reintroduces gradient-based weighting while enhancing robustness against gradient noise. CF-CAM utilizes hierarchical importance weighting strategy to balance discriminative feature preservation and noise elimination. A density-aware channel clustering method via Density-Based Spatial Clustering of Applications with Noise (DBSCAN) groups semantically relevant feature channels and discard noise-prone activations. Additionally, cluster-conditioned gradient filtering leverages Gaussian filters to refine gradient signals, preserving edge-aware localization while suppressing noise impact. Experiment results demonstrate that CF-CAM achieves superior interpretability performance while enhancing computational efficiency, outperforming state-of-the-art CAM methods in faithfulness and robustness. By effectively mitigating gradient instability without excessive computational cost, CF-CAM provides a competitive solution for enhancing the interpretability of deep neural networks in critical applications such as autonomous driving and medical diagnosis.

cs.LG↗

arXiv2023

Quadratic Graph Attention Network (Q-GAT) for Robust Construction of Gene Regulatory Networks

Gene regulatory relationships can be abstracted as a gene regulatory network (GRN), which plays a key role in characterizing complex cellular processes and pathways. Recently, graph neural networks (GNNs), as a class of deep learning models, have emerged as a useful tool to infer gene regulatory relationships from gene expression data. However, deep learning models have been found to be vulnerable to noise, which greatly hinders the adoption of deep learning in constructing GRNs, because high noise is often unavoidable in the process of gene expression measurement. Can we preferably prototype a robust GNN for constructing GRNs? In this paper, we give a positive answer by proposing a Quadratic Graph Attention Network (Q-GAT) with a dual attention mechanism. We study the changes in the predictive accuracy of Q-GAT and 9 state-of-the-art baselines by introducing different levels of adversarial perturbations. Experiments in the E. coli and S. cerevisiae datasets suggest that Q-GAT outperforms the state-of-the-art models in robustness. Lastly, we dissect why Q-GAT is robust through the signal-to-noise ratio (SNR) and interpretability analyses. The former informs that nonlinear aggregation of quadratic neurons can amplify useful signals and suppress unwanted noise, thereby facilitating robustness, while the latter reveals that Q-GAT can leverage more features in prediction thanks to the dual attention mechanism, which endows Q-GAT with the ability to confront adversarial perturbation. We have shared our code in https://github.com/Minorway/Q-GAT_for_Robust_Construction_of_GRN for readers' evaluation.

q-bio.MN↗

arXiv2023

Self-supervised Noise2noise Method Utilizing Corrupted Images with a Modular Network for LDCT Denoising

Deep learning is a very promising technique for low-dose computed tomography (LDCT) image denoising. However, traditional deep learning methods require paired noisy and clean datasets, which are often difficult to obtain. This paper proposes a new method for performing LDCT image denoising with only LDCT data, which means that normal-dose CT (NDCT) is not needed. We adopt a combination including the self-supervised noise2noise model and the noisy-as-clean strategy. First, we add a second yet similar type of noise to LDCT images multiple times. Note that we use LDCT images based on the noisy-as-clean strategy for corruption instead of NDCT images. Then, the noise2noise model is executed with only the secondary corrupted images for training. We select a modular U-Net structure from several candidates with shared parameters to perform the task, which increases the receptive field without increasing the parameter size. The experimental results obtained on the Mayo LDCT dataset show the effectiveness of the proposed method compared with that of state-of-the-art deep learning methods. The developed code is available at https://github.com/XYuan01/Self-supervised-Noise2Noise-for-LDCT.

eess.IV↗

arXiv2023

NL-CS Net: Deep Learning with Non-Local Prior for Image Compressive Sensing

Deep learning has been applied to compressive sensing (CS) of images successfully in recent years. However, existing network-based methods are often trained as the black box, in which the lack of prior knowledge is often the bottleneck for further performance improvement. To overcome this drawback, this paper proposes a novel CS method using non-local prior which combines the interpretability of the traditional optimization methods with the speed of network-based methods, called NL-CS Net. We unroll each phase from iteration of the augmented Lagrangian method solving non-local and sparse regularized optimization problem by a network. NL-CS Net is composed of the up-sampling module and the recovery module. In the up-sampling module, we use learnable up-sampling matrix instead of a predefined one. In the recovery module, patch-wise non-local network is employed to capture long-range feature correspondences. Important parameters involved (e.g. sampling matrix, nonlinear transforms, shrinkage thresholds, step size, $etc.$) are learned end-to-end, rather than hand-crafted. Furthermore, to facilitate practical implementation, orthogonal and binary constraints on the sampling matrix are simultaneously adopted. Extensive experiments on natural images and magnetic resonance imaging (MRI) demonstrate that the proposed method outperforms the state-of-the-art methods while maintaining great interpretability and speed.

cs.CV↗

arXiv2023

3D PETCT Tumor Lesion Segmentation via GCN Refinement

Whole-body PET/CT scan is an important tool for diagnosing various malignancies (e.g., malignant melanoma, lymphoma, or lung cancer), and accurate segmentation of tumors is a key part for subsequent treatment. In recent years, CNN-based segmentation methods have been extensively investigated. However, these methods often give inaccurate segmentation results, such as over-segmentation and under-segmentation. Therefore, to address such issues, we propose a post-processing method based on a graph convolutional neural network (GCN) to refine inaccurate segmentation parts and improve the overall segmentation accuracy. Firstly, nnUNet is used as an initial segmentation framework, and the uncertainty in the segmentation results is analyzed. Certainty and uncertainty nodes establish the nodes of a graph neural network. Each node and its 6 neighbors form an edge, and 32 nodes are randomly selected for uncertain nodes to form edges. The highly uncertain nodes are taken as the subsequent refinement targets. Secondly, the nnUNet result of the certainty nodes is used as label to form a semi-supervised graph network problem, and the uncertainty part is optimized through training the GCN network to improve the segmentation performance. This describes our proposed nnUNet-GCN segmentation framework. We perform tumor segmentation experiments on the PET/CT dataset in the MICCIA2022 autoPET challenge. Among them, 30 cases are randomly selected for testing, and the experimental results show that the false positive rate is effectively reduced with nnUNet-GCN refinement. In quantitative analysis, there is an improvement of 2.12 % on the average Dice score, 6.34 on 95 % Hausdorff Distance (HD95), and 1.72 on average symmetric surface distance (ASSD). The quantitative and qualitative evaluation results show that GCN post-processing methods can effectively improve tumor segmentation performance.

eess.IV↗

arXiv2023

QS-ADN: Quasi-Supervised Artifact Disentanglement Network for Low-Dose CT Image Denoising by Local Similarity Among Unpaired Data

Deep learning has been successfully applied to low-dose CT (LDCT) image denoising for reducing potential radiation risk. However, the widely reported supervised LDCT denoising networks require a training set of paired images, which is expensive to obtain and cannot be perfectly simulated. Unsupervised learning utilizes unpaired data and is highly desirable for LDCT denoising. As an example, an artifact disentanglement network (ADN) relies on unparied images and obviates the need for supervision but the results of artifact reduction are not as good as those through supervised learning.An important observation is that there is often hidden similarity among unpaired data that can be utilized. This paper introduces a new learning mode, called quasi-supervised learning, to empower the ADN for LDCT image denoising.For every LDCT image, the best matched image is first found from an unpaired normal-dose CT (NDCT) dataset. Then, the matched pairs and the corresponding matching degree as prior information are used to construct and train our ADN-type network for LDCT denoising.The proposed method is different from (but compatible with) supervised and semi-supervised learning modes and can be easily implemented by modifying existing networks. The experimental results show that the method is competitive with state-of-the-art methods in terms of noise suppression and contextual fidelity. The code and working dataset are publicly available at https://github.com/ruanyuhui/ADN-QSDL.git.

cs.LG↗

arXiv2022

Attentional Ptycho-Tomography (APT) for three-dimensional nanoscale X-ray imaging with minimal data acquisition and computation time

Noninvasive X-ray imaging of nanoscale three-dimensional objects, e.g. integrated circuits (ICs), generally requires two types of scanning: ptychographic, which is translational and returns estimates of complex electromagnetic field through ICs; and tomographic scanning, which collects complex field projections from multiple angles. Here, we present Attentional Ptycho-Tomography (APT), an approach trained to provide accurate reconstructions of ICs despite incomplete measurements, using a dramatically reduced amount of angular scanning. Training process includes regularizing priors based on typical IC patterns and the physics of X-ray propagation. We demonstrate that APT with 12-time reduced angles achieves fidelity comparable to the gold standard with the original set of angles. With the same set of reduced angles, APT also outperforms baseline reconstruction methods. In our experiments, APT achieves 108-time aggregate reduction in data acquisition and computation without compromising quality. We expect our physics-assisted machine learning framework could also be applied to other branches of nanoscale imaging.

eess.IV↗

arXiv2022

Deep learning at the edge enables real-time streaming ptychographic imaging

Coherent microscopy techniques provide an unparalleled multi-scale view of materials across scientific and technological fields, from structural materials to quantum devices, from integrated circuits to biological cells. Driven by the construction of brighter sources and high-rate detectors, coherent X-ray microscopy methods like ptychography are poised to revolutionize nanoscale materials characterization. However, associated significant increases in data and compute needs mean that conventional approaches no longer suffice for recovering sample images in real-time from high-speed coherent imaging experiments. Here, we demonstrate a workflow that leverages artificial intelligence at the edge and high-performance computing to enable real-time inversion on X-ray ptychography data streamed directly from a detector at up to 2 kHz. The proposed AI-enabled workflow eliminates the sampling constraints imposed by traditional ptychography, allowing low dose imaging using orders of magnitude less data than required by traditional methods.

cs.LG↗

arXiv2022

Quasi-supervised Learning for Super-resolution PET

Low resolution of positron emission tomography (PET) limits its diagnostic performance. Deep learning has been successfully applied to achieve super-resolution PET. However, commonly used supervised learning methods in this context require many pairs of low- and high-resolution (LR and HR) PET images. Although unsupervised learning utilizes unpaired images, the results are not as good as that obtained with supervised deep learning. In this paper, we propose a quasi-supervised learning method, which is a new type of weakly-supervised learning methods, to recover HR PET images from LR counterparts by leveraging similarity between unpaired LR and HR image patches. Specifically, LR image patches are taken from a patient as inputs, while the most similar HR patches from other patients are found as labels. The similarity between the matched HR and LR patches serves as a prior for network construction. Our proposed method can be implemented by designing a new network or modifying an existing network. As an example in this study, we have modified the cycle-consistent generative adversarial network (CycleGAN) for super-resolution PET. Our numerical and experimental results qualitatively and quantitatively show the merits of our method relative to the state-ofthe-art methods. The code is publicly available at https://github.com/PigYang-ops/CycleGAN-QSDL.

eess.IV↗

arXiv2022

An application of Pixel Interval Down-sampling (PID) for dense tiny microorganism counting on environmental microorganism images

This paper proposes a novel pixel interval down-sampling network (PID-Net) for dense tiny object (yeast cells) counting tasks with higher accuracy. The PID-Net is an end-to-end convolutional neural network (CNN) model with an encoder--decoder architecture. The pixel interval down-sampling operations are concatenated with max-pooling operations to combine the sparse and dense features. This addresses the limitation of contour conglutination of dense objects while counting. The evaluation was conducted using classical segmentation metrics (the Dice, Jaccard and Hausdorff distance) as well as counting metrics. The experimental results show that the proposed PID-Net had the best performance and potential for dense tiny object counting tasks, which achieved 96.97\% counting accuracy on the dataset with 2448 yeast cell images. By comparing with the state-of-the-art approaches, such as Attention U-Net, Swin U-Net and Trans U-Net, the proposed PID-Net can segment dense tiny objects with clearer boundaries and fewer incorrect debris, which shows the great potential of PID-Net in the task of accurate counting.

cs.CV↗

arXiv2022

Adaptive Weighted Nonnegative Matrix Factorization for Robust Feature Representation

Nonnegative matrix factorization (NMF) has been widely used to dimensionality reduction in machine learning. However, the traditional NMF does not properly handle outliers, so that it is sensitive to noise. In order to improve the robustness of NMF, this paper proposes an adaptive weighted NMF, which introduces weights to emphasize the different importance of each data point, thus the algorithmic sensitivity to noisy data is decreased. It is very different from the existing robust NMFs that use a slow growth similarity measure. Specifically, two strategies are proposed to achieve this: fuzzier weighted technique and entropy weighted regularized technique, and both of them lead to an iterative solution with a simple form. Experimental results showed that new methods have more robust feature representation on several real datasets with noise than exsiting methods.

cs.LG↗

arXiv2022

CVM-Cervix: A Hybrid Cervical Pap-Smear Image Classification Framework Using CNN, Visual Transformer and Multilayer Perceptron

Cervical cancer is the seventh most common cancer among all the cancers worldwide and the fourth most common cancer among women. Cervical cytopathology image classification is an important method to diagnose cervical cancer. Manual screening of cytopathology images is time-consuming and error-prone. The emergence of the automatic computer-aided diagnosis system solves this problem. This paper proposes a framework called CVM-Cervix based on deep learning to perform cervical cell classification tasks. It can analyze pap slides quickly and accurately. CVM-Cervix first proposes a Convolutional Neural Network module and a Visual Transformer module for local and global feature extraction respectively, then a Multilayer Perceptron module is designed to fuse the local and global features for the final classification. Experimental results show the effectiveness and potential of the proposed CVM-Cervix in the field of cervical Pap smear image classification. In addition, according to the practical needs of clinical work, we perform a lightweight post-processing to compress the model.

cs.CV↗

arXiv2022

Brachial Plexus Nerve Trunk Segmentation Using Deep Learning: A Comparative Study with Doctors' Manual Segmentation

Ultrasound-guided nerve block anesthesia (UGNB) is a high-tech visual nerve block anesthesia method that can observe the target nerve and its surrounding structures, the puncture needle's advancement, and local anesthetics spread in real-time. The key in UGNB is nerve identification. With the help of deep learning methods, the automatic identification or segmentation of nerves can be realized, assisting doctors in completing nerve block anesthesia accurately and efficiently. Here, we establish a public dataset containing 320 ultrasound images of brachial plexus (BP). Three experienced doctors jointly produce the BP segmentation ground truth and label brachial plexus trunks. We design a brachial plexus segmentation system (BPSegSys) based on deep learning. BPSegSys achieves experienced-doctor-level nerve identification performance in various experiments. We evaluate BPSegSys' performance in terms of intersection-over-union (IoU), a commonly used performance measure for segmentation experiments. Considering three dataset groups in our established public dataset, the IoU of BPSegSys are 0.5238, 0.4715, and 0.5029, respectively, which exceed the IoU 0.5205, 0.4704, and 0.4979 of experienced doctors. In addition, we show that BPSegSys can help doctors identify brachial plexus trunks more accurately, with IoU improvement up to 27%, which has significant clinical application value.

eess.IV↗

arXiv2022

A Comprehensive Survey with Quantitative Comparison of Image Analysis Methods for Microorganism Biovolume Measurements

With the acceleration of urbanization and living standards, microorganisms play increasingly important roles in industrial production, bio-technique, and food safety testing. Microorganism biovolume measurements are one of the essential parts of microbial analysis. However, traditional manual measurement methods are time-consuming and challenging to measure the characteristics precisely. With the development of digital image processing techniques, the characteristics of the microbial population can be detected and quantified. The changing trend can be adjusted in time and provided a basis for the improvement. The applications of the microorganism biovolume measurement method have developed since the 1980s. More than 62 articles are reviewed in this study, and the articles are grouped by digital image segmentation methods with periods. This study has high research significance and application value, which can be referred to microbial researchers to have a comprehensive understanding of microorganism biovolume measurements using digital image analysis methods and potential applications.

cs.CV↗

arXiv2022

TOD-CNN: An Effective Convolutional Neural Network for Tiny Object Detection in Sperm Videos

The detection of tiny objects in microscopic videos is a problematic point, especially in large-scale experiments. For tiny objects (such as sperms) in microscopic videos, current detection methods face challenges in fuzzy, irregular, and precise positioning of objects. In contrast, we present a convolutional neural network for tiny object detection (TOD-CNN) with an underlying data set of high-quality sperm microscopic videos (111 videos, $>$ 278,000 annotated objects), and a graphical user interface (GUI) is designed to employ and test the proposed model effectively. TOD-CNN is highly accurate, achieving $85.60\%$ AP$_{50}$ in the task of real-time sperm detection in microscopic videos. To demonstrate the importance of sperm detection technology in sperm quality analysis, we carry out relevant sperm quality evaluation metrics and compare them with the diagnosis results from medical doctors.

cs.CV↗

arXiv2022

Subspace Nonnegative Matrix Factorization for Feature Representation

Traditional nonnegative matrix factorization (NMF) learns a new feature representation on the whole data space, which means treating all features equally. However, a subspace is often sufficient for accurate representation in practical applications, and redundant features can be invalid or even harmful. For example, if a camera has some sensors destroyed, then the corresponding pixels in the photos from this camera are not helpful to identify the content, which means only the subspace consisting of remaining pixels is worthy of attention. This paper proposes a new NMF method by introducing adaptive weights to identify key features in the original space so that only a subspace involves generating the new representation. Two strategies are proposed to achieve this: the fuzzier weighted technique and entropy regularized weighted technique, both of which result in an iterative solution with a simple form. Experimental results on several real-world datasets demonstrated that the proposed methods can generate a more accurate feature representation than existing methods. The code developed in this study is available at https://github.com/WNMF1/FWNMF-ERWNMF.

cs.CV↗