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Yi Lin

Publications and source records attributed to Yi Lin.

At least 91 records · Page 5Linked to original sources
arXiv2024

Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions

Breast cancer has reached the highest incidence rate worldwide among all malignancies since 2020. Breast imaging plays a significant role in early diagnosis and intervention to improve the outcome of breast cancer patients. In the past decade, deep learning has shown remarkable progress in breast cancer imaging analysis, holding great promise in interpreting the rich information and complex context of breast imaging modalities. Considering the rapid improvement in deep learning technology and the increasing severity of breast cancer, it is critical to summarize past progress and identify future challenges to be addressed. This paper provides an extensive review of deep learning-based breast cancer imaging research, covering studies on mammogram, ultrasound, magnetic resonance imaging, and digital pathology images over the past decade. The major deep learning methods and applications on imaging-based screening, diagnosis, treatment response prediction, and prognosis are elaborated and discussed. Drawn from the findings of this survey, we present a comprehensive discussion of the challenges and potential avenues for future research in deep learning-based breast cancer imaging.

eess.IV↗
arXiv2024

Adaptive Tracking and Perching for Quadrotor in Dynamic Scenarios

Perching on the moving platforms is a promising solution to enhance the endurance and operational range of quadrotors, which could benefit the efficiency of a variety of air-ground cooperative tasks. To ensure robust perching, tracking with a steady relative state and reliable perception is a prerequisite. This paper presents an adaptive dynamic tracking and perching scheme for autonomous quadrotors to achieve tight integration with moving platforms. For reliable perception of dynamic targets, we introduce elastic visibility-aware planning to actively avoid occlusion and target loss. Additionally, we propose a flexible terminal adjustment method that adapts the changes in flight duration and the coupled terminal states, ensuring full-state synchronization with the time-varying perching surface at various angles. A relaxation strategy is developed by optimizing the tangential relative speed to address the dynamics and safety violations brought by hard boundary conditions. Moreover, we take SE(3) motion planning into account to ensure no collision between the quadrotor and the platform until the contact moment. Furthermore, we propose an efficient spatiotemporal trajectory optimization framework considering full state dynamics for tracking and perching. The proposed method is extensively tested through benchmark comparisons and ablation studies. To facilitate the application of academic research to industry and to validate the efficiency of our scheme under strictly limited computational resources, we deploy our system on a commercial drone (DJI-MAVIC3) with a full-size sport-utility vehicle (SUV). We conduct extensive real-world experiments, where the drone successfully tracks and perches at 30~km/h (8.3~m/s) on the top of the SUV, and at 3.5~m/s with 60° inclined into the trunk of the SUV.

cs.RO↗
arXiv2024

BoNuS: Boundary Mining for Nuclei Segmentation with Partial Point Labels

Nuclei segmentation is a fundamental prerequisite in the digital pathology workflow. The development of automated methods for nuclei segmentation enables quantitative analysis of the wide existence and large variances in nuclei morphometry in histopathology images. However, manual annotation of tens of thousands of nuclei is tedious and time-consuming, which requires significant amount of human effort and domain-specific expertise. To alleviate this problem, in this paper, we propose a weakly-supervised nuclei segmentation method that only requires partial point labels of nuclei. Specifically, we propose a novel boundary mining framework for nuclei segmentation, named BoNuS, which simultaneously learns nuclei interior and boundary information from the point labels. To achieve this goal, we propose a novel boundary mining loss, which guides the model to learn the boundary information by exploring the pairwise pixel affinity in a multiple-instance learning manner. Then, we consider a more challenging problem, i.e., partial point label, where we propose a nuclei detection module with curriculum learning to detect the missing nuclei with prior morphological knowledge. The proposed method is validated on three public datasets, MoNuSeg, CPM, and CoNIC datasets. Experimental results demonstrate the superior performance of our method to the state-of-the-art weakly-supervised nuclei segmentation methods. Code: https://github.com/hust-linyi/bonus.

cs.CV↗
arXiv2024

PromptMRG: Diagnosis-Driven Prompts for Medical Report Generation

Automatic medical report generation (MRG) is of great research value as it has the potential to relieve radiologists from the heavy burden of report writing. Despite recent advancements, accurate MRG remains challenging due to the need for precise clinical understanding and disease identification. Moreover, the imbalanced distribution of diseases makes the challenge even more pronounced, as rare diseases are underrepresented in training data, making their diagnostic performance unreliable. To address these challenges, we propose diagnosis-driven prompts for medical report generation (PromptMRG), a novel framework that aims to improve the diagnostic accuracy of MRG with the guidance of diagnosis-aware prompts. Specifically, PromptMRG is based on encoder-decoder architecture with an extra disease classification branch. When generating reports, the diagnostic results from the classification branch are converted into token prompts to explicitly guide the generation process. To further improve the diagnostic accuracy, we design cross-modal feature enhancement, which retrieves similar reports from the database to assist the diagnosis of a query image by leveraging the knowledge from a pre-trained CLIP. Moreover, the disease imbalanced issue is addressed by applying an adaptive logit-adjusted loss to the classification branch based on the individual learning status of each disease, which overcomes the barrier of text decoder's inability to manipulate disease distributions. Experiments on two MRG benchmarks show the effectiveness of the proposed method, where it obtains state-of-the-art clinical efficacy performance on both datasets. The code is available at https://github.com/jhb86253817/PromptMRG.

cs.CV↗
arXiv2023

Adversarial Medical Image with Hierarchical Feature Hiding

Deep learning based methods for medical images can be easily compromised by adversarial examples (AEs), posing a great security flaw in clinical decision-making. It has been discovered that conventional adversarial attacks like PGD which optimize the classification logits, are easy to distinguish in the feature space, resulting in accurate reactive defenses. To better understand this phenomenon and reassess the reliability of the reactive defenses for medical AEs, we thoroughly investigate the characteristic of conventional medical AEs. Specifically, we first theoretically prove that conventional adversarial attacks change the outputs by continuously optimizing vulnerable features in a fixed direction, thereby leading to outlier representations in the feature space. Then, a stress test is conducted to reveal the vulnerability of medical images, by comparing with natural images. Interestingly, this vulnerability is a double-edged sword, which can be exploited to hide AEs. We then propose a simple-yet-effective hierarchical feature constraint (HFC), a novel add-on to conventional white-box attacks, which assists to hide the adversarial feature in the target feature distribution. The proposed method is evaluated on three medical datasets, both 2D and 3D, with different modalities. The experimental results demonstrate the superiority of HFC, \emph{i.e.,} it bypasses an array of state-of-the-art adversarial medical AE detectors more efficiently than competing adaptive attacks, which reveals the deficiencies of medical reactive defense and allows to develop more robust defenses in future.

eess.IV↗
arXiv2023

Penalties and Rewards for Fair Learning in Paired Kidney Exchange Programs

A kidney exchange program, also called a kidney paired donation program, can be viewed as a repeated, dynamic trading and allocation mechanism. This suggests that a dynamic algorithm for transplant exchange selection may have superior performance in comparison to the repeated use of a static algorithm. We confirm this hypothesis using a full scale simulation of the Canadian Kidney Paired Donation Program: learning algorithms, that attempt to learn optimal patient-donor weights in advance via dynamic simulations, do lead to improved outcomes. Specifically, our learning algorithms, designed with the objective of fairness (that is, equity in terms of transplant accessibility across cPRA groups), also lead to an increased number of transplants and shorter average waiting times. Indeed, our highest performing learning algorithm improves egalitarian fairness by 10% whilst also increasing the number of transplants by 6% and decreasing waiting times by 24%. However, our main result is much more surprising. We find that the most critical factor in determining the performance of a kidney exchange program is not the judicious assignment of positive weights (rewards) to patient-donor pairs. Rather, the key factor in increasing the number of transplants, decreasing waiting times and improving group fairness is the judicious assignment of a negative weight (penalty) to the small number of non-directed donors in the kidney exchange program.

math.OC↗
arXiv2023

Few Shot Medical Image Segmentation with Cross Attention Transformer

Medical image segmentation has made significant progress in recent years. Deep learning-based methods are recognized as data-hungry techniques, requiring large amounts of data with manual annotations. However, manual annotation is expensive in the field of medical image analysis, which requires domain-specific expertise. To address this challenge, few-shot learning has the potential to learn new classes from only a few examples. In this work, we propose a novel framework for few-shot medical image segmentation, termed CAT-Net, based on cross masked attention Transformer. Our proposed network mines the correlations between the support image and query image, limiting them to focus only on useful foreground information and boosting the representation capacity of both the support prototype and query features. We further design an iterative refinement framework that refines the query image segmentation iteratively and promotes the support feature in turn. We validated the proposed method on three public datasets: Abd-CT, Abd-MRI, and Card-MRI. Experimental results demonstrate the superior performance of our method compared to state-of-the-art methods and the effectiveness of each component. Code: https://github.com/hust-linyi/CAT-Net.

cs.CV↗
arXiv2023

Bi-Modality Medical Image Synthesis Using Semi-Supervised Sequential Generative Adversarial Networks

In this paper, we propose a bi-modality medical image synthesis approach based on sequential generative adversarial network (GAN) and semi-supervised learning. Our approach consists of two generative modules that synthesize images of the two modalities in a sequential order. A method for measuring the synthesis complexity is proposed to automatically determine the synthesis order in our sequential GAN. Images of the modality with a lower complexity are synthesized first, and the counterparts with a higher complexity are generated later. Our sequential GAN is trained end-to-end in a semi-supervised manner. In supervised training, the joint distribution of bi-modality images are learned from real paired images of the two modalities by explicitly minimizing the reconstruction losses between the real and synthetic images. To avoid overfitting limited training images, in unsupervised training, the marginal distribution of each modality is learned based on unpaired images by minimizing the Wasserstein distance between the distributions of real and fake images. We comprehensively evaluate the proposed model using two synthesis tasks based on three types of evaluate metrics and user studies. Visual and quantitative results demonstrate the superiority of our method to the state-of-the-art methods, and reasonable visual quality and clinical significance. Code is made publicly available at https://github.com/hustlinyi/Multimodal-Medical-Image-Synthesis.

eess.IV↗
arXiv2023

Nuclei Segmentation with Point Annotations from Pathology Images via Self-Supervised Learning and Co-Training

Nuclei segmentation is a crucial task for whole slide image analysis in digital pathology. Generally, the segmentation performance of fully-supervised learning heavily depends on the amount and quality of the annotated data. However, it is time-consuming and expensive for professional pathologists to provide accurate pixel-level ground truth, while it is much easier to get coarse labels such as point annotations. In this paper, we propose a weakly-supervised learning method for nuclei segmentation that only requires point annotations for training. First, coarse pixel-level labels are derived from the point annotations based on the Voronoi diagram and the k-means clustering method to avoid overfitting. Second, a co-training strategy with an exponential moving average method is designed to refine the incomplete supervision of the coarse labels. Third, a self-supervised visual representation learning method is tailored for nuclei segmentation of pathology images that transforms the hematoxylin component images into the H&E stained images to gain better understanding of the relationship between the nuclei and cytoplasm. We comprehensively evaluate the proposed method using two public datasets. Both visual and quantitative results demonstrate the superiority of our method to the state-of-the-art methods, and its competitive performance compared to the fully-supervised methods. Code: https://github.com/hust-linyi/SC-Net

eess.IV↗
arXiv2023

Understanding the Tricks of Deep Learning in Medical Image Segmentation: Challenges and Future Directions

Over the past few years, the rapid development of deep learning technologies for computer vision has significantly improved the performance of medical image segmentation (MedISeg). However, the diverse implementation strategies of various models have led to an extremely complex MedISeg system, resulting in a potential problem of unfair result comparisons. In this paper, we collect a series of MedISeg tricks for different model implementation phases (i.e., pre-training model, data pre-processing, data augmentation, model implementation, model inference, and result post-processing), and experimentally explore the effectiveness of these tricks on consistent baselines. With the extensive experimental results on both the representative 2D and 3D medical image datasets, we explicitly clarify the effect of these tricks. Moreover, based on the surveyed tricks, we also open-sourced a strong MedISeg repository, where each component has the advantage of plug-and-play. We believe that this milestone work not only completes a comprehensive and complementary survey of the state-of-the-art MedISeg approaches, but also offers a practical guide for addressing the future medical image processing challenges including but not limited to small dataset, class imbalance learning, multi-modality learning, and domain adaptation. The code and training weights have been released at: https://github.com/hust-linyi/seg_trick.

cs.CV↗
arXiv2023

Rethinking Boundary Detection in Deep Learning Models for Medical Image Segmentation

Medical image segmentation is a fundamental task in the community of medical image analysis. In this paper, a novel network architecture, referred to as Convolution, Transformer, and Operator (CTO), is proposed. CTO employs a combination of Convolutional Neural Networks (CNNs), Vision Transformer (ViT), and an explicit boundary detection operator to achieve high recognition accuracy while maintaining an optimal balance between accuracy and efficiency. The proposed CTO follows the standard encoder-decoder segmentation paradigm, where the encoder network incorporates a popular CNN backbone for capturing local semantic information, and a lightweight ViT assistant for integrating long-range dependencies. To enhance the learning capacity on boundary, a boundary-guided decoder network is proposed that uses a boundary mask obtained from a dedicated boundary detection operator as explicit supervision to guide the decoding learning process. The performance of the proposed method is evaluated on six challenging medical image segmentation datasets, demonstrating that CTO achieves state-of-the-art accuracy with a competitive model complexity.

cs.CV↗
arXiv2023

Enhancing multilingual speech recognition in air traffic control by sentence-level language identification

Automatic speech recognition (ASR) technique is becoming increasingly popular to improve the efficiency and safety of air traffic control (ATC) operations. However, the conversation between ATC controllers and pilots using multilingual speech brings a great challenge to building high-accuracy ASR systems. In this work, we present a two-stage multilingual ASR framework. The first stage is to train a language identifier (LID), that based on a recurrent neural network (RNN) to obtain sentence language identification in the form of one-hot encoding. The second stage aims to train an RNN-based end-to-end multilingual recognition model that utilizes sentence language features generated by LID to enhance input features. In this work, We introduce Featurewise Linear Modulation (FiLM) to improve the performance of multilingual ASR by utilizing sentence language identification. Furthermore, we introduce a new sentence language identification learning module called SLIL, which consists of a FiLM layer and a Squeeze-and-Excitation Networks layer. Extensive experiments on the ATCSpeech dataset show that our proposed method outperforms the baseline model. Compared to the vanilla FiLMed backbone model, the proposed multilingual ASR model obtains about 7.50% character error rate relative performance improvement.

cs.SD↗
arXiv2023

Disorder-invariant Implicit Neural Representation

Implicit neural representation (INR) characterizes the attributes of a signal as a function of corresponding coordinates which emerges as a sharp weapon for solving inverse problems. However, the expressive power of INR is limited by the spectral bias in the network training. In this paper, we find that such a frequency-related problem could be greatly solved by re-arranging the coordinates of the input signal, for which we propose the disorder-invariant implicit neural representation (DINER) by augmenting a hash-table to a traditional INR backbone. Given discrete signals sharing the same histogram of attributes and different arrangement orders, the hash-table could project the coordinates into the same distribution for which the mapped signal can be better modeled using the subsequent INR network, leading to significantly alleviated spectral bias. Furthermore, the expressive power of the DINER is determined by the width of the hash-table. Different width corresponds to different geometrical elements in the attribute space, \textit{e.g.}, 1D curve, 2D curved-plane and 3D curved-volume when the width is set as $1$, $2$ and $3$, respectively. More covered areas of the geometrical elements result in stronger expressive power. Experiments not only reveal the generalization of the DINER for different INR backbones (MLP vs. SIREN) and various tasks (image/video representation, phase retrieval, refractive index recovery, and neural radiance field optimization) but also show the superiority over the state-of-the-art algorithms both in quality and speed. \textit{Project page:} \url{https://ezio77.github.io/DINER-website/}

cs.CV↗
arXiv2023

Exploring Visual Prompts for Whole Slide Image Classification with Multiple Instance Learning

Multiple instance learning (MIL) has emerged as a popular method for classifying histopathology whole slide images (WSIs). However, existing approaches typically rely on pre-trained models from large natural image datasets, such as ImageNet, to generate instance features, which can be sub-optimal due to the significant differences between natural images and histopathology images that lead to a domain shift. In this paper, we present a novel, simple yet effective method for learning domain-specific knowledge transformation from pre-trained models to histopathology images. Our approach entails using a prompt component to assist the pre-trained model in discerning differences between the pre-trained dataset and the target histopathology dataset, resulting in improved performance of MIL models. We validate our method on two publicly available datasets, Camelyon16 and TCGA-NSCLC. Extensive experimental results demonstrate the significant performance improvement of our method for different MIL models and backbones. Upon publication of this paper, we will release the source code for our method.

cs.CV↗
arXiv2023

Learning a Room with the Occ-SDF Hybrid: Signed Distance Function Mingled with Occupancy Aids Scene Representation

Implicit neural rendering, which uses signed distance function (SDF) representation with geometric priors (such as depth or surface normal), has led to impressive progress in the surface reconstruction of large-scale scenes. However, applying this method to reconstruct a room-level scene from images may miss structures in low-intensity areas or small and thin objects. We conducted experiments on three datasets to identify limitations of the original color rendering loss and priors-embedded SDF scene representation. We found that the color rendering loss results in optimization bias against low-intensity areas, causing gradient vanishing and leaving these areas unoptimized. To address this issue, we propose a feature-based color rendering loss that utilizes non-zero feature values to bring back optimization signals. Additionally, the SDF representation can be influenced by objects along a ray path, disrupting the monotonic change of SDF values when a single object is present. To counteract this, we explore using the occupancy representation, which encodes each point separately and is unaffected by objects along a querying ray. Our experimental results demonstrate that the joint forces of the feature-based rendering loss and Occ-SDF hybrid representation scheme can provide high-quality reconstruction results, especially in challenging room-level scenarios. The code would be released.

cs.CV↗
arXiv2023

Parallel Computing Based Solution for Reliability-Constrained Distribution Network Planning

The main goal of distribution network (DN) expansion planning is essentially to achieve minimal investment constrained with specified reliability requirements. The reliability-constrained distribution network planning (RcDNP) problem can be cast an instance of mixed-integer linear programming (MILP) which involves ultra-heavy computation burden especially for large scale DNs. In this paper, we propose a parallel computing-based acceleration algorithm for solve RcDNP problem. The RcDNP is decomposed into a backbone grid and several lateral grid problems with coordination. Then a parallelizable augmented Lagrangian algorithm with acceleration strategy is developed to solve the coordination planning problems. In this method, the lateral grid problems are solved in parallel through coordinating with the backbone grid planning problem. To address the presence of nonconvexity, Gauss-Seidel iteration is adopted on the convex hull of the feasible region constructed by the decomposition method. Under mild conditions, the optimality and convergence of this algorithm is proven. The numerical tests show the proposed method can significantly reduce the computation time and make the RcDNP applicable for real-world problems.

eess.SY↗
arXiv2023

Efficient Implicit Neural Reconstruction Using LiDAR

Modeling scene geometry using implicit neural representation has revealed its advantages in accuracy, flexibility, and low memory usage. Previous approaches have demonstrated impressive results using color or depth images but still have difficulty handling poor light conditions and large-scale scenes. Methods taking global point cloud as input require accurate registration and ground truth coordinate labels, which limits their application scenarios. In this paper, we propose a new method that uses sparse LiDAR point clouds and rough odometry to reconstruct fine-grained implicit occupancy field efficiently within a few minutes. We introduce a new loss function that supervises directly in 3D space without 2D rendering, avoiding information loss. We also manage to refine poses of input frames in an end-to-end manner, creating consistent geometry without global point cloud registration. As far as we know, our method is the first to reconstruct implicit scene representation from LiDAR-only input. Experiments on synthetic and real-world datasets, including indoor and outdoor scenes, prove that our method is effective, efficient, and accurate, obtaining comparable results with existing methods using dense input.

cs.RO↗