arXiv subjects

Dagan Feng

Publications and source records attributed to Dagan Feng.

At least 19 recordsLinked to original sources

arXiv2025

MedCFVQA: A Causal Approach to Mitigate Modality Preference Bias in Medical Visual Question Answering

Medical Visual Question Answering (MedVQA) is crucial for enhancing the efficiency of clinical diagnosis by providing accurate and timely responses to clinicians' inquiries regarding medical images. Existing MedVQA models suffered from modality preference bias, where predictions are heavily dominated by one modality while overlooking the other (in MedVQA, usually questions dominate the answer but images are overlooked), thereby failing to learn multimodal knowledge. To overcome the modality preference bias, we proposed a Medical CounterFactual VQA (MedCFVQA) model, which trains with bias and leverages causal graphs to eliminate the modality preference bias during inference. Existing MedVQA datasets exhibit substantial prior dependencies between questions and answers, which results in acceptable performance even if the model significantly suffers from the modality preference bias. To address this issue, we reconstructed new datasets by leveraging existing MedVQA datasets and Changed their P3rior dependencies (CP) between questions and their answers in the training and test set. Extensive experiments demonstrate that MedCFVQA significantly outperforms its non-causal counterpart on both SLAKE, RadVQA and SLAKE-CP, RadVQA-CP datasets.

cs.CV↗

arXiv2024

3DPX: Single Panoramic X-ray Analysis Guided by 3D Oral Structure Reconstruction

Panoramic X-ray (PX) is a prevalent modality in dentistry practice owing to its wide availability and low cost. However, as a 2D projection of a 3D structure, PX suffers from anatomical information loss and PX diagnosis is limited compared to that with 3D imaging modalities. 2D-to-3D reconstruction methods have been explored for the ability to synthesize the absent 3D anatomical information from 2D PX for use in PX image analysis. However, there are challenges in leveraging such 3D synthesized reconstructions. First, inferring 3D depth from 2D images remains a challenging task with limited accuracy. The second challenge is the joint analysis of 2D PX with its 3D synthesized counterpart, with the aim to maximize the 2D-3D synergy while minimizing the errors arising from the synthesized image. In this study, we propose a new method termed 3DPX - PX image analysis guided by 2D-to-3D reconstruction, to overcome these challenges. 3DPX consists of (i) a novel progressive reconstruction network to improve 2D-to-3D reconstruction and, (ii) a contrastive-guided bidirectional multimodality alignment module for 3D-guided 2D PX classification and segmentation tasks. The reconstruction network progressively reconstructs 3D images with knowledge imposed on the intermediate reconstructions at multiple pyramid levels and incorporates Multilayer Perceptrons to improve semantic understanding. The downstream networks leverage the reconstructed images as 3D anatomical guidance to the PX analysis through feature alignment, which increases the 2D-3D synergy with bidirectional feature projection and decease the impact of potential errors with contrastive guidance. Extensive experiments on two oral datasets involving 464 studies demonstrate that 3DPX outperforms the state-of-the-art methods in various tasks including 2D-to-3D reconstruction, PX classification and lesion segmentation.

eess.IV↗

arXiv2024

SGSeg: Enabling Text-free Inference in Language-guided Segmentation of Chest X-rays via Self-guidance

Segmentation of infected areas in chest X-rays is pivotal for facilitating the accurate delineation of pulmonary structures and pathological anomalies. Recently, multi-modal language-guided image segmentation methods have emerged as a promising solution for chest X-rays where the clinical text reports, depicting the assessment of the images, are used as guidance. Nevertheless, existing language-guided methods require clinical reports alongside the images, and hence, they are not applicable for use in image segmentation in a decision support context, but rather limited to retrospective image analysis after clinical reporting has been completed. In this study, we propose a self-guided segmentation framework (SGSeg) that leverages language guidance for training (multi-modal) while enabling text-free inference (uni-modal), which is the first that enables text-free inference in language-guided segmentation. We exploit the critical location information of both pulmonary and pathological structures depicted in the text reports and introduce a novel localization-enhanced report generation (LERG) module to generate clinical reports for self-guidance. Our LERG integrates an object detector and a location-based attention aggregator, weakly-supervised by a location-aware pseudo-label extraction module. Extensive experiments on a well-benchmarked QaTa-COV19 dataset demonstrate that our SGSeg achieved superior performance than existing uni-modal segmentation methods and closely matched the state-of-the-art performance of multi-modal language-guided segmentation methods.

cs.CV↗

arXiv2024

3DPX: Progressive 2D-to-3D Oral Image Reconstruction with Hybrid MLP-CNN Networks

Panoramic X-ray (PX) is a prevalent modality in dental practice for its wide availability and low cost. However, as a 2D projection image, PX does not contain 3D anatomical information, and therefore has limited use in dental applications that can benefit from 3D information, e.g., tooth angular misa-lignment detection and classification. Reconstructing 3D structures directly from 2D PX has recently been explored to address limitations with existing methods primarily reliant on Convolutional Neural Networks (CNNs) for direct 2D-to-3D mapping. These methods, however, are unable to correctly infer depth-axis spatial information. In addition, they are limited by the in-trinsic locality of convolution operations, as the convolution kernels only capture the information of immediate neighborhood pixels. In this study, we propose a progressive hybrid Multilayer Perceptron (MLP)-CNN pyra-mid network (3DPX) for 2D-to-3D oral PX reconstruction. We introduce a progressive reconstruction strategy, where 3D images are progressively re-constructed in the 3DPX with guidance imposed on the intermediate recon-struction result at each pyramid level. Further, motivated by the recent ad-vancement of MLPs that show promise in capturing fine-grained long-range dependency, our 3DPX integrates MLPs and CNNs to improve the semantic understanding during reconstruction. Extensive experiments on two large datasets involving 464 studies demonstrate that our 3DPX outperforms state-of-the-art 2D-to-3D oral reconstruction methods, including standalone MLP and transformers, in reconstruction quality, and also im-proves the performance of downstream angular misalignment classification tasks.

eess.IV↗

arXiv2024

Correlation-aware Coarse-to-fine MLPs for Deformable Medical Image Registration

Deformable image registration is a fundamental step for medical image analysis. Recently, transformers have been used for registration and outperformed Convolutional Neural Networks (CNNs). Transformers can capture long-range dependence among image features, which have been shown beneficial for registration. However, due to the high computation/memory loads of self-attention, transformers are typically used at downsampled feature resolutions and cannot capture fine-grained long-range dependence at the full image resolution. This limits deformable registration as it necessitates precise dense correspondence between each image pixel. Multi-layer Perceptrons (MLPs) without self-attention are efficient in computation/memory usage, enabling the feasibility of capturing fine-grained long-range dependence at full resolution. Nevertheless, MLPs have not been extensively explored for image registration and are lacking the consideration of inductive bias crucial for medical registration tasks. In this study, we propose the first correlation-aware MLP-based registration network (CorrMLP) for deformable medical image registration. Our CorrMLP introduces a correlation-aware multi-window MLP block in a novel coarse-to-fine registration architecture, which captures fine-grained multi-range dependence to perform correlation-aware coarse-to-fine registration. Extensive experiments with seven public medical datasets show that our CorrMLP outperforms state-of-the-art deformable registration methods.

eess.IV↗

arXiv2024

Dynamic Traceback Learning for Medical Report Generation

Automated medical report generation has demonstrated the potential to significantly reduce the workload associated with time-consuming medical reporting. Recent generative representation learning methods have shown promise in integrating vision and language modalities for medical report generation. However, when trained end-to-end and applied directly to medical image-to-text generation, they face two significant challenges: i) difficulty in accurately capturing subtle yet crucial pathological details, and ii) reliance on both visual and textual inputs during inference, leading to performance degradation in zero-shot inference when only images are available. To address these challenges, this study proposes a novel multimodal dynamic traceback learning framework (DTrace). Specifically, we introduce a traceback mechanism to supervise the semantic validity of generated content and a dynamic learning strategy to adapt to various proportions of image and text input, enabling text generation without strong reliance on the input from both modalities during inference. The learning of cross-modal knowledge is enhanced by supervising the model to recover masked semantic information from a complementary counterpart. Extensive experiments conducted on two benchmark datasets, IU-Xray and MIMIC-CXR, demonstrate that the proposed DTrace framework outperforms state-of-the-art methods for medical report generation.

cs.CV↗

arXiv2023

Full-resolution MLPs Empower Medical Dense Prediction

Dense prediction is a fundamental requirement for many medical vision tasks such as medical image restoration, registration, and segmentation. The most popular vision model, Convolutional Neural Networks (CNNs), has reached bottlenecks due to the intrinsic locality of convolution operations. Recently, transformers have been widely adopted for dense prediction for their capability to capture long-range visual dependence. However, due to the high computational complexity and large memory consumption of self-attention operations, transformers are usually used at downsampled feature resolutions. Such usage cannot effectively leverage the tissue-level textural information available only at the full image resolution. This textural information is crucial for medical dense prediction as it can differentiate the subtle human anatomy in medical images. In this study, we hypothesize that Multi-layer Perceptrons (MLPs) are superior alternatives to transformers in medical dense prediction where tissue-level details dominate the performance, as MLPs enable long-range dependence at the full image resolution. To validate our hypothesis, we develop a full-resolution hierarchical MLP framework that uses MLPs beginning from the full image resolution. We evaluate this framework with various MLP blocks on a wide range of medical dense prediction tasks including restoration, registration, and segmentation. Extensive experiments on six public well-benchmarked datasets show that, by simply using MLPs at full resolution, our framework outperforms its CNN and transformer counterparts and achieves state-of-the-art performance on various medical dense prediction tasks.

eess.IV↗

arXiv2023

AutoFuse: Automatic Fusion Networks for Deformable Medical Image Registration

Deformable image registration aims to find a dense non-linear spatial correspondence between a pair of images, which is a crucial step for many medical tasks such as tumor growth monitoring and population analysis. Recently, Deep Neural Networks (DNNs) have been widely recognized for their ability to perform fast end-to-end registration. However, DNN-based registration needs to explore the spatial information of each image and fuse this information to characterize spatial correspondence. This raises an essential question: what is the optimal fusion strategy to characterize spatial correspondence? Existing fusion strategies (e.g., early fusion, late fusion) were empirically designed to fuse information by manually defined prior knowledge, which inevitably constrains the registration performance within the limits of empirical designs. In this study, we depart from existing empirically-designed fusion strategies and develop a data-driven fusion strategy for deformable image registration. To achieve this, we propose an Automatic Fusion network (AutoFuse) that provides flexibility to fuse information at many potential locations within the network. A Fusion Gate (FG) module is also proposed to control how to fuse information at each potential network location based on training data. Our AutoFuse can automatically optimize its fusion strategy during training and can be generalizable to both unsupervised registration (without any labels) and semi-supervised registration (with weak labels provided for partial training data). Extensive experiments on two well-benchmarked medical registration tasks (inter- and intra-patient registration) with eight public datasets show that our AutoFuse outperforms state-of-the-art unsupervised and semi-supervised registration methods.

eess.IV↗

arXiv2023

Merging-Diverging Hybrid Transformer Networks for Survival Prediction in Head and Neck Cancer

Survival prediction is crucial for cancer patients as it provides early prognostic information for treatment planning. Recently, deep survival models based on deep learning and medical images have shown promising performance for survival prediction. However, existing deep survival models are not well developed in utilizing multi-modality images (e.g., PET-CT) and in extracting region-specific information (e.g., the prognostic information in Primary Tumor (PT) and Metastatic Lymph Node (MLN) regions). In view of this, we propose a merging-diverging learning framework for survival prediction from multi-modality images. This framework has a merging encoder to fuse multi-modality information and a diverging decoder to extract region-specific information. In the merging encoder, we propose a Hybrid Parallel Cross-Attention (HPCA) block to effectively fuse multi-modality features via parallel convolutional layers and cross-attention transformers. In the diverging decoder, we propose a Region-specific Attention Gate (RAG) block to screen out the features related to lesion regions. Our framework is demonstrated on survival prediction from PET-CT images in Head and Neck (H&N) cancer, by designing an X-shape merging-diverging hybrid transformer network (named XSurv). Our XSurv combines the complementary information in PET and CT images and extracts the region-specific prognostic information in PT and MLN regions. Extensive experiments on the public dataset of HEad and neCK TumOR segmentation and outcome prediction challenge (HECKTOR 2022) demonstrate that our XSurv outperforms state-of-the-art survival prediction methods.

eess.IV↗

arXiv2023

Non-iterative Coarse-to-fine Transformer Networks for Joint Affine and Deformable Image Registration

Image registration is a fundamental requirement for medical image analysis. Deep registration methods based on deep learning have been widely recognized for their capabilities to perform fast end-to-end registration. Many deep registration methods achieved state-of-the-art performance by performing coarse-to-fine registration, where multiple registration steps were iterated with cascaded networks. Recently, Non-Iterative Coarse-to-finE (NICE) registration methods have been proposed to perform coarse-to-fine registration in a single network and showed advantages in both registration accuracy and runtime. However, existing NICE registration methods mainly focus on deformable registration, while affine registration, a common prerequisite, is still reliant on time-consuming traditional optimization-based methods or extra affine registration networks. In addition, existing NICE registration methods are limited by the intrinsic locality of convolution operations. Transformers may address this limitation for their capabilities to capture long-range dependency, but the benefits of using transformers for NICE registration have not been explored. In this study, we propose a Non-Iterative Coarse-to-finE Transformer network (NICE-Trans) for image registration. Our NICE-Trans is the first deep registration method that (i) performs joint affine and deformable coarse-to-fine registration within a single network, and (ii) embeds transformers into a NICE registration framework to model long-range relevance between images. Extensive experiments with seven public datasets show that our NICE-Trans outperforms state-of-the-art registration methods on both registration accuracy and runtime.

cs.CV↗

arXiv2023

AdaMSS: Adaptive Multi-Modality Segmentation-to-Survival Learning for Survival Outcome Prediction from PET/CT Images

Survival prediction is a major concern for cancer management. Deep survival models based on deep learning have been widely adopted to perform end-to-end survival prediction from medical images. Recent deep survival models achieved promising performance by jointly performing tumor segmentation with survival prediction, where the models were guided to extract tumor-related information through Multi-Task Learning (MTL). However, these deep survival models have difficulties in exploring out-of-tumor prognostic information. In addition, existing deep survival models are unable to effectively leverage multi-modality images. Empirically-designed fusion strategies were commonly adopted to fuse multi-modality information via task-specific manually-designed networks, thus limiting the adaptability to different scenarios. In this study, we propose an Adaptive Multi-modality Segmentation-to-Survival model (AdaMSS) for survival prediction from PET/CT images. Instead of adopting MTL, we propose a novel Segmentation-to-Survival Learning (SSL) strategy, where our AdaMSS is trained for tumor segmentation and survival prediction sequentially in two stages. This strategy enables the AdaMSS to focus on tumor regions in the first stage and gradually expand its focus to include other prognosis-related regions in the second stage. We also propose a data-driven strategy to fuse multi-modality information, which realizes adaptive optimization of fusion strategies based on training data during training. With the SSL and data-driven fusion strategies, our AdaMSS is designed as an adaptive model that can self-adapt its focus regions and fusion strategy for different training stages. Extensive experiments with two large clinical datasets show that our AdaMSS outperforms state-of-the-art survival prediction methods.

eess.IV↗

arXiv2023

CG-3DSRGAN: A classification guided 3D generative adversarial network for image quality recovery from low-dose PET images

Positron emission tomography (PET) is the most sensitive molecular imaging modality routinely applied in our modern healthcare. High radioactivity caused by the injected tracer dose is a major concern in PET imaging and limits its clinical applications. However, reducing the dose leads to inadequate image quality for diagnostic practice. Motivated by the need to produce high quality images with minimum low-dose, Convolutional Neural Networks (CNNs) based methods have been developed for high quality PET synthesis from its low-dose counterparts. Previous CNNs-based studies usually directly map low-dose PET into features space without consideration of different dose reduction level. In this study, a novel approach named CG-3DSRGAN (Classification-Guided Generative Adversarial Network with Super Resolution Refinement) is presented. Specifically, a multi-tasking coarse generator, guided by a classification head, allows for a more comprehensive understanding of the noise-level features present in the low-dose data, resulting in improved image synthesis. Moreover, to recover spatial details of standard PET, an auxiliary super resolution network - Contextual-Net - is proposed as a second-stage training to narrow the gap between coarse prediction and standard PET. We compared our method to the state-of-the-art methods on whole-body PET with different dose reduction factors (DRFs). Experiments demonstrate our method can outperform others on all DRF.

eess.IV↗

arXiv2023

A Review of Predictive and Contrastive Self-supervised Learning for Medical Images

Over the last decade, supervised deep learning on manually annotated big data has been progressing significantly on computer vision tasks. But the application of deep learning in medical image analysis was limited by the scarcity of high-quality annotated medical imaging data. An emerging solution is self-supervised learning (SSL), among which contrastive SSL is the most successful approach to rivalling or outperforming supervised learning. This review investigates several state-of-the-art contrastive SSL algorithms originally on natural images as well as their adaptations for medical images, and concludes by discussing recent advances, current limitations, and future directions in applying contrastive SSL in the medical domain.

cs.CV↗

arXiv2022

Z-SSMNet: Zonal-aware Self-supervised Mesh Network for Prostate Cancer Detection and Diagnosis with Bi-parametric MRI

Bi-parametric magnetic resonance imaging (bpMRI) has become a pivotal modality in the detection and diagnosis of clinically significant prostate cancer (csPCa). Developing AI-based systems to identify csPCa using bpMRI can transform PCa management by improving efficiency and cost-effectiveness. However, current state-of-the-art methods using convolutional neural networks (CNNs) are limited in learning in-plane and three-dimensional spatial information from anisotropic images. Their performances also depend on the availability of large, diverse, and well-annotated bpMRI datasets. We propose a Zonal-aware Self-supervised Mesh Network (Z-SSMNet) that adaptively integrates multi-dimensional (2D/2.5D/3D) convolutions to learn dense intra-slice information and sparse inter-slice information of the anisotropic bpMRI in a balanced manner. A self-supervised learning (SSL) technique is proposed to pre-train our network using large-scale unlabeled data to learn the appearance, texture, and structure semantics of bpMRI. It aims to capture both intra-slice and inter-slice information during the pre-training stage. Furthermore, we constrained our network to focus on the zonal anatomical regions to further improve the detection and diagnosis capability of csPCa. We conducted extensive experiments on the PI-CAI dataset comprising 10000+ multi-center and multi-scanner data. Our Z-SSMNet excelled in both lesion-level detection (AP score of 0.633) and patient-level diagnosis (AUROC score of 0.881), securing the top position in the Open Development Phase of the PI-CAI challenge and maintained strong performance, achieving an AP score of 0.690 and an AUROC score of 0.909, and securing the second-place ranking in the Closed Testing Phase.

eess.IV↗

arXiv2022

Brain Tumor Sequence Registration with Non-iterative Coarse-to-fine Networks and Dual Deep Supervision

In this study, we focus on brain tumor sequence registration between pre-operative and follow-up Magnetic Resonance Imaging (MRI) scans of brain glioma patients, in the context of Brain Tumor Sequence Registration challenge (BraTS-Reg 2022). Brain tumor registration is a fundamental requirement in brain image analysis for quantifying tumor changes. This is a challenging task due to large deformations and missing correspondences between pre-operative and follow-up scans. For this task, we adopt our recently proposed Non-Iterative Coarse-to-finE registration Networks (NICE-Net) - a deep learning-based method for coarse-to-fine registering images with large deformations. To overcome missing correspondences, we extend the NICE-Net by introducing dual deep supervision, where a deep self-supervised loss based on image similarity and a deep weakly-supervised loss based on manually annotated landmarks are deeply embedded into the NICE-Net. At the BraTS-Reg 2022, our method achieved a competitive result on the validation set (mean absolute error: 3.387) and placed 4th in the final testing phase (Score: 0.3544).

cs.CV↗

arXiv2022

Radiomics-enhanced Deep Multi-task Learning for Outcome Prediction in Head and Neck Cancer

Outcome prediction is crucial for head and neck cancer patients as it can provide prognostic information for early treatment planning. Radiomics methods have been widely used for outcome prediction from medical images. However, these methods are limited by their reliance on intractable manual segmentation of tumor regions. Recently, deep learning methods have been proposed to perform end-to-end outcome prediction so as to remove the reliance on manual segmentation. Unfortunately, without segmentation masks, these methods will take the whole image as input, such that makes them difficult to focus on tumor regions and potentially unable to fully leverage the prognostic information within the tumor regions. In this study, we propose a radiomics-enhanced deep multi-task framework for outcome prediction from PET/CT images, in the context of HEad and neCK TumOR segmentation and outcome prediction challenge (HECKTOR 2022). In our framework, our novelty is to incorporate radiomics as an enhancement to our recently proposed Deep Multi-task Survival model (DeepMTS). The DeepMTS jointly learns to predict the survival risk scores of patients and the segmentation masks of tumor regions. Radiomics features are extracted from the predicted tumor regions and combined with the predicted survival risk scores for final outcome prediction, through which the prognostic information in tumor regions can be further leveraged. Our method achieved a C-index of 0.681 on the testing set, placing the 2nd on the leaderboard with only 0.00068 lower in C-index than the 1st place.

eess.IV↗

arXiv2022

Automatic Tumor Segmentation via False Positive Reduction Network for Whole-Body Multi-Modal PET/CT Images

Multi-modality Fluorodeoxyglucose (FDG) positron emission tomography / computed tomography (PET/CT) has been routinely used in the assessment of common cancers, such as lung cancer, lymphoma, and melanoma. This is mainly attributed to the fact that PET/CT combines the high sensitivity for tumor detection of PET and anatomical information from CT. In PET/CT image assessment, automatic tumor segmentation is an important step, and in recent years, deep learning based methods have become the state-of-the-art. Unfortunately, existing methods tend to over-segment the tumor regions and include regions such as the normal high uptake organs, inflammation, and other infections. In this study, we introduce a false positive reduction network to overcome this limitation. We firstly introduced a self-supervised pre-trained global segmentation module to coarsely delineate the candidate tumor regions using a self-supervised pre-trained encoder. The candidate tumor regions were then refined by removing false positives via a local refinement module. Our experiments with the MICCAI 2022 Automated Lesion Segmentation in Whole-Body FDG-PET/CT (AutoPET) challenge dataset showed that our method achieved a dice score of 0.9324 with the preliminary testing data and was ranked 1st place in dice on the leaderboard. Our method was also ranked in the top 7 methods on the final testing data, the final ranking will be announced during the 2022 MICCAI AutoPET workshop. Our code is available at: https://github.com/YigePeng/AutoPET_False_Positive_Reduction.

eess.IV↗

arXiv2022

Non-iterative Coarse-to-fine Registration based on Single-pass Deep Cumulative Learning

Deformable image registration is a crucial step in medical image analysis for finding a non-linear spatial transformation between a pair of fixed and moving images. Deep registration methods based on Convolutional Neural Networks (CNNs) have been widely used as they can perform image registration in a fast and end-to-end manner. However, these methods usually have limited performance for image pairs with large deformations. Recently, iterative deep registration methods have been used to alleviate this limitation, where the transformations are iteratively learned in a coarse-to-fine manner. However, iterative methods inevitably prolong the registration runtime, and tend to learn separate image features for each iteration, which hinders the features from being leveraged to facilitate the registration at later iterations. In this study, we propose a Non-Iterative Coarse-to-finE registration Network (NICE-Net) for deformable image registration. In the NICE-Net, we propose: (i) a Single-pass Deep Cumulative Learning (SDCL) decoder that can cumulatively learn coarse-to-fine transformations within a single pass (iteration) of the network, and (ii) a Selectively-propagated Feature Learning (SFL) encoder that can learn common image features for the whole coarse-to-fine registration process and selectively propagate the features as needed. Extensive experiments on six public datasets of 3D brain Magnetic Resonance Imaging (MRI) show that our proposed NICE-Net can outperform state-of-the-art iterative deep registration methods while only requiring similar runtime to non-iterative methods.

cs.CV↗