arXiv subjects

Tao Tan

Publications and source records attributed to Tao Tan.

At least 91 records · Page 5Linked to original sources

arXiv2023

A Parameterized Generative Adversarial Network Using Cyclic Projection for Explainable Medical Image Classification

Although current data augmentation methods are successful to alleviate the data insufficiency, conventional augmentation are primarily intra-domain while advanced generative adversarial networks (GANs) generate images remaining uncertain, particularly in small-scale datasets. In this paper, we propose a parameterized GAN (ParaGAN) that effectively controls the changes of synthetic samples among domains and highlights the attention regions for downstream classification. Specifically, ParaGAN incorporates projection distance parameters in cyclic projection and projects the source images to the decision boundary to obtain the class-difference maps. Our experiments show that ParaGAN can consistently outperform the existing augmentation methods with explainable classification on two small-scale medical datasets.

cs.CV↗

arXiv2023

Fine-Grained Unsupervised Cross-Modality Domain Adaptation for Vestibular Schwannoma Segmentation

The domain adaptation approach has gained significant acceptance in transferring styles across various vendors and centers, along with filling the gaps in modalities. However, multi-center application faces the challenge of the difficulty of domain adaptation due to their intra-domain differences. We focus on introducing a fine-grained unsupervised framework for domain adaptation to facilitate cross-modality segmentation of vestibular schwannoma (VS) and cochlea. We propose to use a vector to control the generator to synthesize a fake image with given features. And then, we can apply various augmentations to the dataset by searching the feature dictionary. The diversity augmentation can increase the performance and robustness of the segmentation model. On the CrossMoDA validation phase Leaderboard, our method received a mean Dice score of 0.765 and 0.836 on VS and cochlea, respectively.

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arXiv2023

Pseudo Label-Guided Data Fusion and Output Consistency for Semi-Supervised Medical Image Segmentation

Supervised learning algorithms based on Convolutional Neural Networks have become the benchmark for medical image segmentation tasks, but their effectiveness heavily relies on a large amount of labeled data. However, annotating medical image datasets is a laborious and time-consuming process. Inspired by semi-supervised algorithms that use both labeled and unlabeled data for training, we propose the PLGDF framework, which builds upon the mean teacher network for segmenting medical images with less annotation. We propose a novel pseudo-label utilization scheme, which combines labeled and unlabeled data to augment the dataset effectively. Additionally, we enforce the consistency between different scales in the decoder module of the segmentation network and propose a loss function suitable for evaluating the consistency. Moreover, we incorporate a sharpening operation on the predicted results, further enhancing the accuracy of the segmentation. Extensive experiments on three publicly available datasets demonstrate that the PLGDF framework can largely improve performance by incorporating the unlabeled data. Meanwhile, our framework yields superior performance compared to six state-of-the-art semi-supervised learning methods. The codes of this study are available at https://github.com/ortonwang/PLGDF.

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arXiv2023

Light-VQA: A Multi-Dimensional Quality Assessment Model for Low-Light Video Enhancement

Recently, Users Generated Content (UGC) videos becomes ubiquitous in our daily lives. However, due to the limitations of photographic equipments and techniques, UGC videos often contain various degradations, in which one of the most visually unfavorable effects is the underexposure. Therefore, corresponding video enhancement algorithms such as Low-Light Video Enhancement (LLVE) have been proposed to deal with the specific degradation. However, different from video enhancement algorithms, almost all existing Video Quality Assessment (VQA) models are built generally rather than specifically, which measure the quality of a video from a comprehensive perspective. To the best of our knowledge, there is no VQA model specially designed for videos enhanced by LLVE algorithms. To this end, we first construct a Low-Light Video Enhancement Quality Assessment (LLVE-QA) dataset in which 254 original low-light videos are collected and then enhanced by leveraging 8 LLVE algorithms to obtain 2,060 videos in total. Moreover, we propose a quality assessment model specialized in LLVE, named Light-VQA. More concretely, since the brightness and noise have the most impact on low-light enhanced VQA, we handcraft corresponding features and integrate them with deep-learning-based semantic features as the overall spatial information. As for temporal information, in addition to deep-learning-based motion features, we also investigate the handcrafted brightness consistency among video frames, and the overall temporal information is their concatenation. Subsequently, spatial and temporal information is fused to obtain the quality-aware representation of a video. Extensive experimental results show that our Light-VQA achieves the best performance against the current State-Of-The-Art (SOTA) on LLVE-QA and public dataset. Dataset and Codes can be found at https://github.com/wenzhouyidu/Light-VQA.

cs.CV↗

arXiv2023

IvyGPT: InteractiVe Chinese pathwaY language model in medical domain

General large language models (LLMs) such as ChatGPT have shown remarkable success. However, such LLMs have not been widely adopted for medical purposes, due to poor accuracy and inability to provide medical advice. We propose IvyGPT, an LLM based on LLaMA that is trained and fine-tuned with high-quality medical question-answer (QA) instances and Reinforcement Learning from Human Feedback (RLHF). After supervised fine-tuning, IvyGPT has good multi-turn conversation capabilities, but it cannot perform like a doctor in other aspects, such as comprehensive diagnosis. Through RLHF, IvyGPT can output richer diagnosis and treatment answers that are closer to human. In the training, we used QLoRA to train 33 billion parameters on a small number of NVIDIA A100 (80GB) GPUs. Experimental results show that IvyGPT has outperformed other medical GPT models.

cs.CL↗

arXiv2023

To Raise or Not To Raise: The Autonomous Learning Rate Question

There is a parameter ubiquitous throughout the deep learning world: learning rate. There is likewise a ubiquitous question: what should that learning rate be? The true answer to this question is often tedious and time consuming to obtain, and a great deal of arcane knowledge has accumulated in recent years over how to pick and modify learning rates to achieve optimal training performance. Moreover, the long hours spent carefully crafting the perfect learning rate can come to nothing the moment your network architecture, optimizer, dataset, or initial conditions change ever so slightly. But it need not be this way. We propose a new answer to the great learning rate question: the Autonomous Learning Rate Controller. Find it at https://github.com/fastestimator/ARC/tree/v2.0

cs.LG↗

arXiv2023

DisAsymNet: Disentanglement of Asymmetrical Abnormality on Bilateral Mammograms using Self-adversarial Learning

Asymmetry is a crucial characteristic of bilateral mammograms (Bi-MG) when abnormalities are developing. It is widely utilized by radiologists for diagnosis. The question of 'what the symmetrical Bi-MG would look like when the asymmetrical abnormalities have been removed ?' has not yet received strong attention in the development of algorithms on mammograms. Addressing this question could provide valuable insights into mammographic anatomy and aid in diagnostic interpretation. Hence, we propose a novel framework, DisAsymNet, which utilizes asymmetrical abnormality transformer guided self-adversarial learning for disentangling abnormalities and symmetric Bi-MG. At the same time, our proposed method is partially guided by randomly synthesized abnormalities. We conduct experiments on three public and one in-house dataset, and demonstrate that our method outperforms existing methods in abnormality classification, segmentation, and localization tasks. Additionally, reconstructed normal mammograms can provide insights toward better interpretable visual cues for clinical diagnosis. The code will be accessible to the public.

cs.CV↗

arXiv2023

Synthesis of Contrast-Enhanced Breast MRI Using Multi-b-Value DWI-based Hierarchical Fusion Network with Attention Mechanism

Magnetic resonance imaging (MRI) is the most sensitive technique for breast cancer detection among current clinical imaging modalities. Contrast-enhanced MRI (CE-MRI) provides superior differentiation between tumors and invaded healthy tissue, and has become an indispensable technique in the detection and evaluation of cancer. However, the use of gadolinium-based contrast agents (GBCA) to obtain CE-MRI may be associated with nephrogenic systemic fibrosis and may lead to bioaccumulation in the brain, posing a potential risk to human health. Moreover, and likely more important, the use of gadolinium-based contrast agents requires the cannulation of a vein, and the injection of the contrast media which is cumbersome and places a burden on the patient. To reduce the use of contrast agents, diffusion-weighted imaging (DWI) is emerging as a key imaging technique, although currently usually complementing breast CE-MRI. In this study, we develop a multi-sequence fusion network to synthesize CE-MRI based on T1-weighted MRI and DWIs. DWIs with different b-values are fused to efficiently utilize the difference features of DWIs. Rather than proposing a pure data-driven approach, we invent a multi-sequence attention module to obtain refined feature maps, and leverage hierarchical representation information fused at different scales while utilizing the contributions from different sequences from a model-driven approach by introducing the weighted difference module. The results show that the multi-b-value DWI-based fusion model can potentially be used to synthesize CE-MRI, thus theoretically reducing or avoiding the use of GBCA, thereby minimizing the burden to patients. Our code is available at \url{https://github.com/Netherlands-Cancer-Institute/CE-MRI}.

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arXiv2023

PCDAL: A Perturbation Consistency-Driven Active Learning Approach for Medical Image Segmentation and Classification

In recent years, deep learning has become a breakthrough technique in assisting medical image diagnosis. Supervised learning using convolutional neural networks (CNN) provides state-of-the-art performance and has served as a benchmark for various medical image segmentation and classification. However, supervised learning deeply relies on large-scale annotated data, which is expensive, time-consuming, and even impractical to acquire in medical imaging applications. Active Learning (AL) methods have been widely applied in natural image classification tasks to reduce annotation costs by selecting more valuable examples from the unlabeled data pool. However, their application in medical image segmentation tasks is limited, and there is currently no effective and universal AL-based method specifically designed for 3D medical image segmentation. To address this limitation, we propose an AL-based method that can be simultaneously applied to 2D medical image classification, segmentation, and 3D medical image segmentation tasks. We extensively validated our proposed active learning method on three publicly available and challenging medical image datasets, Kvasir Dataset, COVID-19 Infection Segmentation Dataset, and BraTS2019 Dataset. The experimental results demonstrate that our PCDAL can achieve significantly improved performance with fewer annotations in 2D classification and segmentation and 3D segmentation tasks. The codes of this study are available at https://github.com/ortonwang/PCDAL.

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arXiv2023

TransMRSR: Transformer-based Self-Distilled Generative Prior for Brain MRI Super-Resolution

Magnetic resonance images (MRI) acquired with low through-plane resolution compromise time and cost. The poor resolution in one orientation is insufficient to meet the requirement of high resolution for early diagnosis of brain disease and morphometric study. The common Single image super-resolution (SISR) solutions face two main challenges: (1) local detailed and global anatomical structural information combination; and (2) large-scale restoration when applied for reconstructing thick-slice MRI into high-resolution (HR) iso-tropic data. To address these problems, we propose a novel two-stage network for brain MRI SR named TransMRSR based on the convolutional blocks to extract local information and transformer blocks to capture long-range dependencies. TransMRSR consists of three modules: the shallow local feature extraction, the deep non-local feature capture, and the HR image reconstruction. We perform a generative task to encapsulate diverse priors into a generative network (GAN), which is the decoder sub-module of the deep non-local feature capture part, in the first stage. The pre-trained GAN is used for the second stage of SR task. We further eliminate the potential latent space shift caused by the two-stage training strategy through the self-distilled truncation trick. The extensive experiments show that our method achieves superior performance to other SSIR methods on both public and private datasets. Code is released at https://github.com/goddesshs/TransMRSR.git .

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arXiv2023

LYSTO: The Lymphocyte Assessment Hackathon and Benchmark Dataset

We introduce LYSTO, the Lymphocyte Assessment Hackathon, which was held in conjunction with the MICCAI 2019 Conference in Shenzen (China). The competition required participants to automatically assess the number of lymphocytes, in particular T-cells, in histopathological images of colon, breast, and prostate cancer stained with CD3 and CD8 immunohistochemistry. Differently from other challenges setup in medical image analysis, LYSTO participants were solely given a few hours to address this problem. In this paper, we describe the goal and the multi-phase organization of the hackathon; we describe the proposed methods and the on-site results. Additionally, we present post-competition results where we show how the presented methods perform on an independent set of lung cancer slides, which was not part of the initial competition, as well as a comparison on lymphocyte assessment between presented methods and a panel of pathologists. We show that some of the participants were capable to achieve pathologist-level performance at lymphocyte assessment. After the hackathon, LYSTO was left as a lightweight plug-and-play benchmark dataset on grand-challenge website, together with an automatic evaluation platform. LYSTO has supported a number of research in lymphocyte assessment in oncology. LYSTO will be a long-lasting educational challenge for deep learning and digital pathology, it is available at https://lysto.grand-challenge.org/.

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arXiv2023

IMPORTANT-Net: Integrated MRI Multi-Parameter Reinforcement Fusion Generator with Attention Network for Synthesizing Absent Data

Magnetic resonance imaging (MRI) is highly sensitive for lesion detection in the breasts. Sequences obtained with different settings can capture the specific characteristics of lesions. Such multi-parameter MRI information has been shown to improve radiologist performance in lesion classification, as well as improving the performance of artificial intelligence models in various tasks. However, obtaining multi-parameter MRI makes the examination costly in both financial and time perspectives, and there may be safety concerns for special populations, thus making acquisition of the full spectrum of MRI sequences less durable. In this study, different than naive input fusion or feature concatenation from existing MRI parameters, a novel $\textbf{I}$ntegrated MRI $\textbf{M}$ulti-$\textbf{P}$arameter reinf$\textbf{O}$rcement fusion generato$\textbf{R}$ wi$\textbf{T}$h $\textbf{A}$tte$\textbf{NT}$ion Network (IMPORTANT-Net) is developed to generate missing parameters. First, the parameter reconstruction module is used to encode and restore the existing MRI parameters to obtain the corresponding latent representation information at any scale level. Then the multi-parameter fusion with attention module enables the interaction of the encoded information from different parameters through a set of algorithmic strategies, and applies different weights to the information through the attention mechanism after information fusion to obtain refined representation information. Finally, a reinforcement fusion scheme embedded in a $V^{-}$-shape generation module is used to combine the hierarchical representations to generate the missing MRI parameter. Results showed that our IMPORTANT-Net is capable of generating missing MRI parameters and outperforms comparable state-of-the-art networks. Our code is available at https://github.com/Netherlands-Cancer-Institute/MRI_IMPORTANT_NET.

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arXiv2023

Synthesis-based Imaging-Differentiation Representation Learning for Multi-Sequence 3D/4D MRI

Multi-sequence MRIs can be necessary for reliable diagnosis in clinical practice due to the complimentary information within sequences. However, redundant information exists across sequences, which interferes with mining efficient representations by modern machine learning or deep learning models. To handle various clinical scenarios, we propose a sequence-to-sequence generation framework (Seq2Seq) for imaging-differentiation representation learning. In this study, not only do we propose arbitrary 3D/4D sequence generation within one model to generate any specified target sequence, but also we are able to rank the importance of each sequence based on a new metric estimating the difficulty of a sequence being generated. Furthermore, we also exploit the generation inability of the model to extract regions that contain unique information for each sequence. We conduct extensive experiments using three datasets including a toy dataset of 20,000 simulated subjects, a brain MRI dataset of 1,251 subjects, and a breast MRI dataset of 2,101 subjects, to demonstrate that (1) our proposed Seq2Seq is efficient and lightweight for complex clinical datasets and can achieve excellent image quality; (2) top-ranking sequences can be used to replace complete sequences with non-inferior performance; (3) combining MRI with our imaging-differentiation map leads to better performance in clinical tasks such as glioblastoma MGMT promoter methylation status prediction and breast cancer pathological complete response status prediction. Our code is available at https://github.com/fiy2W/mri_seq2seq.

cs.CV↗

arXiv2022

Network Topology Inference based on Timing Meta-Data

Consider a processor having access only to meta-data consisting of the timings of data packets and acknowledgment (ACK) packets from all nodes in a network. The meta-data report the source node of each packet, but not the destination nodes or the contents of the packets. The goal of the processor is to infer the network topology based solely on such information. Prior work leveraged causality metrics to identify which links are active. If the data timings and ACK timings of two nodes -- say node 1 and node 2, respectively -- are causally related, this may be taken as evidence that node 1 is communicating to node 2 (which sends back ACK packets to node 1). This paper starts with the observation that packet losses can weaken the causality relationship between data and ACK timing streams. To obviate this problem, a new Expectation Maximization (EM)-based algorithm is introduced -- EM-causality discovery algorithm (EM-CDA) -- which treats packet losses as latent variables. EM-CDA iterates between the estimation of packet losses and the evaluation of causality metrics. The method is validated through extensive experiments in wireless sensor networks on the NS-3 simulation platform.

eess.SP↗

arXiv2022

Unsupervised Cross-Modality Domain Adaptation for Vestibular Schwannoma Segmentation and Koos Grade Prediction based on Semi-Supervised Contrastive Learning

Domain adaptation has been widely adopted to transfer styles across multi-vendors and multi-centers, as well as to complement the missing modalities. In this challenge, we proposed an unsupervised domain adaptation framework for cross-modality vestibular schwannoma (VS) and cochlea segmentation and Koos grade prediction. We learn the shared representation from both ceT1 and hrT2 images and recover another modality from the latent representation, and we also utilize proxy tasks of VS segmentation and brain parcellation to restrict the consistency of image structures in domain adaptation. After generating missing modalities, the nnU-Net model is utilized for VS and cochlea segmentation, while a semi-supervised contrastive learning pre-train approach is employed to improve the model performance for Koos grade prediction. On CrossMoDA validation phase Leaderboard, our method received rank 4 in task1 with a mean Dice score of 0.8394 and rank 2 in task2 with Macro-Average Mean Square Error of 0.3941. Our code is available at https://github.com/fiy2W/cmda2022.superpolymerization.

cs.CV↗

arXiv2021

Mass Segmentation in Automated 3-D Breast Ultrasound Using Dual-Path U-net

Automated 3-D breast ultrasound (ABUS) is a newfound system for breast screening that has been proposed as a supplementary modality to mammography for breast cancer detection. While ABUS has better performance in dense breasts, reading ABUS images is exhausting and time-consuming. So, a computer-aided detection system is necessary for interpretation of these images. Mass segmentation plays a vital role in the computer-aided detection systems and it affects the overall performance. Mass segmentation is a challenging task because of the large variety in size, shape, and texture of masses. Moreover, an imbalanced dataset makes segmentation harder. A novel mass segmentation approach based on deep learning is introduced in this paper. The deep network that is used in this study for image segmentation is inspired by U-net, which has been used broadly for dense segmentation in recent years. The system's performance was determined using a dataset of 50 masses including 38 malign and 12 benign lesions. The proposed segmentation method attained a mean Dice of 0.82 which outperformed a two-stage supervised edge-based method with a mean Dice of 0.74 and an adaptive region growing method with a mean Dice of 0.65.

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arXiv2020

Pristine annotations-based multi-modal trained artificial intelligence solution to triage chest X-ray for COVID-19

The COVID-19 pandemic continues to spread and impact the well-being of the global population. The front-line modalities including computed tomography (CT) and X-ray play an important role for triaging COVID patients. Considering the limited access of resources (both hardware and trained personnel) and decontamination considerations, CT may not be ideal for triaging suspected subjects. Artificial intelligence (AI) assisted X-ray based applications for triaging and monitoring require experienced radiologists to identify COVID patients in a timely manner and to further delineate the disease region boundary are seen as a promising solution. Our proposed solution differs from existing solutions by industry and academic communities, and demonstrates a functional AI model to triage by inferencing using a single x-ray image, while the deep-learning model is trained using both X-ray and CT data. We report on how such a multi-modal training improves the solution compared to X-ray only training. The multi-modal solution increases the AUC (area under the receiver operating characteristic curve) from 0.89 to 0.93 and also positively impacts the Dice coefficient (0.59 to 0.62) for localizing the pathology. To the best our knowledge, it is the first X-ray solution by leveraging multi-modal information for the development.

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arXiv2020

Lesion Segmentation in Ultrasound Using Semi-pixel-wise Cycle Generative Adversarial Nets

Breast cancer is the most common invasive cancer with the highest cancer occurrence in females. Handheld ultrasound is one of the most efficient ways to identify and diagnose the breast cancer. The area and the shape information of a lesion is very helpful for clinicians to make diagnostic decisions. In this study we propose a new deep-learning scheme, semi-pixel-wise cycle generative adversarial net (SPCGAN) for segmenting the lesion in 2D ultrasound. The method takes the advantage of a fully convolutional neural network (FCN) and a generative adversarial net to segment a lesion by using prior knowledge. We compared the proposed method to a fully connected neural network and the level set segmentation method on a test dataset consisting of 32 malignant lesions and 109 benign lesions. Our proposed method achieved a Dice similarity coefficient (DSC) of 0.92 while FCN and the level set achieved 0.90 and 0.79 respectively. Particularly, for malignant lesions, our method increases the DSC (0.90) of the fully connected neural network to 0.93 significantly (p$<$0.001). The results show that our SPCGAN can obtain robust segmentation results. The framework of SPCGAN is particularly effective when sufficient training samples are not available compared to FCN. Our proposed method may be used to relieve the radiologists' burden for annotation.

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