arXiv subjects

Yudong Yao

Publications and source records attributed to Yudong Yao.

36 records · Page 2Linked to original sources

arXiv2022

A State-of-the-art Survey of Object Detection Techniques in Microorganism Image Analysis: From Classical Methods to Deep Learning Approaches

Microorganisms play a vital role in human life. Therefore, microorganism detection is of great significance to human beings. However, the traditional manual microscopic detection methods have the disadvantages of long detection cycle, low detection accuracy in large orders, and great difficulty in detecting uncommon microorganisms. Therefore, it is meaningful to apply computer image analysis technology to the field of microorganism detection. Computer image analysis can realize high-precision and high-efficiency detection of microorganisms. In this review, first,we analyse the existing microorganism detection methods in chronological order, from traditional image processing and traditional machine learning to deep learning methods. Then, we analyze and summarize these existing methods and introduce some potential methods, including visual transformers. In the end, the future development direction and challenges of microorganism detection are discussed. In general, we have summarized 142 related technical papers from 1985 to the present. This review will help researchers have a more comprehensive understanding of the development process, research status, and future trends in the field of microorganism detection and provide a reference for researchers in other fields.

cs.CV↗

arXiv2022

AutoPhaseNN: Unsupervised Physics-aware Deep Learning of 3D Nanoscale Bragg Coherent Diffraction Imaging

The problem of phase retrieval, or the algorithmic recovery of lost phase information from measured intensity alone, underlies various imaging methods from astronomy to nanoscale imaging. Traditional methods of phase retrieval are iterative in nature, and are therefore computationally expensive and time consuming. More recently, deep learning (DL) models have been developed to either provide learned priors to iterative phase retrieval or in some cases completely replace phase retrieval with networks that learn to recover the lost phase information from measured intensity alone. However, such models require vast amounts of labeled data, which can only be obtained through simulation or performing computationally prohibitive phase retrieval on hundreds of or even thousands of experimental datasets. Using a 3D nanoscale X-ray imaging modality (Bragg Coherent Diffraction Imaging or BCDI) as a representative technique, we demonstrate AutoPhaseNN, a DL-based approach which learns to solve the phase problem without labeled data. By incorporating the physics of the imaging technique into the DL model during training, AutoPhaseNN learns to invert 3D BCDI data from reciprocal space to real space in a single shot without ever being shown real space images. Once trained, AutoPhaseNN is about one hundred times faster than traditional iterative phase retrieval methods while providing comparable image quality.

physics.app-ph↗

arXiv2022

Improving the Level of Autism Discrimination through GraphRNN Link Prediction

Dataset is the key of deep learning in Autism disease research. However, due to the few quantity and heterogeneity of samples in current dataset, for example ABIDE (Autism Brain Imaging Data Exchange), the recognition research is not effective enough. Previous studies mostly focused on optimizing feature selection methods and data reinforcement to improve accuracy. This paper is based on the latter technique, which learns the edge distribution of real brain network through GraphRNN, and generates the synthetic data which has incentive effect on the discriminant model. The experimental results show that the combination of original and synthetic data greatly improves the discrimination of the neural network. For instance, the most significant effect is the 50-layer ResNet, and the best generation model is GraphRNN, which improves the accuracy by 32.51% compared with the model reference experiment without generation data reinforcement. Because the generated data comes from the learned edge connection distribution of Autism patients and typical controls functional connectivity, but it has better effect than the original data, which has constructive significance for further understanding of disease mechanism and development.

cs.LG↗

arXiv2022

EBHI:A New Enteroscope Biopsy Histopathological H&E Image Dataset for Image Classification Evaluation

Background and purpose: Colorectal cancer has become the third most common cancer worldwide, accounting for approximately 10% of cancer patients. Early detection of the disease is important for the treatment of colorectal cancer patients. Histopathological examination is the gold standard for screening colorectal cancer. However, the current lack of histopathological image datasets of colorectal cancer, especially enteroscope biopsies, hinders the accurate evaluation of computer-aided diagnosis techniques. Methods: A new publicly available Enteroscope Biopsy Histopathological H&E Image Dataset (EBHI) is published in this paper. To demonstrate the effectiveness of the EBHI dataset, we have utilized several machine learning, convolutional neural networks and novel transformer-based classifiers for experimentation and evaluation, using an image with a magnification of 200x. Results: Experimental results show that the deep learning method performs well on the EBHI dataset. Traditional machine learning methods achieve maximum accuracy of 76.02% and deep learning method achieves a maximum accuracy of 95.37%. Conclusion: To the best of our knowledge, EBHI is the first publicly available colorectal histopathology enteroscope biopsy dataset with four magnifications and five types of images of tumor differentiation stages, totaling 5532 images. We believe that EBHI could attract researchers to explore new classification algorithms for the automated diagnosis of colorectal cancer, which could help physicians and patients in clinical settings.

eess.IV↗

arXiv2022

Real-time X-ray Phase-contrast Imaging Using SPINNet -- A Speckle-based Phase-contrast Imaging Neural Network

X-ray phase-contrast imaging has become indispensable for visualizing samples with low absorption contrast. In this regard, speckle-based techniques have shown significant advantages in spatial resolution, phase sensitivity, and implementation flexibility compared with traditional methods. However, their computational cost has hindered their wider adoption. By exploiting the power of deep learning, we developed a new speckle-based phase-contrast imaging neural network (SPINNet) that boosts the phase retrieval speed by at least two orders of magnitude compared to existing methods. To achieve this performance, we combined SPINNet with a novel coded-mask-based technique, an enhanced version of the speckle-based method. Using this scheme, we demonstrate a simultaneous reconstruction of absorption and phase images on the order of 100 ms, where a traditional correlation-based analysis would take several minutes even with a cluster. In addition to significant improvement in speed, our experimental results show that the imaging resolution and phase retrieval quality of SPINNet outperform existing single-shot speckle-based methods. Furthermore, we successfully demonstrate its application in 3D X-ray phase-contrast tomography. Our result shows that SPINNet could enable many applications requiring high-resolution and fast data acquisition and processing, such as in-situ and in-operando 2D and 3D phase-contrast imaging and real-time at-wavelength metrology and wavefront sensing.

eess.IV↗

arXiv2021

Entropy Regularized Iterative Weighted Shrinkage-Thresholding Algorithm (ERIWSTA): An Application to CT Image Restoration

The iterative weighted shrinkage-thresholding algorithm (IWSTA) has shown superiority to the classic unweighted iterative shrinkage-thresholding algorithm (ISTA) for solving linear inverse problems, which address the attributes differently. This paper proposes a new entropy regularized IWSTA (ERIWSTA) that adds an entropy regularizer to the cost function to measure the uncertainty of the weights to stimulate attributes to participate in problem solving. Then, the weights are solved with a Lagrange multiplier method to obtain a simple iterative update. The weights can be explained as the probability of the contribution of an attribute to the problem solution. Experimental results on CT image restoration show that the proposed method has better performance in terms of convergence speed and restoration accuracy than the existing methods.

cs.CV↗

arXiv2021

An Entropy Weighted Nonnegative Matrix Factorization Algorithm for Feature Representation

Nonnegative matrix factorization (NMF) has been widely used to learn low-dimensional representations of data. However, NMF pays the same attention to all attributes of a data point, which inevitably leads to inaccurate representation. For example, in a human-face data set, if an image contains a hat on the head, the hat should be removed or the importance of its corresponding attributes should be decreased during matrix factorizing. This paper proposes a new type of NMF called entropy weighted NMF (EWNMF), which uses an optimizable weight for each attribute of each data point to emphasize their importance. This process is achieved by adding an entropy regularizer to the cost function and then using the Lagrange multiplier method to solve the problem. Experimental results with several data sets demonstrate the feasibility and effectiveness of the proposed method. We make our code available at https://github.com/Poisson-EM/Entropy-weighted-NMF.

cs.LG↗

arXiv2021

Is the aspect ratio of cells important in deep learning? A robust comparison of deep learning methods for multi-scale cytopathology cell image classification: from convolutional neural networks to visual transformers

Cervical cancer is a very common and fatal type of cancer in women. Cytopathology images are often used to screen for this cancer. Given that there is a possibility that many errors can occur during manual screening, a computer-aided diagnosis system based on deep learning has been developed. Deep learning methods require a fixed dimension of input images, but the dimensions of clinical medical images are inconsistent. The aspect ratios of the images suffer while resizing them directly. Clinically, the aspect ratios of cells inside cytopathological images provide important information for doctors to diagnose cancer. Therefore, it is difficult to resize directly. However, many existing studies have resized the images directly and have obtained highly robust classification results. To determine a reasonable interpretation, we have conducted a series of comparative experiments. First, the raw data of the SIPaKMeD dataset are pre-processed to obtain standard and scaled datasets. Then, the datasets are resized to 224 x 224 pixels. Finally, 22 deep learning models are used to classify the standard and scaled datasets. The results of the study indicate that deep learning models are robust to changes in the aspect ratio of cells in cervical cytopathological images. This conclusion is also validated via the Herlev dataset.

cs.CV↗

arXiv2021

GasHisSDB: A New Gastric Histopathology Image Dataset for Computer Aided Diagnosis of Gastric Cancer

Background and Objective: Gastric cancer has turned out to be the fifth most common cancer globally, and early detection of gastric cancer is essential to save lives. Histopathological examination of gastric cancer is the gold standard for the diagnosis of gastric cancer. However, computer-aided diagnostic techniques are challenging to evaluate due to the scarcity of publicly available gastric histopathology image datasets. Methods: In this paper, a noble publicly available Gastric Histopathology Sub-size Image Database (GasHisSDB) is published to identify classifiers' performance. Specifically, two types of data are included: normal and abnormal, with a total of 245,196 tissue case images. In order to prove that the methods of different periods in the field of image classification have discrepancies on GasHisSDB, we select a variety of classifiers for evaluation. Seven classical machine learning classifiers, three Convolutional Neural Network classifiers, and a novel transformer-based classifier are selected for testing on image classification tasks. Results: This study performed extensive experiments using traditional machine learning and deep learning methods to prove that the methods of different periods have discrepancies on GasHisSDB. Traditional machine learning achieved the best accuracy rate of 86.08% and a minimum of just 41.12%. The best accuracy of deep learning reached 96.47% and the lowest was 86.21%. Accuracy rates vary significantly across classifiers. Conclusions: To the best of our knowledge, it is the first publicly available gastric cancer histopathology dataset containing a large number of images for weakly supervised learning. We believe that GasHisSDB can attract researchers to explore new algorithms for the automated diagnosis of gastric cancer, which can help physicians and patients in the clinical setting.

cs.CV↗

arXiv2021

A Comprehensive Review of Image Analysis Methods for Microorganism Counting: From Classical Image Processing to Deep Learning Approaches

Microorganisms such as bacteria and fungi play essential roles in many application fields, like biotechnique, medical technique and industrial domain. Microorganism counting techniques are crucial in microorganism analysis, helping biologists and related researchers quantitatively analyze the microorganisms and calculate their characteristics, such as biomass concentration and biological activity. However, traditional microorganism manual counting methods, such as plate counting method, hemocytometry and turbidimetry, are time-consuming, subjective and need complex operations, which are difficult to be applied in large-scale applications. In order to improve this situation, image analysis is applied for microorganism counting since the 1980s, which consists of digital image processing, image segmentation, image classification and suchlike. Image analysis-based microorganism counting methods are efficient comparing with traditional plate counting methods. In this article, we have studied the development of microorganism counting methods using digital image analysis. Firstly, the microorganisms are grouped as bacteria and other microorganisms. Then, the related articles are summarized based on image segmentation methods. Each part of the article is reviewed by methodologies. Moreover, commonly used image processing methods for microorganism counting are summarized and analyzed to find common technological points. More than 144 papers are outlined in this article. In conclusion, this paper provides new ideas for the future development trend of microorganism counting, and provides systematic suggestions for implementing integrated microorganism counting systems in the future. Researchers in other fields can refer to the techniques analyzed in this paper.

eess.IV↗

arXiv2021

DeepCervix: A Deep Learning-based Framework for the Classification of Cervical Cells Using Hybrid Deep Feature Fusion Techniques

Cervical cancer, one of the most common fatal cancers among women, can be prevented by regular screening to detect any precancerous lesions at early stages and treat them. Pap smear test is a widely performed screening technique for early detection of cervical cancer, whereas this manual screening method suffers from high false-positive results because of human errors. To improve the manual screening practice, machine learning (ML) and deep learning (DL) based computer-aided diagnostic (CAD) systems have been investigated widely to classify cervical pap cells. Most of the existing researches require pre-segmented images to obtain good classification results, whereas accurate cervical cell segmentation is challenging because of cell clustering. Some studies rely on handcrafted features, which cannot guarantee the classification stage's optimality. Moreover, DL provides poor performance for a multiclass classification task when there is an uneven distribution of data, which is prevalent in the cervical cell dataset. This investigation has addressed those limitations by proposing DeepCervix, a hybrid deep feature fusion (HDFF) technique based on DL to classify the cervical cells accurately. Our proposed method uses various DL models to capture more potential information to enhance classification performance. Our proposed HDFF method is tested on the publicly available SIPAKMED dataset and compared the performance with base DL models and the LF method. For the SIPAKMED dataset, we have obtained the state-of-the-art classification accuracy of 99.85%, 99.38%, and 99.14% for 2-class, 3-class, and 5-class classification. Moreover, our method is tested on the Herlev dataset and achieves an accuracy of 98.32% for binary class and 90.32% for 7-class classification.

eess.IV↗

arXiv2021

A Hierarchical Conditional Random Field-based Attention Mechanism Approach for Gastric Histopathology Image Classification

In the Gastric Histopathology Image Classification (GHIC) tasks, which are usually weakly supervised learning missions, there is inevitably redundant information in the images. Therefore, designing networks that can focus on effective distinguishing features has become a popular research topic. In this paper, to accomplish the tasks of GHIC superiorly and to assist pathologists in clinical diagnosis, an intelligent Hierarchical Conditional Random Field based Attention Mechanism (HCRF-AM) model is proposed. The HCRF-AM model consists of an Attention Mechanism (AM) module and an Image Classification (IC) module. In the AM module, an HCRF model is built to extract attention regions. In the IC module, a Convolutional Neural Network (CNN) model is trained with the attention regions selected and then an algorithm called Classification Probability-based Ensemble Learning is applied to obtain the image-level results from patch-level output of the CNN. In the experiment, a classification specificity of 96.67% is achieved on a gastric histopathology dataset with 700 images. Our HCRF-AM model demonstrates high classification performance and shows its effectiveness and future potential in the GHIC field.

cs.CV↗

arXiv2021

A Comprehensive Review of Computer-aided Whole-slide Image Analysis: from Datasets to Feature Extraction, Segmentation, Classification, and Detection Approaches

With the development of computer-aided diagnosis (CAD) and image scanning technology, Whole-slide Image (WSI) scanners are widely used in the field of pathological diagnosis. Therefore, WSI analysis has become the key to modern digital pathology. Since 2004, WSI has been used more and more in CAD. Since machine vision methods are usually based on semi-automatic or fully automatic computers, they are highly efficient and labor-saving. The combination of WSI and CAD technologies for segmentation, classification, and detection helps histopathologists obtain more stable and quantitative analysis results, save labor costs and improve diagnosis objectivity. This paper reviews the methods of WSI analysis based on machine learning. Firstly, the development status of WSI and CAD methods are introduced. Secondly, we discuss publicly available WSI datasets and evaluation metrics for segmentation, classification, and detection tasks. Then, the latest development of machine learning in WSI segmentation, classification, and detection are reviewed continuously. Finally, the existing methods are studied, the applicabilities of the analysis methods are analyzed, and the application prospects of the analysis methods in this field are forecasted.

cs.CV↗

arXiv2021

EMDS-5: Environmental Microorganism Image Dataset Fifth Version for Multiple Image Analysis Tasks

Environmental Microorganism Data Set Fifth Version (EMDS-5) is a microscopic image dataset including original Environmental Microorganism (EM) images and two sets of Ground Truth (GT) images. The GT image sets include a single-object GT image set and a multi-object GT image set. The EMDS-5 dataset has 21 types of EMs, each of which contains 20 original EM images, 20 single-object GT images and 20 multi-object GT images. EMDS-5 can realize to evaluate image preprocessing, image segmentation, feature extraction, image classification and image retrieval functions. In order to prove the effectiveness of EMDS-5, for each function, we select the most representative algorithms and price indicators for testing and evaluation. The image preprocessing functions contain two parts: image denoising and image edge detection. Image denoising uses nine kinds of filters to denoise 13 kinds of noises, respectively. In the aspect of edge detection, six edge detection operators are used to detect the edges of the images, and two evaluation indicators, peak-signal to noise ratio and mean structural similarity, are used for evaluation. Image segmentation includes single-object image segmentation and multi-object image segmentation. Six methods are used for single-object image segmentation, while k-means and U-net are used for multi-object segmentation.We extract nine features from the images in EMDS-5 and use the Support Vector Machine classifier for testing. In terms of image classification, we select the VGG16 feature to test different classifiers. We test two types of retrieval approaches: texture feature retrieval and deep learning feature retrieval. We select the last layer of features of these two deep learning networks as feature vectors. We use mean average precision as the evaluation index for retrieval.

cs.CV↗

arXiv2020

Review of Machine-Learning Methods for RNA Secondary Structure Prediction

Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA secondary structure. Unfortunately, even though new methods have been proposed over the past 40 years, the performance of computational prediction methods has stagnated in the last decade. Recently, with the increasing availability of RNA structure data, new methods based on machine-learning technologies, especially deep learning, have alleviated the issue. In this review, we provide a comprehensive overview of RNA secondary structure prediction methods based on machine-learning technologies and a tabularized summary of the most important methods in this field. The current pending issues in the field of RNA secondary structure prediction and future trends are also discussed.

q-bio.BM↗

arXiv2020

A Comprehensive Review for Breast Histopathology Image Analysis Using Classical and Deep Neural Networks

Breast cancer is one of the most common and deadliest cancers among women. Since histopathological images contain sufficient phenotypic information, they play an indispensable role in the diagnosis and treatment of breast cancers. To improve the accuracy and objectivity of Breast Histopathological Image Analysis (BHIA), Artificial Neural Network (ANN) approaches are widely used in the segmentation and classification tasks of breast histopathological images. In this review, we present a comprehensive overview of the BHIA techniques based on ANNs. First of all, we categorize the BHIA systems into classical and deep neural networks for in-depth investigation. Then, the relevant studies based on BHIA systems are presented. After that, we analyze the existing models to discover the most suitable algorithms. Finally, publicly accessible datasets, along with their download links, are provided for the convenience of future researchers.

eess.IV↗

arXiv2017

Compensation for the setup instability in ptychographic imaging

The high-frequency vibration of the imaging system degrades the quality of the reconstruction of ptychography by acting as a low-pass filter on ideal diffraction patterns. In this study, we demonstrate that by subtracting the deliberately blurred diffraction patterns from the recorded patterns and adding the properly amplified subtraction to the original data, the high-frequency components lost by the vibration of the setup can be recovered, and thus the image quality can be distinctly improved. Because no prior knowledge regarding the vibrating properties of the imaging system is needed, the proposed method is general and simple and has applications in several research fields.

physics.ins-det↗

arXiv2016

Temporally modulated phase retrieval method for weak temporal phase measurement of laser pulses

The measurement of weak temporal phase for picosecond and nanosecond laser pulses is important but quite difficult. We propose a simple iterative algorithm, which is based on a temporally movable phase modulation process, to retrieve the weak temporal phase of laser pulses. This unambiguous method can achieve a high accuracy and simultaneously measure the weak temporal phase and temporal profile of pulses, which are almost transform-limited. Detailed analysis shows that this iterative method has valuable potential applications in the characterization of pulses with weak temporal phase.

physics.optics↗