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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Kuo Guo Yifan Li Hao Chen Hong-Bin Shen Yang Yang Department of Computer Science and Engineering Shanghai Jiao Tong University and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China Computational Biology Department School of Computer Science Carnegie Mellon University Pittsburgh PA USA

Isoforms refer to different mRNA molecules transcribed from the same gene, which can be translated into proteins with varying structures and functions. Predicting the functions of isoforms is an essential topic in bioinformatics as it can provide valuable insights into the intricate mechanisms of gene regulation and biological processes. Conventionally, gene function labels are standardized in Gene Ontology (GO) terms. However, traditional methods for predicting isoform function are largely limited by the absence of isoform-specific labels, sparse annotations, and the vast number of GO terms. To address these issues, we propose HANIso, a deep learning-based method for isoform function prediction. HANIso leverages a pretrained protein language model to extract features from protein sequences. It also integrates heterogeneous information, such as isoform sequence features, GO annotations, and isoform interaction data, using a Heterogeneous Graph Attention Network (HAN). This allows the model to learn the importance of different sources of information and their semantic relationships through the attention mechanism. Our method can predict function labels at both the gene level and isoform level. We conduct experiments on two species datasets, and the results demonstrate that our method outperforms existing methods on both AUROC and AUPRC. HANIso has the potential to overcome the limitations of traditional methods and provide a more accurate and comprehensive understanding of isoform function.

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FREQUENCY-DOMAIN ANALYSIS OF DISCRETE WAVELET TRANSFORM COEFFICIENTS AND THEIR ADAPTIVE SHRINKAGE FOR ANTI-ALIASING

FREQUENCY-DOMAIN ANALYSIS OF DISCRETE WAVELET TRANSFORM COEF...

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IEEE International Conference on image processing

作者： Eunjung Chae Eunsung Lee Wonseok Kang Younghoon Lim Junghoon Jung Taechan Kim Aggelos K. Katsaggelos Joonki Paik Image Processing and Intelligent Systems Laboratory Graduate School of Advanced Imaging Science Multimedia and Film Chung-Ang University Seoul Korea System LSI Samsung Electronics Co. Ltd Suwon Korea Department of Electrical Engineering and Computer Science Northwestern University Evanston IL 60208 USA

ISBN: (纸本)9781479923427

We present an antialiasing method using combined wavelet-Fourier transform and spatially adaptive shrinkage of the transform coefficients. Traditional antialiasing methods employ a simple low-pass filter onto the entire image, so the resulting image loses not only aliasing artifacts but also high-frequency components such as edges and ridges. The proposed algorithm analyzes the property of the LL subband of the discrete wavelet transform (DWT), and reduces aliasing artifacts using patch-adaptive shrinkage of the DWT coefficients. More specifically, an antialiased LL subband is obtained using adaptive patch-based aliasing reduction. To detect an aliased region, we subtract the discrete Fourier transform (DFT) coefficients of the LL subband from the DFT coefficients of antialiased LL subband. The detected aliasing artifacts in the LH, HL, and HH subbands are reduced by patch-wise adaptive shrinkage of the transform coefficients. The resulting antialiased image is obtained using the inverse DWT. The aliasing artifacts can be efficiently reduced by adaptively shrinking wavelet transform coefficients for preserving high-frequency image details. The proposed antialiasing algorithm is suitable for removing aliasing artifacts which frequently occur in imaging sensors with limited resolution.

关键词： Anti-aliasing wavelet-Fourier transform image enhancement patch-adaptive shrinkage antialiasing image enhancement Aliasing shrinkage Artifacts subband domain analysis Coefficients Sensors (image) Frequency-domain analysis discrete Fourier transform

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Voxel-based treatment prediction of glioblastoma multiform tumor using diffusion tensor imaging

Voxel-based treatment prediction of glioblastoma multiform t...

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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： Hadi Sabahi Hamid Soltanian-Zadeh Lisa Scarpace Tom Mikkelsen Control and Intelligent Processing Center of Excellence School of Electrical and Computer Engineering University of Tehran Tehran Iran Image Analysis Laboratory Radiology Department Henry Ford Hospital Detroit MI USA Hermelin Brain Tumor Research Center Neurosurgery Department Henry Ford Health System Detroit MI USA

This paper proposes a method to predict the effect of Bevacizumab therapy on Glioblastoma Multiform (GBM) tumors. The prediction is critical for effective treatment planning. The proposed method is developed and evaluated using Diffusion Tensor Imaging (DTI) and post-contrast T1-weighted Magnetic Resonance images (pc-T1-MRI) of 14 patients with GBM tumors gathered before and after the treatment. First, the proposed method calculates diffusion anisotropy indices (DAI) of all voxels in the brain. These diffusion anisotropy indices are Fractional Anisotropy (FA), Mean Diffusivity (MD), Relative Anisotropy (RA), and Volume Ratio (VR). Then, it registers post-treatment pc-T1-MRI and pre-treatment DAI maps to pre-treatment pc-T1-MRI. Next, it uses a thresholding method to segment the tumor from pc-T1-MRI studies. Comparing Gd-enhanced voxels of the pre- and post-treatment pc-T1-MRI, the DAIs of the tumor are labeled based on their response to the treatment. The voxels of 7 patients are randomly selected to train 4 classifiers (ANN, SVM, KNN, and ANFIS) and then all voxels of the other 7 patients are used to test them. For each classifier, four performance measures (sensitivity, specificity, positive predictive value, and accuracy) are calculated. Experimental results show that the ANFIS is more accurate than the other classifiers in predicting the treatment response.

关键词： Support vector machines Noise Magnetic resonance imaging Sensitivity Tumors Biomedical imaging Artificial neural networks

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Voxel based treatment prediction using diffusion anisotropy indices and spatial information in Glioblastoma Multiform tumor

Voxel based treatment prediction using diffusion anisotropy ...

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Iranian Conference of Biomedical Engineering (ICBME)

In this paper, we propose a method to predict the outcome of Bevacizumab therapy on Glioblastoma Multiform (GBM) tumors. The method uses diffusion anisotropy indices (DAI) and spatial information to predict the treatment response of each tumor voxel. These DAIs are Fractional Anisotropy, Mean Diffusivity, Relative Anisotropy, and Volume Ratio, extracted from Diffusion Tensor Imaging (DTI) data before treatment. The spatial information is considered as the distance of each tumor voxel from the tumor center, extracted from pre-treatment post-contrast T1-weighted Magnetic Resonance images (pc-T1-MRI). DAIs and spatial information of each tumor voxel are considered as feature vector. DTI and pc-T1-MRI are gathered before and after the treatment of seven GBM patients. First, DAIs of all brain voxels and the distance of each tumor voxel from the tumor center are calculated. Second, the method registers pre-treatment DAI maps and post-treatment pc-T1-MRI to pre-treatment pc-T1-MRI. Next, the tumor is segmented using thresholding technique from pc-T1-MRI. Then, Gd-enhanced voxels of the pre- and post-treatment pc-T1-MRI are compared to label the feature vectors. Three classifiers were evaluated, including Support Vector Machine, K-Nearest Neighbor, and Artificial Neural Network. Classification results show a preference for K-Nearest Neighbor based on well-established performance measures.

关键词： Tumors Anisotropic magnetoresistance Diffusion tensor imaging Support vector machines Feature extraction Artificial neural networks

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SliceProp: A Slice-Wise Bidirectional Propagation Model for Interactive 3D Medical image Segmentation

SliceProp: A Slice-Wise Bidirectional Propagation Model for ...

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Medical Artificial Intelligence (MedAI), IEEE International Conference on

作者： Xin Xu Wenjing Lu Jiahao Lei Peng Qiu Hong-Bin Shen Yang Yang Department of Computer Science and Engineering Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai Jiao Tong University Shanghai China Department of Vascular Surgery Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai Jiao Tong University Shanghai China

Interactive medical image segmentation methods have become increasingly popular in recent years. These methods combine manual labeling and automatic segmentation, reducing the workload of annotation while maintaining high accuracy. However, most current interactive segmentation frameworks are limited to 2D image data, and are not suitable for 3D image data due to the large size and high complexity of 3D data, as well as the challenges posed by information asymmetry and sparse annotation. In this paper, we propose SliceProp, an interactive segmentation framework that implements slice-wise Label Bidirectional Propagation (LBP) for 3D medical image segmentation. SliceProp extends the interactive 2D image segmentation algorithm to 3D image segmentation, and can handle 3D data with large size and high complexity. Moreover, equipped with a Backtracking Feedback Check (BFC) module, SliceProp effectively addresses the issues of information asymmetry and spatial sparse annotation in 3D medical image segmentation. Additionally, we adopt an uncertainty-based criterion to pri-oritize the slices to be refined interactively, which enhances the efficiency of the interaction process by enabling the model to focus on the regions with the most unreliable predictions. SliceProp is evaluated on two datasets and achieves promising results compared to state-of-the-art methods.

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High SNR flexible top hat monopole probe for 1.5 T MRI

High SNR flexible top hat monopole probe for 1.5 T MRI

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作者： Mohammadzadeh, M. Shahabadi, M. Soltanian-Zadeh, H. Tavakoli, A. Rafiei, B. Javidnia, D. Oghabian, M.A. Department of Physics Amir-Kabir University of Technology Tehran Iran School of Electrical and Computer Engineering University of Tehran Tehran Iran Control and Intelligent Processing Center of Excellence School of Electrical and Computer Engineering University of Tehran Tehran Iran Image Analysis Laboratory Department of Radiology Henry Ford Health System Detroit MI United States Department of Electrical Engineering Amir-Kabir University of Technology Tehran Iran Medical Imaging Center Imam Khomeyni Hospital Tehran Iran Research Center for Science and Technology in Medicine Tehran University of Medical Sciences Tehran Iran

In this paper, design principles and application of a thin and flexible intravascular top hat monopole probe with increased signal-to-noise ratio (SNR) and improved longitudinal and radial coverage are described and compared with the conventional monopole probe. The top hat probe is constructed by removing a segment of the shield of a coaxial cable. A flexible thin copper foil in contact with the inner conductor of the cable is added to the end section of the cable. The copper foil acts as an antenna top hat load increasing the uniformity of the current distribution on the probe and establishes a uniform region of SNR distribution around the probe. Improvement of the SNR distribution of the top hat probe relative to the conventional monopole probe is evaluated using quantitative indices. Experimental results show that for the top hat probe, the ratio of the maximum image SNR to its relative standard deviation (SR) is 2.73 times higher than that of a conventional probe. © 2006 IOP Publishing Ltd.

关键词： Medical imaging

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Research and application of artificial intelligence based webshell detection model: A literature review

arXiv

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arXiv 2024年

作者： Ma, Mingrui Han, Lansheng Zhou, Chunjie Hubei Key Laboratory of Distributed System Security Hubei Engineering Research Center on Big Data Security School of Cyber Science and Engineering Huazhong University of Science and Technology Wuhan430074 China The Key Laboratory of Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Hubei Wuhan430074 China

Webshell, as the"culprit" behind numerous network attacks, is one of the research hotspots in the field of cybersecurity. However, the complexity, stealthiness, and confusing nature of webshells pose significant challenges to the corresponding detection schemes. With the rise of Artificial Intelligence (AI) technology, researchers have started to apply different intelligent algorithms and neural network architectures to the task of webshell detection. However, the related research still lacks a systematic and standardized methodological process, which is confusing and redundant. Therefore, following the development timeline, we carefully summarize the progress of relevant research in this field, dividing it into three stages: Start Stage, Initial Development Stage, and In-depth Development Stage. We further elaborate on the main characteristics and core algorithms of each stage. In addition, we analyze the pain points and challenges that still exist in this field and predict the future development trend of this field from our point of view. To the best of our knowledge, this is the first review that details the research related to AI-based webshell detection. It is also hoped that this paper can provide detailed technical information for more researchers interested in AI-based webshell detection tasks. Copyright © 2024, The Authors. All rights reserved.

关键词： Machine learning

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Research and application of Transformer based anomaly detection model: A literature review

arXiv

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arXiv 2024年

作者： Ma, Mingrui Han, Lansheng Zhou, Chunjie Hubei Key Laboratory of Distributed System Security Hubei Engineering Research Center on Big Data Security School of Cyber Science and Engineering Huazhong University of Science and Technology Hubei Wuhan430074 China The Key Laboratory of Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Hubei Wuhan430074 China

Transformer, as one of the most advanced neural network models in Natural Language processing (NLP), exhibits diverse applications in the field of anomaly detection. To inspire research on Transformer-based anomaly detection, this review offers a fresh perspective on the concept of anomaly detection. We explore the current challenges of anomaly detection and provide detailed insights into the operating principles of Transformer and its variants in anomaly detection tasks. Additionally, we delineate various application scenarios for Transformer-based anomaly detection models and discuss the datasets and evaluation metrics employed. Furthermore, this review highlights the key challenges in Transformer-based anomaly detection research and conducts a comprehensive analysis of future research trends in this domain. The review includes an extensive compilation of over 100 core references related to Transformer-based anomaly detection. To the best of our knowledge, this is the first comprehensive review that focuses on the research related to Transformer in the context of anomaly detection. We hope that this paper can provide detailed technical information to researchers interested in Transformer-based anomaly detection tasks. Copyright © 2024, The Authors. All rights reserved.

关键词： Anomaly detection

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Utility-Oriented Underwater image Quality Assessment Based on Transfer Learning

arXiv

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arXiv 2022年

作者： Chen, Weiling Lin, Rongfu Liao, Honggang Zhao, Tiesong Gu, Ke Le Callet, Patrick Fujian Key Lab for Intelligent Processing and Wireless Transmission of Media Information Fuzhou University Fuzhou350108 China Peng Cheng Laboratory Shenzhen518000 China The Faculty of Information Technology Beijing University of Technology Engineering Research Center of Intelligent Perception and Autonomous Control Ministry of Education Beijing Key Laboratory of Computational Intelligence and Intelligent System Beijing Artificial Intelligence Institute Beijing100124 China Équipe Image Perception et Interaction Laboratoire des Sciences du Numérique de Nantes Université de Nantes France

The widespread image applications have greatly promoted the vision-based tasks, in which the image Quality Assessment (IQA) technique has become an increasingly significant issue. For user enjoyment in multimedia systems, the IQA exploits image fidelity and aesthetics to characterize user experience;while for other tasks such as popular object recognition, there exists a low correlation between utilities and perceptions. In such cases, the fidelity-based and aesthetics-based IQA methods cannot be directly applied. To address this issue, this paper proposes a utility-oriented IQA in object recognition. In particular, we initialize our research in the scenario of underwater fish detection, which is a critical task that has not yet been perfectly addressed. Based on this task, we build an Underwater image Utility Database (UIUD) and a learning-based Underwater image Utility Measure (UIUM). Inspired by the top-down design of fidelity-based IQA, we exploit the deep models of object recognition and transfer their features to our UIUM. Experiments validate that the proposed transfer-learning-based UIUM achieves promising performance in the recognition task. We envision our research provides insights to bridge the researches of IQA and computer vision. Copyright © 2022, The Authors. All rights reserved.

关键词： Multimedia systems

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A novel method for identification of COPD in inspiratory and expiratory states of CT images

A novel method for identification of COPD in inspiratory and...

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Middle East Conference on Biomedical Engineering (MECBME)

作者： M. Parsa Hosseini Hamid Soltanian-Zadeh Shahram Akhlaghpoor Department of Electrical Engineering Islamic Azad University Tehran Iran Department of Radiology Henry Ford Health System Image Analysis and Communications Laboratory Detroit MI USA Control and Intelligent Processing Center of Excellence School of Electrical and Computer Engineering University of Tehran Tehran Iran Department of Radiology Tehran University of Medical Sciences Sina Hospital Tehran Iran

Chronic obstructive pulmonary disease (COPD) refers to a group of lung diseases that block airflow and cause a huge degree of human suffering. While there is no cure for COPD and the lung damage that results in this disease cannot be reversed, it is very important to diagnose it as early as possible. Additional to diagnosis, using a mathematical model to estimate severity of disease would be helpful for evaluation of treatment effects. This paper presents a new method for identifying COPD from three-dimensional (3-D) pulmonary X-ray CT images. The method has five main steps. First, corresponding positions of lungs in inspiration and expiration are found based on anatomical structures. Then, lung regions are segmented from the CT images by active contours. Next, the left and right lungs are separated using a sequence of morphological operations. Then, parenchyma variations in each lung are found as a relationship between inspiratory and expiratory states. Finally, a classifier is used to decide about the disease and its severity. A t-test is done to evaluate the results. Twelve patients with variable severity of COPD and twelve normal adults were included in this study. The proposed method may assist radiologists in the detection of COPD as a computer aided diagnosis (CAD) system.

关键词： Lungs Computed tomography Diseases image segmentation Biomedical imaging Gaussian distribution

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