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- research-articleDecember 2024
Com-DNB: A novel method for identifying critical states of complex biological processes and its parallelization
BCB '24: Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health InformaticsArticle No.: 29, Pages 1–10https://doi.org/10.1145/3698587.3701338Identifying critical states prior to critical transitions in complex biological processes is essential for disease forecasting and early interventional therapy. Due to the complexity of the underlying mechanisms, the currently proposed methods based on ...
- research-articleOctober 2024
Serial Section Microscopy Image Inpainting Guided by Axial Optical Flow
MM '24: Proceedings of the 32nd ACM International Conference on MultimediaPages 2964–2972https://doi.org/10.1145/3664647.3681023Volume electron microscopy (vEM) is becoming a prominent technique in three-dimensional (3D) cellular visualization. vEM collects a series of two-dimensional (2D) images and reconstructs ultrastructures at the nanometer scale by rational axial ...
- ArticleAugust 2024
IG-GRD: A Model Based on Disentangled Graph Representation Learning for Imaging Genetic Data Fusion
Advanced Intelligent Computing Technology and ApplicationsPages 142–153https://doi.org/10.1007/978-981-97-5581-3_12AbstractIntegrating imaging and genetic data provides a comprehensive approach to analyze brain disorders from different perspectives, which has important implications for the early diagnosis of Alzheimer’s Disease (AD) and the exploration of its ...
- research-articleJuly 2024
Improving the classification of multiple sclerosis and cerebral small vessel disease with interpretable transfer attention neural network
- Wangshu Xu,
- Zhiwei Rong,
- Wenping Ma,
- Bin Zhu,
- Na Li,
- Jiansong Huang,
- Zhilin Liu,
- Yipei Yu,
- Fa Zhang,
- Xinghu Zhang,
- Ming Ge,
- Yan Hou
Computers in Biology and Medicine (CBIM), Volume 176, Issue Chttps://doi.org/10.1016/j.compbiomed.2024.108530AbstractAs an autoimmune-mediated inflammatory demyelinating disease of the central nervous system, multiple sclerosis (MS) is often confused with cerebral small vessel disease (cSVD), which is a regional pathological change in brain tissue with unknown ...
Highlights- The study pioneers an interpretable deep learning models for distinguishing between MS and cSVD based on T2-weighted FLAIR images.
- Employing pre-trained CNNs with attention modules, the model not only enhances feature learning ...
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- research-articleDecember 2023
Realize Generative Yet Complete Latent Representation for Incomplete Multi-View Learning
IEEE Transactions on Pattern Analysis and Machine Intelligence (ITPM), Volume 46, Issue 5Pages 3637–3652https://doi.org/10.1109/TPAMI.2023.3346869In multi-view environment, it would yield missing observations due to the limitation of the observation process. The most current representation learning methods struggle to explore complete information by lacking either cross-generative via simply ...
- ArticleOctober 2023
SaID: Simulation-Aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
AbstractCryo-Electron Microscopy (cryo-EM) is a revolutionary technique for determining the structures of proteins and macromolecules. Physical limitations of the imaging conditions cause a very low Signal-to-Noise Ratio (SNR) in cryo-EM micrographs, ...
- ArticleAugust 2023
GPU Optimization of Biological Macromolecule Multi-tilt Electron Tomography Reconstruction Algorithm
Advanced Intelligent Computing Technology and ApplicationsPages 473–484https://doi.org/10.1007/978-981-99-4749-2_40AbstractThree-dimensional (3D) reconstruction in cryo-electron tomography (cryo-ET) plays an important role in studying in situ biological macromolecular structures at the nanometer level. Owing to limited tilt angle, 3D reconstruction of cryo-ET always ...
- ArticleSeptember 2022
MLCN: Metric Learning Constrained Network for Whole Slide Image Classification with Bilinear Gated Attention Mechanism
Computational Mathematics Modeling in Cancer AnalysisPages 35–46https://doi.org/10.1007/978-3-031-17266-3_4AbstractWhole Slide Image (WSI) classification is an important part of pathological diagnosis. Although previous approaches (such as DSMIL and CLAM) have achieved good results, the classification performance is still unsatisfactory because the learned ...
- ArticleSeptember 2022
Joint Region-Attention and Multi-scale Transformer for Microsatellite Instability Detection from Whole Slide Images in Gastrointestinal Cancer
Medical Image Computing and Computer Assisted Intervention – MICCAI 2022Pages 293–302https://doi.org/10.1007/978-3-031-16434-7_29AbstractMicrosatellite instability (MSI) is a crucial biomarker to clinical immunotherapy in gastrointestinal cancer, while additional immunohistochemical or genetic tests for MSI are generally missing due to lack of medical resources. Deep learning has ...
- research-articleAugust 2022
TransSurv: Transformer-Based Survival Analysis Model Integrating Histopathological Images and Genomic Data for Colorectal Cancer
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 20, Issue 6Pages 3411–3420https://doi.org/10.1109/TCBB.2022.3199244Survival analysis is a significant study in cancer prognosis, and the multi-modal data, including histopathological images, genomic data, and clinical information, provides unprecedented opportunities for its development. However, because of the high ...
- ArticleAugust 2022
Predicting Drug-Disease Associations by Self-topological Generalized Matrix Factorization with Neighborhood Constraints
Intelligent Computing Theories and ApplicationPages 138–149https://doi.org/10.1007/978-3-031-13829-4_12AbstractPredicting drug-disease associations (DDAs) is a significant part of drug discovery. With the continuous accumulation of biomedical data, multidimensional metrics about drugs and diseases are obtained, therefore how to effectively integrate them ...
- research-articleSeptember 2022
Urban traffic optimal solution based on digital twin system technology simulation
ICCMS '22: Proceedings of the 14th International Conference on Computer Modeling and SimulationPages 83–87https://doi.org/10.1145/3547578.3547591At present, with the continuous improvement of residents' quality of life, the increasing number of private cars and the expansion of urban residents, the traffic pressure is increasing. How to choose the best route of urban traffic, shorten the travel ...
- research-articleJune 2022
VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms
Computer Methods and Programs in Biomedicine (CBIO), Volume 221, Issue Chttps://doi.org/10.1016/j.cmpb.2022.106871AbstractBackground and objective: Cryo-electron tomography (cryo-ET) with subtomogram averaging (STA) is indispensable when studying macromolecule structures and functions in their native environments. Due to the low signal-to-noise ratio, the missing ...
- ArticleNovember 2021
PickerOptimizer: A Deep Learning-Based Particle Optimizer for Cryo-Electron Microscopy Particle-Picking Algorithms
AbstractCryo-electron microscopy single particle analysis requires tens of thousands of particle projections for the structural determination of macromolecules. To free researchers from laborious particle picking work, a number of fully automatic and semi-...
- ArticleAugust 2021
Predicting Drug-Disease Associations Based on Network Consistency Projection
Intelligent Computing Theories and ApplicationPages 591–602https://doi.org/10.1007/978-3-030-84532-2_53AbstractWith the increasing cost of traditional drug discovery, drug repositioning methods at low cost have attracting increasing attention. The generation of large amounts of biomedical data also provides unprecedented opportunities for drug ...
- ArticleAugust 2021
Decomposition-and-Fusion Network for HE-Stained Pathological Image Classification
- Rui Yan,
- Jintao Li,
- S. Kevin Zhou,
- Zhilong Lv,
- Xueyuan Zhang,
- Xiaosong Rao,
- Chunhou Zheng,
- Fei Ren,
- Fa Zhang
Intelligent Computing Theories and ApplicationPages 198–207https://doi.org/10.1007/978-3-030-84532-2_18AbstractBuilding upon the clinical evidence supporting that decomposing a pathological image into different components can improve diagnostic value, in this paper we propose a Decomposition-and-Fusion Network (DFNet) for HE-stained pathological image ...