12 research outputs found
LDCSF: Local depth convolution-based Swim framework for classifying multi-label histopathology images
Histopathological images are the gold standard for diagnosing liver cancer.
However, the accuracy of fully digital diagnosis in computational pathology
needs to be improved. In this paper, in order to solve the problem of
multi-label and low classification accuracy of histopathology images, we
propose a locally deep convolutional Swim framework (LDCSF) to classify
multi-label histopathology images. In order to be able to provide local field
of view diagnostic results, we propose the LDCSF model, which consists of a
Swin transformer module, a local depth convolution (LDC) module, a feature
reconstruction (FR) module, and a ResNet module. The Swin transformer module
reduces the amount of computation generated by the attention mechanism by
limiting the attention to each window. The LDC then reconstructs the attention
map and performs convolution operations in multiple channels, passing the
resulting feature map to the next layer. The FR module uses the corresponding
weight coefficient vectors obtained from the channels to dot product with the
original feature map vector matrix to generate representative feature maps.
Finally, the residual network undertakes the final classification task. As a
result, the classification accuracy of LDCSF for interstitial area, necrosis,
non-tumor and tumor reached 0.9460, 0.9960, 0.9808, 0.9847, respectively.
Finally, we use the results of multi-label pathological image classification to
calculate the tumor-to-stromal ratio, which lays the foundation for the
analysis of the microenvironment of liver cancer histopathological images.
Second, we released a multilabel histopathology image of liver cancer, our code
and data are available at https://github.com/panliangrui/LSF.Comment: Submitted to BIBM202
CVFC: Attention-Based Cross-View Feature Consistency for Weakly Supervised Semantic Segmentation of Pathology Images
Histopathology image segmentation is the gold standard for diagnosing cancer,
and can indicate cancer prognosis. However, histopathology image segmentation
requires high-quality masks, so many studies now use imagelevel labels to
achieve pixel-level segmentation to reduce the need for fine-grained
annotation. To solve this problem, we propose an attention-based cross-view
feature consistency end-to-end pseudo-mask generation framework named CVFC
based on the attention mechanism. Specifically, CVFC is a three-branch joint
framework composed of two Resnet38 and one Resnet50, and the independent branch
multi-scale integrated feature map to generate a class activation map (CAM); in
each branch, through down-sampling and The expansion method adjusts the size of
the CAM; the middle branch projects the feature matrix to the query and key
feature spaces, and generates a feature space perception matrix through the
connection layer and inner product to adjust and refine the CAM of each branch;
finally, through the feature consistency loss and feature cross loss to
optimize the parameters of CVFC in co-training mode. After a large number of
experiments, An IoU of 0.7122 and a fwIoU of 0.7018 are obtained on the
WSSS4LUAD dataset, which outperforms HistoSegNet, SEAM, C-CAM, WSSS-Tissue, and
OEEM, respectively.Comment: Submitted to BIBM202
PACS: Prediction and analysis of cancer subtypes from multi-omics data based on a multi-head attention mechanism model
Due to the high heterogeneity and clinical characteristics of cancer, there
are significant differences in multi-omic data and clinical characteristics
among different cancer subtypes. Therefore, accurate classification of cancer
subtypes can help doctors choose the most appropriate treatment options,
improve treatment outcomes, and provide more accurate patient survival
predictions. In this study, we propose a supervised multi-head attention
mechanism model (SMA) to classify cancer subtypes successfully. The attention
mechanism and feature sharing module of the SMA model can successfully learn
the global and local feature information of multi-omics data. Second, it
enriches the parameters of the model by deeply fusing multi-head attention
encoders from Siamese through the fusion module. Validated by extensive
experiments, the SMA model achieves the highest accuracy, F1 macroscopic, F1
weighted, and accurate classification of cancer subtypes in simulated,
single-cell, and cancer multiomics datasets compared to AE, CNN, and GNN-based
models. Therefore, we contribute to future research on multiomics data using
our attention-based approach.Comment: Submitted to BIBM202
Multi-Head Attention Mechanism Learning for Cancer New Subtypes and Treatment Based on Cancer Multi-Omics Data
Due to the high heterogeneity and clinical characteristics of cancer, there
are significant differences in multi-omics data and clinical features among
subtypes of different cancers. Therefore, the identification and discovery of
cancer subtypes are crucial for the diagnosis, treatment, and prognosis of
cancer. In this study, we proposed a generalization framework based on
attention mechanisms for unsupervised contrastive learning (AMUCL) to analyze
cancer multi-omics data for the identification and characterization of cancer
subtypes. AMUCL framework includes a unsupervised multi-head attention
mechanism, which deeply extracts multi-omics data features. Importantly, a
decoupled contrastive learning model (DMACL) based on a multi-head attention
mechanism is proposed to learn multi-omics data features and clusters and
identify new cancer subtypes. This unsupervised contrastive learning method
clusters subtypes by calculating the similarity between samples in the feature
space and sample space of multi-omics data. Compared to 11 other deep learning
models, the DMACL model achieved a C-index of 0.002, a Silhouette score of
0.801, and a Davies Bouldin Score of 0.38 on a single-cell multi-omics dataset.
On a cancer multi-omics dataset, the DMACL model obtained a C-index of 0.016, a
Silhouette score of 0.688, and a Davies Bouldin Score of 0.46, and obtained the
most reliable cancer subtype clustering results for each type of cancer.
Finally, we used the DMACL model in the AMUCL framework to reveal six cancer
subtypes of AML. By analyzing the GO functional enrichment, subtype-specific
biological functions, and GSEA of AML, we further enhanced the interpretability
of cancer subtype analysis based on the generalizable AMUCL framework
Calibration and Distortion Field Compensation of Gradiometer and the Improvement in Object Remote Sensing
Magnetometer, misalignment error and distortion field can reduce the accuracy of gradiometers. So, it is important to calibrate and compensate gradiometers error. Scale factor, bias, nonorthogonality, misalignment and distortion field should be considered. A gradiometer is connected by an aluminium frame, which contains two fluxgate magnetometers. A nonmagnetic rotation equipment is used to change gradiometer attitude, and the compensation parameters are estimated. Experiment results show that, after calibration and compensation, error of each axis is reduced from 888.4 nT, 1292.6 nT and 168.9 nT to 15.3 nT, 22.1 nT and 9.9 nT, respectively. It shows that the proposed method can calibrate gradiometer and compensate distortion field. After calibration and compensation, the object remote sensing performance is improved
Calibration and Distortion Field Compensation of Gradiometer and the Improvement in Object Remote Sensing
Magnetometer, misalignment error and distortion field can reduce the accuracy of gradiometers. So, it is important to calibrate and compensate gradiometers error. Scale factor, bias, nonorthogonality, misalignment and distortion field should be considered. A gradiometer is connected by an aluminium frame, which contains two fluxgate magnetometers. A nonmagnetic rotation equipment is used to change gradiometer attitude, and the compensation parameters are estimated. Experiment results show that, after calibration and compensation, error of each axis is reduced from 888.4 nT, 1292.6 nT and 168.9 nT to 15.3 nT, 22.1 nT and 9.9 nT, respectively. It shows that the proposed method can calibrate gradiometer and compensate distortion field. After calibration and compensation, the object remote sensing performance is improved