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Register a new userA Hierarchical Conditional Random Field-based Attention Mechanism Approach for Gastric Histopathology Image Classification
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Yixin Li
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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.
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Existing deep learning methods for diagnosis of gastric cancer commonly use convolutional neural network. Recently, the Visual Transformer has attracted great attention because of its performance and efficiency, but its applications are mostly in the field of computer vision. In this paper, a multi-scale visual transformer model, referred to as GasHis-Transformer, is proposed for Gastric Histopathological Image Classification (GHIC), which enables the automatic classification of microscopic gastric images into abnormal and normal cases. The GasHis-Transformer model consists of two key modules: A global information module and a local information module to extract histopathological features effectively. In our experiments, a public hematoxylin and eosin (H&E) stained gastric histopathological dataset with 280 abnormal and normal images are divided into training, validation and test sets by a ratio of 1 : 1 : 2. The GasHis-Transformer model is applied to estimate precision, recall, F1-score and accuracy on the test set of gastric histopathological dataset as 98.0%, 100.0%, 96.0% and 98.0%, respectively. Furthermore, a critical study is conducted to evaluate the robustness of GasHis-Transformer, where ten different noises including four adversarial attack and six conventional image noises are added. In addition, a clinically meaningful study is executed to test the gastrointestinal cancer identification performance of GasHis-Transformer with 620 abnormal images and achieves 96.8% accuracy. Finally, a comparative study is performed to test the generalizability with both H&E and immunohistochemical stained images on a lymphoma image dataset and a breast cancer dataset, producing comparable F1-scores (85.6% and 82.8%) and accuracies (83.9% and 89.4%), respectively. In conclusion, GasHisTransformer demonstrates high classification performance and shows its significant potential in the GHIC task.
Subspace learning (SL) plays an important role in hyperspectral image (HSI) classification, since it can provide an effective solution to reduce the redundant information in the image pixels of HSIs. Previous works about SL aim to improve the accuracy of HSI recognition. Using a large number of labeled samples, related methods can train the parameters of the proposed solutions to obtain better representations of HSI pixels. However, the data instances may not be sufficient enough to learn a precise model for HSI classification in real applications. Moreover, it is well-known that it takes much time, labor and human expertise to label HSI images. To avoid the aforementioned problems, a novel SL method that includes the probability assumption called subspace learning with conditional random field (SLCRF) is developed. In SLCRF, first, the 3D convolutional autoencoder (3DCAE) is introduced to remove the redundant information in HSI pixels. In addition, the relationships are also constructed using the spectral-spatial information among the adjacent pixels. Then, the conditional random field (CRF) framework can be constructed and further embedded into the HSI SL procedure with the semi-supervised approach. Through the linearized alternating direction method termed LADMAP, the objective function of SLCRF is optimized using a defined iterative algorithm. The proposed method is comprehensively evaluated using the challenging public HSI datasets. We can achieve stateof-the-art performance using these HSI sets.
GasHisSDB is a New Gastric Histopathology Subsize Image Database with a total of 245196 images. GasHisSDB is divided into 160*160 pixels sub-database, 120*120 pixels sub-database and 80*80 pixels sub-database. GasHisSDB is made to realize the function of valuating image classification. 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 CNN classifiers and a novel transformer-based classifier are selected for testing on image classification tasks. GasHisSDB is available at the URL:https://github.com/NEUhwm/GasHisSDB.git.
Attention modules connecting encoder and decoders have been widely applied in the field of object recognition, image captioning, visual question answering and neural machine translation, and significantly improves the performance. In this paper, we propose a bottom-up gated hierarchical attention (GHA) mechanism for image captioning. Our proposed model employs a CNN as the decoder which is able to learn different concepts at different layers, and apparently, different concepts correspond to different areas of an image. Therefore, we develop the GHA in which low-level concepts are merged into high-level concepts and simultaneously low-level attended features pass to the top to make predictions. Our GHA significantly improves the performance of the model that only applies one level attention, for example, the CIDEr score increases from 0.923 to 0.999, which is comparable to the state-of-the-art models that employ attributes boosting and reinforcement learning (RL). We also conduct extensive experiments to analyze the CNN decoder and our proposed GHA, and we find that deeper decoders cannot obtain better performance, and when the convolutional decoder becomes deeper the model is likely to collapse during training.
The medical image is characterized by the inter-class indistinction, high variability, and noise, where the recognition of pixels is challenging. Unlike previous self-attention based methods that capture context information from one level, we reformulate the self-attention mechanism from the view of the high-order graph and propose a novel method, namely Hierarchical Attention Network (HANet), to address the problem of medical image segmentation. Concretely, an HA module embedded in the HANet captures context information from neighbors of multiple levels, where these neighbors are extracted from the high-order graph. In the high-order graph, there will be an edge between two nodes only if the correlation between them is high enough, which naturally reduces the noisy attention information caused by the inter-class indistinction. The proposed HA module is robust to the variance of input and can be flexibly inserted into the existing convolution neural networks. We conduct experiments on three medical image segmentation tasks including optic disc/cup segmentation, blood vessel segmentation, and lung segmentation. Extensive results show our method is more effective and robust than the existing state-of-the-art methods.
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