Chest X-ray images have been highly involved in clinical diagnosis and treatment planning for thoracic disease. The process of medical images has attracted great attention in the machine learning community. However, the labeled medical images are limited and the regions of lesions are usually much smaller in the image. Most of the existing methods are prone to learning the spurious correlation for classification, resulting in poor generalization. In this paper, we propose a medical generation transformer network based on self-supervised learning and the adversarial strategy to capture the discriminative label-relevant regions with lesions in the images by extending the Chest X-ray images. In the proposed method, we first localize the label-relevant regions in each transformer layer. Then we keep the label-relevant regions to mask the image and construct the masked image with self-supervised learning. Thus we can generate more images to fine-tune the classification network with masked images that keep the label-relevant regions. Since the generated images are usually noisy to fine-tune the classification network, we adopt the adversarial probabilities to weight the importance of each generated image for training. Experimental results on two large-scale and popular chest X-ray datasets show that the proposed method can efficiently leverage the location of lesions to improve the performance of classification.

In a clinical setting, the acquisition of certain medical image modality is often unavailable due to various considerations such as cost, radiation, etc. Therefore, unpaired cross-modality translation techniques, which involve training on the unpaired data and synthesizing the target modality with the guidance of the acquired source modality, are of great interest. Previous methods for synthesizing target medical images are to establish one-shot mapping through generative adversarial networks (GANs). As promising alternatives to GANs, diffusion models have recently received wide interests in generative tasks. In this paper, we propose a target-guided diffusion model (TGDM) for unpaired cross-modality medical image translation. For training, to encourage our diffusion model to learn more visual concepts, we adopted a perception prioritized weight scheme (P2W) to the training objectives. For sampling, a pre-trained classifier is adopted in the reverse process to relieve modality-specific remnants from source data. Experiments on both brain MRI-CT and prostate MRI-US datasets demonstrate that the proposed method achieves a visually realistic result that mimics a vivid anatomical section of the target organ. In addition, we have also conducted a subjective assessment based on the synthesized samples to further validate the clinical value of TGDM.

Protein subcellular localization(PSL) is an important task to study human cell functions and cancer pathogenesis. It has attracted great attention in the computer vision community. However, the huge size of immune histochemical (IHC) images, the disorganized location distribution in different tissue images and the limited training images are always the challenges for the PSL to learn a strong generalization model with deep learning. In this paper, we propose a deep protein subcellular localization method with multi-marginal contrastive learning to perceive the same PSLs in different tissue images and different PSLs within the same tissue image. In the proposed method, we learn the representation of an IHC image by fusing the global features from the downsampled images and local features from the selected patches with the activation map to tackle the oversize of an IHC image. Then a multi-marginal attention mechanism is proposed to generate contrastive pairs with different margins and improve the discriminative features of PSL patterns effectively. Finally, the ensemble prediction of each IHC image is obtained with different patches. The results on the benchmark datasets show that the proposed method achieves significant improvements for the PSL task.

RNA-binding proteins (RBPs) play a significant part in several biological processes in the living cell, such as gene regulation and mRNA localization. Several deep learning methods, especially the model based on convolutional neural network(CNN), have been used to predict the binding sites. However, previous methods fail to represent RNA secondary structure features. The traditional deep learning methods generally transform the RNA secondary structure to a regular matrix that cannot reveal the topological structure information of RNA. To effectively extract the structure features of RNA, we propose an RNA secondary structure representation network (RNASSR-Net) based on graph convolutional neural network (GCN) and convolution neural network (CNN) for RBP binding prediction. RNASSR-Net constructs the graph model derived from the RNA secondary structure to learn the topological properties of RNA. Then, it obtains the spatial importance of each base in RNA with CNN to guide the representation of the RNA secondary structure. Finally, RNASSR-Net combines the structure and sequence features to predict the binding sites. Experimental results demonstrate the proposed method outperforms a few state-of-the-art methods on the benchmark datasets and gets a higher improvement on the small-size data. Besides, the proposed RNASSR-Net is also used to detect the accurate motifs compared with the experimentally verified motifs, which reveals the binding region location and RNA structure interpretation for some biological guidance in the future.