Coronary artery disease (CAD) is responsible for the largest number of human deaths in many countries. Segmentation of coronary artery stenosis is valuable for the diagnosis and treatment of CAD. However, two challenges still exist: 1) Complex structure and various sizes of vessels; 2)Blurry boundaries. In this work, we introduce a novel approach for coronary artery segmentation, namely Kernal-size attention guidance dual-branch network (KSAG-Net). Specifically, a dual-branch network consisting of global branch and detail branch was designed for extracting high-dimensional shape features and low-dimensional texture information of coronary artery, respectively. Further, to make our model more sensitive to complex structure and fine-grained vascular targets, kernel-size attention (KSA) is designed to combine the features extracted by dual-branch extraction and guide the model to form attention to both shape and texture information. And the edge enhancement (EE) module is used to maintain and refine the ambiguous boundaries of the coronary arteries by mining boundary information and incorporating reverse attention. By integrating these modules into our dual-branch encoder, our method is able to segment the coronary arteries more accurately. Experiments on the coronary artery datasets show that our method obtains better results and outperforms many existing 2D methods.

Missed polyps are the major risk factor for colorectal cancer. To minimize misdiagnosis, many methods have been developed. However, they either rely on laborious instance-level annotations, require labeling of prompt points, or lack the ability to filter noise proposals and detect polyps integrally, resulting in severe challenges in this area. In this paper, we propose a novel Cooperation-Based network (CBNet), a two-stage polyp detection framework supervised by image labels that removes wrong proposals through classification in collaboration with segmentation and obtains a more accurate detector by aggregating adaptive multi-level regional features. Specifically, we conduct a Cooperation-Based Region Proposal Network (CBRPN) to reduce the negative impact of noises by deleting proposals without polyps, enabling our network to capture polyp features. Moreover, to enhance location integrity and classification precision of polyps, we aggregate multi-level region of interest (ROI) features under the guidance of the backbone classification layer, namely Adaptive ROI Fusion Module (ARFM). Extensive experiments on the public and private datasets show that our method achieves state-of-the-art performance for weakly supervised methods and even outperforms full supervision in some terms. All code is available at https://github.com/dxqllp/CBNet.

The recognition of DNA- (DBPs) and RNA-binding proteins (RBPs) is not only conducive to understanding cell function, but also a challenging task. Previous studies have shown that these proteins are usually considered separately due to different binding domains. In addition, due to the high similarity between DBPs and RBPs, it is possible for DBPs predictor to predict RBPs as DBPs, and vice versa, which leads to high cross-prediction rate. In this study, we creatively propose a novel deep multi-label joint learning framework to leverage the relationship between multiple labels and binding proteins. First, a multi-label variant network is designed to explore multi-scale context hidden information. Then, multi-label Long Short-Term Memory (multiLSTM) is used to mine the potential relationship between labels. Finally, the calibrated hidden features from variant network are considered for different levels of joint learning so that multiLSTM can better explore the correlation between them. Extensive experiments are also carried out to compare the proposed method with other existing methods. Furthermore, we also provide further insights into the importance of the relevant bioanalysis of proteins obtained from our model and summarize these binding proteins that are significantly related to a disease. Our method is freely available at http://39.108.90.186/dmlj.

The discovery of transcription factor binding sites(TFBSs) is important for modeling potential binding mechanisms and subsequent cellular functions. In recent years, there have been many deep learning methods that have achieved good results in predicting transcription factor binding sites. However, these methods usually follow the fully supervised approach and ignore the weakly supervised information in DNA sequences. In contrast, the currently proposed multiple instance learing(MIL) methods based on weakly supervised learning usually divide the DNA sequence into multiple overlapping subsequences and model each instance separately. These methods do not take into account the connections between overlapping subsequences, and these methods destroy the global information of the sequences in the process of dividing them into overlapping subsequences. In addition, deep learning methods generally perform poorly when there is less training data. We, therefore, propose a new deep learning method, DS-SSB. More specifically, DS-SSB combines the dual-stream multiple instance network with multiple features. First, we combine sequence features and shape features after feature extraction at the instance level to enhance the feature representation of instances. Then, the instance embeddings are aggregated into bag embedding through the dual-stream multiple instance network, and the relationships between the instances are considered in the aggregation process. Finally, the instance features fused into bag features are fused together with the BERT features of the whole sequence at the bag level for the final prediction. Experiments conducted on 690 ChIP-seq datasets showed that DS-SSB achieved good performance in predicting TFBSs. Also, experiments on four datasets further show that our method has an advantage on small datasets as well

Precise segmentation of polyps from colonoscopic images is extremely significant for the early diagnosis and treatment of colorectal cancer. However, it is still a challenging task due to: (1)the boundary between the polyp and the background is blurred makes delineation difficult; (2)the various size and shapes causes feature representation of polyps difficult. In this paper, we propose an integration context-based reverse-contour guidance network (ICGNet) to solve these challenges. The ICGNet firstly utilizes a reverse-contour guidance module to aggregate low-level edge detail information and meanwhile constraint reverse region. Then, the newly designed adaptive context module is used to adaptively extract local-global information of the current layer and complementary information of the previous layer to get larger and denser features. Lastly, an innovative hybrid pyramid pooling fusion module fuses the multi-level features generated from the decoder in the case of considering salient features and less background. Our proposed approach is evaluated on the EndoScene, Kvasir-SEG and CVC-ColonDB datasets with eight evaluation metrics, and gives competitive results compared with other state-of-the-art methods in both learning ability and generalization capability.

The cardiac CT and MRI images depict the various structures of the heart, which are very valuable for analyzing heart function. However, due to the difference in the shape of the cardiac images and imaging techniques, automatic segmentation is challenging. To solve this challenge, in this paper, we propose a new constraint-based unsupervised domain adaptation network. This network first performs mutual translation of images between different domains, it can provide training data for the segmentation model, and ensure domain invariance at the image level. Then, we input the target domain into the source domain segmentation model to obtain pseudo-labels and introduce cross-domain self-supervised learning between the two segmentation models. Here, a new loss function is designed to ensure the accuracy of the pseudo-labels. In addition, a cross-domain consistency loss is also introduced. Finally, we construct a multi-level aggregation segmentation network to obtain more refined target domain information. We validate our method on the public whole heart image segmentation challenge dataset and obtain experimental results of 82.9% and 5.5 on dice and average symmetric surface distance (ASSD), respectively. These experimental results prove that our method can provide important assistance in the clinical evaluation of unannotated cardiac datasets.

Three-dimensional late gadolinium enhanced (LGE) cardiac MR (CMR) of left atrial scar in patients with atrial fibrillation (AF) has recently emerged as a promising technique to stratify patients, to guide ablation therapy and to predict treatment success. This requires a segmentation of the high intensity scar tissue and also a segmentation of the left atrium (LA) anatomy, the latter usually being derived from a separate bright-blood acquisition. Performing both segmentations automatically from a single 3D LGE CMR acquisition would eliminate the need for an additional acquisition and avoid subsequent registration issues. In this paper, we propose a joint segmentation method based on multiview two-task (MVTT) recursive attention model working directly on 3D LGE CMR images to segment the LA (and proximal pulmonary veins) and to delineate the scar on the same dataset. Using our MVTT recursive attention model, both the LA anatomy and scar can be segmented accurately (mean Dice score of 93% for the LA anatomy and 87% for the scar segmentations) and efficiently (∼0.27 s to simultaneously segment the LA anatomy and scars directly from the 3D LGE CMR dataset with 60–68 2D slices). Compared to conventional unsupervised learning and other state-of-the-art deep learning based methods, the proposed MVTT model achieved excellent results, leading to an automatic generation of a patient-specific anatomical model combined with scar segmentation for patients in AF.

Quantitative analysis of the heart is extremely necessary and significant for detecting and diagnosing heart disease, yet there are still some challenges. In this study, we propose a new end-to-end segmentation-based deep multi-task regression learning model (Indices-JSQ) to make a holonomic quantitative analysis of the left ventricle (LV), which contains a segmentation network (Img2Contour) and multi-task regression network (Contour2Indices). First, Img2Contour, which contains a deep convolutional encoder-decoder module, is designed to obtain the LV contour. Then, the predicted contour is fed as input to Contour2Indices for full quantification. On the whole, we take into account the relationship between different tasks, which can serve as a complementary advantage. Meanwhile, instead of using images directly from the original dataset, we creatively use the segmented contour of the original image to estimate the cardiac indices to achieve better and more accurate results. We make experiments on MR sequences of 145 subjects and gain the experimental results of 157 mm2, 2.43 mm, 1.29 mm, and 0.87 on areas, dimensions, regional wall thicknesses, and Dice Metric, respectively. It intuitively shows that the proposed method outperforms the other state-of-the-art methods and demonstrates that our method has a great potential in cardiac MR images segmentation, comprehensive clinical assessment, and diagnosis.