High-quality genome chromosome-scale sequences provide an important basis for genomics downstream analysis, especially the construction of haplotype-resolved and complete genomes, which plays a key role in genome annotation, mutation detection, evolutionary analysis, gene function research, comparative genomics and other aspects. However, genome-wide short-read sequencing is difficult to produce a complete genome in the face of a complex genome with high duplication and multiple heterozygosity. The emergence of long-read sequencing technology has greatly improved the integrity of complex genome assembly. We review a variety of computational methods for complex genome assembly and describe in detail the theories, innovations and shortcomings of collapsed, semi-collapsed and uncollapsed assemblers based on long reads. Among the three methods, uncollapsed assembly is the most correct and complete way to represent genomes. In addition, genome assembly is closely related to haplotype reconstruction, that is uncollapsed assembly realizes haplotype reconstruction, and haplotype reconstruction promotes uncollapsed assembly. We hope that gapless, telomere-to-telomere and accurate assembly of complex genomes can be truly routinely achieved using only a simple process or a single tool in the future.

Automated organ segmentation in CTs is an essential prerequisite for many clinical applications, such as computer-aided diagnosis and intervention. As medical data annotation requires massive human labor from experienced radiologists, how to effectively improve the segmentation performance with limited annotated training data remains a challenging problem. Few-shot learning imitates the learning process of humans, which turns out to be a promising way to overcome the aforementioned challenge. In this paper, we propose a novel anatomical knowledge embedded few-shot network (AKFNet), where an anatomical knowledge embedded support unit (AKSU) is carefully designed to embed the anatomical priors from support images into our model. Moreover, a similarity guidance alignment unit (SGAU) is proposed to impose a mutual alignment between the support and query sets. As a result, AKFNet fully exploits anatomical knowledge and presents good learning capability. Without bells and whistles, AKFNet outperforms the state-of-the-art methods with 0.84-1.76% Dice increase. Transfer learning experiments further verify its learning capability.

With the development of video coding technology, high-efficiency video coding (HEVC) has become a promising alternative, compared with the previous coding standards, for example, H.264. In general, H.264 to HEVC transcoding can be accomplished by fully H.264 decoding and fully HEVC encoding, which suffers from considerable time consumption on the brute-force search of the HEVC coding tree unit (CTU) partition for rate-distortion optimization (RDO). In this paper, we propose a deep learning method to predict the HEVC CTU partition, instead of the brute-force RDO search, for H.264 to HEVC transcoding. First, we build a large-scale H.264 to HEVC transcoding database. Second, we investigate the correlation between the HEVC CTU partition and H.264 features, and analyze both temporal and spatial-temporal similarities of the CTU partition across video frames. Third, we propose a deep learning architecture of a hierarchical long short-term memory (H-LSTM) network to predict the CTU partition of HEVC. Then, the brute-force RDO search of the CTU partition is replaced by the H-LSTM prediction such that the computational time can be significantly reduced for fast H.264 to HEVC transcoding. Finally, the experimental results verify that the proposed H-LSTM method can achieve a better tradeoff between coding efficiency and complexity, compared to the state-of-the-art H.264 to HEVC transcoding methods.

For H.264 to high efficiency video coding (HEVC) transcoding, this paper proposes a hierarchical Long Short-Term Memory (LSTM) method to predict coding unit (CU) splitting. Specifically, we first analyze the correlation between CU splitting patterns and H.264 features. Upon our analysis, we further propose a hierarchical LSTM architecture for predicting CU splitting of HEVC, with regard to the explored H.264 features. The features of H.264, including residual, macroblock (MB) partition and bit allocation, are employed as the input to our LSTM method. Experimental results demonstrate that the proposed method outperforms the state-of-the-art H.264 to HEVC transcoding methods, in terms of both complexity reduction and PSNR performance.

In this letter, we propose a road structure refined convolutional neural network (RSRCNN) approach for road extraction in aerial images. In order to obtain structured output of road extraction, both deconvolutional and fusion layers are designed in the architecture of RSRCNN. For training RSRCNN, a new loss function is proposed to incorporate the geometric information of road structure in cross-entropy loss, thus called road-structure-based loss function. Experimental results demonstrate that the trained RSRCNN model is able to advance the state-of-the-art road extraction for aerial images, in terms of precision, recall, F-score, and accuracy.