Transposable elements (TEs) are DNA sequences that can move within a genome. They constitute a substantial portion of the eukaryotic genome and play essential roles in gene regulation and genome evolution. Accurate classification of these repetitive elements is crucial for investigating their potential impact on the genome. Over the past few decades, several alignment-based tools have been developed to annotate TE types. While these methods rely heavily on prior knowledge and are often computationally expensive, machine learning-based approaches have been proposed to overcome these limitations. However, most of these approaches fail to capture the multiscale features of TEs, resulting in suboptimal performance. Here, we propose a novel framework called CREATE, which simultaneously integrates the global pattern distribution and the local sequence profile of TEs using Convolutional neural networks and Recurrent neural nEtworks with an Attention mechanism for efficient TE classification. Due to the hierarchical structure of TE groups, we trained nine classifiers corresponding to parent nodes within the class hierarchy. We further applied a top-down hierarchical classification strategy to achieve a more complete classification of unknown TEs. Comprehensive experiments demonstrate that CREATE outperforms existing TE-type annotation methods and achieves superior performance in hierarchical classification tasks. In conclusion, CREATE exhibits great potential for improving the accuracy of TE annotation. The source code and demo data are available at https://github.com/yangqi-cs/CREATE.

Accurate prediction of binding between human leukocyte antigen (HLA) class I molecules and antigenic peptide segments is a challenging task and a key bottleneck in personalized immunotherapy for cancer. Although existing prediction tools have demonstrated significant results using established datasets, most can only predict the binding affinity of antigenic peptides to HLA and do not enable the immunogenic interpretation of new antigenic epitopes. This limitation results from the training data for the computational models relying heavily on a large amount of peptide-HLA (pHLA) eluting ligand data, in which most of the candidate epitopes lack immunogenicity. Here, we propose an adaptive immunogenicity prediction model, named MHLAPre, which is trained on the large-scale MS-derived HLA I eluted ligandome (mostly presented by epitopes) that are immunogenic. Allele-specific and pan-allelic prediction models are also provided for endogenous peptide presentation. Using a meta-learning strategy, MHLAPre rapidly assessed HLA class I peptide affinities across the whole pHLA pairs and accurately identified tumor-associated endogenous antigens. During the process of adaptive immune response of T-cells, pHLA-specific binding in the antigen presentation is only a pre-task for CD8+ T-cell recognition. The key factor in activating the immune response is the interaction between pHLA complexes and T-cell receptors (TCRs). Therefore, we performed transfer learning on the pHLA model using the pHLA-TCR dataset. In pHLA binding task, MHLAPre demonstrated significant improvement in identifying neoepitope immunogenicity compared with five state-of-the-art models, proving its effectiveness and robustness. After transfer learning of the pHLA-TCR data, MHLAPre also exhibited relatively superior performance in revealing the mechanism of immunotherapy. MHLAPre is a powerful tool to identify neoepitopes that can interact with TCR and induce immune responses. We believe that the proposed method will greatly contribute to clinical immunotherapy, such as anti-tumor immunity, tumor-specific T-cell engineering, and personalized tumor vaccine.

Comprehensive modeling of the surrounding 3D world is crucial for the success of autonomous driving. However, existing perception tasks like object detection, road structure segmentation, depth & elevation estimation, and open-set object localization each only focus on a small facet of the holistic 3D scene understanding task. This divide-and-conquer strategy simplifies the algorithm development process but comes at the cost of losing an end-to-end unified solution to the problem. In this work, we address this limitation by studying camera-based 3D panoptic segmentation, aiming to achieve a unified occupancy representation for camera-only 3D scene understanding. To achieve this, we introduce a novel method called PanoOcc, which utilizes voxel queries to aggregate spatiotemporal information from multi-frame and multi-view images in a coarse-to-fine scheme, integrating feature learning and scene representation into a unified occupancy representation. We have conducted extensive ablation studies to validate the effectiveness and efficiency of the proposed method. Our approach achieves new state-of-the-art results for camera-based semantic segmentation and panoptic segmentation on the nuScenes dataset. Furthermore, our method can be easily extended to dense occupancy prediction and has demonstrated promising performance on the Occ3D benchmark. The code will be made available at https://github.com/Robertwyq/PanoOcc.

General Instance Re-identification is a very important task in computer vision, which can be widely used in many practical applications, such as person/vehicle re-identification, face recognition, wildlife protection, commodity tracing, snapshots, and so on. To meet the increasing application demand for general instance re-identification, we present FastReID as a widely used software system. In FastReID, the highly modular and extensible design makes it easy for the researcher to achieve new research ideas. Friendly manageable system configuration and engineering deployment functions allow practitioners to quickly deploy models into productions. We have implemented some state-of-the-art projects, including person re-id, partial re-id, cross-domain re-id, and vehicle re-id. Moreover, we plan to release these pre-trained models on multiple benchmark datasets. FastReID is by far the most general and high-performance toolbox that supports single and multiple GPU servers, it can reproduce our project results very easily. The source codes and models have been released at https://github.com/JDAI-CV/fast-reid.

Person re-identification (Re-ID) aims to match pedestrians under dis-joint cameras. Most Re-ID methods formulate it as visual representation learning and image search, and its accuracy is consequently affected greatly by the search space. Spatial-temporal information has been proven to be efficient to filter irrelevant negative samples and significantly improve Re-ID accuracy. However, existing spatial-temporal person Re-ID methods are still rough and do not exploit spatial-temporal information sufficiently. In this paper, we propose a novel Instance-level and Spatial-Temporal Disentangled Re-ID method (InSTD), to improve Re-ID accuracy. In our proposed framework, personalized information such as moving direction is explicitly considered to further narrow down the search space. Besides, the spatial-temporal transferring probability is disentangled from joint distribution to marginal distribution, so that outliers can also be well modeled. Abundant experimental analyses are presented, which demonstrates the superiority and provides more insights into our method. The proposed method achieves mAP of 90.8% on Market-1501 and 89.1% on DukeMTMC-reID, improving from the baseline 82.2% and 72.7%, respectively. Besides, in order to provide a better benchmark for person re-identification, we release a cleaned data list of DukeMTMC-reID with this paper: https://github.com/RenMin1991/cleaned-DukeMTMC-reID/

Multi-Object Tracking (MOT) and Person Search both demand to localize and identify specific targets from raw image frames. Existing methods can be classified into two categories, namely two-step strategy and end-to-end strategy. Two-step approaches have high accuracy but suffer from costly computations, while end-to-end methods show greater efficiency with limited performance. In this paper, we dissect the gap between two-step and end-to-end strategy and propose a simple yet effective end-to-end framework with knowledge distillation. Our proposed framework is simple in concept and easy to benefit from external datasets. Experimental results demonstrate that our model performs competitively with other sophisticated two-step and end-to-end methods in multi-object tracking and person search.

Wireless sensor networks (WSN) have been widely used in the field of industrial Internet of Things (IoT), one of the main security challenges is how to protect the transmission of sensitive data between sensors in the wireless channel. Key management is one of the most challenging work. Most IoT sensors' resources are limited, so the key management scheme should be designed to be as lightweight as possible. Generally, schemes can be divided into two categories: pairwise key management and group key management, but each of them has its limitations. In this paper, we propose a dynamic membership authentication and key management scheme for WSN. In our scheme, we add the access object authentication and key update mechanism, ensure the authenticity of the connected object and key freshness. Compared with other schemes, our solution ensures forward and backward secrecy and resists capture attacks. We finally demonstrate that our scheme is of confidentiality, integrity, and scalability for resource-constrained WSN.

MOTIVATION: Compared with the second-generation sequencing technologies, the third-generation sequencing technologies allows us to obtain longer reads (average ∼10 kbps, maximum 900 kbps), but brings a higher error rate (∼15% error rate). Nanopolish is a variant and methylation detection tool based on hidden Markov model, which uses Oxford Nanopore sequencing data for signal-level analysis. Nanopolish can greatly improve the accuracy of assembly, whereas it is limited by long running time since most executive parts of Nanopolish is a serial and computationally expensive process. RESULTS: In this paper, we present an effective polishing tool, Multithreading Nanopolish (MultiNanopolish), which decomposes the whole process of iterative calculation in Nanopolish into small independent calculation tasks, making it possible to run this process in the parallel mode. Experimental results show that MultiNanopolish reduces running time by 50% with read-uncorrected assembler (Miniasm) and 20% with read-corrected assembler (Canu and Flye) based on 40 threads mode compared to the original Nanopolish. AVAILABILITY AND IMPLEMENTATION: MultiNanopolish is available at GitHub: https://github.com/BioinformaticsCSU/MultiNanopolish. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Assembling genomes from single-cell sequencing data is essential for single-cell studies. However, single-cell assemblies are challenging due to (i) the highly non-uniform read coverage and (ii) the elevated levels of sequencing errors and chimeric reads. Although several assemblers for single-cell data have been proposed in recent years, most of them fail to construct correct long contigs. In this study, we present a new framework called EPGA-SC for de novo assembly of single-cell sequencing reads. The EPGA assembler has designed strategies to solve the problems caused by sequencing errors, sequencing biases, and repetitive regions. However, the extremely unbalanced and richer error types prevent EPGA to achieve high performance in single-cell sequencing data. In this study, we designed EPGA-SC based on EPGA. The main innovations of EPGA-SC are as follows: (i) classifying reads to reduce the proportion of false reads; (ii) using multiple sets of high precision paired-end reads generated from the high precision assemblies produced by other assembler such as SPAdes to overcome the impact of sequencing biases and repetitive regions; and (iii) developing novel algorithms for removing chimeric errors and extending contigs. We test EPGA-SC with seven datasets. The experimental results show that EPGA-SC can generate better assemblies than most current tools in most time in term of MAX contig, N50, NG50, NA50, and NGA50.

Person re-identification (Re-ID) aims at retrieving an input person image from a set of images captured by multiple cameras. Although recent Re-ID methods have made great success, most of them extract features in terms of the attributes of clothing (e.g., color, texture). However, it is common for people to wear black clothes or be captured by surveillance systems in low light illumination, in which cases the attributes of the clothing are severely missing. We call this problem the Black Re-ID problem. To solve this problem, rather than relying on the clothing information, we propose to exploit head-shoulder features to assist person Re-ID. The head-shoulder adaptive attention network (HAA) is proposed to learn the head-shoulder feature and an innovative ensemble method is designed to enhance the generalization of our model. Given the input person image, the ensemble method would focus on the head-shoulder feature by assigning a larger weight if the individual insides the image is in black clothing. Due to the lack of a suitable benchmark dataset for studying the Black Re-ID problem, we also contribute the first Black-reID dataset, which contains 1274 identities in training set. Extensive evaluations on the Black-reID, Market1501 and DukeMTMC-reID datasets show that our model achieves the best result compared with the state-of-the-art Re-ID methods on both Black and conventional Re-ID problems. Furthermore, our method is also proved to be effective in dealing with person Re-ID in similar clothing. Our code and dataset are avaliable on https://github.com/xbq1994/.

BACKGROUND: Repetitive sequences account for a large proportion of eukaryotes genomes. Identification of repetitive sequences plays a significant role in many applications, such as structural variation detection and genome assembly. Many existing de novo repeat identification pipelines or tools make use of assembly of the high-frequency k-mers to obtain repeats. However, a certain degree of sequence coverage is required for assemblers to get the desired assemblies. On the other hand, assemblers cut the reads into shorter k-mers for assembly, which may destroy the structure of the repetitive regions. For the above reasons, it is difficult to obtain complete and accurate repetitive regions in the genome by using existing tools. RESULTS: In this study, we present a new method called RepAHR for de novo repeat identification by assembly of the high-frequency reads. Firstly, RepAHR scans next-generation sequencing (NGS) reads to find the high-frequency k-mers. Secondly, RepAHR filters the high-frequency reads from whole NGS reads according to certain rules based on the high-frequency k-mer. Finally, the high-frequency reads are assembled to generate repeats by using SPAdes, which is considered as an outstanding genome assembler with NGS sequences. CONLUSIONS: We test RepAHR on five data sets, and the experimental results show that RepAHR outperforms RepARK and REPdenovo for detecting repeats in terms of N50, reference alignment ratio, coverage ratio of reference, mask ratio of Repbase and some other metrics.

Due to sequencing bias, sequencing error, and repeat problems, the genome assemblies usually contain misarrangements and gaps. When tackling these problems, current assemblers commonly consider the read libraries as a whole and adopt the same strategy to deal with them. However, if we can divide reads into different categories and take different assembly strategies for different read categories, we expect to reduce the mutual effects on problems in genome assembly and facilitate to produce satisfactory assemblies. In this paper, we present a new pipeline for genome assembly based on read classification (ARC). ARC classifies reads into three categories according to the frequencies of k-mers they contain. The three categories refer to (1) low depth reads, which contain a certain low frequency k-mers and are often caused by sequencing errors or bias; (2) high depth reads, which contain a certain high frequency k-mers and usually come from repetitive regions; and (3) normal depth reads, which are the rest of reads. After read classification, an existing assembler is used to assemble different read categories separately, which is beneficial to resolve problems in the genome assembly. ARC adopts loose assembly parameters for low depth reads, and strict assembly parameters for normal depth and high depth reads. We test ARC using five datasets. The experimental results show that, assemblers combining with ARC can generate better assemblies in terms of NA50, NGA50, and genome fraction.

Next-generation sequencing (NGS) has enabled an exponential growth rate of sequencing data. However, several sequence artifacts, including error reads (base calling errors and small insertions or deletions) and poor quality reads, which can impose significant impact on the downstream sequence processing and analysis. Here, we present PE-Trimmer, a sensitive and special trimming algorithm for NGS sequence. First, PE-Trimmer removes technical sequences in paired-end reads based on the characteristics of low quality reads in NGS data. Second, PE-Trimmer determines the range of reads that need to be trimmed according to the quality score statistics histogram of reads in the library. To improve the accuracy of this algorithm, we design a light-weight and easy-to-explain scoring model to evaluate candidates in the pattern of trimming step. Finally, PE-Trimmer selects the appropriate trimming strategy to process the low quality reads based on the location determined by the scoring model. PE-Trimmer is able to locate and remove adapter residues from the paired-end reads. It is easily configurable and offers superior throughput in the multi-threaded mode. We test PE-Trimmer on five datasets, and compare it with the current five latest methods. The experimental results demonstrate that PE-Trimmer produces more superior results, compared with other trimmers.

The de novo assembly tools aim at reconstructing genomes from next-generation sequencing (NGS) data. However, the assembly tools usually generate a large amount of contigs containing many misassemblies, which are caused by problems of repetitive regions, chimeric reads, and sequencing errors. As they can improve the accuracy of assembly results, detecting and correcting the misassemblies in contigs are appealing, yet challenging. In this study, a novel method, called MEC, is proposed to identify and correct misassemblies in contigs. Based on the insert size distribution of paired-end reads and the statistical analysis of GC-contents, MEC can identify more misassemblies accurately. We evaluate our MEC with the metrics (NA50, NGA50) on four datasets, compared it with the most available misassembly correction tools, and carry out experiments to analyze the influence of MEC on scaffolding results, which shows that MEC can reduce misassemblies effectively and result in quantitative improvements in scaffolding quality. MEC is publicly available at https://github.com/bioinfomaticsCSU/MEC.

This study proposes a simple but strong baseline for deep person re-identification (ReID). Deep person ReID has achieved great progress and high performance in recent years. However, many state-of-the-art methods design complex network structures and concatenate multi-branch features. In the literature, some effective training tricks briefly appear in several papers or source codes. The present study collects and evaluates these effective training tricks in person ReID. By combining these tricks, the model achieves 94.5% rank-1 and 85.9% mean average precision on Market1501 with only using the global features of ResNet50. The performance surpasses all existing global- and part-based baselines in person ReID. We propose a novel neck structure named as batch normalization neck (BNNeck). BNNeck adds a batch normalization layer after global pooling layer to separate metric and classification losses into two different feature spaces because we observe they are inconsistent in one embedding space. Extended experiments show that BNNeck can boost the baseline, and our baseline can improve the performance of existing state-of-the-art methods. Our codes and models are available at: https://github.com/michuanhaohao/reid-strong-baseline.

Repetitive sequences refer to fragments that appear at more than one location in a genome. Numerous studies have shown that the repetitive sequences in genomes play indispensable roles in the evolution, inheritance, variation, gene expression, transcriptional regulation, chromosome construction, and physiological metabolism of organisms. In many sequence and genome analyses such as read alignment, de novo assembly and genome annotation, repetitive sequences can pose major challenges. Detection and classification of repeats is one of the main steps for genome sequence analysis in bioinformatics. However, most existing de novo detection methods are difficult to achieve satisfactory results for marking repetitive regions in both size and accuracy due to the NGS reads are too short to identify long repeats and the raw SMS long reads are with the high error rates. In this study, we present a new de novo repeat detection method called DLR (Detection of Long Repeats) based on PacBio long reads. DLR first converts all long reads into unique k-mers of a certain length, and screens out the k-mers with the high frequency. Then, these high frequency k-mers are aligned to long reads by using multiple sequence alignment, and the high frequency regions on long reads that are covered by those high frequency k-mers are recorded. Finally, the recorded high frequency regions with inclusion relations are merged and the final repetitive sequences are obtained. The experimental results show that DLR achieves optimal results in terms of effective size and accuracy compared with other existing algorithms.

Single-cell RNA-seq (scRNA-seq) data analysis is a powerful tool for biological researches. Similarity plays an important role in clustering scRNA-seq data. Existing similarity measurements are mainly based on local distance information that is calculated between directly connected node pairs, or shared nearest neighbours' information, without considering the global information. Therefore, these similarity measurements may be not very accurate based on the insufficient information. Based on multi-kernel indices in a global feature space and path-based similarity, we proposed a new similarity measurement for single-cell clustering, called multi-kernel and path-based global similarity (MPGS). In MPGS, global information was incorporated by a new feature space from Spearman correlation coefficient, and a global similarity matrix calculated by multi-kernel. A path-based similarity metric was designed to expand the relevant node range. Based on this similaritiy, a modified Louvain community detection method was applied to cluster the scRNA-seq data, named MPGS-Louvain. To validate the performance of MPGS, the clustering performances of several clustering methods combined with different similarity measurements were compared. To demonstrate the performance of MPGS-Louvain, we compared MPGS-Louvain and five scRNA-seq clustering methods on twenty scRNA-seq datasets. The experimental results showed that MPGS outperformed other similarity measurements, and MPGS-Louvain achieved better performance on these datasets. It can be observed that MPGS provided a new insight to improve the accuracy of clustering scRNA-seq data by considering the global information in similarity measurement. MPGS-Louvain automatically detected clusters accurately without prior knowledge.