Accurate identification of N7-methylguanosine (m7G) modification sites plays a critical role in uncovering the regulatory mechanisms of various biological processes, including human development, tumor initiation, and progression. However, existing prediction methods still suffer from limited representational power, redundant feature fusion, insufficient utilization of biological prior knowledge, and poor interpretability. In this study, we propose a novel deep learning model named MCAMEF-BERT. This model adopts a parallel architecture that integrates both a DNABERT-2-based pretrained model branch and multiple traditional feature encoding branches, enabling comprehensive multi-perspective sequence feature extraction. To address the redundancy issue in feature fusion, we introduce a multi-channel attention module. Our model demonstrates superior accuracy and effectiveness on datasets from m7GHub, outperforming other state-of-the-art classifiers. Furthermore, we validate the interpretability of MCAMEF-BERT through in silico saturation mutagenesis experiments, and confirm its robustness in motif recognition. Moreover, its generalization capability is validated across diverse RNA modification site prediction tasks.

MOTIVATION: 5-Methylcytosine (5mC), a fundamental element of DNA methylation in eukaryotes, plays a vital role in gene expression regulation, embryonic development, and other biological processes. Although several computational methods have been proposed for detecting the base modifications in DNA like 5mC sites from Nanopore sequencing data, they face challenges including sensitivity to noise, and ignoring the imbalanced distribution of methylation sites in real-world scenarios. RESULTS: Here, we develop NanoCon, a deep hybrid network coupled with contrastive learning strategy to detect 5mC methylation sites from Nanopore reads. In particular, we adopted a contrastive learning module to alleviate the issues caused by imbalanced data distribution in nanopore sequencing, offering a more accurate and robust detection of 5mC sites. Evaluation results demonstrate that NanoCon outperforms existing methods, highlighting its potential as a valuable tool in genomic sequencing and methylation prediction. In addition, we also verified the effectiveness of our representation learning ability on two datasets by visualizing the dimension reduction of the features of methylation and nonmethylation sites from our NanoCon. Furthermore, cross-species and cross-5mC methylation motifs experiments indicated the robustness and the ability to perform transfer learning of our model. We hope this work can contribute to the community by providing a powerful and reliable solution for 5mC site detection in genomic studies. AVAILABILITY AND IMPLEMENTATION: The project code is available at https://github.com/Challis-yin/NanoCon.

Abstract Nowadays, parents attach importance to their children's primary education but often lack time and correct pedagogical principles to accompany their children's learning. Besides, existing learning systems cannot perceive children's emotional changes. They may also cause children's self‐control and cognitive problems due to smart devices such as mobile phones and tablets. To tackle these issues, we propose an intelligent companion learning system to accompany children in learning English words, namely theIntelligent Augmented Reality Educator (IARE). The IARE realizes the perception and feedback of children's engagement through the intelligent agent (IA) module, and presents the humanized interaction based on projective Augmented Reality (AR). Specifically, IA perceives the children's learning engagement change and spelling status in real‐time through our online lightweight temporal multiple instance attention module and character recognition module, based on which analyses the performance of the individual learning process and gives appropriate feedback and guidance. We allow children to interact with physical letters, thus avoiding the excessive interference of electronic devices. To test the efficacy of our system, we conduct a pilot study with 14 English learning children. The results show that our system can significantly improve children's intrinsic motivation and self‐efficacy.

Video-based automatic assessment of a student's learning engagement on the fly can provide immense values for delivering personalized instructional services, a vehicle particularly important for massive online education. To train such an assessor, a major challenge lies in the collection of sufficient labels at the appropriate temporal granularity since a learner's engagement status may continuously change throughout a study session. Supplying labels at either frame or clip level incurs a high annotation cost. To overcome such a challenge, this paper proposes a novel hierarchical multiple instance learning (MIL) solution, which only requires labels anchored on full-length videos to learn to assess student engagement at an arbitrary temporal granularity and for an arbitrary duration in a study session. The hierarchical model mainly comprises a bottom module and a top module, respectively dedicated to learning the latent relationship between a clip and its constituent frames and that between a video and its constituent clips, with the constraints on the training stage that the average engagements of local clips is that of the video label. To verify the effectiveness of our method, we compare the performance of the proposed approach with that of several state-of-the-art peer solutions through extensive experiments.

With the strong demand for human machine interaction, action recognition has attracted more and more attention in recent years. Traditional video-based approaches are very sensitive to background activity, and also lack the ability to discriminate complex 3D motion. With the emergence and development of commercial depth cameras, action recognition based on 3D skeleton joints is becoming more and more popular. However, a skeleton-based approach is still very challenging because of the large variation in human actions and temporal dynamics. In this paper, we propose a hierarchical model for action recognition. To handle confusing motions in a large feature space, a motion-based grouping method is first proposed, which can efficiently assign each video a group label, and then for each group, a pre-trained classifier is used for frame-labeling. Unlike previous methods, we adopt a bottom-up approach that first performs action recognition for each frame. The final action label is obtained by fusing the classification to its frames, with the effect of each frame being adaptively adjusted based on its local properties. The proposed method is evaluated using two challenge datasets captured by a Kinect. Experiments show that our method can perform more robustly than state-of-the-art approaches.

Massively multiplayer online role playing games feature huge maps that can be partitioned into smaller components called zones to achieve scalability. In peer-to-peer (P2P) systems, those zones can be assigned to peers who are willing to take up the role of zone servers. A seamless map requires inter-zone communications to allow interactions between players across zone boundaries. In assigning zones to peers, it is critical to seek approaches to reduce the inter-zone communication cost in P2P system. In this paper, we formulate the zone assignment problem for P2P system and demonstrate that the problem is NP-hard. We hence propose a low-cost heuristic that partitions the physical network into bins, as well as, aggregating the partitions of the virtual world by clustering neighboring zones in a game map. We then demonstrate that by assigning clustered neighboring zones in the virtual map into peers in common physical network bins, we are able to achieve similar inter-zone communication cost for the zone assignment problem as that can be achieved by the optimization model we formulated, while avoiding the prohibitively high computation cost required by the latter.