Background: Many long non-coding RNAs (lncRNAs) have key roles in different human biologic processes and are closely linked to numerous human diseases, according to cumulative evidence. Predicting potential lncRNA-disease associations can help to detect disease biomarkers and perform disease analysis and prevention. Establishing effective computational methods for lncRNA-disease association prediction is critical.Results: In this paper, we propose a novel model named MAGCNSE to predict underlying lncRNA-disease associations. We first obtain multiple feature matrices from the multi-view similarity graphs of lncRNAs and diseases utilizing graph convolutional network. Then, the weights are adaptively assigned to different feature matrices of lncRNAs and diseases using the attention mechanism. Next, the final representations of lncRNAs and diseases is acquired by further extracting features from the multi-channel feature matrices of lncRNAs and diseases using convolutional neural network. Finally, we employ a stacking ensemble classifier, consisting of multiple traditional machine learning classifiers, to make the final prediction. The results of ablation studies in both representation learning methods and classification methods demonstrate the validity of each module. Furthermore, we compare the overall performance of MAGCNSE with that of six other state-of-the-art models, the results show that it outperforms the other methods. Moreover, we verify the effectiveness of using multi-view data of lncRNAs and diseases. Case studies further reveal the outstanding ability of MAGCNSE in the identification of potential lncRNA-disease associations.Conclusions: The experimental results indicate that MAGCNSE is a useful approach for predicting potential lncRNA-disease associations.

Circular RNA (CircRNA) is widely expressed and has physiological and pathological significance, regulating post-transcriptional processes via its protein-binding activity. However, whereas much work has been done on linear RNA and RNA binding protein (RBP), little is known about the binding sites of CircRNA. The current report is on the development of a medium-term multimodal data fusion strategy, CRBSP, to predict CircRNA-RBP binding sites. CRBSP represents the CircRNA trinucleotide semantic, location, composition and frequency information as the corresponding coding methods of Word to vector (Word2vec), Position-specific trinucleotide propensity (PSTNP), Pseudo trinucleotide composition (PseTNC) and Trinucleotide nucleotide composition (TNC), respectively. CNN (Convolution Neural Networks) was used to extract global information and BiLSTM (bidirectional Long- and Short-Term Memory network) encoder and LSTM (Long- and Short-Term Memory network) decoder for local sequence information. Enhancement of the contributions of key features by the self-attention mechanism was followed by mid-term fusion of the four enhanced features. Logistic Regression (LR) classifier showed that CRBSP gives a mean AUC value of 0.9362 through 5-fold Cross Validation of all 37 datasets, a performance which is superior to five current state-of-the-art models. Similar evaluation of linear RNA-RBP binding sites gave an AUC value of 0.7615 which is also higher than other prediction methods, demonstrating the robustness of CRBSP. The CRBSP method and data are made available at https://github.com/YingLiangjxau/CRBSP .

In the realm of intelligent education, knowledge tracking is a critical study topic. Deep learning-based knowledge tracking models have better predictive performance compared to traditional knowledge tracking models, but the models are less interpretable and also often ignore the intrinsic differences among students (e.g., learning capability, guessing capability, etc.), resulting in a lack of personalization of predictive results. To further reflect the personalized differences among students and enhance the interpretability of the model at the same time, a Deep Knowledge Tracking model integrating Learning Capability and Item Response Theory (DKT-LCIRT) is proposed. The model dynamically calculates students’ learning capability by each time interval and allocates each student to groups with similar learning capabilities to increase the predictive performance of the model. Furthermore, the model introduces item response theory to enhance the interpretability of the model. Substantial experiments on four real datasets were carried out, and the experimental results showed that the DKT-LCIRT model improved the AUC by 3% and the ACC by 2% compared to other models. The results confirmed that the DKT-LCIRT model outperformed other classical models in terms of predictive performance, fully reflecting students’ individualization and adding a more meaningful interpretation to the model.

RNA-protein interaction (RPI) is crucial to the life processes of diverse organisms. Various researchers have identified RPI through long-term and high-cost biological experiments. Although numerous machine learning and deep learning-based methods for predicting RPI currently exist, their robustness and generalizability have significant room for improvement. This study proposes LPI-MFF, an RPI prediction model based on multi-source information fusion, to address these issues. The LPI-MFF employed protein–protein interactions features, sequence features, secondary structure features, and physical and chemical properties as the information sources with the corresponding coding scheme, followed by the random forest algorithm for feature screening. Finally, all information was combined and a classification method based on convolutional neural networks is used. The experimental results of fivefold cross-validation demonstrated that the accuracy of LPI-MFF on RPI1807 and NPInter was 97.60% and 97.67%, respectively. In addition, the accuracy rate on the independent test set RPI1168 was 84.9%, and the accuracy rate on the Mus musculus dataset was 90.91%. Accordingly, LPI-MFF demonstrated greater robustness and generalization than other prevalent RPI prediction methods.

Recent Domain Generalized Semantic Segmentation (DGSS) methods have harnessed vision foundation models (VFMs) to achieve remarkable performance in unseen domains. Two key issues require immediate attention from these methods. First, these methods ignore the learning of contextual information, since VFMs are always pretrained on the image classification task, which means that the frozen backbone of these VFMs struggles to extract contextual information used for dense prediction tasks. Second, these methods focus on enhancing domain-invariant information within the learnable tokens or the features extracted by the frozen backbone (e.g., normalizing their style variances), inevitably losing the effective information. To address these two key issues, this paper proposes a Multi-Granularity Token Learning (MGTL) approach to fine-tune VFMs for DGSS, which uses the visual and text embeddings from the CLIP model for optimizing a set of learnable tokens to learn the domain-invariant information of two granularities, including the domain-invariant contextual and conceptual information. Specifically, first, a contextual relation learning strategy is proposed to assist tokens in capturing and embedding contextual information into VFMs, which is crucial to the semantic segmentation task. Second, a conceptual learning strategy is proposed to acquire instance-level conceptual information for the set of learnable tokens and embed it into VFMs to enhance instance-level domain-invariant information. The proposed MGTL approach is evaluated on multiple DGSS benchmarks, achieving superior performance to recent DGSS methods while maintaining low computational cost in trainable parameters during the fine-tuning stage.

The popularity of Agrocybe cylindracea is increasing due to its unique flavor and nutritional value. The Agrocybe cylindracea cap is a key aspect of the growth process, and high-throughput observation of cap traits in greenhouses by machine vision is a future development trend of smart agriculture. Nevertheless, the segmentation of the Agrocybe cylindracea cap is extremely challenging due to its similarity in color to the rest of the mushroom and the occurrence of mutual occlusion, presenting a major obstacle for the effective application of automation technology. To address this issue, we propose an improved instance segmentation network called Agrocybe cylindracea R-CNN (AC R-CNN) based on the Mask R-CNN model. AC R-CNN incorporates hybrid dilated convolution (HDC) and attention modules into the feature extraction backbone network to enhance the segmentation of adhesive mushroom caps and focus on the segmentation objects. Furthermore, the Mask Branch module is replaced with PointRend to improve the network’s segmentation accuracy at the edges of the mushroom caps. These modifications effectively solve the problems of the original algorithm’s inability to segment adhesive Agrocybe cylindracea caps and low accuracy in edge segmentation. The experimental results demonstrate that AC R-CNN outperforms the original Mask R-CNN in terms of segmentation performance. The average precision (AP) is improved by 12.1%, and the F1 score is improved by 13.7%. Additionally, AC R-CNN outperforms other networks such as Mask Scoring R-CNN and BlendMask. Therefore, the research findings of this study can meet the high-precision segmentation requirements of Agrocybe cylindracea caps and lay a theoretical foundation for the development of subsequent intelligent phenotyping devices and harvesting robots.