Prediction of lncRNA–Disease Associations via Closest Node Weight Graphs of the Spatial Neighborhood Based on the Edge Attention Graph Convolutional Network

Accumulated evidence of biological clinical trials has shown that long non-coding RNAs (lncRNAs) are closely related to the occurrence and development of various complex human diseases. Research works on lncRNA–disease relations will benefit to further understand the pathogenesis of human complex diseases at the molecular level, but only a small proportion of lncRNA–disease associations has been confirmed. Considering the high cost of biological experiments, exploring potential lncRNA–disease associations with computational approaches has become very urgent. In this study, a model based on closest node weight graph of the spatial neighborhood (CNWGSN) and edge attention graph convolutional network (EAGCN), LDA-EAGCN, was developed to uncover potential lncRNA–disease associations by integrating disease semantic similarity, lncRNA functional similarity, and known lncRNA–disease associations. Inspired by the great success of the EAGCN method on the chemical molecule property recognition problem, the prediction of lncRNA–disease associations could be regarded as a component recognition problem of lncRNA–disease characteristic graphs. The CNWGSN features of lncRNA–disease associations combined with known lncRNA–disease associations were introduced to train EAGCN, and correlation scores of input data were predicted with EAGCN for judging whether the input lncRNAs would be associated with the input diseases. LDA-EAGCN achieved a reliable AUC value of 0.9853 in the ten-fold cross-over experiments, which was the highest among five state-of-the-art models. Furthermore, case studies of renal cancer, laryngeal carcinoma, and liver cancer were implemented, and most of the top-ranking lncRNA–disease associations have been proven by recently published experimental literature works. It can be seen that LDA-EAGCN is an effective model for predicting potential lncRNA–disease associations. Its source code and experimental data are available at https://github.com/HGDKMF/LDA-EAGCN.

Eigenvalues, traceability, and perfect matching of a graph

It is well known that the recognition problem of the existence of a perfect matching in a graph, as well as the recognition problem of its Hamiltonicity and traceability, is NP-complete. Quite recently, lower bounds for the size and the spectral radius of a graph that guarantee the existence of a perfect matching in it have been obtained. We improve these bounds, firstly, by using the available bounds for the size of the graph for existence of a Hamiltonian path in it, and secondly, by finding new lower bounds for the spectral radius of the graph that are sufficient for the traceability property. Moreover, we develop the recognition algorithm of the existence of a perfect matching in a graph. This algorithm uses the concept of a (κ,τ)-regular set, which becomes polynomial in the class of graphs with a fixed cyclomatic number.

Human Fatigue Evaluation by Face's Image Analysis Based upon Convolutional Neural Networks

This article presents solutions to the person's fatigue recognition problem by the face's image analysis based on convolutional neural networks. In the present paper, existing algorithms were considered. A new model's architecture was proposed and implemented. Resultant metrics of the model were evaluated.

Isometry Invariant Shape Recognition of Projectively Perturbed Point Clouds by the Mergegram Extending 0D Persistence

Rigid shapes should be naturally compared up to rigid motion or isometry, which preserves all inter-point distances. The same rigid shape can be often represented by noisy point clouds of different sizes. Hence, the isometry shape recognition problem requires methods that are independent of a cloud size. This paper studies stable-under-noise isometry invariants for the recognition problem stated in the harder form when given clouds can be related by affine or projective transformations. The first contribution is the stability proof for the invariant mergegram, which completely determines a single-linkage dendrogram in general position. The second contribution is the experimental demonstration that the mergegram outperforms other invariants in recognizing isometry classes of point clouds extracted from perturbed shapes in images.

Surgical workflow recognition with 3DCNN for Sleeve Gastrectomy

Purpose Surgical workflow recognition is a crucial and challenging problem when building a computer-assisted surgery system. Current techniques focus on utilizing a convolutional neural network and a recurrent neural network (CNN–RNN) to solve the surgical workflow recognition problem. In this paper, we attempt to use a deep 3DCNN to solve this problem. Methods In order to tackle the surgical workflow recognition problem and the imbalanced data problem, we implement a 3DCNN workflow referred to as I3D-FL-PKF. We utilize focal loss (FL) to train a 3DCNN architecture known as Inflated 3D ConvNet (I3D) for surgical workflow recognition. We use prior knowledge filtering (PKF) to filter the recognition results. Results We evaluate our proposed workflow on a large sleeve gastrectomy surgical video dataset. We show that focal loss can help to address the imbalanced data problem. We show that our PKF can be used to generate smoothed prediction results and improve the overall accuracy. We show that the proposed workflow achieves 84.16% frame-level accuracy and reaches a weighted Jaccard score of 0.7327 which outperforms traditional CNN–RNN design. Conclusion The proposed workflow can obtain consistent and smooth predictions not only within the surgical phases but also for phase transitions. By utilizing focal loss and prior knowledge filtering, our implementation of deep 3DCNN has great potential to solve surgical workflow recognition problems for clinical practice.