Con&Net: A Cross-Network Anchor Link Discovery Method Based on Embedding Representation

Cross-network anchor link discovery is an important research problem and has many applications in heterogeneous social network. Existing schemes of cross-network anchor link discovery can provide reasonable link discovery results, but the quality of these results depends on the features of the platform. Therefore, there is no theoretical guarantee to the stability. This article employs user embedding feature to model the relationship between cross-platform accounts, that is, the more similar the user embedding features are, the more similar the two accounts are. The similarity of user embedding features is determined by the distance of the user features in the latent space. Based on the user embedding features, this article proposes an embedding representation-based method Con&Net(Content and Network) to solve cross-network anchor link discovery problem. Con&Net combines the user’s profile features, user-generated content (UGC) features, and user’s social structure features to measure the similarity of two user accounts. Con&Net first trains the user’s profile features to get profile embedding. Then it trains the network structure of the nodes to get structure embedding. It connects the two features through vector concatenating, and calculates the cosine similarity of the vector based on the embedding vector. This cosine similarity is used to measure the similarity of the user accounts. Finally, Con&Net predicts the link based on similarity for account pairs across the two networks. A large number of experiments in Sina Weibo and Twitter networks show that the proposed method Con&Net is better than state-of-the-art method. The area under the curve (AUC) value of the receiver operating characteristic (ROC) curve predicted by the anchor link is 11% higher than the baseline method, and Precision@30 is 25% higher than the baseline method.

DNA Methylation-Driven Genes for Developing Survival Nomogram for Low-Grade Glioma

Low-grade gliomas (LGG) are heterogeneous, and the current predictive models for LGG are either unsatisfactory or not user-friendly. The objective of this study was to establish a nomogram based on methylation-driven genes, combined with clinicopathological parameters for predicting prognosis in LGG. Differential expression, methylation correlation, and survival analysis were performed in 516 LGG patients using RNA and methylation sequencing data, with accompanying clinicopathological parameters from The Cancer Genome Atlas. LASSO regression was further applied to select optimal prognosis-related genes. The final prognostic nomogram was implemented together with prognostic clinicopathological parameters. The predictive efficiency of the nomogram was internally validated in training and testing groups, and externally validated in the Chinese Glioma Genome Atlas database. Three DNA methylation-driven genes, ARL9, CMYA5, and STEAP3, were identified as independent prognostic factors. Together with IDH1 mutation status, age, and sex, the final prognostic nomogram achieved the highest AUC value of 0.930, and demonstrated stable consistency in both internal and external validations. The prognostic nomogram could predict personal survival probabilities for patients with LGG, and serve as a user-friendly tool for prognostic evaluation, optimizing therapeutic regimes, and managing LGG patients.

A Signature of 14 Long Non-Coding RNAs (lncRNAs) as a Step towards Precision Diagnosis for NSCLC

LncRNAs have arisen as new players in the world of non-coding RNA. Disrupted expression of these molecules can be tightly linked to the onset, promotion and progression of cancer. The present study estimated the usefulness of 14 lncRNAs (HAGLR, ADAMTS9-AS2, LINC00261, MCM3AP-AS1, TP53TG1, C14orf132, LINC00968, LINC00312, TP73-AS1, LOC344887, LINC00673, SOX2-OT, AFAP1-AS1, LOC730101) for early detection of non-small-cell lung cancer (NSCLC). The total RNA was isolated from paired fresh-frozen cancerous and noncancerous lung tissue from 92 NSCLC patients diagnosed with either adenocarcinoma (LUAD) or lung squamous cell carcinoma (LUSC). The expression level of lncRNAs was evaluated by a quantitative real-time PCR (qPCR). Based on Ct and delta Ct values, logistic regression and gradient boosting decision tree classifiers were built. The latter is a novel, advanced machine learning algorithm with great potential in medical science. The established predictive models showed that a set of 14 lncRNAs accurately discriminates cancerous from noncancerous lung tissues (AUC value of 0.98 ± 0.01) and NSCLC subtypes (AUC value of 0.84 ± 0.09), although the expression of a few molecules was statistically insignificant (SOX2-OT, AFAP1-AS1 and LOC730101 for tumor vs. normal tissue; and TP53TG1, C14orf132, LINC00968 and LOC730101 for LUAD vs. LUSC). However for subtypes discrimination, the simplified logistic regression model based on the four variables (delta Ct AFAP1-AS1, Ct SOX2-OT, Ct LINC00261, and delta Ct LINC00673) had even stronger diagnostic potential than the original one (AUC value of 0.88 ± 0.07). Our results demonstrate that the 14 lncRNA signature can be an auxiliary tool to endorse and complement the histological diagnosis of non-small-cell lung cancer.

Perfusion-Diffusion Ratio: A New IVIM Approach in Differentiating Solid Benign and Malignant Primary Lesions of the Liver

Introduction. In order to improve the efficacy of intravoxel incoherent motion (IVIM) parameters in characterising specific tissues, a new concept is introduced: the perfusion–diffusion ratio (PDR), which expresses the relationship between the signal S b decline rate as a result of IVIM and the rate of signal S b decline due to diffusion. The aim of this study was to investigate this novel approach in the differentiation of solid primary liver lesions. Material and Methods. Eighty-three patients referred for liver MRI between August 2017 and January 2020 with a suspected liver tumour were prospectively examined with the standard liver MRI protocol extended by DWI-IVIM sequence. Patients with no liver lesions, haemangiomas, or metastases were excluded. The final study population consisted of 34 patients with primary solid liver masses, 9 with FNH, 4 with regenerative nodules, 10 with HCC, and 11 with CCC. The PDR coefficient was introduced, defined as the ratio of the rate of signal S b decrease due to the IVIM effect to the rate of signal S b decrease due to the diffusion process, for b = 0 . Results. No significant differences were found between benign and malignant lesions in the case of IVIM parameters ( f , D , or D ∗ ) and ADC. Significant differences were observed only for PDR, with lower values for malignant lesions ( p = 0.03 ). The ROC analysis yielded an AUC value for PDR equal to 0.74, with a cut-off value of 5.06, sensitivity of 81%, specificity of 77%, and accuracy of 79%. Conclusion. PDR proved to be more effective than IVIM parameters and ADC in the differentiation of solid benign and malignant primary liver lesions.

Mean Received Resources Meet Machine Learning Algorithms to Improve Link Prediction Methods

The analysis of social networks has attracted a lot of attention during the last two decades. These networks are dynamic: new links appear and disappear. Link prediction is the problem of inferring links that will appear in the future from the actual state of the network. We use information from nodes and edges and calculate the similarity between users. The more users are similar, the higher the probability of their connection in the future will be. The similarity metrics play an important role in the link prediction field. Due to their simplicity and flexibility, many authors have proposed several metrics such as Jaccard, AA, and Katz and evaluated them using the area under the curve (AUC). In this paper, we propose a new parameterized method to enhance the AUC value of the link prediction metrics by combining them with the mean received resources (MRRs). Experiments show that the proposed method improves the performance of the state-of-the-art metrics. Moreover, we used machine learning algorithms to classify links and confirm the efficiency of the proposed combination.

Analysis of Predictive Model of Coronary Vulnerable Plaque under Hemodynamic Numerical Simulation

Objective. Vulnerable plaque is considered to be the cause of most clinical coronary arteries, and linear cytokines are an important factor causing plaque instability. Early prediction of vulnerable plaque is of great significance in the treatment of cardiovascular diseases. Methods. Computational fluid dynamics (CFD) was used to simulate the hemodynamics around plaques, and the serum biochemical markers in 224 patients with low-risk acute coronary syndrome (ACS) were analyzed. Vulnerable plaques were predicted according to the distribution of biochemical markers in serum. Results. CFD can accurately capture the hemodynamic characteristics around the plaque. The patient’s age, history of hyperlipidemia, apolipoprotein B (apoB), adiponectin (ADP), and sE-Selection were risk factors for vulnerable plaque. Area under curve (AUC) values corresponding to the five biochemical markers were 0.601, 0.523, 0.562, 0.519, 0.539, and the AUC value after the combination of the five indicators was 0.826. Conclusion. The combination of multiple biochemical markers to predict vulnerable plaque was of high diagnostic value, and this method was convenient and noninvasive, which was worthy of clinical promotion.

DDMF: A Method for Mining Relatively Important Nodes Based on Distance Distribution and Multi-Index Fusion

In research on complex networks, mining relatively important nodes is a challenging and practical work. However, little research has been done on mining relatively important nodes in complex networks, and the existing relatively important node mining algorithms cannot take into account the indicators of both precision and applicability. Aiming at the scarcity of relatively important node mining algorithms and the limitations of existing algorithms, this paper proposes a relatively important node mining method based on distance distribution and multi-index fusion (DDMF). First, the distance distribution of each node is generated according to the shortest path between nodes in the network; then, the cosine similarity, Euclidean distance and relative entropy are fused, and the entropy weight method is used to calculate the weights of different indexes; Finally, by calculating the relative importance score of nodes in the network, the relatively important nodes are mined. Through verification and analysis on real network datasets in different fields, the results show that the DDMF method outperforms other relatively important node mining algorithms in precision, recall, and AUC value.

Association between CHADS2, CHA2DS2-VASc, ATRIA, and Essen Stroke Risk Scores and Unsuccessful Recanalization after Endovascular Thrombectomy in Acute Ischemic Stroke Patients

Background: The CHADS2, CHA2DS2-VASc, ATRIA, and Essen scores have been developed for predicting vascular outcomes in stroke patients. We investigated the association between these stroke risk scores and unsuccessful recanalization after endovascular thrombectomy (EVT). Methods: From the nationwide multicenter registry (Selection Criteria in Endovascular Thrombectomy and Thrombolytic therapy (SECRET)) (Clinicaltrials.gov NCT02964052), we consecutively included 501 patients who underwent EVT. We identified pre-admission stroke risk scores in each included patient. Results: Among 501 patients who underwent EVT, 410 (81.8%) patients achieved successful recanalization (mTICI ≥ 2b). Adjusting for body mass index and p < 0.1 in univariable analysis revealed the association between all stroke risk scores and unsuccessful recanalization (CHADS2 score: odds ratio (OR) 1.551, 95% confidence interval (CI) 1.198–2.009, p = 0.001; CHA2DS2VASc score: OR 1.269, 95% CI 1.080–1.492, p = 0.004; ATRIA score: OR 1.089, 95% CI 1.011–1.174, p = 0.024; and Essen score: OR 1.469, 95% CI 1.167–1.849, p = 0.001). The CHADS2 score had the highest AUC value and differed significantly only from the Essen score (AUC of CHADS2 score; 0.618, 95% CI 0.554–0.681). Conclusion: All stroke risk scores were associated with unsuccessful recanalization after EVT. Our study suggests that these stroke risk scores could be used to predict recanalization in stroke patients undergoing EVT.

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.

Residue–Residue Contact Can Be a Potential Feature for the Prediction of Lysine Crotonylation Sites

Lysine crotonylation (Kcr) is involved in plenty of activities in the human body. Various technologies have been developed for Kcr prediction. Sequence-based features are typically adopted in existing methods, in which only linearly neighboring amino acid composition was considered. However, modified Kcr sites are neighbored by not only the linear-neighboring amino acid but also those spatially surrounding residues around the target site. In this paper, we have used residue–residue contact as a new feature for Kcr prediction, in which features encoded with not only linearly surrounding residues but also those spatially nearby the target site. Then, the spatial-surrounding residue was used as a new scheme for feature encoding for the first time, named residue–residue composition (RRC) and residue–residue pair composition (RRPC), which were used in supervised learning classification for Kcr prediction. As the result suggests, RRC and RRPC have achieved the best performance of RRC at an accuracy of 0.77 and an area under curve (AUC) value of 0.78, RRPC at an accuracy of 0.74, and an AUC value of 0.80. In order to show that the spatial feature is of a competitively high significance as other sequence-based features, feature selection was carried on those sequence-based features together with feature RRPC. In addition, different ranges of the surrounding amino acid compositions’ radii were used for comparison of the performance. After result assessment, RRC and RRPC features have shown competitively outstanding performance as others or in some cases even around 0.20 higher in accuracy or 0.3 higher in AUC values compared with sequence-based features.