scholarly journals Topological and Attribute Link Prediction using Firefly algorithm

2020 ◽  
Vol 10 (1) ◽  
pp. 33-41
Author(s):  
Srilatha Pulipati ◽  
Manjula Ramakrishnan
Keyword(s):  
Link Prediction ◽  
Area Under The Curve ◽  
Similarity Score ◽  
Data Sets ◽  
Prediction Problem ◽  
Recent Past ◽  
Common Neighbor ◽  
Standard Data ◽  
Node Attribute ◽  
Swarm Intelligence Algorithm

AbstractLink prediction problem has received remarkable interest in recent past. In this paper, firefly swarm intelligence algorithm is used to perform link prediction exploiting the topological and node attribute features of social network. Fireflies will be made to traverse on nodes and edges of social networks and the brightness of fireflies will play a major role in their movement. Common neighbor method of link prediction is used to compute similarity score upon each iteration. Performance of the proposed algorithm were analyzed over standard data sets using validation method called ten-fold method. The accuracy of proposed work is measured in terms of Area Under the Curve Characteristics (AUC), Recall and Precision. Experimental results showed that the proposed work outperforms the methods proposed in the literature.

Deep Learning Roles based Approach to Link Prediction in Networks

2020 ◽  
Author(s):  
Aman Gupta ◽  
Yadul Raghav
Keyword(s):  
Deep Learning ◽  
Link Prediction ◽  
Information Science ◽  
Structural Information ◽  
Structural Features ◽  
Similarity Score ◽  
Node Attribute ◽  
Depth Analysis ◽  
Real World Datasets ◽  
Better Than

The problem of predicting links has gained much attention in recent years due to its vast application in various domains such as sociology, network analysis, information science, etc. Many methods have been proposed for link prediction such as RA, AA, CCLP, etc. These methods required hand-crafted structural features to calculate the similarity scores between a pair of nodes in a network. Some methods use local structural information while others use global information of a graph. These methods do not tell which properties are better than others. With an in-depth analysis of these methods, we understand that one way to overcome this problem is to consider network structure and node attribute information to capture the discriminative features for link prediction tasks. We proposed a deep learning Autoencoder based Link Prediction (ALP) architecture for the latent representation of a graph, unified with non-negative matrix factorization to automatically determine the underlying roles in a network, after that assigning a mixed-membership of these roles to each node in the network. The idea is to transfer these roles as a feature vector for the link prediction task in the network. Further, cosine similarity is applied after getting the required features to compute the pairwise similarity score between the nodes. We present the performance of the algorithm on the real-world datasets, where it gives the competitive result compared to other algorithms.

scholarly journals Shall I Work with Them? A Knowledge Graph-Based Approach for Predicting Future Research Collaborations

Entropy ◽  
2021 ◽  
Vol 23 (6) ◽  
pp. 664
Author(s):  
Nikos Kanakaris ◽  
Nikolaos Giarelis ◽  
Ilias Siachos ◽  
Nikos Karacapilidis
Keyword(s):  
Language Processing ◽  
Scientific Knowledge ◽  
Link Prediction ◽  
Performance Metrics ◽  
Future Research ◽  
Knowledge Graph ◽  
Prediction Problem ◽  
Textual Information ◽  
Research Collaborations ◽  
Processing Techniques

We consider the prediction of future research collaborations as a link prediction problem applied on a scientific knowledge graph. To the best of our knowledge, this is the first work on the prediction of future research collaborations that combines structural and textual information of a scientific knowledge graph through a purposeful integration of graph algorithms and natural language processing techniques. Our work: (i) investigates whether the integration of unstructured textual data into a single knowledge graph affects the performance of a link prediction model, (ii) studies the effect of previously proposed graph kernels based approaches on the performance of an ML model, as far as the link prediction problem is concerned, and (iii) proposes a three-phase pipeline that enables the exploitation of structural and textual information, as well as of pre-trained word embeddings. We benchmark the proposed approach against classical link prediction algorithms using accuracy, recall, and precision as our performance metrics. Finally, we empirically test our approach through various feature combinations with respect to the link prediction problem. Our experimentations with the new COVID-19 Open Research Dataset demonstrate a significant improvement of the abovementioned performance metrics in the prediction of future research collaborations.

scholarly journals Software Benchmark—Classification Tree Algorithms for Cell Atlases Annotation Using Single-Cell RNA-Sequencing Data

2021 ◽  
Vol 12 (2) ◽  
pp. 317-334
Author(s):  
Omar Alaqeeli ◽  
Li Xing ◽  
Xuekui Zhang
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Classification Tree ◽  
Area Under The Curve ◽  
Data Sets ◽  
Sequencing Data ◽  
Single Cell Rna Sequencing ◽  
Tree Algorithms ◽  
R Packages

Classification tree is a widely used machine learning method. It has multiple implementations as R packages; rpart, ctree, evtree, tree and C5.0. The details of these implementations are not the same, and hence their performances differ from one application to another. We are interested in their performance in the classification of cells using the single-cell RNA-Sequencing data. In this paper, we conducted a benchmark study using 22 Single-Cell RNA-sequencing data sets. Using cross-validation, we compare packages’ prediction performances based on their Precision, Recall, F1-score, Area Under the Curve (AUC). We also compared the Complexity and Run-time of these R packages. Our study shows that rpart and evtree have the best Precision; evtree is the best in Recall, F1-score and AUC; C5.0 prefers more complex trees; tree is consistently much faster than others, although its complexity is often higher than others.

scholarly journals MUREN: a robust and multi-reference approach of RNA-seq transcript normalization

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yance Feng ◽  
Lei M. Li
Keyword(s):  
Biological Significance ◽  
Housekeeping Genes ◽  
R Package ◽  
Data Sets ◽  
Statistical Regression ◽  
Rna Seq ◽  
Least Trimmed Squares ◽  
Standard Data ◽  
Wide Range ◽  
Multiple References

Abstract Background Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of unwanted confounding factors. Explicitly or implicitly, the justification of normalization requires a set of housekeeping genes. However, the existence of housekeeping genes common for a very large collection of samples, especially under a wide range of conditions, is questionable. Results We propose to carry out pairwise normalization with respect to multiple references, selected from representative samples. Then the pairwise intermediates are integrated based on a linear model that adjusts the reference effects. Motivated by the notion of housekeeping genes and their statistical counterparts, we adopt the robust least trimmed squares regression in pairwise normalization. The proposed method (MUREN) is compared with other existing tools on some standard data sets. The goodness of normalization emphasizes on preserving possible asymmetric differentiation, whose biological significance is exemplified by a single cell data of cell cycle. MUREN is implemented as an R package. The code under license GPL-3 is available on the github platform: github.com/hippo-yf/MUREN and on the conda platform: anaconda.org/hippo-yf/r-muren. Conclusions MUREN performs the RNA-seq normalization using a two-step statistical regression induced from a general principle. We propose that the densities of pairwise differentiations are used to evaluate the goodness of normalization. MUREN adjusts the mode of differentiation toward zero while preserving the skewness due to biological asymmetric differentiation. Moreover, by robustly integrating pre-normalized counts with respect to multiple references, MUREN is immune to individual outlier samples.

scholarly journals Erratum: Corrigendum: Drug Response Prediction as a Link Prediction Problem

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Zachary Stanfield ◽  
Mustafa Coşkun ◽  
Mehmet Koyutürk
Keyword(s):  
Link Prediction ◽  
Drug Response ◽  
Response Prediction ◽  
Prediction Problem

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

Information ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 35
Author(s):  
Jibouni Ayoub ◽  
Dounia Lotfi ◽  
Ahmed Hammouch
Keyword(s):  
Machine Learning ◽  
Link Prediction ◽  
Learning Algorithms ◽  
Area Under The Curve ◽  
Machine Learning Algorithms ◽  
Actual State ◽  
The Future ◽  
Auc Value ◽  
The Mean ◽  
Analysis Of Social Networks

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.

Similarity-based link prediction in social networks: A path and node combined approach

2016 ◽  
Vol 43 (5) ◽  
pp. 683-695 ◽  
Author(s):  
Chuanming Yu ◽  
Xiaoli Zhao ◽  
Lu An ◽  
Xia Lin
Keyword(s):  
Social Networks ◽  
Link Prediction ◽  
Computational Analysis ◽  
Rapid Development ◽  
Area Under The Curve ◽  
Combined Approach ◽  
Topological Features ◽  
Different Types ◽  
Path Dependent ◽  
Analysis Of Social Networks

With the rapid development of the Internet, the computational analysis of social networks has grown to be a salient issue. Various research analyses social network topics, and a considerable amount of attention has been devoted to the issue of link prediction. Link prediction aims to predict the interactions that might occur between two entities in the network. To this aim, this study proposed a novel path and node combined approach and constructed a methodology for measuring node similarities. The method was illustrated with five real datasets obtained from different types of social networks. An extensive comparison of the proposed method against existing link prediction algorithms was performed to demonstrate that the path and node combined approach achieved much higher mean average precision (MAP) and area under the curve (AUC) values than those that only consider common nodes (e.g. Common Neighbours and Adamic/Adar) or paths (e.g. Random Walk with Restart and FriendLink). The results imply that two nodes are more likely to establish a link if they have more common neighbours of lower degrees. The weight of the path connecting two nodes is inversely proportional to the product of degrees of nodes on the pathway. The combination of node and topological features can substantially improve the performance of similarity-based link prediction, compared with node-dependent and path-dependent approaches. The experiments also demonstrate that the path-dependent approaches outperform the node-dependent appraoches. This indicates that topological features of networks may contribute more to improving performance than node features.

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