Biased random walk with restart for essential proteins prediction

Predicting essential proteins is crucial for discovering the process of cellular organization and viability.We propose biased random walk with restart algorithm for essential proteins prediction,called BRWR.Firstly,the common process of practice walk often sets the probability of particles transferring to adjacent nodes to be equal,neglecting the influence of the similarity structure on the transition probability.To address this problem,we redefine a novel transition probability matrix by integrating the gene express similarity and subcellular location similarity.The particles can obtain biased transferring probabilities to perform random walk so as to further exploit biological properties embedded in the network structure.Secondly,we use gene ontology(GO)terms score and subcellular score to calculate the initial probability vector of the random walk with restart.Finally,when the biased random walk with restart process reaches steady state,the protein importance score is obtained.In order to demonstrate superiority of BRWR,we conduct experiments on the YHQ,BioGRID,Krogan and Gavin PPI networks.The results show that the method BRWR is superior to other state-of-the-art methods in essential proteins recognition performance.Especially,compared with the contrast methods,the improvements of BRWR in terms of the ACC results range in 1.4%–5.7%,1.3%–11.9%,2.4%–8.8%,and 0.8%–14.2%,respectively.Therefore,BRWR is effective and reasonable.

Trinity： Walking on a User-Object-Tag Heterogeneous Network for Personalised Recommendations

The rapid evolution of the Internet has been appealing for effective recommender systems to pinpoint useful information from online resources. Although historical rating data has been widely used as the most important information in recommendation methods, recent advancements have been demonstrating the improvement in recommendation performance with the incorporation of tag information. Furthermore, the availability of tag annotations has been well addressed by such fruitful online social tagging applications as CiteULike, MovieLens and BibSonomy, which allow users to express their preferences, upload resources and assign their own tags. Nevertheless, most existing tag-aware recommendation approaches model relationships among users, objects and tags using a tripartite graph, and hence overlook relationships within the same types of nodes. To overcome this limitation, we propose a novel approach, Trinity, to integrate historical data and tag information towards personalised recommendation. Trinity constructs a three-layered object-user-tag network that considers not only interconnections between different types of nodes but also relationships within the same types of nodes. Based on this heterogeneous network, Trinity adopts a random walk with restart model to assign the strength of associations to candidate objects, thereby providing a means of prioritizing the objects for a query user. We validate our approach via a series of large-scale 10-fold cross-validation experiments and evaluate its performance using three comprehensive criteria. Results show that our method outperforms several existing methods, including supervised random walk with restart, simulation of resource allocating processes, and traditional collaborative filtering.

iBole： A Hybrid Multi-Layer Architecture for Doctor Recommendation in Medical Social Networks

In this paper, we try to systematically study how to perform doctor recommendation in medical social net- works （MSNs）. Specifically, employing a real-world medical dataset as the source in our work, we propose iBole, a novel hybrid multi-layer architecture, to solve this problem. First, we mine doctor-patient relationships/ties via a time-constraint probability factor graph model （TPFG）. Second, we extract network features for ranking nodes. Finally, we propose RWR- Model, a doctor recommendation model via the random walk with restart method. Our real-world experiments validate the effectiveness of the proposed methods. Experimental results show that we obtain good accuracy in mining doctor-patient relationships from the network, and the doctor recommendation performance is better than that of the baseline algorithms： traditional Ranking SVM （RSVM） and the individual doctor recommendation model （IDR-Model）. The results of our RWR-Model are more reasonable and satisfactory than those of the baseline approaches.

Topological Features Based Entity Disambiguation

This work proposes an unsupervised topological features based entity disambiguation solution. Most existing studies leverage semantic information to resolve ambiguous references. However, the semantic information is not always accessible because of privacy or is too expensive to access. We consider the problem in a setting that only relationships between references are available. A structure similarity algorithm via random walk with restarts is proposed to measure the similarity of references. The disambiguation is regarded as a clustering problem and a family of graph walk based clustering algorithms are brought to group ambiguous references. We evaluate our solution extensively on two real datasets and show its advantage over two state-of-the-art approaches in accuracy.

ASpediaFI:Functional Interaction Analysis of Alternative Splicing Events

Alternative splicing(AS)regulates biological processes governing phenotypes and diseases.Differential AS(DAS)gene test methods have been developed to investigate important exonic expression from high-throughput datasets.However,the DAS events extracted using statistical tests are insufficient to delineate relevant biological processes.In this study,we developed a novel application,Alternative Splicing Encyclopedia:Functional Interaction(ASpediaFI),to systemically identify DAS events and co-regulated genes and pathways.ASpediaFI establishes a heterogeneous interaction network of genes and their feature nodes(i.e.,AS events and pathways)connected by coexpression or pathway gene set knowledge.Next,ASpediaFI explores the interaction network using the random walk with restart algorithm and interrogates the proximity from a query gene set.Finally,ASpediaFI extracts significant AS events,genes,and pathways.To evaluate the performance of our method,we simulated RNA sequencing(RNA-seq)datasets to consider various conditions of sequencing depth and sample size.The performance was compared with that of other methods.Additionally,we analyzed three public datasets of cancer patients or cell lines to evaluate how well ASpediaFI detects biologically relevant candidates.ASpediaFI exhibits strong performance in both simulated and public datasets.Our integrative approach reveals that DAS events that recognize a global co-expression network and relevant pathways determine the functional importance of spliced genes in the subnetwork.ASpediaFI is publicly available at https://bioconductor.org/packages/ASpediaFI.