arXiv subjects

Ratha Pech

Publications and source records attributed to Ratha Pech.

3 recordsLinked to original sources

arXiv2018

Link prediction via linear optimization

Link prediction is an elemental challenge in network science, which has already found applications in guiding laboratorial experiments, digging out drug targets, recommending friends in social networks, probing mechanisms in network evolution, and so on. With a simple assumption that the likelihood of the existence of a link between two nodes can be unfolded by a linear summation of neighboring nodes' contributions, we obtain the analytical solution of the optimal likelihood matrix, which shows remarkably better performance in predicting missing links than the state-of-the-art algorithms for not only simple networks, but also weighted and directed networks. To our surprise, even some degenerated local similarity indices from the solution outperform well-known local indices, which largely refines our knowledge, for example, the direct count of the number of 3-hop paths between two nodes more accurately predicts missing links than the number of 2-hop paths (i.e., the number of common neighbors), while in the previous studies, as indicated by the local path index and Katz index, the statistics on longer paths are always considered to be complementary to but less important than those on shorter paths.

physics.soc-ph↗

arXiv2017

A generalized method toward drug-target interaction prediction via low-rank matrix projection

Drug-target interaction (DTI) prediction plays a very important role in drug development and drug discovery. Biochemical experiments or \textit{in vitro} methods are very expensive, laborious and time-consuming. Therefore, \textit{in silico} approaches including docking simulation and machine learning have been proposed to solve this problem. In particular, machine learning approaches have attracted increasing attentions recently. However, in addition to the known drug-target interactions, most of the machine learning methods require extra characteristic information such as chemical structures, genome sequences, binding types and so on. Whenever such information is not available, they may perform poor. Very recently, the similarity-based link prediction methods were extended to bipartite networks, which can be applied to solve the DTI prediction problem by using topological information only. In this work, we propose a method based on low-rank matrix projection to solve the DTI prediction problem. On one hand, when there is no extra characteristic information of drugs or targets, the proposed method utilizes only the known interactions. On the other hand, the proposed method can also utilize the extra characteristic information when it is available and the performances will be remarkably improved. Moreover, the proposed method can predict the interactions associated with new drugs or targets of which we know nothing about their associated interactions, but only some characteristic information. We compare the proposed method with ten baseline methods, e.g., six similarity-based methods that utilize only the known interactions and four methods that utilize the extra characteristic information. The datasets and codes implementing the simulations are available at https://github.com/rathapech/DTI_LMP.

cs.LG↗

arXiv2016

Link Prediction via Matrix Completion

Inspired by practical importance of social networks, economic networks, biological networks and so on, studies on large and complex networks have attracted a surge of attentions in the recent years. Link prediction is a fundamental issue to understand the mechanisms by which new links are added to the networks. We introduce the method of robust principal component analysis (robust PCA) into link prediction, and estimate the missing entries of the adjacency matrix. On one hand, our algorithm is based on the sparsity and low rank property of the matrix, on the other hand, it also performs very well when the network is dense. This is because a relatively dense real network is also sparse in comparison to the complete graph. According to extensive experiments on real networks from disparate fields, when the target network is connected and sufficiently dense, whatever it is weighted or unweighted, our method is demonstrated to be very effective and with prediction accuracy being considerably improved comparing with many state-of-the-art algorithms.

cs.SI↗