Background Wet-lab experiments for identification of interactions between drugs and target proteins are time-consuming, costly and labor-intensive. The use of computational prediction of drug–target interactions (DTIs), which is one of the significant points in drug discovery, has been considered by many researchers in recent years. It also reduces the search space of interactions by proposing potential interaction candidates. Results In this paper, a new approach based on unifying matrix factorization and nuclear norm minimization is proposed to find a low-rank interaction. In this combined method, to solve the low-rank matrix approximation, the terms in the DTI problem are used in such a way that the nuclear norm regularized problem is optimized by a bilinear factorization based on Rank-Restricted Soft Singular Value Decomposition (RRSSVD). In the proposed method, adjacencies between drugs and targets are encoded by graphs. Drug–target interaction, drug-drug similarity, target-target, and combination of similarities have also been used as input. Conclusions The proposed method is evaluated on four benchmark datasets known as Enzymes (E), Ion channels (ICs), G protein-coupled receptors (GPCRs) and nuclear receptors (NRs) based on AUC, AUPR, and time measure. The results show an improvement in the performance of the proposed method compared to the state-of-the-art techniques.
Brain tumors are one of the most common causes of death that have been widely investigated by scholars in research areas, including care and prevention. Despite various empirical studies on the brain tumor segmentatin, there is still a need for further investigation. This fact is more needed in the automatic methods of brain tumors detection. In the present study, a new method for improving brain tumor segmentation accuracy based on super-pixel and fast primal dual (PD) algorithms has been proposed. The proposed method detects brain tumor tissue in Flair-MRI imaging in BRATS2012 dataset. This method detects the primary borders of tumors using a super-pixel algorithm, and improves brain tumor borders using fast PD in Markov random field optimization. Then, post-processing processes are used to delete white brain areas. Finally, an active contour algorithm was employed to display tumor area. Different experiments were carried on the proposed method and qualitative and quantitative criteria such as dice similarity measure, accuracy and F-measure were used for evaluation. The obtained results showed the efficiency of the proposed method, such that in the accuracy and sensitivity of 86.59 and 88.57% and F1-Measure 86.37 were obtained, respectively.
Background: Dynamic protein-protein interaction networks (DPPIN) can confirm the conditional and temporal features of proteins and protein complexes. In addition, the relation of protein complexes in dynamic networks can provide useful information in understanding the dynamic functionality of PPI networks.Objective: In this paper, an algorithm is presented to discover the temporal association rule from the dynamic PPIN dataset. Material and Methods:In this analytical study, the static protein-protein interaction network is transformed into a dynamic network using the gene expression thresholding to extract the protein complex relations. The number of presented proteins of the dynamic network is large at each time point. This number will increase for extraction of multidimensional rules at different times. By mapping the gold standard protein complexes as reference protein complexes, the number of items decreases from active proteins to protein complexes at each transaction. Extracted sub graphs as protein complexes, at each time point, are weighted according to the reference protein complexes similarity degrees. Mega-transactions and extended items are created based on occurrence bitmap matrix of the reference complexes. Rules will be extracted based on Mega-transactions of protein complexes. Results:The proposed method has been evaluated using gold standard protein complex rules. The amount of extracted rules from Biogrid datasets and protein complexes are 281, with support 0.2. Conclusion:The characteristic of the proposed algorithm is the simultaneous extraction of intra-transaction and inter-transaction rules. The results evaluation using EBI data shows the efficiency of the proposed algorithm.
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