Protein-protein interaction identification using a hybrid model

Methods of Computational Interactomics for Investigating Interactions of Human Proteoforms

Human genome contains ca. 20,000 protein-coding genes that could be translated into millions of unique protein species (proteoforms). Proteoforms coded by a single gene often have different functions, which implies different protein partners. By interacting with each other, proteoforms create a network reflecting the dynamics of cellular processes in an organism. Perturbations of protein-protein interactions change the network topology, which often triggers pathological processes. Studying proteoforms is a relatively new research area in proteomics, and this is why there are comparatively few experimental studies on the interaction of proteoforms. Bioinformatics tools can facilitate such studies by providing valuable complementary information to the experimental data and, in particular, expanding the possibilities of the studies of proteoform interactions.

Protein-Protein Interaction Identification Using a Similarity-Constrained Graph Model

Protein-protein interaction (PPI) identification is an important task in text mining. Most PPI detection systems make predictions solely based on evidence within a single sentence and often suffer from the heavy burden of manual annotation. This paper approaches PPI detection task from a different paradigm by investigating the context of protein pairs collected from a large corpus and their relations. First, crucial cues in the context are exploited to make initial predictions. Then, relational similarity between protein pairs is calculated. Finally, evidence from the two views is integrated in the framework of minimum cuts algorithm. Experimental results show that the graph model achieves better performance than standard supervised approaches. Using 20 percent data as the training set, our algorithm achieves higher accuracy than support vector machine (SVM) using 80 percent data as training data. Moreover, the semi-supervised settings reveal promising directions for PPI identification exploiting unlabeled data.

Distributed smoothed tree kernel for protein-protein interaction extraction from the biomedical literature

Automatic extraction of protein-protein interaction (PPI) pairs from biomedical literature is a widely examined task in biological information extraction. Currently, many kernel based approaches such as linear kernel, tree kernel, graph kernel and combination of multiple kernels has achieved promising results in PPI task. However, most of these kernel methods fail to capture the semantic relation information between two entities. In this paper, we present a special type of tree kernel for PPI extraction which exploits both syntactic (structural) and semantic vectors information known as Distributed Smoothed Tree kernel (DSTK). DSTK comprises of distributed trees with syntactic information along with distributional semantic vectors representing semantic information of the sentences or phrases. To generate robust machine learning model composition of feature based kernel and DSTK were combined using ensemble support vector machine (SVM). Five different corpora (AIMed, BioInfer, HPRD50, IEPA, and LLL) were used for evaluating the performance of our system. Experimental results show that our system achieves better f-score with five different corpora compared to other state-of-the-art systems.