Interaction network

About: Interaction network is a research topic. Over the lifetime, 2700 publications have been published within this topic receiving 113372 citations.

Identification of essential proteins from weighted protein-protein interaction networks.

Abstract: Identifying essential proteins is very important for understanding the minimal requirements of cellular survival and development. Fast growth in the amount of available protein–protein interactions has produced unprecedented opportunities for detecting protein essentiality on network level. A series of centrality measures have been proposed to discover essential proteins based on network topology. Unfortunately, the protein–protein interactions produced by high-throughput experiments generally have high false positives. Moreover, most of centrality measures based on network topology are sensitive to false positives. We therefore propose a new method for evaluating the confidence of each interaction based on the combination of logistic regression-based model and function similarity. Nine standard centrality measures in weighted network were redefined in this paper. The experimental results on a yeast protein interaction network shows that the weighting method improved the performance of centrality measures considerably. More essential proteins were discovered by the weighted centrality measures than by the original centrality measures used in the unweighted network. Even about 20% improvements were obtained from closeness centrality and subgraph centrality.

MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts

Abstract: The identification of the molecular pathways active in specific contexts, such as disease states or drug responses, often requires an extensive view of the potential interactions between a subset of proteins. This view is not easily obtained: it requires the integration of context-specific protein list or expression data with up-to-date data of protein interactions that are typically spread across multiple databases. The MyProteinNet web server allows users to easily create such context-sensitive protein interaction networks. Users can automatically gather and consolidate data from up to 11 different databases to create a generic protein interaction network (interactome). They can score the interactions based on reliability and filter them by user-defined contexts including molecular expression and protein annotation. The output of MyProteinNet includes the generic and filtered interactome files, together with a summary of their network attributes. MyProteinNet is particularly geared toward building human tissue interactomes, by maintaining tissue expression profiles from multiple resources. The ability of MyProteinNet to facilitate the construction of up-to-date, context-specific interactomes and its applicability to 11 different organisms and to tens of human tissues, make it a powerful tool in meaningful analysis of protein networks. MyProteinNet is available at http://netbio.bgu.ac.il/myproteinnet.

gCoda: Conditional Dependence Network Inference for Compositional Data.

Abstract: The increasing quality and the reducing cost of high-throughput sequencing technologies for 16S rRNA gene profiling enable researchers to directly analyze microbe communities in natural environments. The direct interactions among microbial species of a given ecological system can help us understand the principles of community assembly and maintenance under various conditions. Compositionality and dimensionality of microbiome data are two main challenges for inferring the direct interaction network of microbes. In this article, we use the logistic normal distribution to model the background mechanism of microbiome data, which can appropriately deal with the compositional nature of the data. The direct interaction relationships are then modeled via the conditional dependence network under this logistic normal assumption. We then propose a novel penalized maximum likelihood method called gCoda to estimate the sparse structure of inverse covariance for latent normal variables to address the high dimensionality of the microbiome data. An effective Majorization-Minimization algorithm is proposed to solve the optimization problem in gCoda. Simulation studies show that gCoda outperforms existing methods (e.g., SPIEC-EASI) in edge recovery of inverse covariance for compositional data under a variety of scenarios. gCoda also performs better than SPIEC-EASI for inferring direct microbial interactions of mouse skin microbiome data.

Predicting Vehicle Behaviors Over An Extended Horizon Using Behavior Interaction Network

Abstract: Anticipating possible behaviors of traffic participants is an essential capability of autonomous vehicles. Many behavior detection and maneuver recognition methods only have a very limited prediction horizon that leaves inadequate time and space for planning. To avoid unsatisfactory reactive decisions, it is essential to count long-term future rewards in planning, which requires extending the prediction horizon. In this paper, we uncover that clues to vehicle behaviors over an extended horizon can be found in vehicle interaction, which makes it possible to anticipate the likelihood of a certain behavior, even in the absence of any clear maneuver pattern. We adopt a recurrent neural network (RNN) for observation encoding, and based on that, we propose a novel vehicle behavior interaction network (VBIN) to capture the vehicle interaction from the hidden states and connection feature of each interaction pair. The output of our method is a probabilistic likelihood of multiple behavior classes, which matches the multimodal and uncertain nature of the distant future. A systematic comparison of our method against two state-of-the-art methods and another two baseline methods on a publicly available real highway dataset is provided, showing that our method has superior accuracy and advanced capability for interaction modeling.