SPRINT: Ultrafast protein-protein interaction prediction of the entire human interactome

Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Many computational methods have been proposed among which sequence-based ones are very promising. However, so far no such method is able to predict effectively the entire human interactome: they require too much time or memory. We present SPRINT (Scoring PRotein INTeractions), a new sequence-based algorithm and tool for predicting protein-protein interactions. We comprehensively compare SPRINT with state-of-the-art programs on seven most reliable human PPI datasets and show that it is more accurate while running orders of magnitude faster and using very little memory. SPRINT is the only program that can predict the entire human interactome. Our goal is to transform the very challenging problem of predicting the entire human interactome into a routine task. The source code of SPRINT is freely available from github.com/lucian-ilie/SPRINT/ and the datasets and predicted PPIs from www.csd.uwo.ca/faculty/ilie/SPRINT/

Stochastic single-molecule dynamics of synaptic membrane protein domains

Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic proteins provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the single-molecule trajectories observed for synaptic proteins, and spatially inhomogeneous protein lifetimes at the cell membrane. Our results suggest that central aspects of the single-molecule and collective dynamics observed for membrane protein domains can be understood in terms of stochastic reaction-diffusion processes at the cell membrane.Comment: Main text (7 pages, 4 figures, 1 table) and supplementary material (3 pages, 3 figures

Q-learning Channel Access Methods for Wireless Powered Internet of Things Networks

The Internet of Things (IoT) is becoming critical in our daily life. A key technology of interest in this thesis is Radio Frequency (RF) charging. The ability to charge devices wirelessly creates so called RF-energy harvesting IoT networks. In particular, there is a hybrid access point (HAP) that provides energy in an on-demand manner to RF-energy harvesting devices. These devices then collect data and transmit it to the HAP. In this respect, a key issue is ensuring devices have a high number of successful transmissions. There are a number of issues to consider when scheduling the transmissions of devices in the said network. First, the channel gain to/from devices varies over time. This means the efficiency to deliver energy to devices and to transmit the same amount of data is different over time. Second, during channel access, devices are not aware of the energy level of other devices nor whether they will transmit data. Third, devices have non-causal knowledge of their energy arrivals and channel gain information. Consequently, they do not know whether they should delay their transmissions in hope of better channel conditions or less contention in future time slots or doing so would result in energy overflow

A New Algorithm for Protein-Protein Interaction Prediction

Protein-protein interactions (PPI) are vital processes in molecular biology. However, the current understanding of PPIs is far from satisfactory. Improved methods of pre- dicting PPIs are very much needed. Since experimental methods are labour and time consuming and lack accuracy, the improvement is expected to come from the area of computational methods. We designed and implemented a new algorithm based on protein primary structure to predict PPIs using C++ and OpenMP for parallel computing. We compared our method with four leading methods. Our results are better than the competition for most of the important values. Furthermore, it succeeds in surpassing the consensus of the other methods

Similarity Learning via Kernel Preserving Embedding

Data similarity is a key concept in many data-driven applications. Many algorithms are sensitive to similarity measures. To tackle this fundamental problem, automatically learning of similarity information from data via self-expression has been developed and successfully applied in various models, such as low-rank representation, sparse subspace learning, semi-supervised learning. However, it just tries to reconstruct the original data and some valuable information, e.g., the manifold structure, is largely ignored. In this paper, we argue that it is beneficial to preserve the overall relations when we extract similarity information. Specifically, we propose a novel similarity learning framework by minimizing the reconstruction error of kernel matrices, rather than the reconstruction error of original data adopted by existing work. Taking the clustering task as an example to evaluate our method, we observe considerable improvements compared to other state-of-the-art methods. More importantly, our proposed framework is very general and provides a novel and fundamental building block for many other similarity-based tasks. Besides, our proposed kernel preserving opens up a large number of possibilities to embed high-dimensional data into low-dimensional space.Comment: Published in AAAI 201