Assessment of community efforts to advance network-based prediction of protein-protein interactions

Comprehensive understanding of the human protein-protein interaction (PPI) network, aka the human interactome, can provide important insights into the molecular mechanisms of complex biological processes and diseases. Despite the remarkable experimental efforts undertaken to date to determine the structure of the human interactome, many PPIs remain unmapped. Computational approaches, especially network-based methods, can facilitate the identification of previously uncharacterized PPIs. Many such methods have been proposed. Yet, a systematic evaluation of existing network-based methods in predicting PPIs is still lacking. Here, we report community efforts initiated by the International Network Medicine Consortium to benchmark the ability of 26 representative network-based methods to predict PPIs across six different interactomes of four different organisms: A. thaliana, C. elegans, S. cerevisiae, and H. sapiens. Through extensive computational and experimental validations, we found that advanced similarity-based methods, which leverage the underlying network characteristics of PPIs, show superior performance over other general link prediction methods in the interactomes we considered.

Pavement Distress Estimation via Signal on Graph Processing

A comprehensive representation of the road pavement state of health is of great interest. In recent years, automated data collection and processing technology has been used for pavement inspection. In this paper, a new signal on graph (SoG) model of road pavement distresses is presented with the aim of improving automatic pavement distress detection systems. A novel nonlinear Bayesian estimator in recovering distress metrics is also derived. The performance of the methodology was evaluated on a large dataset of pavement distress values collected in field tests conducted in Kazakhstan. The application of the proposed methodology is effective in recovering acquisition errors, improving road failure detection. Moreover, the output of the Bayesian estimator can be used to identify sections where the measurement acquired by the 3D laser technology is unreliable. Therefore, the presented model could be used to schedule road section maintenance in a better way.

Phase/Amplitude Synchronization of Brain Signals During Motor Imagery BCI Tasks

In the last decade, functional connectivity (FC) has been increasingly adopted based on its ability to capture statistical dependencies between multivariate brain signals. However, the role of FC in the context of brain-computer interface applications is still poorly understood. To address this gap in knowledge, we considered a group of 20 healthy subjects during an EEG-based hand motor imagery (MI) task. We studied two well-established FC estimators, i.e. spectral- and imaginary-coherence, and we investigated how they were modulated by the MI task. We characterized the resulting FC networks by extracting the strength of connectivity of each EEG sensor and we compared the discriminant power with respect to standard power spectrum features. At the group level, results showed that while spectral-coherence based network features were increasing in the sensorimotor areas, those based on imaginary-coherence were significantly decreasing. We demonstrated that this opposite, but complementary, behavior was respectively determined by the increase in amplitude and phase synchronization between the brain signals. At the individual level, we eventually assessed the potential of these network connectivity features in a simple off-line classification scenario. Taken together, our results provide fresh insights into the oscillatory mechanisms subserving brain network changes during MI and offer new perspectives to improve BCI performance.

Green Compressive Sampling Reconstruction in IoT Networks

In this paper, we address the problem of green Compressed Sensing (CS) reconstruction within Internet of Things (IoT) networks, both in terms of computing architecture and reconstruction algorithms. The approach is novel since, unlike most of the literature dealing with energy efficient gathering of the CS measurements, we focus on the energy efficiency of the signal reconstruction stage given the CS measurements. As a first novel contribution, we present an analysis of the energy consumption within the IoT network under two computing architectures. In the first one, reconstruction takes place within the IoT network and the reconstructed data are encoded and transmitted out of the IoT network; in the second one, all the CS measurements are forwarded to off-network devices for reconstruction and storage, i.e., reconstruction is off-loaded. Our analysis shows that the two architectures significantly differ in terms of consumed energy, and it outlines a theoretically motivated criterion to select a green CS reconstruction computing architecture. Specifically, we present a suitable decision function to determine which architecture outperforms the other in terms of energy efficiency. The presented decision function depends on a few IoT network features, such as the network size, the sink connectivity, and other systems’ parameters. As a second novel contribution, we show how to overcome classical performance comparison of different CS reconstruction algorithms usually carried out w.r.t. the achieved accuracy. Specifically, we consider the consumed energy and analyze the energy vs. accuracy trade-off. The herein presented approach, jointly considering signal processing and IoT network issues, is a relevant contribution for designing green compressive sampling architectures in IoT networks.

Reduced complexity rotation invariant texture classification using a blind deconvolution approach

In this paper, we present a texture classification procedure that makes use of a blind deconvolution approach. Specifically, the texture is modeled as the output of a linear system driven by a binary excitation. We show that features computed from one-dimensional slices extracted from the two-dimensional autocorrelation function (ACF) of the binary excitation allows representing the texture for rotation-invariant classification purposes. The two-dimensional classification problem is thus reconduced to a more simple one-dimensional one, which leads to a significant reduction of the classification procedure computational complexity.

Multichannel blind image deconvolution using the Bussgang algorithm: spatial and multiresolution approaches

This work extends the Bussgang blind equalization algorithm to the multichannel case with application to image deconvolution problems. We address the restoration of images with poor spatial correlation as well as strongly correlated (natural) images. The spatial nonlinearity employed in the final estimation step of the Bussgang algorithm is developed according to the minimum mean square error criterion in the case of spatially uncorrelated images. For spatially correlated images, the nonlinearity design is rather conducted using a particular wavelet decomposition that, detecting lines, edges, and higher order structures, carries out a task analogous to those of the (preattentive) stage of the human visual system. Experimental results pertaining to restoration of motion blurred text images, out-of-focus spiky images, and blurred natural images are reported.