MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/.Comment: Accepted by both RECOMB 2014 and PLOS Computational Biolog

Traffic Hotspot localization in 3G and 4G wireless networks using OMC metrics

In recent years, there has been an increasing awareness to traffic localization techniques driven by the emergence of heterogeneous networks (HetNet) with small cells deployment and the green networks. The localization of hotspot data traffic with a very high accuracy is indeed of great interest to know where the small cells should be deployed and how can be managed for sleep mode concept. In this paper, we propose a new traffic localization technique based on the combination of different key performance indicators (KPI) extracted from the operation and maintenance center (OMC). The proposed localization algorithm is composed with five main steps; each one corresponds to the determination of traffic weight per area using only one KPI. These KPIs are Timing Advance (TA), Angle of Arrival (AoA), Neighbor cell level, the load of each cell and the Harmonic mean throughput (HMT) versus the Arithmetic mean throughput (AMT). The five KPIs are finally combined by a function taking as variables the values computed from the five steps. By mixing such KPIs, we show that it is possible to lessen significantly the errors of localization in a high precision attaining small cell dimensions.Comment: 7 pages, 7 figures, published in Proc. IEEE International Symposium on Personal, Indoor and Mobile Radio Communications 2014 (PIMRC); IEEE International Symposium on Personal, Indoor and Mobile Radio Communications 2014 (PIMRC

Modeling Collisional Cascades In Debris Disks: The Numerical Method

We develop a new numerical algorithm to model collisional cascades in debris disks. Because of the large dynamical range in particle masses, we solve the integro-differential equations describing erosive and catastrophic collisions in a particle-in-a-box approach, while treating the orbital dynamics of the particles in an approximate fashion. We employ a new scheme for describing erosive (cratering) collisions that yields a continuous set of outcomes as a function of colliding masses. We demonstrate the stability and convergence characteristics of our algorithm and compare it with other treatments. We show that incorporating the effects of erosive collisions results in a decay of the particle distribution that is significantly faster than with purely catastrophic collisions.Comment: 24 pages, 20 figues, Published in Ap

SIRENA: A CAD environment for behavioural modelling and simulation of VLSI cellular neural network chips

This paper presents SIRENA, a CAD environment for the simulation and modelling of mixed-signal VLSI parallel processing chips based on cellular neural networks. SIRENA includes capabilities for: (a) the description of nominal and non-ideal operation of CNN analogue circuitry at the behavioural level; (b) performing realistic simulations of the transient evolution of physical CNNs including deviations due to second-order effects of the hardware; and, (c) evaluating sensitivity figures, and realize noise and Monte Carlo simulations in the time domain. These capabilities portray SIRENA as better suited for CNN chip development than algorithmic simulation packages (such as OpenSimulator, Sesame) or conventional neural networks simulators (RCS, GENESIS, SFINX), which are not oriented to the evaluation of hardware non-idealities. As compared to conventional electrical simulators (such as HSPICE or ELDO-FAS), SIRENA provides easier modelling of the hardware parasitics, a significant reduction in computation time, and similar accuracy levels. Consequently, iteration during the design procedure becomes possible, supporting decision making regarding design strategies and dimensioning. SIRENA has been developed using object-oriented programming techniques in C, and currently runs under the UNIX operating system and X-Windows framework. It employs a dedicated high-level hardware description language: DECEL, fitted to the description of non-idealities arising in CNN hardware. This language has been developed aiming generality, in the sense of making no restrictions on the network models that can be implemented. SIRENA is highly modular and composed of independent tools. This simplifies future expansions and improvements.Comisión Interministerial de Ciencia y Tecnología TIC96-1392-C02-0

Simultaneous Parameter Calibration, Localization, and Mapping

The calibration parameters of a mobile robot play a substantial role in navigation tasks. Often these parameters are subject to variations that depend either on changes in the environment or on the load of the robot. In this paper, we propose an approach to simultaneously estimate a map of the environment, the position of the on-board sensors of the robot, and its kinematic parameters. Our method requires no prior knowledge about the environment and relies only on a rough initial guess of the parameters of the platform. The proposed approach estimates the parameters online and it is able to adapt to non-stationary changes of the configuration. We tested our approach in simulated environments and on a wide range of real-world data using different types of robotic platforms. (C) 2012 Taylor & Francis and The Robotics Society of Japa

Polyphonic Sound Event Detection by using Capsule Neural Networks

Artificial sound event detection (SED) has the aim to mimic the human ability to perceive and understand what is happening in the surroundings. Nowadays, Deep Learning offers valuable techniques for this goal such as Convolutional Neural Networks (CNNs). The Capsule Neural Network (CapsNet) architecture has been recently introduced in the image processing field with the intent to overcome some of the known limitations of CNNs, specifically regarding the scarce robustness to affine transformations (i.e., perspective, size, orientation) and the detection of overlapped images. This motivated the authors to employ CapsNets to deal with the polyphonic-SED task, in which multiple sound events occur simultaneously. Specifically, we propose to exploit the capsule units to represent a set of distinctive properties for each individual sound event. Capsule units are connected through a so-called "dynamic routing" that encourages learning part-whole relationships and improves the detection performance in a polyphonic context. This paper reports extensive evaluations carried out on three publicly available datasets, showing how the CapsNet-based algorithm not only outperforms standard CNNs but also allows to achieve the best results with respect to the state of the art algorithms

Socially Aware Motion Planning with Deep Reinforcement Learning

For robotic vehicles to navigate safely and efficiently in pedestrian-rich environments, it is important to model subtle human behaviors and navigation rules (e.g., passing on the right). However, while instinctive to humans, socially compliant navigation is still difficult to quantify due to the stochasticity in people's behaviors. Existing works are mostly focused on using feature-matching techniques to describe and imitate human paths, but often do not generalize well since the feature values can vary from person to person, and even run to run. This work notes that while it is challenging to directly specify the details of what to do (precise mechanisms of human navigation), it is straightforward to specify what not to do (violations of social norms). Specifically, using deep reinforcement learning, this work develops a time-efficient navigation policy that respects common social norms. The proposed method is shown to enable fully autonomous navigation of a robotic vehicle moving at human walking speed in an environment with many pedestrians.Comment: 8 page