Abstract: Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.
Abstract: This paper presents a supervised clustering algorithm,
namely Grid-Based Supervised Clustering (GBSC), which is able to
identify clusters of any shapes and sizes without presuming any
canonical form for data distribution. The GBSC needs no prespecified
number of clusters, is insensitive to the order of the input
data objects, and is capable of handling outliers. Built on the
combination of grid-based clustering and density-based clustering,
under the assistance of the downward closure property of density
used in bottom-up subspace clustering, the GBSC can notably reduce
its search space to avoid the memory confinement situation during its
execution. On two-dimension synthetic datasets, the GBSC can
identify clusters with different shapes and sizes correctly. The GBSC
also outperforms other five supervised clustering algorithms when
the experiments are performed on some UCI datasets.
Abstract: This paper develops an unscented grid-based filter
and a smoother for accurate nonlinear modeling and analysis
of time series. The filter uses unscented deterministic sampling
during both the time and measurement updating phases, to approximate
directly the distributions of the latent state variable. A
complementary grid smoother is also made to enable computing
of the likelihood. This helps us to formulate an expectation
maximisation algorithm for maximum likelihood estimation of
the state noise and the observation noise. Empirical investigations
show that the proposed unscented grid filter/smoother compares
favourably to other similar filters on nonlinear estimation tasks.
Abstract: Recent scientific investigations indicate that
multimodal biometrics overcome the technical limitations of
unimodal biometrics, making them ideally suited for everyday life
applications that require a reliable authentication system. However,
for a successful adoption of multimodal biometrics, such systems
would require large heterogeneous datasets with complex multimodal
fusion and privacy schemes spanning various distributed
environments. From experimental investigations of current
multimodal systems, this paper reports the various issues related to
speed, error-recovery and privacy that impede the diffusion of such
systems in real-life. This calls for a robust mechanism that caters to
the desired real-time performance, robust fusion schemes,
interoperability and adaptable privacy policies.
The main objective of this paper is to present a framework that
addresses the abovementioned issues by leveraging on the
heterogeneous resource sharing capacities of Grid services and the
efficient machine learning capabilities of artificial neural networks
(ANN). Hence, this paper proposes a Grid-based neural network
framework for adopting multimodal biometrics with the view of
overcoming the barriers of performance, privacy and risk issues that
are associated with shared heterogeneous multimodal data centres.
The framework combines the concept of Grid services for reliable
brokering and privacy policy management of shared biometric
resources along with a momentum back propagation ANN (MBPANN)
model of machine learning for efficient multimodal fusion and
authentication schemes. Real-life applications would be able to adopt
the proposed framework to cater to the varying business requirements
and user privacies for a successful diffusion of multimodal
biometrics in various day-to-day transactions.
Abstract: This paper presents a novel approach for representing
the spatio-temporal topology of the camera network with overlapping
and non-overlapping fields of view (FOVs). The topology is
determined by tracking moving objects and establishing object
correspondence across multiple cameras. To track people successfully
in multiple camera views, we used the Merge-Split (MS) approach for
object occlusion in a single camera and the grid-based approach for
extracting the accurate object feature. In addition, we considered the
appearance of people and the transition time between entry and exit
zones for tracking objects across blind regions of multiple cameras
with non-overlapping FOVs. The main contribution of this paper is to
estimate transition times between various entry and exit zones, and to
graphically represent the camera topology as an undirected weighted
graph using the transition probabilities.
Abstract: A novel PDE solver using the multidimensional wave
digital filtering (MDWDF) technique to achieve the solution of a 2D
seismic wave system is presented. In essence, the continuous physical
system served by a linear Kirchhoff circuit is transformed to an
equivalent discrete dynamic system implemented by a MD wave
digital filtering (MDWDF) circuit. This amounts to numerically
approximating the differential equations used to describe elements of a
MD passive electronic circuit by a grid-based difference equations
implemented by the so-called state quantities within the passive
MDWDF circuit. So the digital model can track the wave field on a
dense 3D grid of points. Details about how to transform the continuous
system into a desired discrete passive system are addressed. In
addition, initial and boundary conditions are properly embedded into
the MDWDF circuit in terms of state quantities. Graphic results have
clearly demonstrated some physical effects of seismic wave (P-wave
and S–wave) propagation including radiation, reflection, and
refraction from and across the hard boundaries. Comparison between
the MDWDF technique and the finite difference time domain (FDTD)
approach is also made in terms of the computational efficiency.
Abstract: Clustering algorithms help to understand the hidden
information present in datasets. A dataset may contain intrinsic and
nested clusters, the detection of which is of utmost importance. This
paper presents a Distributed Grid-based Density Clustering algorithm
capable of identifying arbitrary shaped embedded clusters as well as
multi-density clusters over large spatial datasets. For handling
massive datasets, we implemented our method using a 'sharednothing'
architecture where multiple computers are interconnected
over a network. Experimental results are reported to establish the
superiority of the technique in terms of scale-up, speedup as well as
cluster quality.