56,948 research outputs found
An empirical comparison of supervised machine learning techniques in bioinformatics
Research in bioinformatics is driven by the experimental data.
Current biological databases are populated by vast amounts of
experimental data. Machine learning has been widely applied to
bioinformatics and has gained a lot of success in this research
area. At present, with various learning algorithms available in the
literature, researchers are facing difficulties in choosing the best
method that can apply to their data. We performed an empirical
study on 7 individual learning systems and 9 different combined
methods on 4 different biological data sets, and provide some
suggested issues to be considered when answering the following
questions: (i) How does one choose which algorithm is best
suitable for their data set? (ii) Are combined methods better than
a single approach? (iii) How does one compare the effectiveness
of a particular algorithm to the others
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Characterisation of FAD-family folds using a machine learning approach
Flavin adenine dinucleotide (FAD) and its derivatives play a crucial role in
biological processes. They are major organic cofactors and electron carriers
in both enzymatic activities and biochemical pathways. We have analysed
the relationships between sequence and structure of FAD-containing proteins
using a machine learning approach. Decision trees were generated using the
C4.5 algorithm as a means of automatically generating rules from biological
databases (TOPS, CATH and PDB). These rules were then used as
background knowledge for an ILP system to characterise the four different
classes of FAD-family folds classified in Dym and Eisenberg (2001). These
FAD-family folds are: glutathione reductase (GR), ferredoxin reductase (FR),
p-cresol methylhydroxylase (PCMH) and pyruvate oxidase (PO). Each FADfamily
was characterised by a set of rules. The âknowledge patternsâ
generated from this approach are a set of rules containing conserved sequence
motifs, secondary structure sequence elements and folding information.
Every rule was then verified using statistical evaluation on the measured
significance of each rule. We show that this machine learning approach is
capable of learning and discovering interesting patterns from large biological
databases and can generate âknowledge patternsâ that characterise the FADcontaining
proteins, and at the same time classify these proteins into four
different families
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Integrative machine learning approach for multi-class SCOP protein fold classification
Classification and prediction of protein structure has been a central research theme in structural bioinformatics. Due to the imbalanced distribution of proteins over multi SCOP classification, most discriminative machine learning suffers the well-known âFalse Positives â problem when learning over these types of problems. We have devised eKISS, an ensemble machine learning specifically designed to increase the coverage of positive examples when learning under multiclass imbalanced data sets. We have applied eKISS to classify 25 SCOP folds and show that our learning system improved over classical learning methods
A heterotic sigma model with novel target geometry
We construct a (1,2) heterotic sigma model whose target space geometry
consists of a transitive Lie algebroid with complex structure on a Kaehler
manifold. We show that, under certain geometrical and topological conditions,
there are two distinguished topological half--twists of the heterotic sigma
model leading to A and B type half--topological models. Each of these models is
characterized by the usual topological BRST operator, stemming from the
heterotic (0,2) supersymmetry, and a second BRST operator anticommuting with
the former, originating from the (1,0) supersymmetry. These BRST operators
combined in a certain way provide each half--topological model with two
inequivalent BRST structures and, correspondingly, two distinct perturbative
chiral algebras and chiral rings. The latter are studied in detail and
characterized geometrically in terms of Lie algebroid cohomology in the
quasiclassical limit.Comment: 83 pages, no figures, 2 references adde
Tunneling spectroscopy studies of aluminum oxide tunnel barrier layers
We report scanning tunneling microscopy and ballistic electron emission
microscopy studies of the electronic states of the uncovered and
chemisorbed-oxygen covered surface of AlOx tunnel barrier layers. These states
change when chemisorbed oxygen ions are moved into the oxide by either flood
gun electron bombardment or by thermal annealing. The former, if sufficiently
energetic, results in locally well defined conduction band onsets at ~1 V,
while the latter results in a progressively higher local conduction band onset,
exceeding 2.3 V for 500 and 600 C thermal anneals
Stray field signatures of N\'eel textured skyrmions in Ir/Fe/Co/Pt multilayer films
Skyrmions are nanoscale spin configurations with topological properties that
hold great promise for spintronic devices. Here, we establish their N\'eel
texture, helicity, and size in Ir/Fe/Co/Pt multilayer films by constructing a
multipole expansion to model their stray field signatures and applying it to
magnetic force microscopy (MFM) images. Furthermore, the demonstrated
sensitivity to inhomogeneity in skyrmion properties, coupled with a unique
capability to estimate the pinning force governing dynamics, portends broad
applicability in the burgeoning field of topological spin textures.Comment: 6 pages, 4 figures, significantly revised and upgraded. For the
updated supplementary material please contact one of the corresponding
author
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