489 research outputs found
In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles
Background: In silico candidate gene prioritisation (CGP) aids the discovery of gene functions by ranking genes according to an objective relevance score. While several CGP methods have been described for identifying human disease genes, corresponding methods for prokaryotic gene function discovery are lacking. Here we present two prokaryotic CGP methods, based on phylogenetic profiles, to assist with this task. Results: Using gene occurrence patterns in sample genomes, we developed two CGP methods (statistical and inductive CGP) to assist with the discovery of bacterial gene functions. Statistical CGP exploits the differences in gene frequency against phenotypic groups, while inductive CGP applies supervised machine learning to identify gene occurrence pattern across genomes. Three rediscovery experiments were designed to evaluate the CGP frameworks. The first experiment attempted to rediscover peptidoglycan genes with 417 published genome sequences. Both CGP methods achieved best areas under receiver operating characteristic curve (AUC) of 0.911 in Escherichia coli K-12 (EC-K12) and 0.978 Streptococcus agalactiae 2603 (SA-2603) genomes, with an average improvement in precision of >3.2-fold and a maximum of >27-fold using statistical CGP. A median AUC of >0.95 could still be achieved with as few as 10 genome examples in each group of genome examples in the rediscovery of the peptidoglycan metabolism genes. In the second experiment, a maximum of 109-fold improvement in precision was achieved in the rediscovery of anaerobic fermentation genes in EC-K12. The last experiment attempted to rediscover genes from 31 metabolic pathways in SA-2603, where 14 pathways achieved AUC >0.9 and 28 pathways achieved AUC >0.8 with the best inductive CGP algorithms. Conclusion: Our results demonstrate that the two CGP methods can assist with the study of functionally uncategorised genomic regions and discovery of bacterial gene-function relationships. Our rediscovery experiments also provide a set of standard tasks against which future methods may be compared.12 page(s
SIMULATING HIERARCHICAL STRUCTURE OF HUMAN VISUAL CORTEX FOR IMAGE CLASSIFICATION
Ph.DDOCTOR OF PHILOSOPH
Generic decoding of seen and imagined objects using hierarchical visual features
Object recognition is a key function in both human and machine vision. While
recent studies have achieved fMRI decoding of seen and imagined contents, the
prediction is limited to training examples. We present a decoding approach for
arbitrary objects, using the machine vision principle that an object category
is represented by a set of features rendered invariant through hierarchical
processing. We show that visual features including those from a convolutional
neural network can be predicted from fMRI patterns and that greater accuracy is
achieved for low/high-level features with lower/higher-level visual areas,
respectively. Predicted features are used to identify seen/imagined object
categories (extending beyond decoder training) from a set of computed features
for numerous object images. Furthermore, the decoding of imagined objects
reveals progressive recruitment of higher to lower visual representations. Our
results demonstrate a homology between human and machine vision and its utility
for brain-based information retrieval
Propagation Kernels
We introduce propagation kernels, a general graph-kernel framework for
efficiently measuring the similarity of structured data. Propagation kernels
are based on monitoring how information spreads through a set of given graphs.
They leverage early-stage distributions from propagation schemes such as random
walks to capture structural information encoded in node labels, attributes, and
edge information. This has two benefits. First, off-the-shelf propagation
schemes can be used to naturally construct kernels for many graph types,
including labeled, partially labeled, unlabeled, directed, and attributed
graphs. Second, by leveraging existing efficient and informative propagation
schemes, propagation kernels can be considerably faster than state-of-the-art
approaches without sacrificing predictive performance. We will also show that
if the graphs at hand have a regular structure, for instance when modeling
image or video data, one can exploit this regularity to scale the kernel
computation to large databases of graphs with thousands of nodes. We support
our contributions by exhaustive experiments on a number of real-world graphs
from a variety of application domains
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