427 research outputs found
Efficient network-guided multi-locus association mapping with graph cuts
As an increasing number of genome-wide association studies reveal the
limitations of attempting to explain phenotypic heritability by single genetic
loci, there is growing interest for associating complex phenotypes with sets of
genetic loci. While several methods for multi-locus mapping have been proposed,
it is often unclear how to relate the detected loci to the growing knowledge
about gene pathways and networks. The few methods that take biological pathways
or networks into account are either restricted to investigating a limited
number of predetermined sets of loci, or do not scale to genome-wide settings.
We present SConES, a new efficient method to discover sets of genetic loci
that are maximally associated with a phenotype, while being connected in an
underlying network. Our approach is based on a minimum cut reformulation of the
problem of selecting features under sparsity and connectivity constraints that
can be solved exactly and rapidly.
SConES outperforms state-of-the-art competitors in terms of runtime, scales
to hundreds of thousands of genetic loci, and exhibits higher power in
detecting causal SNPs in simulation studies than existing methods. On flowering
time phenotypes and genotypes from Arabidopsis thaliana, SConES detects loci
that enable accurate phenotype prediction and that are supported by the
literature.
Matlab code for SConES is available at
http://webdav.tuebingen.mpg.de/u/karsten/Forschung/scones/Comment: 20 pages, 6 figures, accepted at ISMB (International Conference on
Intelligent Systems for Molecular Biology) 201
Realtime market microstructure analysis: online Transaction Cost Analysis
Motivated by the practical challenge in monitoring the performance of a large
number of algorithmic trading orders, this paper provides a methodology that
leads to automatic discovery of the causes that lie behind a poor trading
performance. It also gives theoretical foundations to a generic framework for
real-time trading analysis. Academic literature provides different ways to
formalize these algorithms and show how optimal they can be from a
mean-variance, a stochastic control, an impulse control or a statistical
learning viewpoint. This paper is agnostic about the way the algorithm has been
built and provides a theoretical formalism to identify in real-time the market
conditions that influenced its efficiency or inefficiency. For a given set of
characteristics describing the market context, selected by a practitioner, we
first show how a set of additional derived explanatory factors, called anomaly
detectors, can be created for each market order. We then will present an online
methodology to quantify how this extended set of factors, at any given time,
predicts which of the orders are underperforming while calculating the
predictive power of this explanatory factor set. Armed with this information,
which we call influence analysis, we intend to empower the order monitoring
user to take appropriate action on any affected orders by re-calibrating the
trading algorithms working the order through new parameters, pausing their
execution or taking over more direct trading control. Also we intend that use
of this method in the post trade analysis of algorithms can be taken advantage
of to automatically adjust their trading action.Comment: 33 pages, 12 figure
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