1,913 research outputs found
Automating biomedical data science through tree-based pipeline optimization
Over the past decade, data science and machine learning has grown from a
mysterious art form to a staple tool across a variety of fields in academia,
business, and government. In this paper, we introduce the concept of tree-based
pipeline optimization for automating one of the most tedious parts of machine
learning---pipeline design. We implement a Tree-based Pipeline Optimization
Tool (TPOT) and demonstrate its effectiveness on a series of simulated and
real-world genetic data sets. In particular, we show that TPOT can build
machine learning pipelines that achieve competitive classification accuracy and
discover novel pipeline operators---such as synthetic feature
constructors---that significantly improve classification accuracy on these data
sets. We also highlight the current challenges to pipeline optimization, such
as the tendency to produce pipelines that overfit the data, and suggest future
research paths to overcome these challenges. As such, this work represents an
early step toward fully automating machine learning pipeline design.Comment: 16 pages, 5 figures, to appear in EvoBIO 2016 proceeding
Substance Use and Mild Traumatic Brain Injury Risk Reduction and Prevention: A Novel Model for Treatment
Traumatic brain injury (TBI) and substance use disorders (SUDs) frequently co-occur. Individuals with histories of alcohol or other drug use are at greater risk for sustaining TBI, and individuals with TBI frequently misuse substances before and after injury. Further, a growing body of literature supports the relationship between comorbid histories of mild TBI (mTBI) and SUDs and negative outcomes. Alcohol and other drug use are strongly associated with risk taking. Disinhibition, impaired executive function, and/or impulsivity as a result of mTBI also contribute to an individual's proclivity towards risk-taking. Risk-taking behavior may therefore, be a direct result of SUD and/or history of mTBI, and risky behaviors may predispose individuals for subsequent injury or continued use of substances. Based on these findings, evaluation of risk-taking behavior associated with the co-occurrence of SUD and mTBI should be a standard clinical practice. Interventions aimed at reducing risky behavior among members of this population may assist in decreasing negative outcomes. A novel intervention (Substance Use and Traumatic Brain Injury Risk Reduction and Prevention (STRRP)) for reducing and preventing risky behaviors among individuals with co-occurring mTBI and SUD is presented. Areas for further research are discussed
Asymmetrical crossing barriers in angiosperms
Patterns of reproductive isolation between species may provide insight into the mechanisms and evolution of barriers to interspeci¢c gene exchange. We used data from published interspeci¢c hybridization experiments from 14 genera of angiosperms in order to test for the presence of asymmetrical barriers to gene exchange. Reproductive isolation was examined at three life-history stages: the ability of interspeci¢c crosses to produce seeds, the viability of F 1 hybrids, and the fertility of F 1 hybrids. Statistically signi¢cant asymmetries in the strength of reproductive isolation between species were detected in all genera and at each of the three life-history stages. Asymmetries in seed production may be caused by a variety of mechanisms including di¡erences in stigma/style lengths, self compatibility and di¡erential fruit abortion. Asymmetries in post-zygotic isolation are probably caused by nuclear^cytoplasmic interactions. Asymmetrical reproductive isolation between plant taxa may have important implications for the dynamics of hybrid zones, the direction of genetic introgression and the probability of reinforcement
Two-dimensional hydrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic fluid flow through porous media
The behaviour of two dimensional binary and ternary amphiphilic fluids under
flow conditions is investigated using a hydrodynamic lattice gas model. After
the validation of the model in simple cases (Poiseuille flow, Darcy's law for
single component fluids), attention is focussed on the properties of binary
immiscible fluids in porous media. An extension of Darcy's law which explicitly
admits a viscous coupling between the fluids is verified, and evidence of
capillary effects are described. The influence of a third component, namely
surfactant, is studied in the same context. Invasion simulations have also been
performed. The effect of the applied force on the invasion process is reported.
As the forcing level increases, the invasion process becomes faster and the
residual oil saturation decreases. The introduction of surfactant in the
invading phase during imbibition produces new phenomena, including
emulsification and micellisation. At very low fluid forcing levels, this leads
to the production of a low-resistance gel, which then slows down the progress
of the invading fluid. At long times (beyond the water percolation threshold),
the concentration of remaining oil within the porous medium is lowered by the
action of surfactant, thus enhancing oil recovery. On the other hand, the
introduction of surfactant in the invading phase during drainage simulations
slows down the invasion process -- the invading fluid takes a more tortuous
path to invade the porous medium -- and reduces the oil recovery (the residual
oil saturation increases).Comment: 48 pages, 26 figures. Phys. Rev. E (in press
Bethe--Salpeter equation in QCD
We extend to regular QCD the derivation of a confining
Bethe--Salpeter equation previously given for the simplest model of scalar QCD
in which quarks are treated as spinless particles. We start from the same
assumptions on the Wilson loop integral already adopted in the derivation of a
semirelativistic heavy quark potential. We show that, by standard
approximations, an effective meson squared mass operator can be obtained from
our BS kernel and that, from this, by expansion the
corresponding Wilson loop potential can be reobtained, spin--dependent and
velocity--dependent terms included. We also show that, on the contrary,
neglecting spin--dependent terms, relativistic flux tube model is reproduced.Comment: 23 pages, revte
Charged multifluids in general relativity
The exact 1+3 covariant dynamical fluid equations for a multi-component
plasma, together with Maxwell's equations are presented in such a way as to
make them suitable for a gauge-invariant analysis of linear density and
velocity perturbations of the Friedmann-Robertson-Walker model. In the case
where the matter is described by a two component plasma where thermal effects
are neglected, a mode representing high-frequency plasma oscillations is found
in addition to the standard growing and decaying gravitational instability
picture. Further applications of these equations are also discussed.Comment: 14 pages (example added), to appear in Class. Quantum Gra
Three dimensional hysdrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic flow through porous media
We report the results of a study of multiphase flow in porous media. A
Darcy's law for steady multiphase flow was investigated for both binary and
ternary amphiphilic flow. Linear flux-forcing relationships satisfying Onsager
reciprocity were shown to be a good approximation of the simulation data. The
dependence of the relative permeability coefficients on water saturation was
investigated and showed good qualitative agreement with experimental data.
Non-steady state invasion flows were investigated, with particular interest in
the asymptotic residual oil saturation. The addition of surfactant to the
invasive fluid was shown to significantly reduce the residual oil saturation.Comment: To appear in Phys. Rev.
Three-dimensional adaptive evolution of gravitational waves in numerical relativity
Adaptive techniques are crucial for successful numerical modeling of
gravitational waves from astrophysical sources such as coalescing compact
binaries, since the radiation typically has wavelengths much larger than the
scale of the sources. We have carried out an important step toward this goal,
the evolution of weak gravitational waves using adaptive mesh refinement in the
Einstein equations. The 2-level adaptive simulation is compared with unigrid
runs at coarse and fine resolution, and is shown to track closely the features
of the fine grid run.Comment: REVTeX, 7 pages, including three figures; submitted to Physical
Review
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