pwc-archive/papers-with-abstracts huggingface dataset:
Spatial Auditory Brain-computer Interface using Head Related Impulse Response
Date: 2015-01-19 00:00:00
Tasks: Brain Computer Interface

This study reports on a head related impulse response (HRIR) application to
an auditory spatial brain-computer interface (BCI) speller paradigm. Six
experienced and five BCI-naive users participated in an experimental spelling
set up based on five Japanese vowels. Obtained auditory evoked potentials
resulted with encouragingly good and stable P300-responses in online BCI
experiments. Our case study indicated that the headphone reproduced auditory
(HRIR- based) spatial sound paradigm could be a viable alternative to the
established multi-loudspeaker surround sound BCI-speller applications, as far
as healthy pilot study users are concerned.
The 'Power of Then': The Uniquely Human Capacity to Imagine Beyond the Present
Date: 2015-01-19 00:00:00

Humans appear to be uniquely in their ability to transcend the present and
reflect on current ideas in terms of what was experienced in the past, or
fantasize about the future. This paper presents an account, in layperson terms,
of how this ability came about, its importance in modern life, and why it
defines our human-ness.
How a Generation Was Misled About Natural Selection
Date: 2015-01-19 00:00:00

This article explains how natural selection works and how it has been
inappropriately applied to the description of cultural change. It proposes an
alternative evolutionary explanation for cultural evolution that describes it
in terms of communal exchange.
How Creative Ideas Take Shape
Date: 2015-01-19 00:00:00

According to the honing theory of creativity, creative thought works not on
individually considered, discrete, predefined representations but on a
contextually-elicited amalgam of items which exist in a state of potentiality
and may not be readily separable. This leads to the prediction that analogy
making proceeds not by mapping correspondences from candidate sources to
target, as predicted by the structure mapping theory of analogy, but by weeding
out non-correspondences, thereby whittling away at potentiality. Participants
were given an analogy problem, interrupted before they had time to solve it,
and asked to write down what they had by way of a solution. Na\"ive judges
categorized responses as significantly more supportive of the predictions of
honing theory than those of structure mapping.
Food web assembly rules
Date: 2015-06-17 00:00:00

In food webs, many interacting species coexist despite the restrictions
imposed by the competitive exclusion principle and apparent competition. For
the generalized Lotka-Volterra equations, sustainable coexistence necessitates
nonzero determinant of the interaction matrix. Here we show that this
requirement is equivalent to demanding that each species be part of a
non-overlapping pairing, which substantially constrains the food web structure.
We demonstrate that a stable food web can always be obtained if a
non-overlapping pairing exists. If it does not, the matrix rank can be used to
quantify the lack of niches, corresponding to unpaired species. For the species
richness at each trophic level, we derive the food web assembly rules, which
specify sustainable combinations. In neighboring levels, these rules allow the
higher level to avert competitive exclusion at the lower, thereby incorporating
apparent competition. In agreement with data, the assembly rules predict high
species numbers at intermediate levels and thinning at the top and bottom.
Using comprehensive food web data, we demonstrate how omnivores or parasites
with hosts at multiple trophic levels can loosen the constraints and help
obtain coexistence in food webs. Hence, omnivory may be the glue that keeps
communities intact even under extinction or ecological release of species.
Responding to Retrieval: A Proposal to Use Retrieval Information for Better Presentation of Website Content
Authors: Chowdary C Ravindranath, Singh Anil Kumar, Nelakanti Anil
Date: 2015-01-19 00:00:00
Tasks: Information Retrieval, Management, Retrieval

Retrieval and content management are assumed to be mutually exclusive. In
this paper we suggest that they need not be so. In the usual information
retrieval scenario, some information about queries leading to a website (due to
`hits' or `visits') is available to the server administrator of the concerned
website. This information can used to better present the content on the
website. Further, we suggest that some more information can be shared by the
retrieval system with the content provider. This will enable the content
provider (any website) to have a more dynamic presentation of the content that
is in tune with the query trends, without violating the privacy of the querying
user. The result will be a better synchronization between retrieval systems and
content providers, with the purpose of improving the user's web search
experience. This will also give the content provider a say in this process,
given that the content provider is the one who knows much more about the
content than the retrieval system. It also means that the content presentation
may change in response to a query. In the end, the user will be able to find
the relevant content more easily and quickly.
Effect of Volatility Clustering on Indifference Pricing of Options by Convex Risk Measures
Date: 2015-01-19 00:00:00
Tasks: Clustering

In this article, we look at the effect of volatility clustering on the risk
indifference price of options described by Sircar and Sturm in their paper
(Sircar, R., & Sturm, S. (2012). From smile asymptotics to market risk
measures. Mathematical Finance. Advance online publication.
doi:10.1111/mafi.12015). The indifference price in their article is obtained by
using dynamic convex risk measures given by backward stochastic differential
equations. Volatility clustering is modelled by a fast mean-reverting
volatility in a stochastic volatility model for stock price. Asymptotics of the
indifference price of options and their corresponding implied volatility are
obtained in this article, as the mean-reversion time approaches zero.
Correction terms to the asymptotic option price and implied volatility are also
obtained.
An optimal trading problem in intraday electricity markets
Date: 2015-01-19 00:00:00

We consider the problem of optimal trading for a power producer in the
context of intraday electricity markets. The aim is to minimize the imbalance
cost induced by the random residual demand in electricity, i.e. the consumption
from the clients minus the production from renewable energy. For a simple
linear price impact model and a quadratic criterion, we explicitly obtain
approximate optimal strategies in the intraday market and thermal power
generation, and exhibit some remarkable properties of the trading rate.
Furthermore, we study the case when there are jumps on the demand forecast and
on the intraday price, typically due to error in the prediction of wind power
generation. Finally, we solve the problem when taking into account delay
constraints in thermal power production.
Statistical Problems in a Paper on Variation In Cancer Risk Among Tissues, and New Discoveries
Date: 2015-01-19 00:00:00

Tomasetti and Vogelstein (2015) collected data on 31 different tissue types
and found a correlation of 0.8 between the logarithms of the incidence of
cancer (LCI), and the estimated number of stem cell divisions in those tissues
(LSCD). Some of their conclusions however are statistically erroneous. Their
excess risk score, "ERS" (log10 LCI x log10 LSCD), is non-monotonic under a
change of time units for the rates, which renders meaningless the results
derived from it, including a cluster of 22 "R-tumor" types for which they
conclude, "primary prevention measures are not likely to be very effective".
Further, r = 0.8 is consistent with the three orders of magnitude variation in
other unmeasured factors, leaving room for the possibility of primary
prevention if such factors can be intervened upon. Further exploration of the
data reveals additional findings: (1) that LCI grows at approximately the
square root of LSCD, which may provide a clue to the biology; (2) among
different possible combinations of the primary data, the one maximizing the
correlations with LCI is almost precisely the formula used by Tomasetti and
Vogelstein to estimate LSCD, giving support to stem cell divisions as an
independent factor in carcinogenesis, while not excluding other such factors.
Fast, approximate kinetics of RNA folding
Date: 2015-01-19 00:00:00
Tasks: Benchmarking

In this paper, we introduce the software suite, Hermes, which provides fast,
novel algorithms for RNA secondary structure kinetics. Using the fast Fourier
transform to efficiently compute the Boltzmann probability that a secondary
structure S of a given RNA sequence has base pair distance x [resp. y] from
reference structure A [resp. B], Hermes computes the exact kinetics of folding
from A to B in this coarse-grained model. In particular, Hermes computes the
mean first passage time from the transition probability matrix by using matrix
inversion, and also computes the equilibrium time from the rate matrix by using
spectral decomposition. Due to the model granularity and the speed of Hermes,
it is capable of determining secondary structure refolding kinetics for large
RNA sequences, beyond the range of other methods. Comparative benchmarking of
Hermes with other methods indicates that Hermes provides refolding kinetics of
accuracy suitable for use in computational design of RNA, an important area of
synthetic biology. Source code and documentation for Hermes are available at
http://bioinformatics. bc.edu/clotelab/Hermes/.
Similarities as Evidence for Common Ancestry -- A Likelihood Epistemology
Date: 2015-01-19 00:00:00

Darwin claims in the {\em Origin} that similarity is evidence for common
ancestry, but that adaptive similarities are "almost valueless" as evidence.
This claim seems reasonable for some adaptive similarities but not for others.
Here we clarify and evaluate these and related matters by using the law of
likelihood as an analytic tool and by considering mathematical models of three
evolutionary processes -- directional selection, stabilizing selection, and
drift. Our results apply both to Darwin's theory of evolution and to modern
evolutionary biology.
The paradoxical relationship of difficulty and lateral frontal cortex activity
Date: 2015-01-20 00:00:00

Task difficulty is widely cited in current theory regarding cognitive control
and fronto-parietal function. Ongoing debate surrounds the extent to which
global difficulty across multiple cognitive demands is the main driver of
lateral frontal activity. Here, we examine a commonly cited behavioral marker
of difficulty in these accounts: time-on-task (ToT), as assessed by response
time. Specifically, we investigate the task-dependent scaling of frontal BOLD
responses with ToT during hierarchical cognitive control. We observe a
paradoxical relationship, whereby rostral regions show greater scaling with ToT
on a first-order task, despite showing greater recruitment on a second-order
task; caudal regions show the converse relationships. Together, these results
demonstrate that ToT does not reflect a single dimension of difficulty that
uniformly drives lateral frontal activity. Rather, this discrepancy in the mean
and scaling of BOLD requires that multiple, distinct processes are instantiated
across these fronto-parietal regions in the service of cognitive control
function.
Modularity Enhances the Rate of Evolution in a Rugged Fitness Landscape
Date: 2015-01-20 00:00:00

Biological systems are modular, and this modularity affects the evolution of
biological systems over time and in different environments. We here develop a
theory for the dynamics of evolution in a rugged, modular fitness landscape. We
show analytically how horizontal gene transfer couples to the modularity in the
system and leads to more rapid rates of evolution at short times. The model, in
general, analytically demonstrates a selective pressure for the prevalence of
modularity in biology. We use this model to show how the evolution of the
influenza virus is affected by the modularity of the proteins that are
recognized by the human immune system. Approximately 25\% of the observed rate
of fitness increase of the virus could be ascribed to a modular viral
landscape.
Strabismic syndromes and syndromic strabismus - a brief review
Date: 2015-01-20 00:00:00

Strabismus can be found in association with congenital heart diseases, for
examples, in velocardiofacial (DiGeorge) syndrome, Down syndrome, mild
dysmorphic features, in CHARGE association, Turner syndrome, Ullrich-Turner
syndrome, cardiofaciocutaneous syndrome.1-4 Some types of strabismus is
heritable (e.g. infantile esotropia syndrome), particularly the ones associated
with multisystem disorders, e.g. Moebius syndrome, Prader-Willi syndrome,
craniofacial dysostoses, and mitochondrial myopathies.5 Due to the complexities
that a case of strabismus may pertain to, it is worthwhile to get to know more
about the strabismic syndromes and syndromic strabismus. This brief review -as
its name implied- does not attempt to cover every angle of the syndromic
conditions, but offers a refreshment on our knowledge about more prevalent
strabismus-related syndromes.
Real-time growth rate for general stochastic SIR epidemics on unclustered networks
Date: 2015-04-20 00:00:00
Tasks: Epidemiology

Networks have become an important tool for infectious disease epidemiology.
Most previous theoretical studies of transmission network models have either
considered simple Markovian dynamics at the individual level, or have focused
on the invasion threshold and final outcome of the epidemic. Here, we provide a
general theory for early real-time behaviour of epidemics on large
configuration model networks (i.e. static and locally unclustered), in
particular focusing on the computation of the Malthusian parameter that
describes the early exponential epidemic growth. Analytical, numerical and
Monte-Carlo methods under a wide variety of Markovian and non-Markovian
assumptions about the infectivity profile are presented. Numerous examples
provide explicit quantification of the impact of the network structure on the
temporal dynamics of the spread of infection and provide a benchmark for
validating results of large scale simulations.
Output stream of leaky integrate and fire neuron
Date: 2015-12-29 00:00:00
Tasks: Form

Probability density function of output interspike intervals is found in exact
form for leaky integrate and fire neuron stimulated with Poisson stream. The
diffusion approximation is not exploited.
CITEX: A new citation index to measure the relative importance of authors and papers in scientific publications
Authors: Pal Arindam, Ruj Sushmita
Date: 2015-01-20 00:00:00

Evaluating the performance of researchers and measuring the impact of papers
written by scientists is the main objective of citation analysis. Various
indices and metrics have been proposed for this. In this paper, we propose a
new citation index CITEX, which gives normalized scores to authors and papers
to determine their rankings. To the best of our knowledge, this is the first
citation index which simultaneously assigns scores to both authors and papers.
Using these scores, we can get an objective measure of the reputation of an
author and the impact of a paper.
  We model this problem as an iterative computation on a publication graph,
whose vertices are authors and papers, and whose edges indicate which author
has written which paper. We prove that this iterative computation converges in
the limit, by using a powerful theorem from linear algebra. We run this
algorithm on several examples, and find that the author and paper scores match
closely with what is suggested by our intuition. The algorithm is theoretically
sound and runs very fast in practice. We compare this index with several
existing metrics and find that CITEX gives far more accurate scores compared to
the traditional metrics.
Approximate statistical alignment by iterative sampling of substitution matrices
Date: 2015-01-19 00:00:00

We outline a procedure for jointly sampling substitution matrices and
multiple sequence alignments, according to an approximate posterior
distribution, using an MCMC-based algorithm. This procedure provides an
efficient and simple method by which to generate alternative alignments
according to their expected accuracy, and allows appropriate parameters for
substitution matrices to be selected in an automated fashion. In the cases
considered here, the sampled alignments with the highest likelihood have an
accuracy consistently higher than alignments generated using the standard
BLOSUM62 matrix.
Ion mediated crosslink driven mucous swelling kinetics
Date: 2015-01-20 00:00:00

We present an experimentally guided, multi-phasic, multi-species ionic gel
model to compare and make qualitative predictions on the rheology of mucus of
healthy individuals (Wild Type) versus those infected with Cystic Fibrosis. The
mixture theory consists of the mucus (polymer phase) and water (solvent phase)
as well as several different ions: H+, Na+ and Ca++. The model is linearized to
study the hydration of spherically symmetric mucus gels and calibrated against
the experimental data of mucus diffusivities. Near equilibrium, the linearized
form of the equation describing the radial size of the gel, reduces to the
well-known expression used in the kinetic theory of swelling hydrogels.
Numerical studies reveal that the Donnan potential is the dominating mechanism
driving the mucus swelling/deswelling transition. However, the altered swelling
kinetics of the Cystic Fibrosis infected mucus is not merely governed by the
hydroelectric composition of the swelling media, but also due to the altered
movement of electrolytes as well as due to the defective properties of the
mucin polymer network.
Chapter 9 TISSUE ENGINEERING
Date: 2015-01-20 00:00:00

Tissue Engineering (TE) is an interdisciplinary field dealing with the
principles of engineering and life sciences toward the development of
biological substitutes that restore, maintain, or improve tissue function or a
whole organ. Currently, TE is emerging as an invaluable field of study and is
one of the most promising fields for the next century. The ultimate goal is to
develop powerful new therapies for biological substitutes - that will
successfully restore the structural and functional disorders of human and
animal system.
Simple model for the Darwinian transition in early evolution
Date: 2015-01-21 00:00:00

It has been hypothesized that in the era just before the last universal
common ancestor emerged, life on earth was fundamentally collective. Ancient
life forms shared their genetic material freely through massive horizontal gene
transfer (HGT). At a certain point, however, life made a transition to the
modern era of individuality and vertical descent. Here we present a minimal
model for this hypothesized "Darwinian transition." The model suggests that
HGT-dominated dynamics may have been intermittently interrupted by
selection-driven processes during which genotypes became fitter and decreased
their inclination toward HGT. Stochastic switching in the population dynamics
with three-point (hypernetwork) interactions may have destabilized the
HGT-dominated collective state and led to the emergence of vertical descent and
the first well-defined species in early evolution. A nonlinear analysis of a
stochastic model dynamics covering key features of evolutionary processes (such
as selection, mutation, drift and HGT) supports this view. Our findings thus
suggest a viable route from early collective evolution to the start of
individuality and vertical Darwinian evolution, enabling the emergence of the
first species.
Characterizing the neural correlates of reasoning
Date: 2015-04-19 00:00:00

The brain did not develop a dedicated device for reasoning. This fact bears
dramatic consequences. While for perceptuo-motor functions neural activity is
shaped by the input's statistical properties, and processing is carried out at
high speed in hardwired spatially segregated modules, in reasoning, neural
activity is driven by internal dynamics, and processing times, stages, and
functional brain geometry are largely unconstrained a priori. Here, it is shown
that the complex properties of spontaneous activity, which can be ignored in a
short-lived event-related world, become prominent at the long time scales of
certain forms of reasoning which stretch over sufficiently long periods of
time. It is argued that the neural correlates of reasoning should in fact be
defined in terms of non-trivial generic properties of spontaneous brain
activity, and that this implies resorting to concepts, analytical tools, and
ways of designing experiments that are as yet non-standard in cognitive
neuroscience. The implications in terms of models of brain activity, shape of
the neural correlates, methods of data analysis, observability of the
phenomenon and experimental designs are discussed.
Rapid Sequence Identification of Potential Pathogens Using Techniques from Sparse Linear Algebra
Date: 2015-01-21 00:00:00

The decreasing costs and increasing speed and accuracy of DNA sample
collection, preparation, and sequencing has rapidly produced an enormous volume
of genetic data. However, fast and accurate analysis of the samples remains a
bottleneck. Here we present D$^{4}$RAGenS, a genetic sequence identification
algorithm that exhibits the Big Data handling and computational power of the
Dynamic Distributed Dimensional Data Model (D4M). The method leverages linear
algebra and statistical properties to increase computational performance while
retaining accuracy by subsampling the data. Two run modes, Fast and Wise, yield
speed and precision tradeoffs, with applications in biodefense and medical
diagnostics. The D$^{4}$RAGenS analysis algorithm is tested over several
datasets, including three utilized for the Defense Threat Reduction Agency
(DTRA) metagenomic algorithm contest.
Combining Alphas via Bounded Regression
Date: 2015-10-22 00:00:00
Tasks: regression

We give an explicit algorithm and source code for combining alpha streams via
bounded regression. In practical applications typically there is insufficient
history to compute a sample covariance matrix (SCM) for a large number of
alphas. To compute alpha allocation weights, one then resorts to (weighted)
regression over SCM principal components. Regression often produces alpha
weights with insufficient diversification and/or skewed distribution against,
e.g., turnover. This can be rectified by imposing bounds on alpha weights
within the regression procedure. Bounded regression can also be applied to
stock and other asset portfolio construction. We discuss illustrative examples.