pwc-archive/papers-with-abstracts huggingface dataset:
Optimally Investing to Reach a Bequest Goal
Date: 2016-05-24 00:00:00

We determine the optimal strategy for investing in a Black-Scholes market in
order to maximize the probability that wealth at death meets a bequest goal
$b$, a type of goal-seeking problem, as pioneered by Dubins and Savage (1965,
1976). The individual consumes at a constant rate $c$, so the level of wealth
required for risklessly meeting consumption equals $c/r$, in which $r$ is the
rate of return of the riskless asset.
  Our problem is related to, but different from, the goal-reaching problems of
Browne (1997). First, Browne (1997, Section 3.1) maximizes the probability that
wealth reaches $b < c/r$ before it reaches $a < b$. Browne's game ends when
wealth reaches $b$. By contrast, for the problem we consider, the game
continues until the individual dies or until wealth reaches 0; reaching $b$ and
then falling below it before death does not count.
  Second, Browne (1997, Section 4.2) maximizes the expected discounted reward
of reaching $b > c/r$ before wealth reaches $c/r$. If one interprets his
discount rate as a hazard rate, then our two problems are {\it mathematically}
equivalent for the special case for which $b > c/r$, with ruin level $c/r$.
However, we obtain different results because we set the ruin level at 0,
thereby allowing the game to continue when wealth falls below $c/r$.
Maximum sustainable yields from a spatially-explicit harvest model
Date: 2015-09-26 00:00:00
Tasks: Management

Spatial heterogeneity plays an important role in complex ecosystem dynamics,
and therefore is also an important consideration in sustainable resource
management. However, little is known about how spatial effects can influence
management targets derived from a non-spatial harvest model. Here, we extended
the Schaefer model, a conventional non-spatial harvest model that is widely
used in resource management, to a spatially-explicit harvest model by
integrating environmental heterogeneities, as well as species exchange between
patches. By comparing the maximum sustainable yields (MSY), one of the central
management targets in resource management, obtained from the spatially extended
model with that of the conventional model, we examined the effect of spatial
heterogeneity. When spatial heterogeneity exists, we found that the Schaefer
model tends to overestimate the MSY, implying potential for causing
overharvesting. In addition, by assuming a well-mixed population in the
heterogeneous environment, we showed analytically that the Schaefer model
always overestimate the MSY, regardless of the number of patches existing. The
degree of overestimation becomes significant when spatial heterogeneity is
marked. Collectively, these results highlight the importance of integrating the
spatial structure to conduct sustainable resource management.
Genome-wide modelling of transcription kinetics reveals patterns of RNA production delays
Date: 2015-07-16 00:00:00
Tasks: parameter estimation

Genes with similar transcriptional activation kinetics can display very
different temporal mRNA profiles due to differences in transcription time,
degradation rate and RNA processing kinetics. Recent studies have shown that a
splicing-associated RNA production delay can be significant. We introduce a
joint model of transcriptional activation and mRNA accumulation which can be
used for inference of transcription rate, RNA production delay and degradation
rate given genome-wide data from high-throughput sequencing time course
experiments. We combine a mechanistic differential equation model with a
non-parametric statistical modelling approach allowing us to capture a broad
range of activation kinetics, and use Bayesian parameter estimation to quantify
the uncertainty in the estimates of the kinetic parameters. We apply the model
to data from estrogen receptor (ER-{\alpha}) activation in the MCF-7 breast
cancer cell line. We use RNA polymerase II (pol-II) ChIP-Seq time course data
to characterise transcriptional activation and mRNA-Seq time course data to
quantify mature transcripts. We find that 11% of genes with a good signal in
the data display a delay of more than 20 minutes between completing
transcription and mature mRNA production. The genes displaying these long
delays are significantly more likely to be short. We also find a statistical
association between high delay and late intron retention in pre-mRNA data,
indicating significant splicing-associated production delays in many genes.
Assessing a human mediated current awareness service
Authors: Carevic Zeljko, Krichel Thomas, Mayr Philipp
Date: 2015-03-15 00:00:00

In this paper, we present an approach for analyzing the behavior of editors
in the large current awareness service "NEP: New Economics Papers". We
processed data from more than 38,000 issues derived from 90 different NEP
reports over the past ten years. The aim of our analysis was to gain an inside
to the editor behaviour when creating an issue and to look for factors that
influence the success of a report. In our study we looked at the following
features: average editing time, the average number of papers in an issue and
the editor effort measured on presorted issues as relative search length (RSL).
We found an average issue size of 12.4 documents per issue. The average editing
time is rather low with 14.5 minute. We get to the point that the success of a
report is mainly driven by its topic and the number of subscribers, as well as
proactive action by the editor to promote the report in her community.
Model reduction of biochemical reactions networks by tropical analysis methods
Date: 2015-05-26 00:00:00

We discuss a method of approximate model reduction for networks of
biochemical reactions. This method can be applied to networks with polynomial
or rational reaction rates and whose parameters are given by their orders of
magnitude. In order to obtain reduced models we solve the problem of tropical
equilibration that is a system of equations in max-plus algebra. In the case of
networks with nonlinear fast cycles we have to solve the problem of tropical
equilibration at least twice, once for the initial system and a second time for
an extended system obtained by adding to the initial system the differential
equations satisfied by the conservation laws of the fast subsystem. The two
steps can be reiterated until the fast subsystem has no conservation laws
different from the ones of the full model. Our method can be used for formal
model reduction in computational systems biology.
Constructing Analytically Tractable Ensembles of Non-Stationary Covariances with an Application to Financial Data
Date: 2015-07-14 00:00:00

In complex systems, crucial parameters are often subject to unpredictable
changes in time. Climate, biological evolution and networks provide numerous
examples for such non-stationarities. In many cases, improved statistical
models are urgently called for. In a general setting, we study systems of
correlated quantities to which we refer as amplitudes. We are interested in the
case of non-stationarity, i.e., seemingly random covariances. We present a
general method to derive the distribution of the covariances from the
distribution of the amplitudes. To ensure analytical tractability, we construct
a properly deformed Wishart ensemble of random matrices. We apply our method to
financial returns where the wealth of data allows us to carry out statistically
significant tests. The ensemble that we find is characterized by an algebraic
distribution which improves the understanding of large events.
Hierarchical Bond Graph Modelling of Biochemical Networks
Date: 2015-10-26 00:00:00

The bond graph approach to modelling biochemical networks is extended to
allow hierarchical construction of complex models from simpler components. This
is made possible by representing the simpler components as thermodynamically
open systems exchanging mass and energy via ports. A key feature of this
approach is that the resultant models are robustly thermodynamically compliant:
the thermodynamic compliance is not dependent on precise numerical values of
parameters. Moreover, the models are reusable due to the well-defined interface
provided by the energy ports.
  To extract bond graph model parameters from parameters found in the
literature, general and compact formulae are developed to relate free-energy
constants and equilibrium constants. The existence and uniqueness of solutions
is considered in terms of fundamental properties of stoichiometric matrices.
The approach is illustrated by building a hierarchical bond graph model of
glycogenolysis in skeletal muscle.
Shadows of the SIS immortality transition in small networks
Date: 2015-05-13 00:00:00

Much of the research on the behavior of the SIS model on networks has
concerned the infinite size limit; in particular the phase transition between a
state where outbreaks can reach a finite fraction of the population, and a
state where only a finite number would be infected. For finite networks, there
is also a dynamic transition---the immortality transition---when the
per-contact transmission probability $\lambda$ reaches one. If $\lambda < 1$,
the probability that an outbreak will survive by an observation time $t$ tends
to zero as $t \rightarrow \infty$; if $\lambda = 1$, this probability is one.
We show that treating $\lambda = 1$ as a critical point predicts the
$\lambda$-dependence of the survival probability also for more moderate
$\lambda$-values. The exponent, however, depends on the underlying network.
This fact could, by measuring how a vertex' deletion changes the exponent, be
used to evaluate the role of a vertex in the outbreak. Our work also confirms
an extremely clear separation between the early die-off (from the outbreak
failing to take hold in the population) and the later extinctions
(corresponding to rare stochastic events of several consecutive transmission
events failing to occur).
Where are your eyes going to look during reading? A critical evaluation of saccade targeting hypothesis
Date: 2015-03-18 00:00:00

The word-based account of saccades drawn by a central gravity of the PVL is
supported by two pillars of evidences. The first is the finding of the initial
fixation location on a word resembled a normal distribution (Rayner, 1979). The
other is the finding of a moderate slope coefficient between the launch site
and the landing site (b=0.49, see McConkie, Kerr, Reddix, & Zola, 1988). Four
simulations on different saccade targeting strategies and one eye-movement
experiment of Chinese reading have been conducted to evaluate the two findings.
We demonstrated that the current understanding of the word-based account is not
conclusive by showing an alternative strategy of the word-based account and
identifying the problem with the calculation of the slope coefficient. Although
almost all the computational models of eye-movement control during reading have
built on the two findings, future efforts should be directed to understand the
precise contribution of different saccade targeting strategies, and to know how
their weighting might vary across desperate writing systems.
Exploiting the adaptation dynamics to predict the distribution of beneficial fitness effects
Date: 2015-12-25 00:00:00

Adaptation of asexual populations is driven by beneficial mutations and
therefore the dynamics of this process, besides other factors, depend on the
distribution of beneficial fitness effects. It is known that on uncorrelated
fitness landscapes, this distribution can only be of three types: truncated,
exponential and power law. We performed extensive stochastic simulations to
study the adaptation dynamics on rugged fitness landscapes, and identified two
quantities that can be used to distinguish the underlying distribution of
beneficial fitness effects. The first quantity studied here is the fitness
difference between successive mutations that spread in the population, which is
found to decrease in the case of truncated distributions, remain nearly a
constant for exponentially decaying distributions and increase when the fitness
distribution decays as a power law. The second quantity of interest, namely,
the rate of change of fitness with time also shows quantitatively different
behaviour for different beneficial fitness distributions. The patterns
displayed by the two aforementioned quantities are found to hold for both low
and high mutation rates. We discuss how these patterns can be exploited to
determine the distribution of beneficial fitness effects in microbial
experiments.
Rhythmic inhibition allows neural networks to search for maximally consistent states
Date: 2015-03-10 00:00:00

Gamma-band rhythmic inhibition is a ubiquitous phenomenon in neural circuits
yet its computational role still remains elusive. We show that a model of
Gamma-band rhythmic inhibition allows networks of coupled cortical circuit
motifs to search for network configurations that best reconcile external inputs
with an internal consistency model encoded in the network connectivity. We show
that Hebbian plasticity allows the networks to learn the consistency model by
example. The search dynamics driven by rhythmic inhibition enable the described
networks to solve difficult constraint satisfaction problems without making
assumptions about the form of stochastic fluctuations in the network. We show
that the search dynamics are well approximated by a stochastic sampling
process. We use the described networks to reproduce perceptual multi-stability
phenomena with switching times that are a good match to experimental data and
show that they provide a general neural framework which can be used to model
other 'perceptual inference' phenomena.
Unravelling Graph-Exchange File Formats
Authors: Roughan Matthew, Tuke Jonathan
Date: 2015-03-10 00:00:00

A graph is used to represent data in which the relationships between the
objects in the data are at least as important as the objects themselves. Over
the last two decades nearly a hundred file formats have been proposed or used
to provide portable access to such data. This paper seeks to review these
formats, and provide some insight to both reduce the ongoing creation of
unnecessary formats, and guide the development of new formats where needed.
Generalized modeling of empirical social-ecological systems
Date: 2017-05-24 00:00:00

Modeling social-ecological systems is difficult due to the complexity of
ecosystems and of individual and collective human behavior. Key components of
the social-ecological system are often over-simplified or omitted. Generalized
modeling is a dynamical systems approach that can overcome some of these
challenges. It can rigorously analyze qualitative system dynamics such as
regime shifts despite incomplete knowledge of the model's constituent
processes. Here, we review generalized modeling and use a recent study on the
Baltic Sea cod fishery's boom and collapse to demonstrate its application to
modeling the dynamics of empirical social-ecological systems. These empirical
applications demand new methods of analysis suited to larger, more complicated
generalized models. Generalized modeling is a promising tool for rapidly
developing mathematically rigorous, process-based understanding of a
social-ecological system's dynamics despite limited knowledge of the system.
Effects of spike-triggered negative feedback on receptive-field properties
Date: 2015-03-10 00:00:00

Sensory neurons are often described in terms of a receptive field, that is, a
linear kernel through which stimuli are filtered before they are further
processed. If information transmission is assumed to proceed in a feedforward
cascade, the receptive field may be interpreted as the external stimulus'
profile maximizing neuronal output. The nervous system, however, contains many
feedback loops, and sensory neurons filter more currents than the ones
representing the transduced external stimulus. Some of the additional currents
are generated by the output activity of the neuron itself, and therefore
constitute feedback signals. By means of a time-frequency analysis of the
input/output transformation, here we show how feedback modifies the receptive
field. The model is applicable to various types of feedback processes, from
spike triggered intrinsic conductances to inhibitory synaptic inputs from
nearby neurons. We distinguish between the intrinsic receptive field (filtering
all input currents) and the effective receptive field (filtering only external
stimuli). Whereas the intrinsic receptive field summarizes the biophysical
properties of the neuron associated to subthreshold integration and spike
generation, only the effective receptive field can be interpreted as the
external stimulus' profile maximizing neuronal output. We demonstrate that
spike-triggered feedback shifts low-pass filtering towards band-pass
processing, transforming integrator neurons into resonators. For strong
feedback, a sharp resonance in the spectral neuronal selectivity may appear.
Our results provide a unified framework to interpret a collection of previous
experimental studies where specific feedback mechanisms were shown to modify
the filtering properties of neurons.
Two-step Input Spatial Auditory BCI for Japanese Kana Characters
Date: 2015-03-10 00:00:00
Tasks: Brain Computer Interface, EEG, Electroencephalogram (EEG), ERP, Vocal Bursts Valence Prediction

We present an auditory stimulus optimization and a pilot study of a two-step
input speller application combined with a spatial auditory brain-computer
interface (saBCI) for paralyzed users. The application has been developed for
45, out of 48 defining the full set, Japanese kana characters in a two-step
input procedure setting for an easy-to-use BCI-speller interface. The user
first selects the representative letter of a subset, defining the second step.
In the second step, the final choice is made. At each interfacing step, the
choices are classified based on the P300 event related potential (ERP)
responses captured in the EEG, as in the classic oddball paradigm. The BCI
online experiment and EEG responses classification results of the pilot study
confirm the effectiveness of the proposed spelling method.
Energy cost and optimisation in breath-hold diving
Date: 2016-01-19 00:00:00

We present a new model for calculating locomotion costs in breath-hold
divers. Starting from basic mechanics principles, we calculate the work that
the diver must provide through propulsion to counterbalance the action of drag,
the buoyant force and weight during immersion. Compared to those in previous
studies, the model presented here accurately analyses breath-hold divers which
alternate active swimming with prolonged glides during the dive (as is the case
in mammals). The energy cost of the dive is strongly dependent on these
prolonged gliding phases. Here we investigate the length and impacts on energy
cost of these glides with respect to the diver characteristics, and compare
them with those observed in different breath-hold diving species. Taking into
account the basal metabolic rate and chemical energy to propulsion
transformation efficiency, we calculate optimal swim velocity and the
corresponding total energy cost (including metabolic rate) and compare them
with observations. Energy cost is minimised when the diver passes through
neutral buoyancy conditions during the dive. This generally implies the
presence of prolonged gliding phases in both ascent and descent, where the
buoyancy (varying with depth) is best used against the drag, reducing energy
cost. This is in agreement with past results (Miller et al., 2012; Sato et al.,
2013) where, when the buoyant force is considered constant during the dive, the
energy cost was minimised for neutral buoyancy. In particular, our model
confirms the good physical adaption of dolphins for diving, compared to other
breath-hold diving species which are mostly positively buoyant (penguins for
example). The presence of prolonged glides implies a non-trivial dependency of
optimal speed on maximal depth of the dive. This extends previous findings
(Sato et al., 2010; Watanabe et al., 2011) which found no dependency of optimal
speed on dive depth for particular conditions. The energy cost of the dive can
be further diminished by reducing the volume of gas-filled body parts in divers
close to neutral buoyancy. This provides a possible additional explanation for
the observed exhalation of air before diving in phocid seals to minimise dive
energy cost. Until now the only explanation for this phenomenon has been a
reduction in the risk of decompression sickness.
Modelling Computational Resources for Next Generation Sequencing Bioinformatics Analysis of 16S rRNA Samples
Date: 2015-03-10 00:00:00
Tasks: Denoising

In the rapidly evolving domain of next generation sequencing and
bioinformatics analysis, data generation is one aspect that is increasing at a
concomitant rate. The burden associated with processing large amounts of
sequencing data has emphasised the need to allocate sufficient computing
resources to complete analyses in the shortest possible time with manageable
and predictable costs. A novel method for predicting time to completion for a
popular bioinformatics software (QIIME), was developed using key variables
characteristic of the input data assumed to impact processing time. Multiple
Linear Regression models were developed to determine run time for two denoising
algorithms and a general bioinformatics pipeline. The models were able to
accurately predict clock time for denoising sequences from a naturally
assembled community dataset, but not an artificial community. Speedup and
efficiency tests for AmpliconNoise also highlighted that caution was needed
when allocating resources for parallel processing of data. Accurate modelling
of computational processing time using easily measurable predictors can assist
NGS analysts in determining resource requirements for bioinformatics software
and pipelines. Whilst demonstrated on a specific group of scripts, the
methodology can be extended to encompass other packages running on multiple
architectures, either in parallel or sequentially.
Some new results on Dufffie-type OTC markets
Date: 2015-03-10 00:00:00
Tasks: Vocal Bursts Type Prediction

The extended Wild sums considered in this article generalize the classi- cal
Wild sums of statistical physics. We first show how to obtain explicit
solutions for the evolution equation of a large system where the interactions
are given by a single, but general, interacting kernel which involves m
components, for a fixed m >= 2. We then show how to retain the explicit
formulas for the case of OTC market models where the dynamics is more directly
described by two (or more) kernels.
Experimental Estimation of Number of Clusters Based on Cluster Quality
Authors: Grace G. Hannah, Desikan Kalyani
Date: 2015-03-10 00:00:00
Tasks: Clustering, Text Clustering

Text Clustering is a text mining technique which divides the given set of
text documents into significant clusters. It is used for organizing a huge
number of text documents into a well-organized form. In the majority of the
clustering algorithms, the number of clusters must be specified apriori, which
is a drawback of these algorithms. The aim of this paper is to show
experimentally how to determine the number of clusters based on cluster
quality. Since partitional clustering algorithms are well-suited for clustering
large document datasets, we have confined our analysis to a partitional
clustering algorithm.
Symmetry structure and solution of evolution-type equations with time dependent parameters in financial Mathematics
Date: 2015-03-11 00:00:00

Mathematical models with time dependent parameters are of great interest in
financial Mathematics because they capture real life scenarios in the financial
market. In this study, via the Lie group technique, we analyse evolution-type
equations with time dependent parameters and give the general symmetry
structure of these equations. In addition, we illustrate this method by looking
at an example of exotic options called the power options. Our model parameters
are time dependent and the option gives a continuous yield dividend at
different time intervals. We present new solutions, satisfying the boundary
conditions, to this important problem.