pwc-archive/papers-with-abstracts huggingface dataset:
An Exchange Rate Target Zone Model with a Terminal Condition and Mean-Reverting Fundamentals
Date: 2015-06-16 00:00:00
Tasks: Form

This paper proposes a target zones exchange rate model with a terminal
condition of entering a currency zone. It is assumed that the exchange rate is
a function of the fundamental and time. Another essential assumptions of the
model is that the fundamental process is bounded inside a band and that
terminal condition for the exchange rate holds. The fundamental is specified in
two ways: as a regulated Brownian motion and Ornstein-Uhlenbeck processes. For
the case of the Brownian motion process the closed form solution of the problem
is obtained, whereas for the Ornstein-Uhlenbeck process the closed form
solution does not exist, therefore we had to use numerical method for solving
of the problem. Both specifications are compared numerically.
Network-based model of the growth of termite nests
Date: 2015-12-10 00:00:00

We present a model for the growth of the transportation network inside nests
of the social insect subfamily Termitinae (Isoptera, termitidae). These nests
consist of large chambers (nodes) connected by tunnels (edges). The model based
on the empirical analysis of the real nest networks combined with pruning (edge
removal, either random or weighted by betweenness centrality) and a memory
effect (preferential growth from the latest added chambers) successfully
predicts emergent nest properties (degree distribution, size of the largest
connected component, average path lengths, backbone link ratios, and local
graph redundancy). The two pruning alternatives can be associated with
different genuses in the subfamily. A sensitivity analysis on the pruning and
memory parameters indicates that Termitinae networks favor fast internal
transportation over efficient defense strategies against ant predators. Our
results provide an example of how complex network organization and efficient
network properties can be generated from simple building rules based on local
interactions and contribute to our understanding of the mechanisms that come
into play for the formation of termite networks and of biological
transportation networks in general.
Multiscale modelling of intestinal crypt organization and carcinogenesis
Date: 2015-06-16 00:00:00

Colorectal cancers are the third most common type of cancer. They originate
from intestinal crypts, glands that descend from the intestinal lumen into the
underlying connective tissue. Normal crypts are thought to exist in a dynamic
equilibrium where the rate of cell production at the base of a crypt is matched
by that of loss at the top. Understanding how genetic alterations accumulate
and proceed to disrupt this dynamic equilibrium is fundamental to understanding
the origins of colorectal cancer. Colorectal cancer emerges from the
interaction of biological processes that span several spatial scales, from
mutations that cause inappropriate intracellular responses to changes at the
cell/tissue level, such as uncontrolled proliferation and altered motility and
adhesion. Multiscale mathematical modelling can provide insight into the
spatiotemporal organisation of such a complex, highly regulated and dynamic
system. Moreover, the aforementioned challenges are inherent to the multiscale
modelling of biological tissue more generally. In this review we describe the
mathematical approaches that have been applied to investigate multiscale
aspects of crypt behaviour, highlighting a number of model predictions that
have since been validated experimentally. We also discuss some of the key
mathematical and computational challenges associated with the multiscale
modelling approach. We conclude by discussing recent efforts to derive
coarse-grained descriptions of such models, which may offer one way of reducing
the computational cost of simulation by leveraging well-established tools of
mathematical analysis to address key problems in multiscale modelling.
Models, measurement and inference in epithelial tissue dynamics
Date: 2015-06-16 00:00:00

The majority of solid tumours arise in epithelia and therefore much research
effort has gone into investigating the growth, renewal and regulation of these
tissues. Here we review different mathematical and computational approaches
that have been used to model epithelia. We compare different models and
describe future challenges that need to be overcome in order to fully exploit
new data which present, for the first time, the real possibility for detailed
model validation and comparison.
On the Origins and Control of Community Types in the Human Microbiome
Date: 2016-01-21 00:00:00

Microbiome-based stratification of healthy individuals into compositional
categories, referred to as "community types", holds promise for drastically
improving personalized medicine. Despite this potential, the existence of
community types and the degree of their distinctness have been highly debated.
Here we adopted a dynamic systems approach and found that heterogeneity in the
interspecific interactions or the presence of strongly interacting species is
sufficient to explain community types, independent of the topology of the
underlying ecological network. By controlling the presence or absence of these
strongly interacting species we can steer the microbial ecosystem to any
desired community type. This open-loop control strategy still holds even when
the community types are not distinct but appear as dense regions within a
continuous gradient. This finding can be used to develop viable therapeutic
strategies for shifting the microbial composition to a healthy configuration
CARGO: Effective format-free compressed storage of genomic information
Date: 2015-06-17 00:00:00

The recent super-exponential growth in the amount of sequencing data
generated worldwide has put techniques for compressed storage into the focus.
Most available solutions, however, are strictly tied to specific bioinformatics
formats, sometimes inheriting from them suboptimal design choices; this hinders
flexible and effective data sharing. Here we present CARGO (Compressed
ARchiving for GenOmics), a high-level framework to automatically generate
software systems optimized for the compressed storage of arbitrary types of
large genomic data collections. Straightforward applications of our approach to
FASTQ and SAM archives require a few lines of code, produce solutions that
match and sometimes outperform specialized format-tailored compressors, and
scale well to multi-TB datasets.
Defending Grey Attacks by Exploiting Wavelet Analysis in Collaborative Filtering Recommender Systems
Authors: Yang Zhihai
Date: 2015-06-19 00:00:00
Tasks: Collaborative Filtering, Recommendation Systems

"Shilling" attacks or "profile injection" attacks have always major
challenges in collaborative filtering recommender systems (CFRSs). Many efforts
have been devoted to improve collaborative filtering techniques which can
eliminate the "shilling" attacks. However, most of them focused on detecting
push attack or nuke attack which is rated with the highest score or lowest
score on the target items. Few pay attention to grey attack when a target item
is rated with a lower or higher score than the average score, which shows a
more hidden rating behavior than push or nuke attack. In this paper, we present
a novel detection method to make recommender systems resistant to such attacks.
To characterize grey ratings, we exploit rating deviation of item to
discriminate between grey attack profiles and genuine profiles. In addition, we
also employ novelty and popularity of item to construct rating series. Since it
is difficult to discriminate between the rating series of attacker and genuine
users, we incorporate into discrete wavelet transform (DWT) to amplify these
differences based on the rating series of rating deviation, novelty and
popularity, respectively. Finally, we respectively extract features from rating
series of rating deviation-based, novelty-based and popularity-based by using
amplitude domain analysis method and combine all clustered results as our
detection results. We conduct a list of experiments on both the Book-Crossing
and HetRec-2011 datasets in diverse attack models. Experimental results were
included to validate the effectiveness of our approach in comparison with the
benchmarked methods.
The structure of the genotype-phenotype map strongly constrains the evolution of non-coding RNA
Date: 2015-09-25 00:00:00

The prevalence of neutral mutations implies that biological systems typically
have many more genotypes than phenotypes. But can the way that genotypes are
distributed over phenotypes determine evolutionary outcomes? Answering such
questions is difficult because the number of genotypes can be
hyper-astronomically large. By solving the genotype-phenotype (GP) map for RNA
secondary structure for systems up to length $L=126$ nucleotides (where the set
of all possible RNA strands would weigh more than the mass of the visible
universe) we show that the GP map strongly constrains the evolution of
non-coding RNA (ncRNA). Simple random sampling over genotypes predicts the
distribution of properties such as the mutational robustness or the number of
stems per secondary structure found in naturally occurring ncRNA with
surprising accuracy. Since we ignore natural selection, this strikingly close
correspondence with the mapping suggests that structures allowing for
functionality are easily discovered, despite the enormous size of the genetic
spaces. The mapping is extremely biased: the majority of genotypes map to an
exponentially small portion of the morphospace of all biophysically possible
structures. Such strong constraints provide a non-adaptive explanation for the
convergent evolution of structures such as the hammerhead ribozyme. These
results presents a particularly clear example of bias in the arrival of
variation strongly shaping evolutionary outcomes and may be relevant to Mayr's
distinction between proximate and ultimate causes in evolutionary biology.
Universal Laws of Human Society's Income Distribution
Date: 2015-05-22 00:00:00
Tasks: Fairness

General equilibrium equations in economics play the same role with many-body
Newtonian equations in physics. Accordingly, each solution of the general
equilibrium equations can be regarded as a possible microstate of the economic
system. Since Arrow's Impossibility Theorem and Rawls' principle of social
fairness will provide a powerful support for the hypothesis of equal
probability, then the principle of maximum entropy is available in a just and
equilibrium economy so that an income distribution will occur spontaneously
(with the largest probability). Remarkably, some scholars have observed such an
income distribution in some democratic countries, e.g. USA. This result implies
that the hypothesis of equal probability may be only suitable for some "fair"
systems (economic or physical systems). From this meaning, the non-equilibrium
systems may be "unfair" so that the hypothesis of equal probability is
unavailable.
Bermuda: Bidirectional de novo assembly of transcripts with new insights for handling uneven coverage
Date: 2015-06-18 00:00:00

Motivation: RNA-seq has made feasible the analysis of a whole set of
expressed mRNAs. Mapping-based assembly of RNA-seq reads sometimes is
infeasible due to lack of high-quality references. However, de novo assembly is
very challenging due to uneven expression levels among transcripts and also the
read coverage variation within a single transcript. Existing methods either
apply de Bruijn graphs of single-sized k-mers to assemble the full set of
transcripts, or conduct multiple runs of assembly, but still apply graphs of
single-sized k-mers at each run. However, a single k-mer size is not suitable
for all the regions of the transcripts with varied coverage. Contribution: This
paper presents a de novo assembler Bermuda with new insights for handling
uneven coverage. Opposed to existing methods that use a single k-mer size for
all the transcripts in each run of assembly, Bermuda self-adaptively uses a few
k-mer sizes to assemble different regions of a single transcript according to
their local coverage. As such, Bermuda can deal with uneven expression levels
and coverage not only among transcripts, but also within a single transcript.
Extensive tests show that Bermuda outperforms popular de novo assemblers in
reconstructing unevenly-expressed transcripts with longer length, better
contiguity and lower redundancy. Further, Bermuda is computationally efficient
with moderate memory consumption.
Genetic Toggle Switch in the Absence of Cooperative Binding: Exact Results
Date: 2015-10-22 00:00:00

We present an analytical treatment of a genetic switch model consisting of
two mutually inhibiting genes operating without cooperative binding of the
corresponding transcription factors. Previous studies have numerically shown
that these systems can exhibit bimodal dynamics without possessing two stable
fixed points at the deterministic level. We analytically show that bimodality
is induced by the noise and find the critical repression strength that controls
a transition between the bimodal and non-bimodal regimes. We also identify
characteristic polynomial scaling laws of the mean switching time between
bimodal states. These results, independent of the model under study, reveal
essential differences between these systems and systems with cooperative
binding, where there is no critical threshold for bimodality and the mean
switching time scales exponentially with the system size.
Analyzing Web Behavior in Indoor Retail Spaces
Authors: Ren Yongli, Tomko Martin, Salim Flora, Ong Kevin, Sanderson Mark
Date: 2015-06-18 00:00:00

We analyze 18 million rows of Wi-Fi access logs collected over a one year
period from over 120,000 anonymized users at an inner-city shopping mall. The
anonymized dataset gathered from an opt-in system provides users' approximate
physical location, as well as Web browsing and some search history. Such data
provides a unique opportunity to analyze the interaction between people's
behavior in physical retail spaces and their Web behavior, serving as a proxy
to their information needs. We find: (1) the use of Wi-Fi network maps the
opening hours of the mall; (2) there is a weekly periodicity in users' visits
to the mall; (3) around 60% of registered Wi-Fi users actively browse the Web
and around 10% of them use Wi-Fi for accessing Web search engines; (4) people
are likely to spend a relatively constant amount of time browsing the Web while
their visiting duration may vary; (5) people tend to visit similar mall
locations and Web content during their repeated visits to the mall; (6) the
physical spatial context has a small but significant influence on the Web
content that indoor users browse; (7) accompanying users tend to access
resources from the same Web domains.
A unified model for wild resistance dynamics and weed control using herbicide
Date: 2015-06-18 00:00:00

A major issue in the modelling of weed resistance to herbicide lies in
effectively handling the wild dynamics, that is, the allele frequency prior to
the herbicide application, and in particular when starting to use the
herbicide. The wild allele frequency is a key variable as the resistance
evolution is highly sensitive to it, moreover it is extremely difficult to
measure in the agricultural field. In this paper we propose a model for weed
control that handles the allele frequency in a direct manner, grounded on the
very dynamics of the weed life cycle, with no need of a priori distributions
nor the use of the Hardy-Weinberg equilibrium. The proposed model is individual
based, stochastic, and considers some phenomena like the relative fitnesses and
mutation that are prominent in the resistance dynamics without herbicide. A
case study is presented for the herbicide nicosulfuron in a field with the weed
Bidens pilosa. Another two models having a standard deterministic dynamics are
compared with ours in terms of the initial allele frequency, its time
evolution, and the resistance visualization in the field, indicating that the
proposed model is effective to provide more realistic simulations for the weed
resistance.
Query Expansion for Survey Question Retrieval in the Social Sciences
Authors: Dulisch Nadine, Kempf Andreas Oskar, Schaer Philipp
Date: 2015-06-18 00:00:00
Tasks: Retrieval

In recent years, the importance of research data and the need to archive and
to share it in the scientific community have increased enormously. This
introduces a whole new set of challenges for digital libraries. In the social
sciences typical research data sets consist of surveys and questionnaires. In
this paper we focus on the use case of social science survey question reuse and
on mechanisms to support users in the query formulation for data sets. We
describe and evaluate thesaurus- and co-occurrence-based approaches for query
expansion to improve retrieval quality in digital libraries and research data
archives. The challenge here is to translate the information need and the
underlying sociological phenomena into proper queries. As we can show retrieval
quality can be improved by adding related terms to the queries. In a direct
comparison automatically expanded queries using extracted co-occurring terms
can provide better results than queries manually reformulated by a domain
expert and better results than a keyword-based BM25 baseline.
Hedging, arbitrage and optimality with superlinear frictions
Date: 2015-06-19 00:00:00

In a continuous-time model with multiple assets described by c\`{a}dl\`{a}g
processes, this paper characterizes superhedging prices, absence of arbitrage,
and utility maximizing strategies, under general frictions that make execution
prices arbitrarily unfavorable for high trading intensity. Such frictions
induce a duality between feasible trading strategies and shadow execution
prices with a martingale measure. Utility maximizing strategies exist even if
arbitrage is present, because it is not scalable at will.
Seasonal Stochastic Volatility and Correlation together with the Samuelson Effect in Commodity Futures Markets
Date: 2015-06-19 00:00:00

We introduce a multi-factor stochastic volatility model based on the
CIR/Heston volatility process that incorporates seasonality and the Samuelson
effect. First, we give conditions on the seasonal term under which the
corresponding volatility factor is well-defined. These conditions appear to be
rather mild. Second, we calculate the joint characteristic function of two
futures prices for different maturities in the proposed model. This
characteristic function is analytic. Finally, we provide numerical
illustrations in terms of implied volatility and correlation produced by the
proposed model with five different specifications of the seasonality pattern.
The model is found to be able to produce volatility smiles at the same time as
a volatility term-structure that exhibits the Samuelson effect with a seasonal
component. Correlation, instantaneous or implied from calendar spread option
prices via a Gaussian copula, is also found to be seasonal.
Numerical Methods for a Poisson-Nernst-Planck-Fermi Model
Date: 2015-06-19 00:00:00

Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi
(PNPF) model for studying ion transport through biological ion channels. PNPF
contains many more correlations than most models and simulations of channels,
because it includes water and calculates dielectric properties consistently as
outputs. This model accounts for the steric effect of ions and water molecules
with different sizes and interstitial voids, the correlation effect of crowded
ions with different valences, and the screening effect of polarized water
molecules in an inhomogeneous aqueous electrolyte. The steric energy is shown
to be comparable to the electrical energy under physiological conditions,
demonstrating the crucial role of the excluded volume of particles and the
voids in the natural function of channel proteins. Water is shown to play a
critical role in both correlation and steric effects in the model. We extend
the classical Scharfetter-Gummel (SG) method for semiconductor devices to
include the steric potential for ion channels, which is a fundamental physical
property not present in semiconductors. Together with a simplified matched
interface and boundary (SMIB) method for treating molecular surfaces and
singular charges of channel proteins, the extended SG method is shown to
exhibit important features in flow simulations such as optimal convergence,
efficient nonlinear iterations, and physical conservation. Two different
methods --- called the SMIB and multiscale methods --- are proposed for two
different types of channels, namely, the gramicidin A channel and an L-type
calcium channel, depending on whether water is allowed to pass through the
channel. The PNPF currents are in accord with the experimental I-V (V for
applied voltages) data of the gramicidin A channel and I-C (C for bath
concentrations) data of the calcium channel.
Annuitization and asset allocation
Date: 2015-06-19 00:00:00

This paper examines the optimal annuitization, investment and consumption
strategies of a utility-maximizing retiree facing a stochastic time of death
under a variety of institutional restrictions. We focus on the impact of aging
on the optimal purchase of life annuities which form the basis of most Defined
Benefit pension plans. Due to adverse selection, acquiring a lifetime payout
annuity is an irreversible transaction that creates an incentive to delay.
Under the institutional all-or-nothing arrangement where annuitization must
take place at one distinct point in time (i.e. retirement), we derive the
optimal age at which to annuitize and develop a metric to capture the loss from
annuitizing prematurely. In contrast, under an open-market structure where
individuals can annuitize any fraction of their wealth at anytime, we locate a
general optimal annuity purchasing policy. In this case, we find that an
individual will initially annuitize a lump sum and then buy annuities to keep
wealth to one side of a separating ray in wealth-annuity space. We believe our
paper is the first to integrate life annuity products into the portfolio choice
literature while taking into account realistic institutional restrictions which
are unique to the market for mortality-contingent claims.