pwc-archive/papers-with-abstracts huggingface dataset:
Topic-focused Dynamic Information Filtering in Social Media
Authors: Zhu Yadong, Lan Yanyan, Guo Jiafeng, Cheng Xueqi
Date: 2015-04-20 00:00:00
Tasks: Diversity

With the quick development of online social media such as twitter or sina
weibo in china, many users usually track hot topics to satisfy their desired
information need. For a hot topic, new opinions or ideas will be continuously
produced in the form of online data stream. In this scenario, how to
effectively filter and display information for a certain topic dynamically,
will be a critical problem. We call the problem as Topic-focused Dynamic
Information Filtering (denoted as TDIF for short) in social media. In this
paper, we start open discussions on such application problems. We first analyze
the properties of the TDIF problem, which usually contains several typical
requirements: relevance, diversity, recency and confidence. Recency means that
users want to follow the recent opinions or news. Additionally, the confidence
of information must be taken into consideration. How to balance these factors
properly in online data stream is very important and challenging. We propose a
dynamic preservation strategy on the basis of an existing feature-based utility
function, to solve the TDIF problem. Additionally, we propose new dynamic
diversity measures, to get a more reasonable evaluation for such application
problems. Extensive exploratory experiments have been conducted on TREC public
twitter dataset, and the experimental results validate the effectiveness of our
approach.
On the Origin of Risk Sensitivity: the Energy Budget Rule Revisited
Date: 2015-11-17 00:00:00
Tasks: Sensitivity

The risk-sensitive foraging theory formulated in terms of the (daily) energy
budget rule has been influential in behavioural ecology as well as other
disciplines. Predicting risk-aversion on positive budgets and risk-proneness on
negative budgets, however, the budget rule has recently been challenged both
empirically and theoretically. In this paper, we critically review these
challenges as well as the original derivation of the budget rule and propose a
`gradual' budget rule, which is normatively derived from a gradual nature of
risk sensitivity and encompasses the conventional budget rule as a special
case. The gradual budget rule shows that the conventional budget rule holds
when the expected reserve is close enough to a threshold for overnight
survival, selection pressure being significant. The gradual view also reveals
that the conventional budget rule does not need to hold when the expected
reserve is not close enough to the threshold, selection pressure being
insignificant. The proposed gradual budget rule better fits the empirical
findings including those that used to challenge the conventional budget rule.
Dynamical patterns of p53 states driven by PML
Date: 2015-04-20 00:00:00

Recent studies suggest that PML (Promyelocytic Leukemia) suppresses p53
protein degradation by inhibiting MDM2 protein in the nucleus [1], and
regulates a number of biological functions [2]. We modeled a PML-MDM2-p53
regulatory network by integrating p53-MDM2 autoregulatory model [3] and related
PML pathways. We found that p53 dynamics switched at various dynamical states
induced by PML which corresponds to different cellular states. Our results show
clear transitions among the stabilized, damped and sustain states under
different stress conditions induced by PML in the system. These states in p53
dynamics is the signature of existence of various cellular states and the phase
transition like behaviour of these states involve various biological
significance.
Improving the Presentation and Understanding of Risk Models
Date: 2015-04-20 00:00:00

The key concepts (calibration, discrimination, and discordance) important in
understanding and comparing risk models are best conveyed graphically. To
illustrate this, models predicting death and acute kidney injury in a large
cohort of PCI patients differing in the number of predictors included are
presented. Calibration plots, often presented in the current literature,
present the agreement between predicted and observed risk for deciles of risk.
Risk distribution curves present the frequency of different levels of risk.
Scatterplots of the risks assigned to individuals by different models show the
discordance of the individual risk estimates. Increasing the number of
predictors in these models produce increasingly disperse and progressively
skewed risk distribution curves. These resemble the lognormal distributions
expected when risk predictors interact multiplicatively. These changes in the
risk distribution curves correlate with improved measures of discrimination.
A Mathematical Model of Motion Sickness in 6DOF Motion and Its Application to Vehicle Passengers
Date: 2015-04-20 00:00:00

A mathematical model of motion sickness incidence (MSI) is derived by
integrating neurophysiological knowledge of the vestibular system to predict
the severity of motion sickness of humans. Bos et al. proposed the successful
mathematical model of motion sickness based on the neurophysiological mechanism
based on the subject vertical conflict (SVC) theory. We expand this model to
6-DOF motion, including head rotation, by introducing the otolith-canal
interaction. Then the model is applied to an analysis of passengers' comfort.
It is known that the driver is less susceptible to motion sickness than are the
passengers. In addition, it is known that the driver tilts his/her head toward
the curve direction when curve driving, whereas the passengers' head movement
is likely to occur in the opposite direction. Thus, the effect of the head tilt
strategy on motion sickness was investigated by the proposed mathematical
model. The head movements of drivers and passengers were measured in slalom
driving. Then, the MSI of the drivers and that of the passengers predicted by
the proposed model were compared. The results revealed that the head movement
toward the centripetal direction has a significant effect in reducing the MSI
in the sense of SVC theory.
HPV and cervical cancer in Moldova, epidemiological model with intervention cost vs benefit and effectiveness analysis
Date: 2015-04-21 00:00:00

Human papillomavirus, or HPV, is a sexually transmittable virus infection,
which is necessary risk factor for developing cervical cancer, first most
common type of cancer in working age women in Moldova. We observe both
behavioral change (sexuality increase) and demographical change (population
ageing). We used data since 1998 (Moldovan peace treaty) to adjust model
parameter and we project till around 2030 (for vaccination till 2050).
According to provided information, interdisciplinary model was proposed. It iss
set of deterministic differential equations. Stochasticity was introduced in
sexual partner change rates. The model has aggregated the most important paths
of infection, cancer development and prevention scenarios (more than 100
equations and 200 parameters). Moldovan cervical cancer perspective looks much
better, than in central western Europe countries, because of relatively young
society. In our setup, obligatory vaccination seems to not be so crucial (for
none of realistic scenarios increase of cancer cases is possible) for public
health, as in most countries in European Union. However, screening practice
could be verified in terms of efficiency, when cost benefit calculation would
be done. We propose more optimal screening guidelines (with prevention cost 5
-10k EUR per QALY), which could provide saving perspective in 10-15 year in
range 150-300k EUR yearly. Targeted vaccination could be also consider, because
costs are similar to high frequencies screening schema with the same cancer
cases projection. However, some positive side effects of vaccination as
reduction of pathogen circulation in society, will cause decrease of other
pathologies related to HPV like genital warts and other cancer.
A Macroscopic Behavioral Violation of No Signaling In Time Inequalities
Date: 2015-04-19 00:00:00

In this paper we applied the no-signaling in time (NSIT) formalism discussed
by Kofler and Brukner to investigate temporal entanglement between binary human
behavioral unconscious choices at t1 with binary random outcomes at t2. NSIT
consists of a set of inequalities and represents mathematical conditions for
macro-realism which require only two measurements in time. The analyses of
three independent experiments show a strong violation of NSIT in two out of
three of them, supporting the hypothesis of a quantum-like temporal
entanglement between human choices at t1 with binary random outcomes at t2
iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition
Date: 2015-04-21 00:00:00
Tasks: Drug Discovery, Tree Decomposition

Protein side-chain packing is a critical component in obtaining the 3D
coordinates of a structure and drug discovery. Single-domain protein side-chain
packing has been thoroughly studied. A major challenge in generalizing these
methods to protein complexes is that they, unlike monomers, often have very
large treewidth, and thus algorithms such as TreePack cannot be directly
applied. To address this issue, SCWRL4 treats the complex effectively as a
monomer, heuristically excluding weak interactions to decrease treewidth; as a
result, SCWRL4 generates poor packings on protein interfaces. To date, few
side-chain packing methods exist that are specifically designed for protein
complexes. In this paper, we introduce a method, iTreePack, which solves the
side-chain packing problem for complexes by using a novel combination of dual
decomposition and tree decomposition. In particular, iTreePack overcomes the
problem of large treewidth by decomposing a protein complex into smaller
subgraphs and novelly reformulating the complex side-chain packing problem as a
dual relaxation problem; this allows us to solve the side-chain packing of each
small subgraph separately using tree-decomposition. A projected subgradient
algorithm is applied to enforcing the consistency among the side-chain packings
of all the small subgraphs. Computational results demonstrate that our
iTreePack program outperforms SCWRL4 on protein complexes. In particular,
iTreePack places side-chain atoms much more accurately on very large complexes,
which constitute a significant portion of protein-protein interactions.
Moreover, the advantage of iTreePack over SCWRL4 increases with respect to the
treewidth of a complex. Even for monomeric proteins, iTreePack is much more
efficient than SCWRL and slightly more accurate.
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing
Date: 2015-04-21 00:00:00

Genetic variation in the tomato clade was explored by sequencing a selection
of 84 tomato accessions and related wild species representative for the
Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups. We present a
reconstruction of three new reference genomes in support of our comparative
genome analyses. Sequence diversity in commercial breeding lines appears
extremely low, indicating the dramatic genetic erosion of crop tomatoes. This
is reflected by the SNP count in wild species which can exceed 10 million i.e.
20 fold higher than in crop accessions. Comparative sequence alignment reveals
group, species, and accession specific polymorphisms, which explain
characteristic fruit traits and growth habits in tomato accessions. Using gene
models from the annotated Heinz reference genome, we observe a bias in dN/dS
ratio in fruit and growth diversification genes compared to a random set of
genes, which probably is the result of a positive selection. We detected highly
divergent segments in wild S. lycopersicum species, and footprints of
introgressions in crop accessions originating from a common donor accession.
Phylogenetic relationships of fruit diversification and growth specific genes
from crop accessions show incomplete resolution and are dependent on the
introgression donor. In contrast, whole genome SNP information has sufficient
power to resolve the phylogenetic placement of each accession in the four main
groups in the Lycopersicon clade using Maximum Likelihood analyses.
Phylogenetic relationships appear correlated with habitat and mating type and
point to the occurrence of geographical races within these groups and thus are
of practical importance for introgressive hybridization breeding. Our study
illustrates the need for multiple reference genomes in support of tomato
comparative genomics and Solanum genome evolution studies.
Introgression Browser: High throughput whole-genome SNP visualization
Date: 2015-04-21 00:00:00
Tasks: Vocal Bursts Intensity Prediction

Breeding by introgressive hybridization is a pivotal strategy to broaden the
genetic basis of crops. Usually, the desired traits are monitored in
consecutive crossing generations by marker-assisted selection, but their
analyses fail in chromosome regions where crossover recombinants are rare or
not viable. Here, we present the Introgression Browser (IBROWSER), a novel
bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP
accuracy. The software selects homozygous SNPs from Variant Call Format (VCF)
information and filters out heterozygous SNPs, Multi-Nucleotide Polymorphisms
(MNPs) and insertion-deletions (InDels). For data analysis IBROWSER makes use
of sliding windows, but if needed it can generate any desired fragmentation
pattern through General Feature Format (GFF) information. In an example of
tomato (Solanum lycopersicum) accessions we visualize SNP patterns and
elucidate both position and boundaries of the introgressions. We also show that
our tool is capable of identifying alien DNA in a panel of the closely related
S. pimpinellifolium by examining phylogenetic relationships of the introgressed
segments in tomato. In a third example, we demonstrate the power of the
IBROWSER in a panel of 600 Arabidopsis accessions, detecting the boundaries of
a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short
arm of chromosome 4. The architecture and functionality of IBROWSER makes the
software appropriate for a broad set of analyses including SNP mining, genome
structure analysis, and pedigree analysis. Its functionality, together with the
capability to process large data sets and efficient visualization of sequence
variation, makes IBROWSER a valuable breeding tool.
Surface deformation and shear flow in ligand mediated cell adhesion
Date: 2015-04-22 00:00:00

We present a single, unified, multi-scale model to study the
attachment\detachment dynamics of two deforming, near spherical cells, coated
with binding ligands and subject to a slow, homogeneous shear flow in a viscous
fluid medium. The binding ligands on the surface of the cells experience
attractive and repulsive forces in an ionic medium and exhibit finite
resistance to rotation via bond tilting. The macroscale drag forces and couples
describing the fluid flow inside the small separation gap between the cells,
are calculated using a combination of methods in lubrication theory and
previously published numerical results. For a select range of material and
fluid parameters, a hysteretic transition of the sticking probability curves
between the adhesion and fragmentation domain is attributed to a nonlinear
relation between the total microscale binding forces and the separation gap
between the cells. We show that adhesion is favored in highly ionic fluids,
increased deformability of the cells, elastic binders and a higher fluid shear
rate (until a critical value). Continuation of the limit points predict a
bistable region, indicating an abrupt switching between the adhesion and
fragmentation regimes at critical shear rates, and suggesting that adhesion of
two deformable surfaces in shearing fluids may play a significant dynamical
role in some cell adhesion applications.
Quasispecies on class-dependent fitness landscapes
Date: 2016-04-26 00:00:00

We study Eigen's quasispecies model in the asymptotic regime where the length
of the genotypes goes to infinity and the mutation probability goes to 0. We
give several explicit formulas for the stationary solutions of the limiting
system of differential equations.
Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
Date: 2015-04-22 00:00:00
Tasks: Specificity

Gene expression is controlled primarily by interactions between transcription
factor proteins (TFs) and the regulatory DNA sequence, a process that can be
captured well by thermodynamic models of regulation. These models, however,
neglect regulatory crosstalk: the possibility that non-cognate TFs could
initiate transcription, with potentially disastrous effects for the cell. Here
we estimate the importance of crosstalk, suggest that its avoidance strongly
constrains equilibrium models of TF binding, and propose an alternative
non-equilibrium scheme that implements kinetic proofreading to suppress
erroneous initiation. This proposal is consistent with the observed covalent
modifications of the transcriptional apparatus and would predict increased
noise in gene expression as a tradeoff for improved specificity. Using
information theory, we quantify this tradeoff to find when optimal proofreading
architectures are favored over their equilibrium counterparts.
Agent-based mapping of credit risk for sustainable microfinance
Date: 2015-04-22 00:00:00

Inspired by recent ideas on how the analysis of complex financial risks can
benefit from analogies with independent research areas, we propose an
unorthodox framework for mapping microfinance credit risk---a major obstacle to
the sustainability of lenders outreaching to the poor. Specifically, using the
elements of network theory, we constructed an agent-based model that obeys the
stylised rules of microfinance industry. We found that in a deteriorating
economic environment confounded with adverse selection, a form of latent moral
hazard may cause a regime shift from a high to a low loan repayment
probability. An after-the-fact recovery, when possible, required the economic
environment to improve beyond that which led to the shift in the first place.
These findings suggest a small set of measurable quantities for mapping
microfinance credit risk and, consequently, for balancing the requirements to
reasonably price loans and to operate on a fully self-financed basis. We
illustrate how the proposed mapping works using a 10-year monthly data set from
one of the best-known microfinance representatives, Grameen Bank in Bangladesh.
Finally, we discuss an entirely new perspective for managing microfinance
credit risk based on enticing spontaneous cooperation by building social
capital.
Flagellar swimmers oscillate between pusher- and puller-type swimming
Date: 2015-04-22 00:00:00
Tasks: Vocal Bursts Type Prediction

Self-propulsion of cellular microswimmers generates flow signatures, commonly
classified as pusher- and puller-type, which characterize hydrodynamic
interactions with other cells or boundaries. Using experimentally measured beat
patterns, we compute that flagellated alga and sperm oscillate between pusher
and puller. Beyond a typical distance of 100 um from the swimmer, inertia
attenuates oscillatory micro-flows. We show that hydrodynamic interactions
between swimmers oscillate in time and are of similar magnitude as stochastic
swimming fluctuations.
SMC-ABC methods for the estimation of stochastic simulation models of the limit order book
Date: 2015-04-22 00:00:00
Tasks: Attribute

In this paper we consider classes of models that have been recently developed
for quantitative finance that involve modelling a highly complex multivariate,
multi-attribute stochastic process known as the Limit Order Book (LOB). The LOB
is the primary data structure recorded each day intra-daily for all assets on
every electronic exchange in the world in which trading takes place. As such,
it represents one of the most important fundamental structures to study from a
stochastic process perspective if one wishes to characterize features of
stochastic dynamics for price, volume, liquidity and other important attributes
for a traded asset. In this paper we aim to adopt the model structure which
develops a stochastic model framework for the LOB of a given asset and to
explain how to perform calibration of this stochastic model to real observed
LOB data for a range of different assets.
A Study of Correlations in the Stock Market
Date: 2015-04-22 00:00:00
Tasks: Management, Portfolio Optimization

We study the various sectors of the Bombay Stock Exchange(BSE) for a period
of 8 years from April 2006 - March 2014. Using the data of daily returns of a
period of eight years we make a direct model free analysis of the pattern of
the sectorial indices movement and the correlations among them. Our analysis
shows significant auto correlation among the individual sectors and also strong
cross-correlation among sectors. We also find that auto correlations in some of
the sectors persist in time. This is a very significant result and has not been
reported so far in Indian context These findings will be very useful in model
building for prediction of price movement of equities, derivatives and
portfolio management. We show that the Random Walk Hypothesis is not applicable
in modeling the Indian market and Mean-Variance-Skewness-Kurtosis based
portfolio optimization might be required. We also find that almost all sectors
are highly correlated during large fluctuation periods and have only moderate
correlation during normal periods.
Impact of density-dependent migration flows on epidemic outbreaks in heterogeneous metapopulations
Date: 2015-07-29 00:00:00

We investigate the role of migration patterns on the spread of epidemics in
complex networks. We enhance the SIS-diffusion model on metapopulations to a
nonlinear diffusion. Specifically, individuals move randomly over the network
but at a rate depending on the population of the departure patch. In the
absence of epidemics, the migration-driven equilibrium is described by
quantifying the total number of individuals living in heavily/lightly populated
areas. Our analytical approach reveals that strengthening the migration from
populous areas contains the infection at the early stage of the epidemic.
Moreover, depending on the exponent of the nonlinear diffusion rate, epidemic
outbreaks do not always occur in the most populated areas as one might expect.