pwc-archive/papers-with-abstracts huggingface dataset:
The spatial dynamics of ecosystem engineers
Date: 2017-08-10 00:00:00

The changes on abiotic features of ecosystems have rarely been taken into
account by population dynamics models, which typically focus on trophic and
competitive interactions between species. However, understanding the population
dynamics of organisms that must modify their habitats in order to survive, the
so-called ecosystem engineers, requires the explicit incorporation of abiotic
interactions in the models. Here we study a model of ecosystem engineers that
is discrete both in space and time, and where the engineers and their habitats
are arranged in patches fixed to the sites of regular lattices. The growth of
the engineer population is modeled by Ricker equation with a density-dependent
carrying capacity that is given by the number of modified habitats. A diffusive
dispersal stage ensures that a fraction of the engineers move from their birth
patches to neighboring patches. We find that dispersal influences the
metapopulation dynamics only in the case that the local or single-patch
dynamics exhibits chaotic behavior. In that case, it can suppress the chaotic
behavior and avoid extinctions in the regime of large intrinsic growth rate of
the population.
Thermodynamic competition between membrane protein oligomeric states
Date: 2016-11-28 00:00:00
Tasks: Diversity

Self-assembly of protein monomers into distinct membrane protein oligomers
provides a general mechanism for diversity in the molecular architectures, and
resulting biological functions, of membrane proteins. We develop a general
physical framework describing the thermodynamic competition between different
oligomeric states of membrane proteins. Using the mechanosensitive channel of
large conductance as a model system, we show how the dominant oligomeric states
of membrane proteins emerge from the interplay of protein concentration in the
cell membrane, protein-induced lipid bilayer deformations, and direct
monomer-monomer interactions. Our results suggest general physical mechanisms
and principles underlying regulation of protein function via control of
membrane protein oligomeric state.
Forward Backward Similarity Search in Knowledge Networks
Authors: Shi Baoxu, Yang Lin, Weninger Tim
Date: 2016-11-28 00:00:00
Tasks: Link Prediction

Similarity search is a fundamental problem in social and knowledge networks
like GitHub, DBLP, Wikipedia, etc. Existing network similarity measures are
limited because they only consider similarity from the perspective of the query
node. However, due to the complicated topology of real-world networks, ignoring
the preferences of target nodes often results in odd or unintuitive
performance. In this work, we propose a dual perspective similarity metric
called Forward Backward Similarity (FBS) that efficiently computes topological
similarity from the perspective of both the query node and the perspective of
candidate nodes. The effectiveness of our method is evaluated by traditional
quantitative ranking metrics and large-scale human judgement on four large real
world networks. The proposed method matches human preference and outperforms
other similarity search algorithms on community overlap and link prediction.
Finally, we demonstrate top-5 rankings for five famous researchers on an
academic collaboration network to illustrate how our approach captures
semantics more intuitively than other approaches.
diagno-syst: a tool for accurate inventories in metabarcoding
Date: 2016-11-28 00:00:00

Metabarcoding on amplicons is rapidly expanding as a method to produce
molecular based inventories of microbial communities. Here, we work on
freshwater diatoms, which are microalgae possibly inventoried both on a
morphological and a molecular basis. We have developed an algorithm, in a
program called diagno-syst, based a the notion of informative read, which
carries out supervised clustering of reads by mapping them exactly one by one
on all reads of a well curated and taxonomically annotated reference database.
This program has been run on a HPC (and HTC) infrastructure to address
computation load. We compare optical and molecular based inventories on 10
samples from L\'eman lake, and 30 from Swedish rivers. We track all
possibilities of mismatches between both approaches, and compare the results
with standard pipelines (with heuristics) like Mothur. We find that the
comparison with optics is more accurate when using exact calculations, at the
price of a heavier computation load. It is crucial when studying the long tail
of biodiversity, which may be overestimated by pipelines or algorithms using
heuristics instead (more false positive). This work supports the analysis that
these methods will benefit from progress in, first, building an agreement
between molecular based and morphological based systematics and, second, having
as complete as possible publicly available reference databases.
A Graph-based Push Service Platform
Authors: Guo Huifeng, Tang Ruiming, Ye Yunming, Li Zhenguo, He Xiuqiang
Date: 2016-11-29 00:00:00
Tasks: Recommendation Systems

It is well known that learning customers' preference and making
recommendations to them from today's information-exploded environment is
critical and non-trivial in an on-line system. There are two different modes of
recommendation systems, namely pull-mode and push-mode. The majority of the
recommendation systems are pull-mode, which recommend items to users only when
and after users enter Application Market. While push-mode works more actively
to enhance or re-build connection between Application Market and users. As one
of the most successful phone manufactures,both the number of users and apps
increase dramatically in Huawei Application Store (also named Hispace Store),
which has approximately 0.3 billion registered users and 1.2 million apps until
2016 and whose number of users is growing with high-speed. For the needs of
real scenario, we establish a Push Service Platform (shortly, PSP) to discover
the target user group automatically from web-scale user operation log data with
an additional small set of labelled apps (usually around 10 apps),in Hispace
Store. As presented in this work,PSP includes distributed storage layer,
application layer and evaluation layer. In the application layer, we design a
practical graph-based algorithm (named A-PARW) for user group discovery, which
is an approximate version of partially absorbing random walk. Based on I mode
of A-PARW, the effectiveness of our system is significantly improved, compared
to the predecessor to presented system, which uses Personalized Pagerank in its
application layer.
Hierarchical Neural Representation of Dreamed Objects Revealed by Brain Decoding with Deep Neural Network Features
Date: 2017-01-23 00:00:00
Tasks: Brain Decoding, Object, Object Recognition

Dreaming is generally thought to be generated by spontaneous brain activity
during sleep with patterns common to waking experience. This view is supported
by a recent study demonstrating that dreamed objects can be predicted from
brain activity during sleep using statistical decoders trained with
stimulus-induced brain activity. However, it remains unclear whether and how
visual image features associated with dreamed objects are represented in the
brain. In this study, we used a deep neural network (DNN) model for object
recognition as a proxy for hierarchical visual feature representation, and DNN
features for dreamed objects were analyzed with brain decoding of fMRI data
collected during dreaming. The decoders were first trained with
stimulus-induced brain activity labeled with the feature values of the stimulus
image from multiple DNN layers. The decoders were then used to decode DNN
features from the dream fMRI data, and the decoded features were compared with
the averaged features of each object category calculated from a large-scale
image database. We found that the feature values decoded from the dream fMRI
data positively correlated with those associated with dreamed object categories
at mid- to high-level DNN layers. Using the decoded features, the dreamed
object category could be identified at above-chance levels by matching them to
the averaged features for candidate categories. The results suggest that
dreaming recruits hierarchical visual feature representations associated with
objects, which may support phenomenal aspects of dream experience.
Tip-enhanced Raman spectroscopic detection of aptamers
Date: 2016-11-29 00:00:00
Tasks: Position

Single molecule detection, sequencing and conformational mapping of aptamers
are important for improving medical and biosensing technologies and for better
understanding of biological processes at the molecular level. We obtain
vibrational signals of single aptamers immobilized on gold substrates using
tip-enhanced Raman spectroscopy (TERS). We compare topographic and optical
signals and investigate the fluctuations of the position-dependent TERS
spectra. TERS mapping provides information about the chemical composition and
conformation of aptamers, and paves the way to future single-molecule
label-free sequencing.
Stability of two-species communities: drift, environmental stochasticity, storage effect and selection
Date: 2016-11-29 00:00:00

The dynamics of two competing species in a finite size community is one of
the most studied problems in population genetics and community ecology.
Stochastic fluctuations lead, inevitably, to the extinction of one of the
species, but the relevant timescale depends on the underlying dynamics. The
persistence time of the community has been calculated for neutral models, where
the only drive of the system is drift (demographic stochasticity) and for
models with strong selection. Following recent analyses that stress the
importance of environmental stochasticity in empirical systems, we present here
a general theory of persistence time of two-species community where drift,
environmental variations and time independent selective advantage are all taken
into account.
Spatial organization and cyclic dominance in asymmetric predator-prey spatial games
Date: 2017-07-11 00:00:00

Predators may attack isolated or grouped prey in a cooperative, collective
way. Whether a gregarious behavior is advantageous to each species depends on
several conditions and game theory is a useful tool to deal with such a
problem. We here extend the Lett-Auger-Gaillard model [Theor. Pop. Biol. 65
(2004) 263] to spatially distributed populations and compare the resulting
behavior with their mean-field predictions for the coevolving densities of
predator and prey strategies. Besides its richer behavior in the presence of
spatial organization, we also show that the coexistence phase in which
collective and individual strategies for each group are present is stable
because of an effective, cyclic dominance mechanism similar to a well-studied
generalization of the Rock-Paper-Scissors game with four species, a further
example of how ubiquitous this coexistence mechanism is.
Cover's universal portfolio, stochastic portfolio theory and the numeraire portfolio
Date: 2016-11-29 00:00:00

Cover's celebrated theorem states that the long run yield of a properly
chosen "universal" portfolio is as good as the long run yield of the best
retrospectively chosen constant rebalanced portfolio. The "universality"
pertains to the fact that this result is model-free, i.e., not dependent on an
underlying stochastic process. We extend Cover's theorem to the setting of
stochastic portfolio theory as initiated by R. Fernholz: the rebalancing rule
need not to be constant anymore but may depend on the present state of the
stock market. This model-free result is complemented by a comparison with the
log-optimal numeraire portfolio when fixing a stochastic model of the stock
market. Roughly speaking, under appropriate assumptions, the optimal long run
yield coincides for the three approaches mentioned in the title of this paper.
We present our results in discrete and continuous time.
PeBLes: Prediction of B-cell epitope using molecular layers
Date: 2016-11-29 00:00:00
Tasks: Prediction

Characterization of B-cell protein epitope and developing critical parameters
for its identification is one of the long standing interests. Using Layers
algorithm, we introduced the concept of anchor residues to identify epitope. We
have shown that majority of the epitope is composed of anchor residues and have
significant bias in epitope for these residues. We optimized the search space
reduction for epitope identification. We used Layers to non-randomly sample the
antigen surface reducing the molecular surface to an average of 75 residues
while preserving 50% of the epitope in the sample surface. To facilitate the
comparison of favorite methods of researchers we compared the popular
techniques used to identify epitope with their sampling performance and
evaluation. We proposed an optimum Sr of 16 {\AA} to sample the antigen
molecules to reduce the search space, in which epitope is identified using
buried surface area method. We used the combinations of molecular surface
sampling, anchor residue intensity in surface, secondary structure and sequence
information to predict epitope at an accuracy of 89%. A web application is made
available at
http://www.csb.iitkgp.ernet.in/applications/b_cell_epitope_pred/main.
Interspecific allometric scaling of unicellular organisms as an evolutionary process of food chain creation
Date: 2016-11-29 00:00:00

Metabolism of living organisms is a foundation of life. The metabolic rate
(energy production per unit time) increases slower than organisms' mass. When
this phenomenon is considered across different species, it is called
interspecific allometric scaling, whose causes are unknown. We argue that the
cause of interspecific allometric scaling is the total effect of physiological
and adaptation mechanisms inherent to organisms composing a food chain.
Together, the workings of these mechanisms are united by a primary goal of any
living creature - its successful reproduction. This primary necessity of each
organism and of the entire food chain is that common denominator, to which all
organisms adjust their metabolic rates. In this article, we consider
unicellular organisms, while the second paper studies multicellular organisms
and the entire concept in more detail. Here, using the proposed concepts and
experimentally verified growth models of five different unicellular organisms,
we obtain close to experimental findings values of allometric exponents of
0.757 for the end of growth and 0.853 for the beginning of growth. These
results comply with experimental observations and prove our theory that the
requirement of successful reproduction within the food chain is an important
factor shaping interspecific allometric scaling.
Exploring the Uncharted Export: an Analysis of Tourism-Related Foreign Expenditure with International Spend Data
Date: 2016-11-29 00:00:00

Tourism is one of the most important economic activities in the world: for
many countries it represents the single largest product in their export basket.
However, it is a product difficult to chart: "exporters" of tourism do not ship
it abroad, but they welcome importers inside the country. Current research uses
social accounting matrices and general equilibrium models, but the standard
industry classifications they use make it hard to identify which domestic
industries cater to foreign visitors. In this paper, we make use of open source
data and of anonymized and aggregated transaction data giving us insights about
the spend behavior of foreigners inside two countries, Colombia and the
Netherlands, to inform our research. With this data, we are able to describe
what constitutes the tourism sector, and to map the most attractive
destinations for visitors. In particular, we find that countries might observe
different geographical tourists' patterns -- concentration versus
decentralization --; we show the importance of distance, a country's reported
wealth and cultural affinity in informing tourism; and we show the potential of
combining open source data and anonymized and aggregated transaction data on
foreign spend patterns in gaining insight as to the evolution of tourism from
one year to another.
The optimal rate for resolving a near-polytomy in a phylogeny
Date: 2017-03-10 00:00:00

The reconstruction of phylogenetic trees from discrete character data
typically relies on models that assume the characters evolve under a
continuous-time Markov process operating at some overall rate $\lambda$. When
$\lambda$ is too high or too low, it becomes difficult to distinguish a short
interior edge from a polytomy (the tree that results from collapsing the edge).
In this note, we investigate the rate that maximizes the expected
log-likelihood ratio (i.e. the Kullback--Leibler separation) between the
four-leaf unresolved (star) tree and a four-leaf binary tree with interior edge
length $\epsilon$. For a simple two-state model, we show that as $\epsilon$
converges to $0$ the optimal rate also converges to zero when the four pendant
edges have equal length. However, when the four pendant branches have unequal
length, two local optima can arise, and it is possible for the globally optimal
rate to converge to a non-zero constant as $\epsilon \rightarrow 0$. Moreover,
in the setting where the four pendant branches have equal lengths and either
(i) we replace the two-state model by an infinite-state model or (ii) we retain
the two-state model and replace the Kullback--Leibler separation by Euclidean
distance as the maximization goal, then the optimal rate also converges to a
non-zero constant.
Vocabulary and the Brain: Evidence from Neuroimaging Studies
Date: 2016-11-30 00:00:00
Tasks: Retrieval

In summary of the research findings presented in this paper, various brain
regions are correlated with vocabulary and vocabulary acquisition. Semantic
associations for vocabulary seem to be located near brain areas that vary
according to the type of vocabulary, e.g. ventral temporal regions important
for words for things that can be seen. Semantic processing is believed to be
strongly associated with the ANG. Phonological ability has been closely related
to the anterior surfaces of the SMG. Pathways through the posterior SMG are
thought to link the anterior SMG and the ANG. In vocabulary tasks,
mediotemporal structures may be related to long-term memory processing, with
left hippocampal and parahippocampal regions related to long-term and working
memory, respectively. Precentral structures are associated with phonological
retrieval. Furthermore, many more regions of the brain are of interest in
vocabulary tasks, particularly in areas important for visual and auditory
processing. Furthermore, differences between brain anatomies can be attributed
to vocabulary demands of different languages.
Lipidomic approach for stratification of Acute Myeloid Leukemia patients
Date: 2016-11-30 00:00:00
Tasks: Diagnostic

The pathogenesis and progression of many tumors, including hematologic
malignancies is highly dependent on enhanced lipogenesis. De novo fatty-acid
synthesis permits accelerated proliferation of tumor cells by providing
structural components to build the membranes. It may also lead to alterations
of physicochemical properties of the formed membranes, which can have an impact
on signaling or even increase resistance to drugs in cancer cells. Cancer
type-specific lipid profiles would allow understanding the actual effects of
lipid changes and therefore could potentially serve as fingerprints for
individual tumors and be explored as diagnostic markers. We have used shotgun
MS approach to identify lipid patterns in different types of acute myeloid
leukemia (AML) patients that either show no karyotype changes or belong to
t(8;21) or inv16 types. The observed differences in lipidomes of t(8;21) and
inv(16) patients, as compared to AML patients without karyotype changes,
concentrate mostly on substantial modulation of ceramides/sphingolipids
synthesis. Also significant changes in the physicochemical properties of the
membranes, between the t(8;21) and the other patients, were noted that were
related to a marked alteration in the saturation levels of lipids. The revealed
differences in lipid profiles of various AML types increase our understanding
of the affected biochemical pathways and can potentially serve as diagnostic
tools.
A framework to reconcile frequency scaling measurements, from intracellular recordings, local-field potentials, up to EEG and MEG signals
Date: 2016-11-30 00:00:00
Tasks: EEG, Electroencephalogram (EEG)

In this viewpoint article, we discuss the electric properties of the medium
around neurons, which are important to correctly interpret extracellular
potentials or electric field effects in neural tissue. We focus on how these
electric properties shape the frequency scaling of brain signals at different
scales, such as intracellular recordings, the local field potential (LFP), the
electroencephalogram (EEG) or the magnetoencephalogram (MEG). These signals
display frequency-scaling properties which are not consistent with resistive
media. The medium appears to exert a frequency filtering scaling as
$1/\sqrt{f}$, which is the typical frequency scaling of ionic diffusion. Such a
scaling was also found recently by impedance measurements in physiological
conditions. Ionic diffusion appears to be the only possible explanation to
reconcile these measurements and the frequency-scaling properties found in
different brain signals. However, other measurements suggest that the
extracellular medium is essentially resistive. To resolve this discrepancy, we
show new evidence that metal-electrode measurements can be perturbed by shunt
currents going through the surface of the brain. Such a shunt may explain the
contradictory measurements, and together with ionic diffusion, provides a
framework where all observations can be reconciled. Finally, we propose a
method to perform measurements avoiding shunting effects, thus enabling to test
the predictions of this framework.
Invasive competition with Fokker-Planck diffusion and noise
Date: 2016-11-30 00:00:00

Defeat and success of the competitive invasion of a populated area is
described with a standard Lotka-Volterra competition model. The resident is
adapted to the heterogeneous living conditions, i.e., its motion is modelled as
space-dependent, so-called Fokker-Planck diffusion. The invader's diffusion is
taken as neutral Fickian. Furthermore, it is studied how multiplicative
environmental noise fosters or hinders the invasion.
A rare mutation model in a spatial heterogeneous environment: the Hawk and Dove game
Date: 2016-11-30 00:00:00

We propose a stochastic model in evolutionary game theory where individuals
(or subpopulations) can mutate changing their strategies randomly (but rarely)
and explore the external environment. This environment affects the selective
pressure by modifying the payoff arising from the interactions between
strategies. We derive a Fokker-Plank integro-differential equation and provide
Monte-Carlo simulations for the Hawks vs Doves game. In particular we show
that, in some cases, taking into account the external environment favors the
persistence of the low-fitness strategy.
Assessing pattern recognition or labeling in streams of temporal data
Authors: Marteau Pierre-François  EXPRESSION
Date: 2016-11-30 00:00:00

In the data deluge context, pattern recognition or labeling in streams is
becoming quite an essential and pressing task as data flows inside always
bigger streams. The assessment of such tasks is not so easy when dealing with
temporal data, namely patterns that have a duration (a beginning and an end
time-stamp). This paper details an approach based on an editing distance to
first align a sequence of labeled temporal segments with a ground truth
sequence, and then, by back-tracing an optimal alignment path, to provide a
confusion matrix at the label level. From this confusion matrix, standard
evaluation measures can easily be derived as well as other measures such as the
"latency" that can be quite important in (early) pattern detection
applications.