1,693 research outputs found
Higher order organizational features can distinguish protein interaction networks of disease classes: a case study of neoplasms and neurological diseases
Neoplasms (NPs) and neurological diseases and disorders (NDDs) are amongst
the major classes of diseases underlying deaths of a disproportionate number of
people worldwide. To determine if there exist some distinctive features in the
local wiring patterns of protein interactions emerging at the onset of a
disease belonging to either of these two classes, we examined 112 and 175
protein interaction networks belonging to NPs and NDDs, respectively. Orbit
usage profiles (OUPs) for each of these networks were enumerated by
investigating the networks' local topology. 56 non-redundant OUPs (nrOUPs) were
derived and used as network features for classification between these two
disease classes. Four machine learning classifiers, namely, k-nearest neighbour
(KNN), support vector machine (SVM), deep neural network (DNN), random forest
(RF) were trained on these data. DNN obtained the greatest average AUPRC
(0.988) among these classifiers. DNNs developed on node2vec and the proposed
nrOUPs embeddings were compared using 5-fold cross validation on the basis of
average values of the six of performance measures, viz., AUPRC, Accuracy,
Sensitivity, Specificity, Precision and MCC. It was found that nrOUPs based
classifier performed better in all of these six performance measures.Comment: 14 pages, 3 figures, 3 table
DeepAutoPIN: An automorphism orbits based deep neural network for characterizing the organizational diversity of protein interactomes across the tree of life
The enormous diversity of life forms thriving in drastically different
environmental milieus involves a complex interplay among constituent proteins
interacting with each other. However, the organizational principles
characterizing the evolution of protein interaction networks (PINs) across the
tree of life are largely unknown. Here we study 4,738 PINs belonging to 16
phyla to discover phyla-specific architectural features and examine if there
are some evolutionary constraints imposed on the networks' topologies. We
utilized positional information of a network's nodes by normalizing the
frequencies of automorphism orbits appearing in graphlets of sizes 2-5. We
report that orbit usage profiles (OUPs) of networks belonging to the three
domains of life are contrastingly different not only at the domain level but
also at the scale of phyla. Integrating the information related to protein
families, domains, subcellular location, gene ontology, and pathways, our
results indicate that wiring patterns of PINs in different phyla are not
randomly generated rather they are shaped by evolutionary constraints imposed
on them. There exist subtle but substantial variations in the wiring patterns
of PINs that enable OUPs to differentiate among different superfamilies. A deep
neural network was trained on differentially expressed orbits resulting in a
prediction accuracy of 85%.Comment: 29 pages, 4 figures, 1 algorithm, 2 supplementary file
Design and Development of a User Specific Dynamic E-Magazine
Internet and electronic media gaining more popularity due to ease and speed,
the count of Internet users has increased tremendously. The world is moving
faster each day with several events taking place at once and the Internet is
flooded with information in every field. There are categories of information
ranging from most relevant to user, to the information totally irrelevant or
less relevant to specific users. In such a scenario getting the information
which is most relevant to the user is indispensable to save time. The
motivation of our solution is based on the idea of optimizing the search for
information automatically. This information is delivered to user in the form of
an interactive GUI. The optimization of the contents or information served to
him is based on his social networking profiles and on his reading habits on the
proposed solution. The aim is to get the user's profile information based on
his social networking profile considering that almost every Internet user has
one. This helps us personalize the contents delivered to the user in order to
produce what is most relevant to him, in the form of a personalized e-magazine.
Further the proposed solution learns user's reading habits for example the news
he saves or clicks the most and makes a decision to provide him with the best
contents.Comment: 19 pages, 6 figure
Inferring interaction networks from transcriptomic data: methods and applications
Transcriptomic data is a treasure-trove in modern molecular biology, as it
offers a comprehensive viewpoint into the intricate nuances of gene expression
dynamics underlying biological systems. This genetic information must be
utilised to infer biomolecular interaction networks that can provide insights
into the complex regulatory mechanisms underpinning the dynamic cellular
processes. Gene regulatory networks and protein-protein interaction networks
are two major classes of such networks. This chapter thoroughly investigates
the wide range of methodologies used for distilling insightful revelations from
transcriptomic data that include association based methods (based on
correlation among expression vectors), probabilistic models (using Bayesian and
Gaussian models), and interologous methods. We reviewed different approaches
for evaluating the significance of interactions based on the network topology
and biological functions of the interacting molecules, and discuss various
strategies for the identification of functional modules. The chapter concludes
with highlighting network based techniques of prioritising key genes, outlining
the centrality based, diffusion based and subgraph based methods. The chapter
provides a meticulous framework for investigating transcriptomic data to
uncover assembly of complex molecular networks for their adaptable analyses
across a broad spectrum of biological domains.Comment: 48 pages, 3 figure
Stochastic Coalitional Better-response Dynamics and Strong Nash Equilibrium
We consider coalition formation among players in an n-player finite strategic
game over infinite horizon. At each time a randomly formed coalition makes a
joint deviation from a current action profile such that at new action profile
all players from the coalition are strictly benefited. Such deviations define a
coalitional better-response (CBR) dynamics that is in general stochastic. The
CBR dynamics either converges to a strong Nash equilibrium or stucks in a
closed cycle. We also assume that at each time a selected coalition makes
mistake in deviation with small probability that add mutations (perturbations)
into CBR dynamics. We prove that all strong Nash equilibria and closed cycles
are stochastically stable, i.e., they are selected by perturbed CBR dynamics as
mutations vanish. Similar statement holds for strict strong Nash equilibrium.
We apply CBR dynamics to the network formation games and we prove that all
strongly stable networks and closed cycles are stochastically stable
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