10,574 research outputs found
Elephant Search with Deep Learning for Microarray Data Analysis
Even though there is a plethora of research in Microarray gene expression
data analysis, still, it poses challenges for researchers to effectively and
efficiently analyze the large yet complex expression of genes. The feature
(gene) selection method is of paramount importance for understanding the
differences in biological and non-biological variation between samples. In
order to address this problem, a novel elephant search (ES) based optimization
is proposed to select best gene expressions from the large volume of microarray
data. Further, a promising machine learning method is envisioned to leverage
such high dimensional and complex microarray dataset for extracting hidden
patterns inside to make a meaningful prediction and most accurate
classification. In particular, stochastic gradient descent based Deep learning
(DL) with softmax activation function is then used on the reduced features
(genes) for better classification of different samples according to their gene
expression levels. The experiments are carried out on nine most popular Cancer
microarray gene selection datasets, obtained from UCI machine learning
repository. The empirical results obtained by the proposed elephant search
based deep learning (ESDL) approach are compared with most recent published
article for its suitability in future Bioinformatics research.Comment: 12 pages, 5 Tabl
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Collaborative analysis of multi-gigapixel imaging data using Cytomine
Motivation: Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries.
Results: We developed Cytomine to foster active and distributed collaboration of multidisciplinary teams for large-scale image-based studies. It uses web development methodologies and machine learning in order to readily organize, explore, share and analyze (semantically and quantitatively) multi-gigapixel imaging data over the internet. We illustrate how it has been used in several biomedical applications
Reconstructing the Forest of Lineage Trees of Diverse Bacterial Communities Using Bio-inspired Image Analysis
Cell segmentation and tracking allow us to extract a plethora of cell
attributes from bacterial time-lapse cell movies, thus promoting computational
modeling and simulation of biological processes down to the single-cell level.
However, to analyze successfully complex cell movies, imaging multiple
interacting bacterial clones as they grow and merge to generate overcrowded
bacterial communities with thousands of cells in the field of view,
segmentation results should be near perfect to warrant good tracking results.
We introduce here a fully automated closed-loop bio-inspired computational
strategy that exploits prior knowledge about the expected structure of a
colony's lineage tree to locate and correct segmentation errors in analyzed
movie frames. We show that this correction strategy is effective, resulting in
improved cell tracking and consequently trustworthy deep colony lineage trees.
Our image analysis approach has the unique capability to keep tracking cells
even after clonal subpopulations merge in the movie. This enables the
reconstruction of the complete Forest of Lineage Trees (FLT) representation of
evolving multi-clonal bacterial communities. Moreover, the percentage of valid
cell trajectories extracted from the image analysis almost doubles after
segmentation correction. This plethora of trustworthy data extracted from a
complex cell movie analysis enables single-cell analytics as a tool for
addressing compelling questions for human health, such as understanding the
role of single-cell stochasticity in antibiotics resistance without losing site
of the inter-cellular interactions and microenvironment effects that may shape
it
Social Fingerprinting: detection of spambot groups through DNA-inspired behavioral modeling
Spambot detection in online social networks is a long-lasting challenge
involving the study and design of detection techniques capable of efficiently
identifying ever-evolving spammers. Recently, a new wave of social spambots has
emerged, with advanced human-like characteristics that allow them to go
undetected even by current state-of-the-art algorithms. In this paper, we show
that efficient spambots detection can be achieved via an in-depth analysis of
their collective behaviors exploiting the digital DNA technique for modeling
the behaviors of social network users. Inspired by its biological counterpart,
in the digital DNA representation the behavioral lifetime of a digital account
is encoded in a sequence of characters. Then, we define a similarity measure
for such digital DNA sequences. We build upon digital DNA and the similarity
between groups of users to characterize both genuine accounts and spambots.
Leveraging such characterization, we design the Social Fingerprinting
technique, which is able to discriminate among spambots and genuine accounts in
both a supervised and an unsupervised fashion. We finally evaluate the
effectiveness of Social Fingerprinting and we compare it with three
state-of-the-art detection algorithms. Among the peculiarities of our approach
is the possibility to apply off-the-shelf DNA analysis techniques to study
online users behaviors and to efficiently rely on a limited number of
lightweight account characteristics
On combinatorial optimisation in analysis of protein-protein interaction and protein folding networks
Abstract: Protein-protein interaction networks and protein folding networks represent prominent research topics at the intersection of bioinformatics and network science. In this paper, we present a study of these networks from combinatorial optimisation point of view. Using a combination of classical heuristics and stochastic optimisation techniques, we were able to identify several interesting combinatorial properties of biological networks of the COSIN project. We obtained optimal or near-optimal solutions to maximum clique and chromatic number problems for these networks. We also explore patterns of both non-overlapping and overlapping cliques in these networks. Optimal or near-optimal solutions to partitioning of these networks into non-overlapping cliques and to maximum independent set problem were discovered. Maximal cliques are explored by enumerative techniques. Domination in these networks is briefly studied, too. Applications and extensions of our findings are discussed
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