43,092 research outputs found
Using Neural Networks for Relation Extraction from Biomedical Literature
Using different sources of information to support automated extracting of
relations between biomedical concepts contributes to the development of our
understanding of biological systems. The primary comprehensive source of these
relations is biomedical literature. Several relation extraction approaches have
been proposed to identify relations between concepts in biomedical literature,
namely, using neural networks algorithms. The use of multichannel architectures
composed of multiple data representations, as in deep neural networks, is
leading to state-of-the-art results. The right combination of data
representations can eventually lead us to even higher evaluation scores in
relation extraction tasks. Thus, biomedical ontologies play a fundamental role
by providing semantic and ancestry information about an entity. The
incorporation of biomedical ontologies has already been proved to enhance
previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1
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Heterogeneous network embedding enabling accurate disease association predictions.
BackgroundIt is significant to identificate complex biological mechanisms of various diseases in biomedical research. Recently, the growing generation of tremendous amount of data in genomics, epigenomics, metagenomics, proteomics, metabolomics, nutriomics, etc., has resulted in the rise of systematic biological means of exploring complex diseases. However, the disparity between the production of the multiple data and our capability of analyzing data has been broaden gradually. Furthermore, we observe that networks can represent many of the above-mentioned data, and founded on the vector representations learned by network embedding methods, entities which are in close proximity but at present do not actually possess direct links are very likely to be related, therefore they are promising candidate subjects for biological investigation.ResultsWe incorporate six public biological databases to construct a heterogeneous biological network containing three categories of entities (i.e., genes, diseases, miRNAs) and multiple types of edges (i.e., the known relationships). To tackle the inherent heterogeneity, we develop a heterogeneous network embedding model for mapping the network into a low dimensional vector space in which the relationships between entities are preserved well. And in order to assess the effectiveness of our method, we conduct gene-disease as well as miRNA-disease associations predictions, results of which show the superiority of our novel method over several state-of-the-arts. Furthermore, many associations predicted by our method are verified in the latest real-world dataset.ConclusionsWe propose a novel heterogeneous network embedding method which can adequately take advantage of the abundant contextual information and structures of heterogeneous network. Moreover, we illustrate the performance of the proposed method on directing studies in biology, which can assist in identifying new hypotheses in biological investigation
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
Link Prediction in Complex Networks: A Survey
Link prediction in complex networks has attracted increasing attention from
both physical and computer science communities. The algorithms can be used to
extract missing information, identify spurious interactions, evaluate network
evolving mechanisms, and so on. This article summaries recent progress about
link prediction algorithms, emphasizing on the contributions from physical
perspectives and approaches, such as the random-walk-based methods and the
maximum likelihood methods. We also introduce three typical applications:
reconstruction of networks, evaluation of network evolving mechanism and
classification of partially labelled networks. Finally, we introduce some
applications and outline future challenges of link prediction algorithms.Comment: 44 pages, 5 figure
Ontology-based knowledge representation of experiment metadata in biological data mining
According to the PubMed resource from the U.S. National Library of Medicine,
over 750,000 scientific articles have been published in the ~5000 biomedical journals
worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes
edge2vec: Representation learning using edge semantics for biomedical knowledge discovery
Representation learning provides new and powerful graph analytical approaches
and tools for the highly valued data science challenge of mining knowledge
graphs. Since previous graph analytical methods have mostly focused on
homogeneous graphs, an important current challenge is extending this
methodology for richly heterogeneous graphs and knowledge domains. The
biomedical sciences are such a domain, reflecting the complexity of biology,
with entities such as genes, proteins, drugs, diseases, and phenotypes, and
relationships such as gene co-expression, biochemical regulation, and
biomolecular inhibition or activation. Therefore, the semantics of edges and
nodes are critical for representation learning and knowledge discovery in real
world biomedical problems. In this paper, we propose the edge2vec model, which
represents graphs considering edge semantics. An edge-type transition matrix is
trained by an Expectation-Maximization approach, and a stochastic gradient
descent model is employed to learn node embedding on a heterogeneous graph via
the trained transition matrix. edge2vec is validated on three biomedical domain
tasks: biomedical entity classification, compound-gene bioactivity prediction,
and biomedical information retrieval. Results show that by considering
edge-types into node embedding learning in heterogeneous graphs,
\textbf{edge2vec}\ significantly outperforms state-of-the-art models on all
three tasks. We propose this method for its added value relative to existing
graph analytical methodology, and in the real world context of biomedical
knowledge discovery applicability.Comment: 10 page
New Method of Measuring TCP Performance of IP Network using Bio-computing
The measurement of performance of Internet Protocol IP network can be done by
Transmission Control Protocol TCP because it guarantees send data from one end
of the connection actually gets to the other end and in the same order it was
send, otherwise an error is reported. There are several methods to measure the
performance of TCP among these methods genetic algorithms, neural network, data
mining etc, all these methods have weakness and can't reach to correct measure
of TCP performance. This paper proposed a new method of measuring TCP
performance for real time IP network using Biocomputing, especially molecular
calculation because it provides wisdom results and it can exploit all
facilities of phylogentic analysis. Applying the new method at real time on
Biological Kurdish Messenger BIOKM model designed to measure the TCP
performance in two types of protocols File Transfer Protocol FTP and Internet
Relay Chat Daemon IRCD. This application gives very close result of TCP
performance comparing with TCP performance which obtains from Little's law
using same model (BIOKM), i.e. the different percentage of utilization (Busy or
traffic industry) and the idle time which are obtained from a new method base
on Bio-computing comparing with Little's law was (nearly) 0.13%.
KEYWORDS Bio-computing, TCP performance, Phylogenetic tree, Hybridized Model
(Normalized), FTP, IRCDComment: 17 Pages,10 Figures,5 Table
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