Search results for "NG networks"
showing 10 items of 33 documents
Deep learning architectures for prediction of nucleosome positioning from sequences data
2018
Abstract Background Nucleosomes are DNA-histone complex, each wrapping about 150 pairs of double-stranded DNA. Their function is fundamental for one of the primary functions of Chromatin i.e. packing the DNA into the nucleus of the Eukaryote cells. Several biological studies have shown that the nucleosome positioning influences the regulation of cell type-specific gene activities. Moreover, computational studies have shown evidence of sequence specificity concerning the DNA fragment wrapped into nucleosomes, clearly underlined by the organization of particular DNA substrings. As the main consequence, the identification of nucleosomes on a genomic scale has been successfully performed by com…
Deep learning network for exploiting positional information in nucleosome related sequences
2017
A nucleosome is a DNA-histone complex, wrapping about 150 pairs of double-stranded DNA. The role of nucleosomes is to pack the DNA into the nucleus of the Eukaryote cells to form the Chromatin. Nucleosome positioning genome wide play an important role in the regulation of cell type-specific gene activities. Several biological studies have shown sequence specificity of nucleosome presence, clearly underlined by the organization of precise nucleotides substrings. Taking into consideration such advances, the identification of nucleosomes on a genomic scale has been successfully performed by DNA sequence features representation and classical supervised classification methods such as Support Vec…
Recurrent Deep Neural Networks for Nucleosome Classification
2020
Nucleosomes are the fundamental repeating unit of chromatin. A nucleosome is an 8 histone proteins complex, in which approximately 147–150 pairs of DNA bases bind. Several biological studies have clearly stated that the regulation of cell type-specific gene activities are influenced by nucleosome positioning. Bioinformatic studies have improved those results showing proof of sequence specificity in nucleosomes’ DNA fragment. In this work, we present a recurrent neural network that uses nucleosome sequence features representation for their classification. In particular, we implement an architecture which stacks convolutional and long short-term memory layers, with the main purpose to avoid t…
CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification
2020
Abstract Background Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. Results In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel …
Assessment of Deep Learning Methodology for Self-Organizing 5G Networks
2019
In this paper, we present an auto-encoder-based machine learning framework for self organizing networks (SON). Traditional machine learning approaches, for example, K Nearest Neighbor, lack the ability to be precisely predictive. Therefore, they can not be extended for sequential data in the true sense because they require a batch of data to be trained on. In this work, we explore artificial neural network-based approaches like the autoencoders (AE) and propose a framework. The proposed framework provides an advantage over traditional machine learning approaches in terms of accuracy and the capability to be extended with other methods. The paper provides an assessment of the application of …
Deep Learning Architectures for DNA Sequence Classification
2016
DNA sequence classification is a key task in a generic computational framework for biomedical data analysis, and in recent years several machine learning technique have been adopted to successful accomplish with this task. Anyway, the main difficulty behind the problem remains the feature selection process. Sequences do not have explicit features, and the commonly used representations introduce the main drawback of the high dimensionality. For sure, machine learning method devoted to supervised classification tasks are strongly dependent on the feature extraction step, and in order to build a good representation it is necessary to recognize and measure meaningful details of the items to cla…
Defining the genomic signature of totipotency and pluripotency during early human development.
2013
The genetic mechanisms governing human pre-implantation embryo development and the in vitro counterparts, human embryonic stem cells (hESCs), still remain incomplete. Previous global genome studies demonstrated that totipotent blastomeres from day-3 human embryos and pluripotent inner cell masses (ICMs) from blastocysts, display unique and differing transcriptomes. Nevertheless, comparative gene expression analysis has revealed that no significant differences exist between hESCs derived from blastomeres versus those obtained from ICMs, suggesting that pluripotent hESCs involve a new developmental progression. To understand early human stages evolution, we developed an undifferentiation netw…
A study of mobility and reachability in ad hoc networks using stochastic activity networks
2006
The integration of ad-hoc networks into real environments is now becoming more and more common and supervision and control systems are no exception. The efficiency of the communication in these networks as well as various other factors, are governed by the working area, the number of nodes, mobility, transmission power, etc. In this paper, the mobility and reachability of mobile nodes appearing spontaneously in a large installation such as can be found in a water purification system are studied. These nodes form an ad-hoc network and communicate between each other in order to finally reach a fixed node which can offer them information from the rest of the system in real time or act as a gat…
Two Levels SPF-Based System to Interconnect Partially Decentralized P2P File Sharing Networks
2005
Partially decentralized P2P (PDP2P) networks are a subset of P2P networks. Roles of nodes are different according to their functionality in the network. Nowadays, there are many PDP2P networks, with different characteristics. It is necessary to find a way to join those autonomous networks. We have not found any interconnection system, so in this article we present a new hierarchical system for interconnecting peers from different PDP2P networks. It will allow sharing data, content and resources between networks. It can be employed between sensor networks, P2P networks, and generally, overlay networks. Oldest superpeers or brokers with higher bandwidth in the PDP2P network will belong to hig…
Optimization of Long-Run Average-Flow Cost in Networks With Time-Varying Unknown Demand
2010
We consider continuous-time robust network flows with capacity constraints and unknown but bounded time-varying demand. The problem of interest is to design a control strategy off-line with no knowledge of the demand realization. Such a control strategy regulates the flow on-line as a function of the realized demand. We address both the case of systems without and with buffers. The main novelty in this work is that we consider a convex cost which is a function of the long-run average-flow and average-demand. We distinguish a worst-case scenario where the demand is the worst-one from a deterministic scenario where the demand has a neutral behavior. The resulting strategies are called min-max…