Search results for "NETWORKS"
showing 10 items of 3260 documents
Demo
2017
We present an innovative smartphone-centric tracking system for indoor and outdoor environments, based on the joint utilization of dead-reckoning and computer vision (CV) techniques. The system is explicitly designed for visually impaired people (although it could be easily generalized to other users) and it is built under the assumption that special reference signals, such as painted lines, colored tapes or tactile pavings are deployed in the environment for guiding visually impaired users along pre-defined paths. Thanks to highly optimized software, we are able to execute the CV and sensor-fusion algorithms in run-time on low power hardware such as a normal smartphone, precisely tracking …
Clustering of low-correlated spatial gene expression patterns in the mouse brain in the Allen Brain Atlas
2018
In this paper, clustering techniques are applied to spatial gene expression patterns with a low genomic correlation between the sagittal and coronal projections. The data analysed here are hosted on an available public DB named ABA (Allen Brain Atlas). The results are compared to those obtained by Bohland et al. on the complementary dataset (high correlation values). We prove that, by analysing a reduced dataset,hence reducing the computational burden, we get the same accuracy in highlighting different neuroanatomical region.
Discovering discriminative graph patterns from gene expression data
2016
We consider the problem of mining gene expression data in order to single out interesting features characterizing healthy/unhealthy samples of an input dataset. We present an approach based on a network model of the input gene expression data, where there is a labelled graph for each sample. To the best of our knowledge, this is the first attempt to build a different graph for each sample and, then, to have a database of graphs for representing a sample set. Our main goal is that of singling out interesting differences between healthy and unhealthy samples, through the extraction of "discriminative patterns" among graphs belonging to the two different sample sets. Differently from the other…
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…
Retrieving infinite numbers of patterns in a spin-glass model of immune networks
2013
The similarity between neural and immune networks has been known for decades, but so far we did not understand the mechanism that allows the immune system, unlike associative neural networks, to recall and execute a large number of memorized defense strategies {\em in parallel}. The explanation turns out to lie in the network topology. Neurons interact typically with a large number of other neurons, whereas interactions among lymphocytes in immune networks are very specific, and described by graphs with finite connectivity. In this paper we use replica techniques to solve a statistical mechanical immune network model with `coordinator branches' (T-cells) and `effector branches' (B-cells), a…
Identification of microRNAS differentially regulated by water deficit in relation to mycorrhizal treatment in wheat.
2019
Arbuscular mycorrhizal fungi (AMF) are soil microrganisms that establish symbiosis with plants positively influencing their resistance to abiotic stresses. The aim of this work was to identify wheat miRNAs differentially regulated by water deficit conditions in presence or absence of AMF treatment. Small RNA libraries were constructed for both leaf and root tissues considering four conditions: control (irrigated) or water deficit in presence/absence of mycorrhizal (AMF) treatment. A total of 12 miRNAs were significantly regulated by water deficit in leaves: five in absence and seven in presence of AMF treatment. In roots, three miRNAs were water deficit-modulated in absence of mycorrhizal t…
Analyzing the feasibility of time correlated spectral entropy for the assessment of neuronal synchrony
2016
In this paper, we study neuronal network analysis based on microelectrode measurements. We search for potential relations between time correlated changes in spectral distributions and synchrony for neuronal network activity. Spectral distribution is quantified by spectral entropy as a measure of uniformity/complexity and this measure is calculated as a function of time for the recorded neuronal signals, i.e., time variant spectral entropy. Time variant correlations in the spectral distributions between different parts of a neuronal network, i.e., of concurrent measurements via different microelectrodes, are calculated to express the relation with a single scalar. We demonstrate these relati…
Multiple steady states and the form of response functions to antigen in a model for the initiation of T cell activation
2017
The aim of this paper is to study the qualitative behaviour predicted by a mathematical model for the initial stage of T-cell activation. The state variables in the model are the concentrations of phosphorylation states of the T-cell receptor (TCR) complex and the phosphatase SHP-1 in the cell. It is shown that these quantities cannot approach zero and that the model possesses more than one positive steady state for certain values of the parameters. It can also exhibit damped oscillations. It is proved that the chemical concentration which represents the degree of activation of the cell, that of the maximally phosphorylated form of the TCR complex, is, in general, a non-monotone function of…
Reactome diagram viewer: data structures and strategies to boost performance
2017
Abstract Motivation Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. Results The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partit…
Gene-based and semantic structure of the Gene Ontology as a complex network
2012
The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The information accumulated time-by-time and included in the GO is encoded in the definition of terms and in the setting up of semantic relations amongst terms. This approach might be usefully complemented by a bottom-up approach based on the knowledge of relationships amongst genes. To this end, we investigate the Gene Ontology from a complex network perspective. We consider the semantic network of terms naturally associated with the semantic relationships provided by the Gene Ontology consortium and a gene-based …