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Improving gene-network inference with graph-wavelets and making insights about ageing associated regulatory changes in lungs [article]

Shreya Mishra, Vibhor Kumar
2020 bioRxiv   pre-print
Here we devise a conceptually different method using graph-wavelet filters for improving gene-network (GWNet) based analysis of the transcriptome.  ...  Using gene-regulatory-networks based approach for single-cell expression profiles can reveal unprecedented details about the effects of external and internal stress on cells.  ...  ACKNOWLEDGEMENTS We thank Dr Gaurav Ahuja for providing us valuable advice on analysis of single-cell expression profile of ageing cells. Conflict of interest statement. None declared.  ... 
doi:10.1101/2020.07.24.219196 fatcat:rww7gelmojd5zihj3p4ciyleby

Text Analysis Using Different Graph-Based Representations

Esteban Castillo Juarez, Ofelia Cervantes Villagómez, Darnes Vilariño Ayala
2018 Journal of Computacion y Sistemas  
The core of this manuscript is to highlight the importance of enriched/non-enriched co-occurrence graphs as an alternative to traditional features representation models like vector representation, where  ...  For each text classification task the type of graph created as well as the benefits of using it are presented and discussed.  ...  The authors would also like to thank Daniel Macías Galindo and David Báez López for their invaluable help reviewing this manuscript.  ... 
doi:10.13053/cys-21-4-2551 fatcat:oheaazjd4fabdayuehpfvpg65e


I. Elachkar, H. Ouzif, H. Labriji
2020 The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences  
Whatever the user profile model used, it's updating and enrichment is a very essential step in the information research process in order to obtain more interesting and satisfactory results, which lead  ...  In this paper, we propose a new approach to express the similarity between users profiles by developing a structural similarity measure to calculate the similarity between user profiles based on SimRank  ...  to apply the SimRank measure on user profiles in order to study the similarity between them using a weighted bipartite graph.  ... 
doi:10.5194/isprs-archives-xliv-4-w3-2020-203-2020 fatcat:m54skprz6bc6fiqyfbvbiae7im

Comparison of single gene and module-based methods for modeling gene regulatory networks [article]

Mikel Hernaez, Olivier Gevaert
2018 bioRxiv   pre-print
We also perform a topological and gene set enrichment analysis and compare several module-based approaches to single gene network approaches where a graph is built from the gene expression profiles without  ...  First, modules are created iteratively using a regression approach that links co-expressed genes with few regulatory genes.  ...  profile of a given target gene, that gene is removed from the graph.  ... 
doi:10.1101/307884 fatcat:u2iebublbzbgbkr3rsfoiwzmkq

Towards the Modelling of Veillance based Citizen Profiling using Knowledge Graphs

Siraj Munir, Syed Imran Jami, Shaukat Wasi
2021 Open Computer Science  
For representation of Citizen Profile Temporal Knowledge Graph has been used through which we can answer semantic queries.  ...  In this work we have proposed a model for Citizen Profiling. It uses veillance (Surveillance and Sousveillance) for data acquisition.  ...  Song and Park [56] proposed a Knowledge Graph enrichment scheme, based on translation-based embedding.  ... 
doi:10.1515/comp-2020-0209 fatcat:zay5zfuhkvfdfnzoxe353pjpa4

Experimental assessment of the TARGET adaptive ontology-based Web search framework

Nicolas Guelfi, Cedric Pruski, Chantal Reynaud
2010 2010 10th Annual International Conference on New Technologies of Distributed Systems (NOTERE)  
This is done first by introducing the TARGET approach. We will briefly present the used ontologies and their ability to adapt to domain evolution.  ...  Finding relevant information on the Web can be a complex task for most of the users.  ...  Such an approach has been proposed in [6] where the authors build a profile of the user based on information related to his Web navigation history. The approach proposed by Liu et al.  ... 
doi:10.1109/notere.2010.5536622 dblp:conf/notere/GuelfiPR10 fatcat:omb54p3q7ffexbyyc4hkylpv4e

A Case Study on the Influence of the User Profile Enrichment on Buzz Propagation in Social Media: Experiments on Delicious [chapter]

Manel Mezghani, Sirinya On-at, André Péninou, Marie-Françoise Canut, Corinne Amel Zayani, Ikram Amous, Florence Sedes
2015 Communications in Computer and Information Science  
We will use the result of our previous work on dynamic user profile enrichment in order to analyse the influence of this enrichment in the buzz propagation. 3)we analyse each enriched user profile in order  ...  to show if the enrichment approach anticipate the buzz propagation.  ...  It represents, for each tag, its popularity (number of use) in Delicious and its use in enriching profiles (number of times it is used to enrich a profile) The graphs above show that the studied tags are  ... 
doi:10.1007/978-3-319-23201-0_57 fatcat:ibkiwblcenh43m4iffq6ionhiq

Graph Representation Learning on Tissue-Specific Multi-Omics [article]

Amine Amor
2021 arXiv   pre-print
In this study, we leverage a graph embedding model (i.e VGAE) to perform link prediction on tissue-specific Gene-Gene Interaction (GGI) networks.  ...  Our evaluation shows that the integration of gene methylation profiles and RNA-sequencing data significantly improves the link prediction performance.  ...  The first step consists of training two separate GCN (Graph Convolutional Neural Network) encoders on a GGI network enriched with RNA sequencing data and a GGI network enriched with gene methylation data  ... 
arXiv:2107.11856v1 fatcat:5pb2e3h3jrcx5l7sxo4muzkqb4

On the performance of de novo pathway enrichment

Richa Batra, Nicolas Alcaraz, Kevin Gitzhofer, Josch Pauling, Henrik J. Ditzel, Marc Hellmuth, Jan Baumbach, Markus List
2017 npj Systems Biology and Applications  
De novo pathway enrichment is a powerful approach to discover previously uncharacterized molecular mechanisms in addition to already known pathways.  ...  We identified 19 tools and selected seven representative candidates for a comparative analysis with more than 12,000 runs, spanning different biological networks, molecular profiles, and parameters.  ...  ACKNOWLEDGEMENTS The research is supported in part by Villum foundation, ERC grant 676858-IMCIS, and the National Experimental Therapy Partnership (NEXT), which is financed by a grant from Innovation Fund  ... 
doi:10.1038/s41540-017-0007-2 pmid:28649433 pmcid:PMC5445589 fatcat:654syyw725fv7kmdacgz72ucfq


A. Famili
2015 Intelligent Data Analysis  
To evaluate the performance of their proposed approach the authors use real data sets from a US website.  ...  The authors propose a new algorithm for a logic-based alerts correlation approach that integrates domain knowledge into the entire filtering process.  ... 
doi:10.3233/ida-140692 fatcat:h3uw3s2nzjgxzcb6boywt3xxaa

Capturing single-cell heterogeneity via data fusion improves image-based profiling

Mohammad H. Rohban, Hamdah S. Abbasi, Shantanu Singh, Anne E. Carpenter
2019 Nature Communications  
a gene's pathway.  ...  Here, we summarize cell populations by adding features' dispersion and covariances to population averages, in the context of image-based profiling.  ...  Acknowledgements The authors gratefully acknowledge contributions from members of the Carpenter laboratory, Ted Natoli, Lev Litichevskiy, Rajiv Narayan, and Karthik Shekhar for their helpful feedback.  ... 
doi:10.1038/s41467-019-10154-8 pmid:31064985 pmcid:PMC6504923 fatcat:p2mw46hzjrarlaztf4p4dphdvy

TuBA: Tunable Biclustering Algorithm Reveals Clinically Relevant Tumor Transcriptional Profiles in Breast Cancer [article]

Amartya Singh, Gyan Bhanot, Hossein Khiabanian
2018 bioRxiv   pre-print
We propose a Tunable Biclustering Algorithm (TuBA) based on a novel pairwise proximity measure among gene pairs, which examines the relationship of samples at the extremes of genes' expression profiles  ...  Robust biclusters are then identified in these graphs iteratively.  ...  Moreover, the graph-based approach allows us to infer the relative importance of each gene within a bicluster, based on its degree.  ... 
doi:10.1101/245712 fatcat:xyal3ytdtrcmzmplxpiy6ar4wm

Dynamic enrichment of social users' interests

Manel Mezghani, Corinne Amel Zayani, Ikram Amous, Andre Peninou, Florence Sedes
2014 2014 IEEE Eighth International Conference on Research Challenges in Information Science (RCIS)  
In this paper, we propose a new approach for enriching the user profile in an evolutionary environment such as a social network.  ...  The originality of our approach relies on combining information tags, users and resources in a way that guarantees a better enrichment for the social user profile.  ...  ACKNOWLEDGMENT The authors would like to thank Souha Bouhali for participating to this work.  ... 
doi:10.1109/rcis.2014.6861066 dblp:conf/rcis/MezghaniZAPS14 fatcat:gg24ki36org25pq2yar2vpy7yy

Capturing single-cell heterogeneity via data fusion improves image-based profiling [article]

Mohammad Hossein Rohban, Shantanu Singh, Anne E Carpenter
2018 bioRxiv   pre-print
) and a gene's pathway.  ...  Here, we summarize cell populations by adding features' dispersion and covariances to population averages, in the context of image-based profiling.  ...  A graph diffusion process then is used to combine the graph for each data type into the final network, which encodes the pairwise similarity values.  ... 
doi:10.1101/328542 fatcat:3yixlomupfcyfj4sjqkhz5s2re

Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment

Tamasin N Doig, David A Hume, Thanasis Theocharidis, John R Goodlad, Christopher D Gregory, Tom C Freeman
2013 BMC Genomics  
Results: Using a novel 3D network-based approach we have analysed six large human cancer microarray datasets derived from more than 1,000 individuals.  ...  were also found to be largely conserved in a number of independent datasets.  ...  Acknowledgements This work was funded by Leukaemia Research and The Roslin Institute is supported by a BBSRC Institute Strategic Programme Grant.  ... 
doi:10.1186/1471-2164-14-469 pmid:23845084 pmcid:PMC3721986 fatcat:4rqromfwefhttj4envlpsp2mia
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