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On the Natural Hierarchical Composition of Cliques in Cell Assemblies

Thomas Wennekers
2009 Cognitive Computation  
Hebbian cell assemblies can be formalised as sets of tightly connected cells in auto-and hetero-associative memories.  ...  The excitatory cells can further learn incrementally using a Hebbian coincidence learning rule. Implications of the model for retrieval in auto-associative memories are further outlined.  ...  Acknowledgement The author acknowledges support by the Engineering and Physical Sciences Research Council (grant EP/ C010841/1, COLAMN-A Novel Computing Architecture for Cognitive Systems based on the  ... 
doi:10.1007/s12559-008-9004-5 fatcat:5mi46cjcivh6xd6s63tu3spyiu

Automated deep lineage tree analysis using a Bayesian single cell tracking approach [article]

Kristina Ulicna, Giulia Vallardi, Guillaume Charras, Alan R Lowe
2020 bioRxiv   pre-print
Here, we developed an open-source Python library, btrack, to facilitate retrieval of deep lineage information from live-cell imaging data.  ...  We acquired 3,500 hours of time-lapse microscopy data of epithelial cells in culture and used our software to extract 22,519 fully annotated single-cell trajectories.  ...  A graph-based search is used to then assemble the tracks into lineage trees, and propagate lineage information such as generational depth, parent and root IDs.  ... 
doi:10.1101/2020.09.10.276980 fatcat:xszglctzznfzbdtqkdc74thnuy

Representing and Analysing Molecular and Cellular Function Using the Computer

Jacques van Helden, Avi Naim, Renato Mancuso, Mattew Eldridge, Lorenz Wernisch, David Gilbert, Shoshana J. Wodak
2000 Biological chemistry  
Determining the biological function of a myriad of genes, and understanding how they interact to yield a living cell, is the major challenge of the post genome-sequencing era.  ...  In a second part, we present a new general data model, currently under development, which describes information on molecular function and cellular processes in a rigorous manner.  ...  useful discussion.  ... 
doi:10.1515/bc.2000.113 pmid:11076023 fatcat:4va2kv2abbfbdonv2yaitu7dj4

Finding gene regulatory network candidates using the gene expression knowledge base

Aravind Venkatesan, Sushil Tripathi, Alejandro Sanz de Galdeano, Ward Blondé, Astrid Lægreid, Vladimir Mironov, Martin Kuiper
2014 BMC Bioinformatics  
We show how a combination of specific query definitions and additional selection criteria derived from gene expression data and prior knowledge concerning candidate proteins can be used to retrieve a set  ...  This work illustrates how GeXKB can be used in combination with gene expression results and literature information to identify new potential candidates that may be considered for extending a gene regulatory  ...  Acknowledgements Technical support was provided by the High-Performance Computing team at the Norwegian University of Science and Technology. The work was supported by The Norwegian Cancer Society.  ... 
doi:10.1186/s12859-014-0386-y pmid:25490885 pmcid:PMC4279962 fatcat:s2he2zgr3bbflg36gq2yl2qi5i

Post and pre-compensatory Hebbian learning for categorisation

Christian R. Huyck, Ian G. Mitchell
2014 Cognitive Neurodynamics  
A novel compensatory Hebbian learning algorithm is used that considers the total synaptic weight coming into a neuron. The network is unsupervised and entirely self-organising.  ...  A system with some degree of biological plausibility is developed to categorise items from a widely used machine learning benchmark.  ...  Acknowledgments Thanks to Zhijun Yang and Dan Diaper for comments on this paper.  ... 
doi:10.1007/s11571-014-9282-4 pmid:25009672 pmcid:PMC4079900 fatcat:3iud2kjc2fdvbh6zyxd2e7qspa

Redundancy gain in semantic categorisation

Peter Shepherdson, Jeff Miller
2014 Acta Psychologica  
of a single stimulus.  ...  I am also thankful to the Department of Psychology at the University of Otago for providing an ideal working environment, and to the Government and taxpayers of New Zealand for indirectly funding my study  ...  Acknowledgements Given the horror stories one sometimes hears about completing a PhD thesis, I found conducting and writing up the following experiments to be a surprisingly enjoyable experience.  ... 
doi:10.1016/j.actpsy.2014.01.011 pmid:24508611 fatcat:zn3gng7fx5dh5krpkmd5oe3dpi

E-Branding: A New Approach for Promoting Polyhouse

Sudeepthi Govathoti, Deepthi Kamidi, N.Thirupathi Rao, Debnath Bhattacharyya, Hye-jin Kim
2017 International Journal of u- and e- Service, Science and Technology  
The polyhouse information is collected from different resources by using sampling method.  ...  In the current work we considered and proposed a framework which could able to collect the information related to polyhouse atmosphere and harvest status and manage the polyhouse automatically based on  ...  Latent Semantic Indexing Latent linguistics categorisation (LSI) is a categorisation and retrieval methodology that victimisation one mathematical technique that known as singular price decomposition (  ... 
doi:10.14257/ijunesst.2017.10.10.01 fatcat:233yenvo5bdkdhvzij7azdasbu

RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)

Joey Ee Uli, Christina Seok Yien Yong, Swee Keong Yeap, Jeffrine J. Rovie-Ryan, Nurulfiza Mat Isa, Soon Guan Tan, Noorjahan Banu Alitheen
2017 PeerJ  
This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing  ...  Enriched Immune system pathways include Platelet activation pathway, Antigen processing and presentation, B cell receptor signalling pathway, and Intestinal immune network for IgA production.  ...  ADDITIONAL INFORMATION AND DECLARATIONS Funding This research was supported by Research University Grant Scheme (Project No: GP-IPB/2013/9413602) provided by Universiti Putra Malaysia, Malaysia.  ... 
doi:10.7717/peerj.3566 pmid:28828235 pmcid:PMC5563440 fatcat:r5b73ddwlzccxajgx7jsuwuryq

Understanding the Exacerbating Role of the Metalloproteinase Meprin during AKI, an In Silico Approach

Deepyan Chatterjee
2016 International Letters of Natural Sciences  
The data obtained using literature search from PubMed and interaction networks analysis software STRING strongly support the concept that meprin acts as a major matrix degrading enzyme in the kidney, and  ...  The present study discerns the structure of meprin alpha subunit using in silico tools SWISS-MODE, Phyre2 web server and identify the active site and critical amino acid residues in the active site using  ...  , analysis and druggability assessment were used. 4) Interaction networks analysis: A list of protein-protein interaction and substrates for meprin was obtained using STRING (Search Tool for the Retrieval  ... 
doi:10.18052/www.scipress.com/ilns.57.18 fatcat:hykadn5lsfecjmzs72ubda4de4

Offline handwritten mathematical symbol recognition utilising deep learning [article]

Azadeh Nazemi, Niloofar Tavakolian, Donal Fitzpatrick, Chandrik a Fernando, Ching Y. Suen
2019 arXiv   pre-print
intensity of raw image for 66 classes. 87 classes using modified LeNet represents 90% accuracy.  ...  This paper initially addresses the issue regarding segmentation using Simple Linear Iterative Clustering (SLIC).  ...  Recognition uses a modified LeNet network and of pre-trained SqueezeNet.  ... 
arXiv:1910.07395v1 fatcat:ld6i4awluvextoyjdqzfhtgfva

Assessing nanotechnology potentials: interplay between the paths of knowledge evolution and the patterns of competence building

Alfonso Ávila Robinson, Kumiko Miyazaki
2014 International Journal of Technology Intelligence and Planning (IJTIP)  
To analyse the case, this research makes use of intensive bibliometric and social network methods based on scientific publications.  ...  A series of implications for policy makers and researchers on the critical role of micro and nanofabrication technologies within the N&N field will be described in this paper.  ...  For the construction of the collapsed network, the sum of the interactions between and within the different technological categorisations was used.  ... 
doi:10.1504/ijtip.2014.066709 fatcat:nvbd5o2q4jhqppbyulmwlln2tq

Oncogenes and pathway identification using filter-based approaches between various carcinoma types in lung

Mahesh Visvanathan, Michael Netzer, Michael Seger, Bhargav S. Adagarla, Christian Baumgartner, Sitta Sittampalam, Gerald H. Lushington
2009 International Journal of Computational Biology and Drug Design  
The IG lacked the ability to clearly categorise genes into the proposed scheme when using the clustering approach (Figure 3) , resulting in a high number of primary genes (2531 Visvanathan et al.  ...  Second, feature-selection-based Particle Swarm Optimisation (PSO), Information Gain (IG) and the Biomarker Identifier (BMI) for the identification of different types of lung cancer were used.  ...  Acknowledgments This publication was made possible by grant number P20 RR016475 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH) and the Austrian  ... 
doi:10.1504/ijcbdd.2009.030115 pmid:20090162 pmcid:PMC2825752 fatcat:prldp5ja6ve3fgxcwiozheqthq

Distributed Architecture for Intelligent Robotic Assembly Part III: Design of the Invariant Object Recognition System [chapter]

Mario Pena, Ismael Lopez
2006 Manufacturing the Future  
This interdisciplinary and comprehensive volume, consisting of 30 chapters, covers a survey of trends in distributed manufacturing, modern manufacturing equipment, product design process, rapid prototyping  ...  , quality assurance, from technological and organisational point of view and aspects of supply chain management.  ...  The table shows the results for 18 assembly cycles using the vision system and the assembly system of the cell.  ... 
doi:10.5772/5056 fatcat:u3dxua7rcjadlgunqferqdfvei

Network integration and graph analysis in mammalian molecular systems biology

A. Ma'ayan
2008 IET Systems Biology  
interactions, metabolic, generegulation and cell-signalling networks.  ...  A first step towards assembling this 3D puzzle is identifying protein-protein interactions, their localisation and the functional relationship among the components [5] .  ...  Text mining is used to extract interactions using natural language processing (NLP) and information retrieval technologies [86] .  ... 
doi:10.1049/iet-syb:20070075 pmid:19045817 pmcid:PMC2745214 fatcat:t55zchkczrfflpdeolrf7wxn2y

A review of cell assemblies

Christian R. Huyck, Peter J. Passmore
2013 Biological cybernetics  
Since the Cell Assembly (CA) was hypothesised, it has gained substantial support and is believed to be the neural basis of psychological concepts.  ...  A range of models have been used to simulate CA behaviour including associative memory and more process oriented tasks such as natural language parsing.  ...  CAs have been used as the model of the basic categorising unit in networks that categorise visual input (Bogacz, 2007) .  ... 
doi:10.1007/s00422-013-0555-5 pmid:23559034 fatcat:hy2mcv25vjbbzm4sgqannuezzm
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