41,537 research outputs found
Growing Attributed Networks through Local Processes
This paper proposes an attributed network growth model. Despite the knowledge
that individuals use limited resources to form connections to similar others,
we lack an understanding of how local and resource-constrained mechanisms
explain the emergence of rich structural properties found in real-world
networks. We make three contributions. First, we propose a parsimonious and
accurate model of attributed network growth that jointly explains the emergence
of in-degree distributions, local clustering, clustering-degree relationship
and attribute mixing patterns. Second, our model is based on biased random
walks and uses local processes to form edges without recourse to global network
information. Third, we account for multiple sociological phenomena: bounded
rationality, structural constraints, triadic closure, attribute homophily, and
preferential attachment. Our experiments indicate that the proposed Attributed
Random Walk (ARW) model accurately preserves network structure and attribute
mixing patterns of six real-world networks; it improves upon the performance of
eight state-of-the-art models by a statistically significant margin of 2.5-10x.Comment: 11 pages, 13 figure
A Survey of Adaptive Resonance Theory Neural Network Models for Engineering Applications
This survey samples from the ever-growing family of adaptive resonance theory
(ART) neural network models used to perform the three primary machine learning
modalities, namely, unsupervised, supervised and reinforcement learning. It
comprises a representative list from classic to modern ART models, thereby
painting a general picture of the architectures developed by researchers over
the past 30 years. The learning dynamics of these ART models are briefly
described, and their distinctive characteristics such as code representation,
long-term memory and corresponding geometric interpretation are discussed.
Useful engineering properties of ART (speed, configurability, explainability,
parallelization and hardware implementation) are examined along with current
challenges. Finally, a compilation of online software libraries is provided. It
is expected that this overview will be helpful to new and seasoned ART
researchers
Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
BackgroundSingle-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve.ResultsWe introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods.ConclusionsSlingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression
Genomic analysis of the function of the transcription factor gata3 during development of the Mammalian inner ear
We have studied the function of the zinc finger transcription factor gata3 in auditory system development by analysing temporal profiles of gene expression during differentiation of conditionally immortal cell lines derived to model specific auditory cell types and developmental stages. We tested and applied a novel probabilistic method called the gamma Model for Oligonucleotide Signals to analyse hybridization signals from Affymetrix oligonucleotide arrays. Expression levels estimated by this method correlated closely (p<0.0001) across a 10-fold range with those measured by quantitative RT-PCR for a sample of 61 different genes. In an unbiased list of 26 genes whose temporal profiles clustered most closely with that of gata3 in all cell lines, 10 were linked to Insulin-like Growth Factor signalling, including the serine/threonine kinase Akt/PKB. Knock-down of gata3 in vitro was associated with a decrease in expression of genes linked to IGF-signalling, including IGF1, IGF2 and several IGF-binding proteins. It also led to a small decrease in protein levels of the serine-threonine kinase Akt2/PKB beta, a dramatic increase in Akt1/PKB alpha protein and relocation of Akt1/PKB alpha from the nucleus to the cytoplasm. The cyclin-dependent kinase inhibitor p27(kip1), a known target of PKB/Akt, simultaneously decreased. In heterozygous gata3 null mice the expression of gata3 correlated with high levels of activated Akt/PKB. This functional relationship could explain the diverse function of gata3 during development, the hearing loss associated with gata3 heterozygous null mice and the broader symptoms of human patients with Hearing-Deafness-Renal anomaly syndrome
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