7,639 research outputs found
Model-free reconstruction of neuronal network connectivity from calcium imaging signals
A systematic assessment of global neural network connectivity through direct
electrophysiological assays has remained technically unfeasible even in
dissociated neuronal cultures. We introduce an improved algorithmic approach
based on Transfer Entropy to reconstruct approximations to network structural
connectivities from network activity monitored through calcium fluorescence
imaging. Based on information theory, our method requires no prior assumptions
on the statistics of neuronal firing and neuronal connections. The performance
of our algorithm is benchmarked on surrogate time-series of calcium
fluorescence generated by the simulated dynamics of a network with known
ground-truth topology. We find that the effective network topology revealed by
Transfer Entropy depends qualitatively on the time-dependent dynamic state of
the network (e.g., bursting or non-bursting). We thus demonstrate how
conditioning with respect to the global mean activity improves the performance
of our method. [...] Compared to other reconstruction strategies such as
cross-correlation or Granger Causality methods, our method based on improved
Transfer Entropy is remarkably more accurate. In particular, it provides a good
reconstruction of the network clustering coefficient, allowing to discriminate
between weakly or strongly clustered topologies, whereas on the other hand an
approach based on cross-correlations would invariantly detect artificially high
levels of clustering. Finally, we present the applicability of our method to
real recordings of in vitro cortical cultures. We demonstrate that these
networks are characterized by an elevated level of clustering compared to a
random graph (although not extreme) and by a markedly non-local connectivity.Comment: 54 pages, 8 figures (+9 supplementary figures), 1 table; submitted
for publicatio
Linking Visual Cortical Development to Visual Perception
Defense Advanced Research Projects Agency and the Office of Naval Research (N00014-95-1-0409); National Science Foundation (IRI-97-20333); Office of Naval Research (N00014-95-1-0657
edge2vec: Representation learning using edge semantics for biomedical knowledge discovery
Representation learning provides new and powerful graph analytical approaches
and tools for the highly valued data science challenge of mining knowledge
graphs. Since previous graph analytical methods have mostly focused on
homogeneous graphs, an important current challenge is extending this
methodology for richly heterogeneous graphs and knowledge domains. The
biomedical sciences are such a domain, reflecting the complexity of biology,
with entities such as genes, proteins, drugs, diseases, and phenotypes, and
relationships such as gene co-expression, biochemical regulation, and
biomolecular inhibition or activation. Therefore, the semantics of edges and
nodes are critical for representation learning and knowledge discovery in real
world biomedical problems. In this paper, we propose the edge2vec model, which
represents graphs considering edge semantics. An edge-type transition matrix is
trained by an Expectation-Maximization approach, and a stochastic gradient
descent model is employed to learn node embedding on a heterogeneous graph via
the trained transition matrix. edge2vec is validated on three biomedical domain
tasks: biomedical entity classification, compound-gene bioactivity prediction,
and biomedical information retrieval. Results show that by considering
edge-types into node embedding learning in heterogeneous graphs,
\textbf{edge2vec}\ significantly outperforms state-of-the-art models on all
three tasks. We propose this method for its added value relative to existing
graph analytical methodology, and in the real world context of biomedical
knowledge discovery applicability.Comment: 10 page
Non-negative mixtures
This is the author's accepted pre-print of the article, first published as M. D. Plumbley, A. Cichocki and R. Bro. Non-negative mixtures. In P. Comon and C. Jutten (Ed), Handbook of Blind Source Separation: Independent Component Analysis and Applications. Chapter 13, pp. 515-547. Academic Press, Feb 2010. ISBN 978-0-12-374726-6 DOI: 10.1016/B978-0-12-374726-6.00018-7file: Proof:p\PlumbleyCichockiBro10-non-negative.pdf:PDF owner: markp timestamp: 2011.04.26file: Proof:p\PlumbleyCichockiBro10-non-negative.pdf:PDF owner: markp timestamp: 2011.04.2
Improved observer dependent perception of weak edges when scanning an image in real time indicated by introducing 1/f noise into the primary visual cortex V1. Theory and experimental support
We present results of a new process for generating 1/f type noise sequences and introducing the noise in the primary visual cortex which then enables improved perception of weak edges when an observer is scanning a complex image in real time to detect detail such as in mammogram reading sessions. It can be explained by an adaptation of information theory for functional rather than previous task-based methods for formulating processes for edge formation in early vision. This is enabled from a two "species" classification of the interaction of opposing on-centre and off-centre neuron processes. We show that non-stationary stochastic resonances predicted by theory can occur with 1/f noise in the primary visual cortex V1 and suggest that signalling exchanges between V1 and the lateral geniculate nucleus (LGN) of the thalamus can initiate neural activity for saccadic action (and observer attention) for weak edge perception. Improvements predicted by our theory were shown from 600 observations by two groups of observers of limited experience and an experienced radiologist for reference (but not for diagnosis). They scanned and rated the definition of microcalcification in clusters separately rated by the experienced radiologist. The results and supporting theory showed dependence on the observer's attention and orderly scanning. Using a compact simplified equipment configuration the methodology has important clinical applications for conjunction searches of features and for detection of objects in poor light conditions for vehicles. Copyright © 2009 ACPSEM
- …