233 research outputs found
Incremental Mutual Information: A New Method for Characterizing the Strength and Dynamics of Connections in Neuronal Circuits
Understanding the computations performed by neuronal circuits requires characterizing the strength and dynamics of the connections between individual neurons. This characterization is typically achieved by measuring the correlation in the activity of two neurons. We have developed a new measure for studying connectivity in neuronal circuits based on information theory, the incremental mutual information (IMI). By conditioning out the temporal dependencies in the responses of individual neurons before measuring the dependency between them, IMI improves on standard correlation-based measures in several important ways: 1) it has the potential to disambiguate statistical dependencies that reflect the connection between neurons from those caused by other sources (e. g. shared inputs or intrinsic cellular or network mechanisms) provided that the dependencies have appropriate timescales, 2) for the study of early sensory systems, it does not require responses to repeated trials of identical stimulation, and 3) it does not assume that the connection between neurons is linear. We describe the theory and implementation of IMI in detail and demonstrate its utility on experimental recordings from the primate visual system
On directed information theory and Granger causality graphs
Directed information theory deals with communication channels with feedback.
When applied to networks, a natural extension based on causal conditioning is
needed. We show here that measures built from directed information theory in
networks can be used to assess Granger causality graphs of stochastic
processes. We show that directed information theory includes measures such as
the transfer entropy, and that it is the adequate information theoretic
framework needed for neuroscience applications, such as connectivity inference
problems.Comment: accepted for publications, Journal of Computational Neuroscienc
Fractional quantum Hall effect in a quantum point contact at filling fraction 5/2
Recent theories suggest that the excitations of certain quantum Hall states
may have exotic braiding statistics which could be used to build topological
quantum gates. This has prompted an experimental push to study such states
using confined geometries where the statistics can be tested. We study the
transport properties of quantum point contacts (QPCs) fabricated on a
GaAs/AlGaAs two dimensional electron gas that exhibits well-developed
fractional quantum Hall effect, including at bulk filling fraction 5/2. We find
that a plateau at effective QPC filling factor 5/2 is identifiable in point
contacts with lithographic widths of 1.2 microns and 0.8 microns, but not 0.5
microns. We study the temperature and dc-current-bias dependence of the 5/2
plateau in the QPC, as well as neighboring fractional and integer plateaus in
the QPC while keeping the bulk at filling factor 3. Transport near QPC filling
factor 5/2 is consistent with a picture of chiral Luttinger liquid edge-states
with inter-edge tunneling, suggesting that an incompressible state at 5/2 forms
in this confined geometry
Microwave studies of the fractional Josephson effect in HgTe-based Josephson junctions
The rise of topological phases of matter is strongly connected to their
potential to host Majorana bound states, a powerful ingredient in the search
for a robust, topologically protected, quantum information processing. In order
to produce such states, a method of choice is to induce superconductivity in
topological insulators. The engineering of the interplay between
superconductivity and the electronic properties of a topological insulator is a
challenging task and it is consequently very important to understand the
physics of simple superconducting devices such as Josephson junctions, in which
new topological properties are expected to emerge. In this article, we review
recent experiments investigating topological superconductivity in topological
insulators, using microwave excitation and detection techniques. More
precisely, we have fabricated and studied topological Josephson junctions made
of HgTe weak links in contact with two Al or Nb contacts. In such devices, we
have observed two signatures of the fractional Josephson effect, which is
expected to emerge from topologically-protected gapless Andreev bound states.
We first recall the theoretical background on topological Josephson junctions,
then move to the experimental observations. Then, we assess the topological
origin of the observed features and conclude with an outlook towards more
advanced microwave spectroscopy experiments, currently under development.Comment: Lectures given at the San Sebastian Topological Matter School 2017,
published in "Topological Matter. Springer Series in Solid-State Sciences,
vol 190. Springer
Beyond element-wise interactions: identifying complex interactions in biological processes
Background: Biological processes typically involve the interactions of a number of elements (genes, cells) acting on each others. Such processes are often modelled as networks whose nodes are the elements in question and edges pairwise relations between them (transcription, inhibition). But more often than not, elements actually work cooperatively or competitively to achieve a task. Or an element can act on the interaction between two others, as in the case of an enzyme controlling a reaction rate. We call “complex” these types of interaction and propose ways to identify them from time-series observations.
Methodology: We use Granger Causality, a measure of the interaction between two signals, to characterize the influence of an enzyme on a reaction rate. We extend its traditional formulation to the case of multi-dimensional signals in order to capture group interactions, and not only element interactions. Our method is extensively tested on simulated data and applied to three biological datasets: microarray data of the Saccharomyces cerevisiae yeast, local field potential recordings of two brain areas and a metabolic reaction.
Conclusions: Our results demonstrate that complex Granger causality can reveal new types of relation between signals and is particularly suited to biological data. Our approach raises some fundamental issues of the systems biology approach since finding all complex causalities (interactions) is an NP hard problem
Ballistic Josephson junctions in edge-contacted graphene
Hybrid graphene-superconductor devices have attracted much attention since
the early days of graphene research. So far, these studies have been limited to
the case of diffusive transport through graphene with poorly defined and modest
quality graphene-superconductor interfaces, usually combined with small
critical magnetic fields of the superconducting electrodes. Here we report
graphene based Josephson junctions with one-dimensional edge contacts of
Molybdenum Rhenium. The contacts exhibit a well defined, transparent interface
to the graphene, have a critical magnetic field of 8 Tesla at 4 Kelvin and the
graphene has a high quality due to its encapsulation in hexagonal boron
nitride. This allows us to study and exploit graphene Josephson junctions in a
new regime, characterized by ballistic transport. We find that the critical
current oscillates with the carrier density due to phase coherent interference
of the electrons and holes that carry the supercurrent caused by the formation
of a Fabry-P\'{e}rot cavity. Furthermore, relatively large supercurrents are
observed over unprecedented long distances of up to 1.5 m. Finally, in the
quantum Hall regime we observe broken symmetry states while the contacts remain
superconducting. These achievements open up new avenues to exploit the Dirac
nature of graphene in interaction with the superconducting state.Comment: Updated version after peer review. Includes supplementary material
and ancillary file with source code for tight binding simulation
Quantum oscillations of the critical current and high-field superconducting proximity in ballistic graphene
Graphene-based Josephson junctions provide a novel platform for studying the
proximity effect due to graphene's unique electronic spectrum and the
possibility to tune junction properties by gate voltage. Here we describe
graphene junctions with a mean free path of several micrometres, low contact
resistance and large supercurrents. Such devices exhibit pronounced
Fabry-P\'erot oscillations not only in the normal-state resistance but also in
the critical current. The proximity effect is mostly suppressed in magnetic
fields below 10mT, showing the conventional Fraunhofer pattern. Unexpectedly,
some proximity survives even in fields higher than 1 T. Superconducting states
randomly appear and disappear as a function of field and carrier concentration,
and each of them exhibits a supercurrent carrying capacity close to the
universal quantum limit. We attribute the high-field Josephson effect to
mesoscopic Andreev states that persist near graphene edges. Our work reveals
new proximity regimes that can be controlled by quantum confinement and
cyclotron motion
Recursive regularization for inferring gene networks from time-course gene expression profiles
<p>Abstract</p> <p>Background</p> <p>Inferring gene networks from time-course microarray experiments with vector autoregressive (VAR) model is the process of identifying functional associations between genes through multivariate time series. This problem can be cast as a variable selection problem in Statistics. One of the promising methods for variable selection is the elastic net proposed by Zou and Hastie (2005). However, VAR modeling with the elastic net succeeds in increasing the number of true positives while it also results in increasing the number of false positives.</p> <p>Results</p> <p>By incorporating relative importance of the VAR coefficients into the elastic net, we propose a new class of regularization, called recursive elastic net, to increase the capability of the elastic net and estimate gene networks based on the VAR model. The recursive elastic net can reduce the number of false positives gradually by updating the importance. Numerical simulations and comparisons demonstrate that the proposed method succeeds in reducing the number of false positives drastically while keeping the high number of true positives in the network inference and achieves two or more times higher true discovery rate (the proportion of true positives among the selected edges) than the competing methods even when the number of time points is small. We also compared our method with various reverse-engineering algorithms on experimental data of MCF-7 breast cancer cells stimulated with two ErbB ligands, EGF and HRG.</p> <p>Conclusion</p> <p>The recursive elastic net is a powerful tool for inferring gene networks from time-course gene expression profiles.</p
- …