Automated data integration for developmental biological research

In an era exploding with genome-scale data, a major challenge for developmental biologists is how to extract significant clues from these publicly available data to benefit our studies of individual genes, and how to use them to improve our understanding of development at a systems level. Several studies have successfully demonstrated new approaches to classic developmental questions by computationally integrating various genome-wide data sets. Such computational approaches have shown great potential for facilitating research: instead of testing 20,000 genes, researchers might test 200 to the same effect. We discuss the nature and state of this art as it applies to developmental research

A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data

Deducing the structure of neural circuits is one of the central problems of modern neuroscience. Recently-introduced calcium fluorescent imaging methods permit experimentalists to observe network activity in large populations of neurons, but these techniques provide only indirect observations of neural spike trains, with limited time resolution and signal quality. In this work we present a Bayesian approach for inferring neural circuitry given this type of imaging data. We model the network activity in terms of a collection of coupled hidden Markov chains, with each chain corresponding to a single neuron in the network and the coupling between the chains reflecting the network's connectivity matrix. We derive a Monte Carlo Expectation--Maximization algorithm for fitting the model parameters; to obtain the sufficient statistics in a computationally-efficient manner, we introduce a specialized blockwise-Gibbs algorithm for sampling from the joint activity of all observed neurons given the observed fluorescence data. We perform large-scale simulations of randomly connected neuronal networks with biophysically realistic parameters and find that the proposed methods can accurately infer the connectivity in these networks given reasonable experimental and computational constraints. In addition, the estimation accuracy may be improved significantly by incorporating prior knowledge about the sparseness of connectivity in the network, via standard L$_1$ penalization methods.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS303 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

MORPH: A Reference Architecture for Configuration and Behaviour Self-Adaptation

An architectural approach to self-adaptive systems involves runtime change of system configuration (i.e., the system's components, their bindings and operational parameters) and behaviour update (i.e., component orchestration). Thus, dynamic reconfiguration and discrete event control theory are at the heart of architectural adaptation. Although controlling configuration and behaviour at runtime has been discussed and applied to architectural adaptation, architectures for self-adaptive systems often compound these two aspects reducing the potential for adaptability. In this paper we propose a reference architecture that allows for coordinated yet transparent and independent adaptation of system configuration and behaviour

Efficient variational quantum simulator incorporating active error minimisation

One of the key applications for quantum computers will be the simulation of other quantum systems that arise in chemistry, materials science, etc, in order to accelerate the process of discovery. It is important to ask: Can this be achieved using near future quantum processors, of modest size and under imperfect control, or must it await the more distant era of large-scale fault-tolerant quantum computing? Here we propose a variational method involving closely integrated classical and quantum coprocessors. We presume that all operations in the quantum coprocessor are prone to error. The impact of such errors is minimised by boosting them artificially and then extrapolating to the zero-error case. In comparison to a more conventional optimised Trotterisation technique, we find that our protocol is efficient and appears to be fundamentally more robust against error accumulation.Comment: 13 pages, 5 figures; typos fixed and small update