Accelerated parallel algorithm for gene network reverse engineering

CNET: an algorithm for Reverse Engineering of Causal Gene Networks

We present a novel Reverse Engineering algorithm, CNET, to reconstruct Gene Regulatory Networks from microarray time series data. CNET can be considered an improvement of the Mutual Information approach, present in the REVEAL [5] algorithm, with an innovative scoring function, to cope with noise, quantization errors and gene characteristic transcription delays. We tested the algorithm on simula...

Reverse Engineering of Network Software Binary Codes for Identification of Syntax and Semantics of Protocol Messages

Reverse engineering of network applications especially from the security point of view is of high importance and interest. Many network applications use proprietary protocols which specifications are not publicly available. Reverse engineering of such applications could provide us with vital information to understand their embedded unknown protocols. This could facilitate many tasks including d...

Combining multiple results of a reverse-engineering algorithm: application to the DREAM five-gene network challenge.

The output of reverse-engineering methods for biological networks is often not a single network prediction, but an ensemble of networks that are consistent with the experimentally measured data. In this paper, we consider the problem of combining the information contained within such an ensemble in order to (1) make more accurate network predictions and (2) estimate the reliability of these pre...

Algorithm Engineering for Parallel Computation

The emerging discipline of algorithm engineering has primarily focussed on transforming pencil-and-paper sequential algorithms into robust, efficient, well tested, and easily used implementations. As parallel computing becomes ubiquitous, we need to extend algorithm engineering techniques to parallel computation. Such an extension adds significant complications. After a short review of algorith...

Reverse engineering the ovine gene network under Psoroptes Ovis infestation