MOTIVATION: A digenic genetic interaction (GI) is observed when mutations in two genes within the same organism yield a phenotype that is different from the expected, given each mutation's individual effects. While multiplicative scoring is widely applied to define GIs, revealing underlying gene functions, it remains unclear if it is the most suitable choice for scoring GIs in Escherichia coli. Here, we assess many different definitions, including the multiplicative model, for mapping functional links between genes and pathways in E.coli. RESULTS: Using our published E.coli GI datasets, we show computationally that a machine learning Gaussian process (GP)-based definition better identifies functional associations among genes than a multiplicative model, which we have experimentally confirmed on a set of gene pairs. Overall, the GP definition improves the detection of GIs, biological reasoning of epistatic connectivity, as well as the quality of GI maps in E.coli, and, potentially, other microbes. AVAILABILITY AND IMPLEMENTATION: The source code and parameters used to generate the machine learning models in WEKA software were provided in the Supplementary information. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Passive star-coupled optical interconnects with wavelength-division multiplexing hold a strong potential for realizing flexible large-scale multicomputer networks. Virtual point-to-point regular connectivities can be defined and modified in a network with broadcast-select routing via distributed wavelength assignment to the nodes. The system size in this approach is bound by the number of separable wavelength channels. The paper proposes a network class that achieves scalability by grouping the nodes into clusters and employing a separate pair of broadcast and select couplers with each cluster. Interconnecting the clusters according to a regular topology results in a modular architecture with reconfigurable partitions and significantly reduced fiber link density. This approach efficiently combines wavelength-division with direct space interconnection, taking advantage of the properties of each. For the topologies of most significance to parallel computing, the paper studies conflict-free wavelength assignment that maximizes spatial reuse, identifies the valid network partitions, and evaluates the fiber link density and both space and wavelength channel throughput improvement. The results show that cube and shuffle networks take most advantage of the proposed approach in terms of maximizing wavelength reuse.>

A passive optical realization of large expandable shuffle networks is considered, where the general (p, k) shuffle function interconnects star-coupled clusters of time and/or wavelength multiplexed nodes. This configuration enables network partitioning into independent subnetworks that can emulate various indirect cube topologies on a virtual point-to-point basis. Node transmitters are assigned fixed channels and reconfiguring the partition and/or the individual sub-network topologies is achieved by monitoring the appropriate channels. The considered network configuration can function as a general-purpose optical interconnect for a variety of heterogeneous traffic sources, such as multicomputers and ATM network interface units, communicating independently within logically defined subnetworks. The paper derives a conflict-free channel partition and assignment map for a general (p, k) cluster shuffle using a minimal number of channel sets.

The above paper by L. Bhuyan and D.P. Agrawal (1984) described a hierarchical, all-optical wavelength division multiplexed (WDM) network that is being built to support the communication requirements of a large distributed shared memory system. Dynamically adaptable bandwidth allocation is supported, both within and between levels of the hierarchy, and is highly scalable through wavelength re-use at each hierarchical level. The mixed radix scheme introduced was used for processor numbering, but was not specified. The system was described in term of a time multiplexed access protocol, generalized to the multichannel WDM environment, which has static slot assignment that provides excellent throughput but long latencies due to cycle synchronization. The actual system implementation will use a hybrid WDMA strategy, which is collisionless, provides low latency support, dynamic bandwidth allocation within a hierarchical level, and a fast reliable broadcast.>

This paper introduces a hierarchical optical structure for processor interconnection and evaluates its performance. The architecture is based on wavelength division multiplexing (WDM) which enables multiple multi-access channels to be realized on a single optical fiber. The objective of the hierarchical architecture is to achieve scalability yet avoid the requirement of multiple wavelength tunable devices per node as with the WDM-based hypercube interconnection scheme. Furthermore, single-hop communication is achieved: a packet remains in the optical form from source to destination and does not require cross dimensional intermediate routing. The wavelength multiplexed hierarchical structure features wavelength channel re-use at each level, allowing scalability to very large system sizes. It employs acousto-optic tunable filters in conjunction with passive couplers to partition the traffic between different levels of the hierarchy without electronic intervention. A significant advantage of the proposed structure is its ability to dynamically vary the bandwidth provided to different levels of the hierarchy. The architecture is compared to a wavelength-flat architecture in terms of physical and performance scalability.>

Introduces two hierarchical optical structures for processor interconnection and compares their performance through analytic models and discrete-event simulation. Both architectures are based on wavelength division multiplexing (WDM) which enables multiple multi-access channels to be realized on a single optical fiber. The objective of the hierarchical architectures is to achieve scalability yet avoid the requirement of multiple wavelength tunable devices per node. Furthermore, both hierarchical architectures are single-hop: a packet remains in the optical form from source to destination and does not require cross dimensional intermediate routing.>