NETGEM: Network Embedded Temporal GEnerative Model for gene expression data

Background: Temporal analysis of gene expression data has been limited to identifying genes whose expression varies with time and/or correlation between genes that have similar temporal profiles. Often, the methods do not consider the underlying network constraints that connect the genes. It is becoming increasingly evident that interactions change substantially with time. Thus far, there is no systematic method to relate the temporal changes in gene expression to the dynamics of interactions between them. Information on interaction dynamics would open up possibilities for discovering new mechanisms of regulation by providing valuable insight into identifying time-sensitive interactions as well as permit studies on the effect of a genetic perturbation. Results: We present NETGEM, a tractable model rooted in Markov dynamics, for analyzing the dynamics of the interactions between proteins based on the dynamics of the expression changes of the genes that encode them. The model treats the interaction strengths as random variables which are modulated by suitable priors. This approach is necessitated by the extremely small sample size of the datasets, relative to the number of interactions. The model is amenable to a linear time algorithm for efficient inference. Using temporal gene expression data, NETGEM was successful in identifying (i) temporal interactions and determining their strength, (ii) functional categories of the actively interacting partners and (iii) dynamics of interactions in perturbed networks. Conclusions: NETGEM represents an optimal trade-off between model complexity and data requirement. It was able to deduce actively interacting genes and functional categories from temporal gene expression data. It permits inference by incorporating the information available in perturbed networks. Given that the inputs to NETGEM are only the network and the temporal variation of the nodes, this algorithm promises to have widespread applications, beyond biological systems. The source code for NETGEM is available from https://github.com/vjethava/NETGEM

Packet Reordering in Network Processors

Network processors today consist of multiple parallel processors (micro engines) with support for multiple threads to exploit packet level parallelism inherent in network workloads. With such concurrency, packet ordering at the output of the network processor cannot be guaranteed. This paper studies the effect of concurrency in network processors on packet ordering. We use a validated Petri net model of a commercial network processor, Intel IXP 2400, to determine the extent of packet reordering for IPv4 forwarding application. Our study indicates that in addition to the parallel processing in the network processor, the allocation scheme for the transmit buffer also adversely impacts packet ordering. In particular, our results reveal that these packet reordering results in a packet retransmission rate of up to 61%. We explore different transmit buffer allocation schemes namely, contiguous, strided, local, and global which reduces the packet retransmission to 24%. We propose an alternative scheme, packet sort, which guarantees complete packet ordering while achieving a throughput of 2.5 Gbps. Further, packet sort outperforms the in-built packet ordering schemes in the IXP processor by up to 35%.

Exploiting Programmable Network Interfaces for Parallel Query Execution in Workstation Clusters

Workstation clusters equipped with high performance interconnect having programmable network processors facilitate interesting opportunities to enhance the performance of parallel application run on them. In this paper, we propose schemes where certain application level processing in parallel database query execution is performed on the network processor. We evaluate the performance of TPC-H queries executing on a high end cluster where all tuple processing is done on the host processor, using a timed Petri net model, and find that tuple processing costs on the host processor dominate the execution time. These results are validated using a small cluster. We therefore propose 4 schemes where certain tuple processing activity is offloaded to the network processor. The first 2 schemes offload the tuple splitting activity - computation to identify the node on which to process the tuples, resulting in an execution time speedup of 1.09 relative to the base scheme, but with I/O bus becoming the bottleneck resource. In the 3rd scheme in addition to offloading tuple processing activity, the disk and network interface are combined to avoid the I/O bus bottleneck, which results in speedups up to 1.16, but with high host processor utilization. Our 4th scheme where the network processor also performs apart of join operation along with the host processor, gives a speedup of 1.47 along with balanced system resource utilizations. Further we observe that the proposed schemes perform equally well even in a scaled architecture i.e., when the number of processors is increased from 2 to 64

Queuing Network Models for Aircraft Availability and Spares Management

Interactions of major activities involved in airfleet operations, maintenance, and logistics are investigated in the framework of closed queuing networks with finite number of customers. The system is viewed at three levels, namely: operations at the flying-base, maintenance at the repair-depot, and logistics for subsystems and their interactions in achieving the system objectives. Several performance measures (eg, availability of aircraft at the flying-base, mean number of aircraft on ground at different stages of repair, use of repair facilities, and mean time an aircraft spends in various stages of repair) can easily be computed in this framework. At the subsystem level the quantities of interest are the unavailability (probability of stockout) of a spare and the duration of its unavailability. The repair-depot capability is affected by the unavailability of a spare which in turn, adversely affects the availability of aircraft at the flying-base level. Examples illustrate the utility of the proposed models.

Network pricing for QoS: A 'Regulation' approach

V. S. Borkar’s work was supported in part by grant number III.5(157)/99-ET from the Department of Science and Technology, Government of India. D. Manjunath’s work was supported in part by grant number 1(1)/2004-E-Infra from the Ministry of Information Technology, Government of India.

Smoothed functional and Quasi-Newton algorithms for routing in multi-stage queueing network with constraints

We consider the problem of optimal routing in a multi-stage network of queues with constraints on queue lengths. We develop three algorithms for probabilistic routing for this problem using only the total end-to-end delays. These algorithms use the smoothed functional (SF) approach to optimize the routing probabilities. In our model all the queues are assumed to have constraints on the average queue length. We also propose a novel quasi-Newton based SF algorithm. Policies like Join Shortest Queue or Least Work Left work only for unconstrained routing. Besides assuming knowledge of the queue length at all the queues. If the only information available is the expected end-to-end delay as with our case such policies cannot be used. We also give simulation results showing the performance of the SF algorithms for this problem.

Sufficient conditions for formation of a network topology by self-interested agents

Networks such as organizational network of a global company play an important role in a variety of knowledge management and information diffusion tasks. The nodes in these networks correspond to individuals who are self-interested. The topology of these networks often plays a crucial role in deciding the ease and speed with which certain tasks can be accomplished using these networks. Consequently, growing a stable network having a certain topology is of interest. Motivated by this, we study the following important problem: given a certain desired network topology, under what conditions would best response (link addition/deletion) strategies played by self-interested agents lead to formation of a pairwise stable network with only that topology. We study this interesting reverse engineering problem by proposing a natural model of recursive network formation. In this model, nodes enter the network sequentially and the utility of a node captures principal determinants of network formation, namely (1) benefits from immediate neighbors, (2) costs of maintaining links with immediate neighbors, (3) benefits from indirect neighbors, (4) bridging benefits, and (5) network entry fee. Based on this model, we analyze relevant network topologies such as star graph, complete graph, bipartite Turan graph, and multiple stars with interconnected centers, and derive a set of sufficient conditions under which these topologies emerge as pairwise stable networks. We also study the social welfare properties of the above topologies.

Regulation of Off-Network Pricing in a Nonneutral Network

Representatives of several Internet service providers (ISPs) have expressed their wish to see a substantial change in the pricing policies of the Internet. In particular, they would like to see content providers (CPs) pay for use of the network, given the large amount of resources they use. This would be in clear violation of the ``network neutrality'' principle that had characterized the development of the wireline Internet. Our first goal in this article is to propose and study possible ways of implementing such payments and of regulating their amount. We introduce a model that includes the users' behavior, the utilities of the ISP and of the CPs, and, the monetary flow that involves the content users, the ISP and CP, and, in pUrticular, the CP's revenues from advertisements. We consider various game models and study the resulting equilibria; they are all combinations of a noncooperative game (in which the ISPs and CPs determine how much they will charge the users) with a ``cooperative'' one on how the CP and the ISP share the payments. We include in our model a possible asymmetric weighting parameter (that varies between zero to one). We also study equilibria that arise when one of the CPs colludes with the TSP. We also study two dynamic game models as well as the convergence of prices to the equilibrium values.

Emergency Handling in MICS based Body Area Network

Body Area Network, a new wireless networking paradigm, promises to revolutionize the healthcare applications. A number of tiny sensor nodes are strategically placed in and around the human body to obtain physiological information. The sensor nodes are connected to a coordinator or a data collector to form a Body Area Network. The tiny devices may sense physiological parameters of emergency in nature (e.g. abnormality in heart bit rate, increase of glucose level above the threshold etc.) that needs immediate attention of a physician. Due to ultra low power requirement of wireless body area network, most of the time, the coordinator and devices are expected to be in the dormant mode, categorically when network is not operational. This leads to an open question, how to handle and meet the QoS requirement of emergency data when network is not operational? Emergency handling becomes more challenging at the MAC layer, if the channel access related information is unknown to the device with emergency message. The aforementioned scenarios are very likely scenarios in a MICS (Medical Implant Communication Service, 402-405 MHz) based healthcare systems. This paper proposes a mechanism for timely and reliable transfer of emergency data in a MICS based Body Area Network. We validate our protocol design with simulation in a C++ framework. Our simulation results show that more than 99 p ercentage of the time emergency messages are reached at the coordinator with a delay of 400ms.