6321522
Biclustering of Expression Data
An efficient node-deletion algorithm is introduced to find submatrices in expression data that have low mean squared residue scores and it is shown to perform well in finding co-regulation patterns in yeast and human. This introduces "biclustering", or simultaneous clustering of both genes and conditions, to knowledge discovery from expression data. This approach overcomes some problems associated with traditional clustering methods, by allowing automatic discovery of similarity based on a subset of attributes, simultaneous clustering of genes and conditions, and overlapped grouping that provides a better representation for genes with multiple functions or regulated by many factors.
216020825
Mean Shift, Mode Seeking, and Clustering
Mean shift, a simple iterative procedure that shifts each data point to the average of data points in its neighborhood, is generalized and analyzed in this paper. This generalization makes some k-m...
44320241
Convergence and Ordering of Kohonen's Batch Map
The convergence and ordering of Kohonen's batch-mode self-organizing map with Heskes and Kappen's (1993) winner selection are proved. Selim and Ismail's (1984) objective function for k-means clustering is generalized in the convergence proof of the self-organizing map. It is shown that when the neighborhood relation is doubly decreasing, order in the map is preserved. An unordered map becomes ordered when a degenerate state of ordering is entered, where the number of distinct winners is one or two. One strategy to enter this state is to run the algorithm with a broad neighborhood relation.
14172108
Context-dependent similarity
Attribute weighting and differential weighting, two major mechanisms for computing context-dependent similarity or dissimilarity measures are studied and compared. A dissimilarity measure based on subset size in the context is proposed and its metrization and application are given. It is also shown that while all attribute weighting dissimilarity measures are metrics differential weighting dissimilarity measures are usually non-metric.
10297562
Computational Models for the Helix Tilt Angle
The concept of hydrophobic imbalance and that of hydrophobic and hydrophilic centers are used along with side chain models in the computation of helix orientation and tilt angle in or near a membrane. Rotamer statistics are used to infer typical side chain positions and chain length for each amino acid, and the results are used in fast computation of helix orientation. Sliding windows are used to compute local tilt angles on long alpha-helices that defy idealized modeling and generate tilt angle profiles. Seven different procedures based on different formulas and hydrophobicity scales are used for comparison. These procedures generated very similar tilt angle profiles. These profiles provide insights into helix deformation, membrane destabilization, and similarity and differences between membrane proteins.
18245224
Distributed Pairwise Key Establishment in Wireless Sensor Networks
Abstract - Security is a big challenge when wireless sensor networks are deployed in a hostile environment. Due to the computational and storage overheads, traditional asymmetric-key based security protocols are not suitable for the resource-constrained wireless sensors. Several symmetric-key distribution protocols have been proposed in literature to establish shared cryptographic keys between sensor nodes, but most of them only work for small-scale networks due to their linearly increased communication overhead and key storage overhead. Furthermore, existing protocols are not secure when the number of compromised nodes exceeds a threshold value. In this paper, we propose a new distributed pairwise key establishment method for large-scale wireless sensor networks. Compared with existing key distribution protocols, our scheme guarantees any two sensors to establish a pairwise key between them with low overheads. A high level network security also can be achieved in our scheme even a large number of sensors are compromised.
15648291
An improved key distribution mechanism for large-scale hierarchical wireless sensor networks
Abstract Wireless sensor networks are often deployed in hostile environments and operated on an unattended mode. In order to protect the sensitive data and the sensor readings, secret keys should be used to encrypt the exchanged messages between communicating nodes. Due to their expensive energy consumption and hardware requirements, asymmetric key based cryptographies are not suitable for resource-constrained wireless sensors. Several symmetric-key pre-distribution protocols have been investigated recently to establish secure links between sensor nodes, but most of them are not scalable due to their linearly increased communication and key storage overheads. Furthermore, existing protocols cannot provide sufficient security when the number of compromised nodes exceeds a critical value. To address these limitations, we propose an improved key distribution mechanism for large-scale wireless sensor networks. Based on a hierarchical network model and bivariate polynomial-key generation mechanism, our scheme guarantees that two communicating parties can establish a unique pairwise key between them. Compared with existing protocols, our scheme can provide sufficient security no matter how many sensors are compromised. Fixed key storage overhead, full network connectivity, and low communication overhead can also be achieved by the proposed scheme.
852380
Switching classes of directed graphs
By analogy with Seidel switching classes of graphs, and two-graphs, this paper develops a theory of switching classes of directed graphs. The elements of the theory are these: there is a one-to-one correspondence among switching classes of directed graphs, two-digraphs, and cyclic triple covers of the complete digraph. If G is a group of automorphisms of a switching class of digraphs, there is a cohomological invariant γ which vanishes if and only if some digraph in the switching class is fixed by G. If G is cyclic then γ ≠ 0 if and only if all orbits on vertices have size divisible by 3 and a certain sum (defined in Theorem 3.5) is nonzero. There is a second cohomological invariant β which vanishes if and only if G can be realized as a group of automorphisms of the cyclic triple cover associated with the switching class. If G is cyclic, then β ≠ 0 if and only if G has a subgroup of order 3 for which γ ≠ 0. There is a formula for the number of isomorphism types of two-digraphs on n vertices which is a sum over the symmetric group Sn of a simple function of the cycle structure of its elements. Finally, the only elements of Sn which fix a digraph in every switching class of digraphs they fix are those elements containing a cycle whose length is not divisible by 3.
11793175
Internet Traffic Characterization Using Packet-Pair Probing
This paper presents an edge-based Internet traffic characterization approach. Our objective is to estimate the marginal distribution and the correlation structure of the packet arrival process at a queue, by sending probe packet pairs with a specific dispersion to sample the traffic. The aggregate work load process inferred from the output dispersions is a compound process of the packet arrival process and the packet size distribution. We show that the packet arrival marginal distribution and the packet size distribution can be decoupled by using the probability generating function; given one of the distributions, the other can then be estimated. We use the fact that the Internet packet size follows a known multi-modal distribution. Moreover, multiple series of packet pairs with different input dispersions can be used to estimate the packet arrival process at different time scales, and therefore to estimate the Hurst parameter, which characterizes the long-range dependence, by generating the variance-time plot. While the traffic characterization techniques are developed and validated in a single-queue context, we indicate how the techniques can be applied to a black box system for end-to-end quality of service provisioning along a multi-hop path.
15761102
Dynamic inter-SLA resource sharing in path-oriented differentiated services networks
This paper proposes novel resource sharing schemes for differentiated services (DiffServ) networks, to achieve both high resource utilization and quality of service (QoS) guarantee. Service level agreements (SLAs) are negotiated at network boundaries and supported by path-oriented resource mapping within the network. The recently proposed SLA management scheme based on virtual partitioning (Bouillet et al., 2002) allows overloaded SLAs to exploit the spare capacity of underloaded SLAs for efficient resource utilization, however, at the the cost of possible SLA violation of the underloaders. In the bandwidth borrowing scheme proposed here, the dedicated bandwidth for underloaded SLAs is determined and adaptively adjusted at network boundaries according to the actual traffic load and QoS policies; the available spare capacity is then properly distributed to related links for lending to others. On the other hand, the traffic flows admitted with borrowed bandwidth are tagged and may be preempted later when the original bandwidth owner needs to claim back the resources. Through a detailed implementation design and extensive computer simulation results we show that, by bandwidth borrowing, both SLA compliance and high resource utilization can be achieved in various load conditions, with some side benefits such as call-level service differentiation, small admission overhead, and convenience for policy-based management. In addition, we propose a distributed bandwidth pushing scheme that can dynamically adjust the spare bandwidth distribution over the network. Combining bandwidth pushing with bandwidth borrowing, the resource utilization can be further improved